CARTILAGE-HOMING PEPTIDES
Peptides that home, target, migrate to, are directed to, are retained by, or accumulate in and/or binds to the cartilage of a subject are disclosed. Pharmaceutical compositions and uses for peptides or peptide-active agent complexes comprising such peptides are also disclosed. Such compositions can be formulated for targeted delivery of a drug to a target region, tissue, structure or cell in the cartilage. Targeted compositions of the disclosure can deliver peptide or peptide-active agent complexes to target regions, tissues, structures or cells targeted by the peptide.
This application is a divisional of U.S. Application No. 17/353,447, filed Jun. 21, 2021, which is a continuation of U.S. Application No. 15/758,320, filed Mar. 7, 2018, now U.S. Pat. No. 11,090,358, which is a U.S. National Phase Application under 35 U.S.C. § 371 of International Application No. PCT/US2016/051166, filed Sep. 9, 2016, which claims priority to U.S. Provisional Pat. Application No. 62/216,331, filed Sep. 9, 2015; U.S. Provisional Pat. Application No. 62/278,929, filed Jan. 14, 2016; and U.S. Provisional Pat. Application No. 62/385,734, filed Sep. 9, 2016, each of which are herein incorporated by reference in their entireties.
SEQUENCE LISTINGThis application includes an electronically submitted sequence listing in eXtensible Markup Language (XML file). The XML file contains a sequence listing entitled “438705-710081_ST26.xm1” created on Mar. 2, 2023, and is 773 kilobytes in size. The sequence listing contained in this XML file is part of the specification and is hereby incorporated by reference herein in its entirety.
BACKGROUNDCartilage comprises chondrocytes, a specialized cell-type which produces components of the extracellular matrix, mainly including collagen, proteoglycans (e.g., aggrecan), and elastic fibers. The extracellular matrix proteins provide support, cushion, and durability to cartilage-rich portions of the body such as joints, ears, nose and windpipe. Cartilage is one of few tissues in the body which does not contain blood vessels and is considered an avascular tissue. Unlike many cells in the body which rely on a combination of blood flow and diffusion, chondrocytes rely on diffusion. Because it does not have a direct blood supply, compared to other connective tissues, cartilage grows and repairs much more slowly. As a result, cartilage disorders are particularly difficult to treat.
SUMMARYThe present disclosure relates to compositions and methods for treatment of cartilage disorders. Described herein are peptides that home to, migrate to, accumulate in, bind to, are retained by, or are directed to, and/or bind in cartilage following administration in a subject. In some embodiments, the homing peptides of the present disclosure are used to deliver a detection agent to image and/or diagnose cartilage. In other embodiments, the homing peptides of the present disclosure are used to deliver an active agent to a region, tissue, structure, or cell thereof.
In various aspects, the present disclosure provides a knotted peptide, wherein upon administration to a subject the knotted peptide homes, targets, migrates to, accumulates in, binds to, is retained by, or is directed to a cartilage of the subject.
In some aspects, the knotted peptide comprises a sequence of any one of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 or a fragment thereof. In other aspects, the knotted peptide comprises a sequence that has at least 80% sequence identity with any one of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 or a fragment thereof. In still other aspects, the knotted peptide comprises a sequence that has at least 85%, at least 90%, or at least 95% sequence identity with any one of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 or a fragment thereof.
In some aspects, the knotted peptide comprises a sequence of any one of SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 or a fragment thereof. In other aspects, the knotted peptide comprises a sequence that has at least 80% sequence identity with any one of SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 or a fragment thereof. In still other aspects, the knotted peptide comprises a sequence that has at least 85%, at least 90%, or at least 95% sequence identity with any one of SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 or a fragment thereof.
In some aspects, the knotted peptide comprises a sequence of any one of SEQ ID NO: 1 -SEQ ID NO: 20 or a fragment thereof. In other aspects, the knotted peptide comprises a sequence of any one of SEQ ID NO: 217 - SEQ ID NO: 236 or a fragment thereof.
In other aspects, the knotted peptide is at least 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 95% identical to any one of SEQ ID NO: 436 - SEQ ID NO: 482. In further aspects, the knotted peptide of claim 10, wherein the knotted peptide is SEQ ID NO: 24. In other aspects, the knotted peptide is SEQ ID NO: 111.
In some aspects, the knotted peptide comprises 4 or more cysteine residues. In further aspects, the knotted peptide comprises three or more disulfide bridges formed between cysteine residues, wherein one of the disulfide bridges passes through a loop formed by two other disulfide bridges. In still further aspects, the knotted peptide comprises a plurality of disulfide bridges formed between cysteine residues. In other aspects, the knotted peptide comprises a disulfide through a disulfide knot.
In some aspects, at least one amino acid residue of the knotted peptide is in an L configuration or, wherein at least one amino acid residue of the knotted peptide is in a D configuration.
In some aspects, the sequence comprises at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46, at least 47, at least 48, at least 49, at least 50, at least 51, at least 52, at least 53, at least 54, at least 55, at least 56, at least 57, at least 58 residues, at least 59, at least 60, at least 61, at least 62, at least 63, at least 64, at least 65, at least 66, at least 67, at least 68, at least 69, at least 70, at least 71, at least 72, at least 73, at least 74, at least 75, at least 76, at least 77, at least 78, at least 79, at least 80, or at least 81 residues.
In some aspects, any one or more K residues are replaced by an R residue or wherein any one or more R residues are replaced by for a K residue. In other aspects, any one or more M residues are replaced by any one of the I, L, or V residues. In still other aspects, any one or more L residues are replaced by any one of the V, I, or M residues.
In other aspects, any one or more I residues are replaced by any of the M, L, or V residues. In still other aspects, any one or more V residues are replaced by any of the M, I, or L residues. In some aspects, any one or more G residues are replaced by an A residue or wherein any one or more A residues are replaced by a G residue. In other aspects, any one or more S residues are replaced by a T residue or wherein any one or more T residues are replaced by for an S residue.
In still other aspects, any one or more Q residues are replaced by an N residue or wherein any one or more N residues are replaced by a Q residue. In some aspects, any one or more D residues are replaced by an E residue or wherein any one or more E residues are replaced by a D residue.
In some aspects, the knotted peptide has a charge distribution comprising an acidic region and a basic region. In further aspects, the acidic region is a nub. In other aspects, the basic region is a patch. In some aspects, the knotted peptide comprises 6 or more basic residues and 2 or fewer acidic residues. In some aspects, the knotted peptide comprises a 4-19 amino acid residue fragment containing at least 2 cysteine residues, and at least 2 positively charged amino acid residues.
In other aspects, the knotted peptide comprises a 20-70 amino acid residue fragment containing at least 2 cysteine residues, no more than 2 basic residues and at least 2 positively charged amino acid residues. In still other aspects, the knotted peptide comprises at least 3 positively charged amino acid residues. In some aspects, the positively charged amino acid residues are selected from K, R, or a combination thereof.
In some aspects, the knotted peptide has a charge greater than 2 at physiological pH. In other aspects, the knotted peptide has a charge greater than 3.5 at physiological pH. In still other aspects, the knotted peptide has a charge greater than 4.5 at physiological pH. In some aspects, the knotted peptide has a charge greater than 5.5 at physiological pH. In other aspects, the knotted peptide has a charge greater than 6.5 at physiological pH. In other aspects, the knotted peptide has a charge greater than 7.5 at physiological pH.
In some aspects, the knotted peptide is selected from a potassium channel agonist, a potassium channel antagonist, a portion of a potassium channel, a sodium channel agonist, a sodium channel antagonist, a calcium channel agonist, a calcium channel antagonist, a hadrucalcin, a theraphotoxin, a huwentoxin, a kaliotoxin, a cobatoxin or a lectin.
In further aspects, the lectin is SHL-Ib2. In some aspects, the knotted peptide is arranged in a multimeric structure with at least one other knotted peptide.
In some aspects, at least one residue of the knotted peptide comprises a chemical modification. In further aspects, the chemical modification is blocking the N-terminus of the knotted peptide. In still further aspects, the chemical modification is methylation, acetylation, or acylation. In other aspects, the chemical modification is: methylation of one or more lysine residues or analogue thereof; methylation of the N-terminus; or methylation of one or more lysine residue or analogue thereof and methylation of the N-terminus. In some aspects, the knotted peptide is linked to an acyl adduct.
In some aspects, the knotted peptide is linked to an active agent. In further aspects, the active agent is fused with the knotted peptide at an N-terminus or a C-terminus of the knotted peptide. In some aspects, the active agent is an antibody. In other aspects, the active agent is an Fc domain. In still other aspects, the knotted peptide fused with an Fc domain comprises a contiguous sequence.
In further aspects, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 active agents are linked to the knotted peptide. In still further aspects, the knotted peptide is linked to the active agent via a cleavable linker. In some aspects, the knotted peptide is linked to the active agent at an N-terminus, at the epsilon amine of an internal lysine residue, at the carboxylic acid of an aspartic acid or glutamic acid residue, or a C-terminus of the knotted peptide by a linker. In some aspects, the knotted peptide further comprises a non-natural amino acid, wherein the non-natural amino acid is an insertion, appendage, or substitution for another amino acid.
In some aspects, the knotted peptide is linked to the active agent at the non-natural amino acid by a linker. In some aspects, the linker comprises an amide bond, an ester bond, a carbamate bond, a carbonate bond, a hydrazone bond, an oxime bond, a disulfide bond, a thioester bond, or a carbon-nitrogen bond. In further aspects, the cleavable linker comprises a cleavage site for matrix metalloproteinases, thrombin, cathepsins, or beta-glucuronidase. In other aspects, the linker is a hydrolytically labile linker. In still other aspects, the knotted peptide is linked to the active agent via a noncleavable linker.
In some aspects, the active agent is: a peptide, an oligopeptide, a polypeptide, a polynucleotide, a polyribonucleotide, a DNA, a cDNA, a ssDNA, a RNA, a dsRNA, a micro RNA, an oligonucleotide, an antibody, an antibody fragment, an aptamer, a cytokine, an enzyme, a growth factor, a chemokine, a neurotransmitter, a chemical agent, a fluorophore, a metal, a metal chelate, an X-ray contrast agent, a PET agent, a radioisotope, a photosensitizer, a radiosensitizer, a radionuclide chelator, a therapeutic small molecule, a steroid, a corticosteroid, an anti-inflammatory agent, an immune modulator, a protease inhibitor, an amino sugar, a chemotherapeutic agent, a cytotoxic chemical, a toxin, a tyrosine kinase inhibitor, an anti-infective agent, an antibiotic, an anti-viral agent, an anti-fungal agent, an aminoglycoside, a nonsteroidal anti-inflammatory drug (NSAID), a statin, a nanoparticle, a liposome, a polymer, a biopolymer, a polysaccharide, a proteoglycan, a glycosaminoglycan, a glucocorticoid, an anti-cytokine agent, a pain-reducing agent, a dendrimer, a fatty acid, an Fc region, or a combination thereof.
In some aspects, the NSAID is ketorolac. In other aspects, the NSAID is ibuprofen. In some aspects, the steroid is dexamethasone. In other aspects, the steroid is budesonide. In some aspects, the active agent induces programmed cell death. In further aspects, the programmed cell death is apoptosis. In some aspects, the active agent is a tumor necrosis factor alpha inhibitor. In further aspects, the active agent is a TNF receptor family activator. In still further aspects, the active agent is a TNF alpha antibody. In some aspects, the protease inhibitor is a collagenase inhibitor, elastase inhibitor, or a matrix metalloprotease inhibitor. In further aspects, the matrix metalloprotease is MMP13.
In some aspects, the knotted peptide is linked to a detectable agent. In further aspects, the detectable agent is fused with the knotted peptide at an N-terminus or a C-terminus of the knotted peptide. In still further aspects, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 detectable agents are linked to the knotted peptide. In some aspects, the knotted peptide is linked to the detectable agent via a cleavable linker.
In some aspects, the knotted peptide is linked to the detectable agent at an N-terminus, at the epsilon amine of an internal lysine residue, or a C-terminus of the knotted peptide by a linker. In further aspects, the peptide further comprises a non-natural amino acid, wherein the non-natural amino acid is an insertion, appendage, or substitution for another amino acid. In still further aspects, the knotted peptide is linked to the active agent at the non-natural amino acid by a linker.
In still further aspects, the linker comprises an amide bond, an ester bond, a carbamate bond, a hydrazone bond, an oxime bond, or a carbon-nitrogen bond. In some aspects, the cleavable linker comprises a cleavage site for matrix metalloproteinases, thrombin, cathepsins, or beta-glucuronidase. In other aspects, the knotted peptide is linked to the detectable agent via a noncleavable linker.
In some aspects, the detectable agent is a fluorophore, a near-infrared dye, a contrast agent, a nanoparticle, a metal-containing nanoparticle, a metal chelate, an X-ray contrast agent, a PET agent, a radioisotope, or a radionuclide chelator. In further aspects, the detectable agent is a fluorescent dye. In some aspects, the knotted peptide has an isoelectric point of about 9.
In some aspects, the knotted peptide is SEQ ID NO: 24. In other aspects, the knotted peptide is SEQ ID NO: 111.
In various aspects, the present disclosure provides a pharmaceutical composition comprising any of the above compositions or a salt thereof, and a pharmaceutically acceptable carrier.
In further aspects, the pharmaceutical composition is formulated for administration to a subject. In still further aspects, the pharmaceutical composition is formulated for inhalation, intranasal administration, oral administration, topical administration, intravenous administration, subcutaneous administration, intra-articular administration, intramuscular administration, intraperitoneal administration, or a combination thereof.
In various aspects, the present disclosure provides a method of treating a condition in a subject in need thereof, the method comprising: administering to the subject a knotted peptide comprising any of the above compositions or any of the above pharmaceutical compositions.
In some aspects, the composition is administered by inhalation, intranasally, orally, topically, intravenously, subcutaneously, intra-articularly, intramuscularly administration, intraperitoneally, or a combination thereof. In further aspects, the composition homes, targets, or migrates to cartilage of the subject following administration.
In some aspects, the condition is associated with a function of cartilage. In some aspects, the condition is an inflammation, a cancer, a degradation, a growth disturbance, genetic, a tear, an infection, or an injury. In other aspects, the condition is a chondrodystrophy. In still other aspects, the condition is a traumatic rupture or detachment. In some aspects, the condition is a costochondritis. In other aspects, the condition is a herniation. In still other aspects, the condition is a polychondritis.
In other aspects, the condition is a chordoma. In some aspects, the condition is a type of arthritis. In further aspects, the type of arthritis is rheumatoid arthritis. In other aspects, the type of arthritis is osteoarthritis. In some aspects, the condition is achondroplasia. In some aspects, the cancer is benign chondroma or malignant chondrosarcoma. In other aspects, the condition is bursitis, tendinitis, gout, pseudogout, an arthropathy, or an infection.
In some aspects, the composition is administered to treat the injury, to repair a tissue damaged by the injury, or to treat a pain caused by the injury. In further aspects, the composition is administered to treat the tear or to repair a tissue damaged by the tear.
In various aspects, the present disclosure provides a method of imaging an organ or body region of a subject, the method comprising: administering to the subject composition of any one of knotted peptide previously described or a pharmaceutical composition as previously described; and imaging the subject.
In some aspects, the method further comprises detecting a cancer or diseased region, tissue, structure or cell. In further aspects, the method further comprises performing surgery on the subject. In some aspects, the method further comprises treating the cancer.
In other aspects, the surgery comprises removing the cancer or the diseased region, tissue, structure or cell of the subject. In still other aspects, the method further comprises imaging the cancer or diseased region, tissue, structure, or cell of the subject after surgical removal.
INCORPORATION BY REFERENCEAll publications, patents, and patent applications mentioned, disclosed or referenced in this specification are herein incorporated by reference in their entirety and to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.
The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which:
The present disclosure relates generally to compositions and methods for cartilage therapy. In some embodiments, the compositions and methods herein utilize peptides that home, target, are directed to, are retained by, accumulate in, migrate to, and/or bind to cartilage following administration to a subject. In some embodiments, the cartilage homing peptides of the present disclosure are used to deliver an active agent to cartilage or tissue or cell thereof. The active agent can exert a therapeutic effect on cartilage or tissue or cell thereof. For example, in certain embodiments, the active agent allows for localized delivery of an anti-inflammatory agent to cartilage or tissue or cell thereof. As another example, the active agent is a fluorophore that can be used for imaging of cartilage. In certain embodiments, the peptide itself induces therapeutic responses.
Cartilage disorders are particularly difficult to treat. A direct route for drug administration can be intravenously, intra-articularly, or orally. However, cartilage can be avascular thus intravenous administration of drugs can fail to reach the cartilage. Drugs for cartilage diseases, such as osteoarthritis, can be injected directly locally into the affected area, for example, directly injected into the j oint. Few drugs aimed at treating cartilage disorders have proved therapeutically viable with lack of access to target tissue being a primary reason for failure. The lack of access to the target tissue can also lead to administration of doses that are higher than would be necessary if a drug could home, target, or be directed to, is retained by, and/or binds to a target region, tissue, structure or cell. Thus, treatment of cartilage conditions often requires the use of high concentrations of non-specific drugs. In addition, a number of therapeutics are of interest in treating joint disorders, but are problematic because of the level of side effects caused by systemic administration of the drug (Dancevic and McCulloch, Arthritis Research & Therapy 16:429 (2014)).
Specific and potent drugs that are capable of contacting the cartilage can counteract the non-specificity of many treatments by selectively targeting and delivering compounds to specific regions, tissues, cells and structures. Such drugs can also be useful to modulate ion channels, protein-protein interactions, extracellular matrix remodeling (i.e., protease inhibition), and the like. Such targeted therapy can allow for lower dosing, reduced side effects, improved patient compliance, and improvement in therapeutic outcomes, which would be advantageous not only in acute disease of the cartilage, but in chronic conditions as well.
The present disclosure describes a class of peptides derived from knottins that can effectively contact cartilage and be used either directly or as carriers of active drugs, peptides, or molecules to treat a cartilage condition. For instance, osteoarthritis is a cartilage condition that is associated with the thinning of cartilage covering the ends of bones resulting in bone directly contacting bone within the joint. Over time, the ends of the bones are subjected to increased levels of friction which causes erosion of the end of the bone. Individuals suffering from osteoarthritis experience reduced motion and increased pain. A therapeutic peptide that could contact the cartilage at the joint and ends of the bone to interact with the chondrocytes and induce increased expression of extracellular matrix proteins could be used in the treatment and prevention of osteoarthritis by increasing expression of collagen through, for example, the rate of production, amount of production, inhibition of proteins which degrade collagen, promote expression of other proteins which maintain the integrity of existing collagen proteins, or other mechanism. A peptide could also affect nearby tissues or cells such as the bone, osteoclasts, osteoblasts, ligaments, muscle, tendons, and bursa. The peptides of the disclosure can be used to treat the symptoms of various conditions. The peptides of the disclosure can bind to chondrocytes, to cartilage, to extracellular matrix, to collagen, hyaluranon, aggrecan (also known as cartilage-specific proteoglycan core protein (CSPCP)), or other components of the extracellular matrix, or to other components in joints and cartilaginous tissues.
Also described herein are peptides that selectively home, target, are directed to, migrate to, are retained by, or accumulate in and/or bind to specific regions, tissues, structures or cells of the cartilage that aid in managing, decreasing, ablating or reducing pain (e.g., joint pain) due to chronic disease or cartilage injury or other therapeutic indications as described herein. A peptide that homes, targets, migrates to, is directed to, is retained by, or accumulates in and/or binds to one or more specific regions, tissues, structures or cells of the cartilage can have fewer off-target and potentially negative effects, for example, side effects that often limit use and efficacy of pain drugs. In addition, such peptides can reduce dosage and increase the efficacy of existing drugs by directly targeting them to a specific region, tissue, structure or cell of the cartilage and helping the contact the cartilage or increasing the local concentration of agent. The peptide itself can modulate pain or it can be conjugated to an agent that modulates pain. Such pain modulation may operate by various mechanisms such as modulating inflammation, autoimmune responses, direct or indirect action on pain receptors, cell killing, or programmed cell death (whether via an apoptotic and/or non-apoptotic pathway of diseased cells or tissues, and the like (Tait et al. J Cell Sci 127(Pt 10):2135-44 (2014)).
Peptides of this disclosure that home, target, are directed to, migrate to, are retained by, accumulate in, or bind to specific regions, tissues, structures or cells of the cartilage can do so with different degrees of efficiency. Peptides can have a higher concentration in cartilage than in other locations, such as blood or muscle. Peptides can be recorded as having a signal in cartilage as a percentage of signal in blood. For example, a cartilage signal of 200% indicates that the signal in cartilage is twice as high as the signal in blood. In some embodiments, peptides that have cartilage homing properties can have a cartilage signal of >170% by radio densitometry measurements. In other embodiments, peptides that are cartilage homers can have a cartilage signal of >200% by radio densitometry measurements. In other embodiments, peptides that are more efficient cartilage homers can have a cartilage signal of >300% by radio densitometry measurements. In other embodiments, peptides that are more efficient cartilage homers can have a cartilage signal of >400% by radio densitometry measurements. In other embodiments, peptides that are strongest cartilage homers of highest interest can have a cartilage signal of >500% by radio densitometry measurements.
Peptides that selectively home, target, are directed to, migrate to, are retained by, or accumulate in and/or bind to specific regions, tissues, structures or cells of the cartilage can occur after administration of the peptide to a subject. A subject can be a human or a non-human animal.
The peptides disclosed herein can be used as active agents such a fluorophores for imaging or to carry agents such as anti-inflammatory agents to the joint to treat inflammation.
The peptides disclosed herein can be used to bind cartilage explants ex vivo. Cartilage explants can be from any subject, such as a human or an animal. Assessment of peptide binding to cartilage explants can be used to screen peptides that may efficiently home to cartilage in vivo.
Additional aspects and advantages of the present disclosure will become apparent to those skilled in this art from the following detailed description, wherein illustrative embodiments of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different embodiments, and its several details are capable of modifications in various respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive.
As used herein, the abbreviations for the natural L-enantiomeric amino acids are conventional and are as follows: alanine (A, Ala); arginine (R, Arg); asparagine (N, Asn); aspartic acid (D, Asp); cysteine (C, Cys); glutamic acid (E, Glu); glutamine (Q, Gln); glycine (G, Gly); histidine (H, His); isoleucine (I, Ile); leucine (L, Leu); lysine (K, Lys); methionine (M, Met); phenylalanine (F, Phe); proline (P, Pro); serine (S, Ser); threonine (T, Thr); tryptophan (W, Trp); tyrosine (Y, Tyr); valine (V, Val). Typically, Xaa can indicate any amino acid. In some embodiments, X can be asparagine (N), glutamine (Q), histidine (H), lysine (K), or arginine (R).
Some embodiments of the disclosure contemplate D-amino acid residues of any standard or non-standard amino acid or analogue thereof. When an amino acid sequence is represented as a series of three-letter or one-letter amino acid abbreviations, the left-hand direction is the amino terminal direction and the right-hand direction is the carboxy terminal direction, in accordance with standard usage and convention.
PeptidesKnottins are a class of peptides, usually ranging from about 20 to about 80 amino acids in length that are often folded into a compact structure. Knottins are typically assembled into a complex tertiary structure that is characterized by a number of intramolecular disulfide crosslinks and may contain beta strands and other secondary structures. The presence of the disulfide bonds gives knottins remarkable environmental stability, allowing them to withstand extremes of temperature and pH and to resist the proteolytic enzymes of the blood stream.
A wider examination of the sequence structure and homology of knottins reveals that they have arisen by convergent evolution in all kinds of animals and plants. In animals, they are typically found in venoms, for example, the venoms of spiders and scorpions and have been implicated in the modulation of ion channels. Many of this class of peptide can be protease inhibitors, and as such can both home to cartilage and inhibit collagenase or a matrix metalloprotease that breaks down cartilage (e.g., matrix metalloprotease 13 (MMP13)). The knottin proteins of plants can inhibit the proteolytic enzymes of animals or have antimicrobial activity, suggesting that knottins can function in the native defense of plants. Many of this class of peptides can have antimicrobial activity, and as such one of these can both home to cartilage and treat microbial infections. Therefore, knottin peptides can interact with ion channels, and as such can home to cartilage and interact (bind, block, activate) with ion channels such as those in chondrocytes that are known to effect proliferation, mechanotransduction, and other functions (Potassium Ion Channels in Articular Chondrocytes, Ali Mobasheri, in Mechanosensitive Ion Channels Mechanosensitivity in Cells and Tissues Volume 1, 2008, pp 157-178).
The knotted peptides of the present disclosure provide certain advantages. For instance, the presence of the disulfide bonds gives knotted peptides remarkable environmental stability, allowing them to withstand extremes of temperature and pH and to resist the proteolytic enzymes of the blood stream, the gastrointestinal tract, and elsewhere in the body. The resistance of knotted peptides to degradation can be beneficial in terms of reducing immunogenicity. The rigidity of knotted peptides also allows them to bind to targets without paying the “entropic penalty” that a floppy peptide accrues upon binding a target. The knotted peptides can bind targets with antibody-like affinity. The knotted peptides can modulate the activity of a plurality of cartilage regions, tissues, structures or cells. Some of the cartilage regions, tissues, structures include: (a) elastic cartilage; (b) hyaline cartilage, such as articular cartilage and physeal cartilage; (c) fibrocartilage; and (d) any cells or cell types in (a) - (c) above. Some of the areas where the knottin peptide can home to cartilage include joints such as knees, hips, or digits, nasal cartilage, spinal cartilage, tracheal cartilage, and rib cartilage. In various aspects, cartilage components include aggrecan and type II collagen. Additionally, in some embodiments, knotted peptides can penetrate into cells. In other embodiments, knotted peptides exhibit more rapid clearance and cellular uptake compared to other types of molecules.
The present disclosure provides peptides that comprise or are derived from these knotted peptides (or knottins). As used herein, the term “knotted peptide” is considered to be interchangeable with the terms “knottin” and “optide.”
The peptides of the present disclosure can comprise cysteine amino acid residues. In some cases, the peptide has at least 4 cysteine amino acid residues. In some cases, the peptide has at least 6 cysteine amino acid residues. In other cases, the peptide has at least 8 cysteine amino acid residues, at least 10 cysteine amino acid residues, at least 12 cysteine amino acid residues, at least 14 cysteine amino acid residues or at least 16 cysteine amino acid residues.
A knotted peptide can comprise disulfide bridges. A knotted peptide can be a peptide wherein 5% or more of the residues are cysteines forming intramolecular disulfide bonds. A disulfide-linked peptide can be a drug scaffold. In some embodiments, the disulfide bridges form an inhibitor knot. A disulfide bridge can be formed between cysteine residues, for example, between cysteines 1 and 4, 2 and 5, or, 3 and 6. In some cases, one disulfide bridge passes through a loop formed by the other two disulfide bridges, for example, to form the inhibitor knot. In other cases, the disulfide bridges can be formed between any two cysteine residues.
The present disclosure further includes peptide scaffolds that, e.g., can be used as a starting point for generating additional peptides that can target and home to cartilage. In some embodiments, these scaffolds can be derived from a variety of knotted peptides (or knottins). In certain embodiments, knotted peptides are assembled into a complex tertiary structure that is characterized by a number of intramolecular disulfide crosslinks, and optionally contain beta strands and other secondary structures such as an alpha helix. For example, knotted peptides include, in some embodiments, small disulfide-rich proteins characterized by a disulfide through disulfide knot. This knot can be, e.g., obtained when one disulfide bridge crosses the macrocycle formed by two other disulfides and the interconnecting backbone. In some embodiments, the knotted peptides can include growth factor cysteine knots or inhibitor cysteine knots. Other possible peptide structures can include peptide having two parallel helices linked by two disulfide bridges without β- sheets (e.g., hefutoxin).
A knotted peptide can comprise at least one amino acid residue in an L configuration. A knotted peptide can comprise at least one amino acid residue in a D configuration. In some embodiments, a knotted peptide is 15-40 amino acid residues long. In other embodiments, a knotted peptide is 11-57 amino acid residues long. In further embodiments, a knotted peptide is at least 20 amino acid residues long.
These kinds of peptides can be derived from a class of proteins known to be present or associated with toxins or venoms. In some cases, the peptide can be derived from toxins or venoms associated with scorpions or spiders. The peptide can be derived from venoms and toxins of spiders and scorpions of various genus and species. For example, the peptide can be derived from a venom or toxin of the Leiurus quinquestriatus hebraeus, Buthus occitanus tunetanus, Hottentotta judaicus, Mesobuthus eupeus, Buthus occitanus israelis, Hadrurus gertschi, Androctonus australis, Centruroides noxius, Heterometrus laoticus, Opistophthalmus carinatus, Haplopelma schmidti, Isometrus maculatus, Grammostola rosea or another suitable genus or species of scorpion. In some cases, a peptide can be derived from a Buthus martensii Karsh (scorpion) toxin.
In some embodiments, the peptides are members of the pfam00451:toxin_2 family. The pfam00451:toxin_2 structural class family can include a peptide of any one of SEQ ID NO: 436 - SEQ ID NO: 482. A cartilage homoing peptide of this disclosure can be a variant of any peptide members of the pfam00451:toxin_2 family. In some embodiments, an exemplary cartilage homing peptide of this disclosure that is a variant of the pfam00451:toxin_2 structural class family is a peptide of SEQ ID NO: 24. In other embodiments, an exemplary cartilage homing peptide of this disclosure that is a variant of the pfam00451:toxin_2 structural class family is a peptide of SEQ ID NO: 111. In other embodiments, the variant peptides are at least 30% identical to a peptide of the structural class pfam00451:toxin_2 family. In some embodiments, the variant peptides are 30%, 40%, 50%, 60%, 80%, 90% or 95% identical to a peptide of the structural class pfam00451:toxin_2 family. In some embodiments, the variant peptides are at least 30%, at least 40%, at least 50%, at least 60%, at least 80%, at least 90% or at least 95% identical to a peptide of the structural class pfam00451:toxin_2 family. The pfam00451:toxin_2 family comprises peptide family members found as portions of various scorpion toxins, often functioning to block potassium channels. Features of the pfam00451:toxin_2 family include, but are not limited to, a features associated with members of a knottin 1 (CL0054) clan, which has at least 120 family members. For example, the average family member amino acid residue lengths is 31.4 amino acid residues, the average identity of family member sequence homology to the consensus sequence is 46%, and family members are derived from at least the following organisms: Tityus costatus, Centruroides noxius, Tityus serrulatus, Mesobuthus gibbosus, Centruroides elegans, Hottentotta judaicus, Mesobuthus eupeus, Parabuthus transvaalicus, Isometroides vescus, Hottentotta tamulus sindicus, Centruroides margaritatus, Centruroides suffusus suffusus, Buthus occitanus israelis, Centruroides limpidus limpidus, Leiurus quinquestriatus hebraeus, Odontobuthus doriae, Mesobuthus tamulus, Tityus stigmurus, Lychas mucronatus, Androctonus australis, Orthochirus scrobiculosus, Mesobuthus martensii, Androctonus mauretanicus mauretanicus, Centruroides limbatus, Isometrus maculatus, Tityus discrepans, Androctonus amoreuxi, Buthus occitanus tunetanus, Tityus trivittatus and Tityus obscurus (Amazonian scorpion).
In some embodiments, cartilage homing peptides are members of family with the sequence GSXVXXXVKCXGSKQCXXPCKRXXGXRXGKCINKKXCKCYXXX (SEQ ID NO: 9), in which this sequence is based on the most common elements found in the following sequences:
and
where the following residues may be independently interchanged in the sequences: K and R; M, I, L, and V; G and A; S and T; Q and N; and X can independently be any number of any amino acid or no amino acid. The N-terminal GS sequence can be included or excluded between the peptides of the present disclosure.
In other embodiments, peptides are members of family with the sequence GSXXXGCVXXXXKCRPGXKXCCXPXKRCSRRFGXXXXKKCKXXXXXX (SEQ ID NO: 10), in which the sequence is based on the most common elements found in the following sequences:
and
where the following residues may be independently interchanged in the sequences: K and R; M, I, L, and V; G and A; S and T; Q and N; and X can independently be any number of any amino acid or no amino acid. The N-terminal GS sequence can be included or excluded between the peptides of the present disclosure.
In some embodiments, a peptide comprises the sequence GSGVX1IX2X3KCX4GSKQCX5DPCKX6X7X8GX9RX10GKCX11NKKCKCX12X13X14X15 (SEQ ID NO: 1), wherein X1, X2, X3, X4, X5, X6, X7, X8, X9, X10, X11, X12, X13, X14 and X15 are each individually any amino acid or amino acid analogue or null. In some cases, the peptide comprises the sequence GSGVX1IX2X3KCX4GSKQCX5DPCKX6X7X8GX9RX10GKCX11NKKCKCX12X13X14X15 (SEQ ID NO: 2), where X1 is selected from P or R, wherein X2 is selected from P or N, wherein X3 is selected from V or I, wherein X4 is selected from S, T, R or K, wherein X5 is selected from Y or L, wherein X6 is selected from Q, R or K, wherein X7 is selected from A, K or R, wherein X8 is selected from T or A, wherein X9 is selected from C or M, wherein X10 is selected from F or N, wherein X11 is selected from M or I, wherein X12 is selected from Y or T, wherein X13 is selected from G or P, wherein X14 is selected from C or null, and wherein X15 is selected from G or null.
In some embodiments, a peptide comprises the sequence X1X2X3X4IX5CX6GSKQCYX7PCKX8X9TGCX10X11X12KCX13X14KX15CKCYGCG (SEQ ID NO: 3), wherein X1, X2, X3, X4, X5, X6, X7, X8, X9, X10, X11, X12, X13, X14, and X15 are each individually any amino acid or amino acid analogue or null. In some cases, the peptide comprises the sequence X1X2X3X4IX5CX6GSKQCYX7PCKX8X9TGCX10X11X12KCX13X14KX15CKCYGCG, (SEQ ID NO: 4), where X1 is selected from G or null, wherein X2 is selected from S or null, wherein X3 is selected from E, G or null, wherein X4 is selected from V, S, or null, wherein X5 is selected from R or S, wherein X6 is selected from S or T, wherein X7 is selected from G or D, wherein X8 is selected from Q or R, wherein X9 is selected from Q or K, wherein X10 is selected from T or P, wherein X11 is selected from N or Q, wherein X12 is selected from S or A, wherein X13 is selected from M or L, wherein X14 is selected from N or Q, and wherein X15 is selected from V or S.
In some embodiments, a peptide comprises the sequence X1X2X3VX41X5VX6CX7X8SX9X10CLX11PCKX12 AGMRFGKCX13NX14KCX15CTPX16 (SEQ ID NO: 5), wherein X1, X2, X3, X4, X5, X6, X7, X8, X9, X10, X11, X12, X13, X14, X15, X16 are each individually any amino acid or amino acid analogue or null. In some cases, the peptide comprises the sequence X1X2X3VX41X5VX6CX7X8SX9X10CLX11PCKX12 AGMRFGKCX13NX14KCX15CTPX16 (SEQ ID NO: 6), where X1 is selected from G or null, wherein X2 is selected from G, S or null, wherein X3 is selected from G, S or null, wherein X4 is selected from P or R, wherein X5 is selected from N or P, wherein X6 is selected from K or S, wherein X7 is selected from R or K, wherein X8 is selected from G or H, wherein X9 is selected from R or G, wherein X10 is selected from D or Q, wherein X11 is selected from D or K, wherein X12 is selected from K or D, wherein X13 is selected from I or M, wherein X14 is selected from S or G, wherein X15 is selected from H or D, and wherein X16 is selected from K or null.
In some embodiments, a peptide comprises the sequence XVXVKCXGSKQCXPCKRXGXRXGKCINKKXCKCYX (SEQ ID NO: 7) or XGCVXKCRPGXKXCCXPXKRCSRRFGXKKCKX (SEQ ID NO: 8), wherein each letter is each individually any amino acid or amino acid analogue and where X is no amino acid or a 1-10 amino acid long peptide fragment wherein each amino acid within such peptide fragment can in each case be any amino acid or amino acid analogue.
In some embodiments, a peptide comprises the sequence GSGVX1IX2X3RCX4GSRQCX5DPCRX6X7X8GX9RX10GRCX11NRRCRCX12X13X14X15 (SEQ ID NO: 11), wherein X1, X2, X3, X4, X5, X6, X7, X8, X9, X10, X11, X12, X13, X14 and X15 are each individually any amino acid or amino acid analogue or null. In some cases, the peptide comprises the sequence GSGVX1IX2X3RCX4GSRQCX5DPCRX6X7X8GX9RX10GRCX11NRRCRCX12X13X14X15 (SEQ ID NO: 12), where X1 is selected from P or R, wherein X2 is selected from P or N, wherein X3 is selected from V or I, wherein X4 is selected from S, T, R or K, wherein X5 is selected from Y or L, wherein X6 is selected from Q, R or K, wherein X7 is selected from A, K or R, wherein X8 is selected from T or A, wherein X9 is selected from C or M, wherein X10 is selected from F or N, wherein X11 is selected from M or I, wherein X12 is selected from Y or T, wherein X13 is selected from G or P, wherein X14 is selected from C or null, and wherein X15 is selected from G or null.
In some embodiments, a peptide comprises the sequence X1X2X3X4IX5CX6GSRQCYX7PCRX8X9TGCX10X11X12RCX13X14RX15CRCYGCG (SEQ ID NO: 13), wherein X1, X2, X3, X4, X5, X6, X7, X8 X9, X10, X11, X12, X13, X14, and X15are each individually any amino acid or amino acid analogue or null. In some cases, the peptide comprises the sequence X1X2X3X4IX5CX6GSRQCYX7PCRX8X9TGCX10X11X12RCX13X14RX15CRCYGCG, (SEQ ID NO: 14), where X1 is selected from G or null, wherein X2 is selected from S or null, wherein X3 is selected from E, G or null, wherein X4 is selected from V, S, or null, wherein X5 is selected from R or S, wherein X6 is selected from S or T, wherein X7 is selected from G or D, wherein X8 is selected from Q or R, wherein X9 is selected from Q, R, or K, wherein X10 is selected from T or P, wherein X11 is selected from N or Q, wherein X12 is selected from S or A, wherein X13 is selected from M or L, wherein X14 is selected from N or Q, and wherein X15 is selected from V or S.
In some embodiments, a peptide comprises the sequence X1X2X3VX4IX5VX6CX7X8SX9X10CLX11PCRX12AGMRFGRCX13NX14RCX15CTPX16 (SEQ ID NO: 15), wherein X1, X2, X3, X4, X5, X6, X7, X8, X9, X10, X11, X12, X13, X14, X15, X16 are each individually any amino acid or amino acid analogue or null. In some cases, the peptide comprises the sequence X1X2X3VX4IX5VX6CX7X8SX9X10CLX11PCRX12AGMRFGRCX13NX14RCX15CTPX16 (SEQ ID NO: 16), where X1 is selected from G or null, wherein X2 is selected from G, S or null, wherein X3 is selected from G, S or null, wherein X4 is selected from P or R, wherein X5 is selected from N or P, wherein X6 is selected from R, K or S, wherein X7 is selected from R or K, wherein X8 is selected from G or H, wherein X9 is selected from R or G, wherein X10 is selected from D or Q, wherein X11 is selected from D, R, or K, wherein X12 is selected from K, R, or D, wherein X13 is selected from I or M, wherein X14 is selected from S or G, wherein X15 is selected from H or D, and wherein X16 is selected from K, R, or null.
In some embodiments, a peptide comprises the sequence XVXVRCXGSRQCXPCRRXGXRXGRCINRRXCRCYX (SEQ ID NO: 17) or XGCVXRCRPGXRXCCXPXRRCSRRFGXRRCRX (SEQ ID NO: 18), wherein each letter is each individually any amino acid or amino acid analogue and where X is no amino acid or a 1-10 amino acid long peptide fragment wherein each amino acid within such peptide fragment can in each case be any amino acid or amino acid analogue.
In some embodiments, a peptide comprises one or more of the following peptide fragments: SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 191, SEQ ID NO: 193, and SEQ ID NO: 194.
TABLE 1 lists some exemplary peptides according to the present disclosure.
In any of SEQ ID NO: 1 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 or fragment thereof, any one or more K residues can be replaced by an R residue or any one or more R residues can be replaced by a K residue. In any of SEQ ID NO: 1 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 or any fragment thereof, any one or more M residues can be replaced by any one of I, L, or V residues, any one or more L residues can be replaced by any one of V, I, or M residues, any one or more I residues can be replaced by any one of M, L, or V residues, or any one or more V residues can be replaced by any one of I, L, or M residues. In any embodiment, at least one of the amino acids alone or in combination can be interchanged in the peptides or peptide fragments as follows: K/R, M/ I/ L/V, G/A, S/T, Q/N, and D/E wherein each letter is each individually any amino acid or amino acid analogue. In some instances, the peptide can contain only one lysine residue, or no lysine residue. In any of SEQ ID NO: 1 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 or any fragment thereof, X can independently be any number of any amino acid or no amino acid. In some cases, a peptide can include the first two N-terminal amino acids GS, as with peptides of SEQ ID NO: 1 - SEQ ID NO: 194, SEQ ID NO: 196, and SEQ ID NO: 198 - SEQ ID NO: 216, or such N-terminal amino acids (GS) can be substituted by any other one or two amino acids. In other cases, a peptide does not include the first two N-terminal amino acids GS, as with peptides of SEQ ID NO: 217 - SEQ ID NO: 410, SEQ ID NO: 412, and SEQ ID NO: 414 - SEQ ID NO: 432. In some cases, the N-terminus of the peptide is blocked, such as by an acetyl group; in other instances the C-terminus of the peptide is block, such as by an amide group.
In some instances, the peptide is any one of SEQ ID NO: 1 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 or a functional fragment thereof. In other embodiments, the peptide of the disclosure further comprises a peptide with 99%, 95%, 90%, 85%, or 80% homology to any one of SEQ ID NO: 1 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432. In further embodiments, the peptide fragment comprises a contiguous fragment of any one of SEQ ID NO: 1 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 that is at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 31, at least 32, at least 33, at least 34, at least 35, at least 36, at least 37, at least 38, at least 39, at least 40, at least 41, at least 42, at least 43, at least 44, at least 45, at least 46 residues long, wherein the peptide fragment is selected from any portion of the peptide. In some embodiments, such peptide fragments contact the cartilage and exhibit properties of those described herein for peptide and peptide-active agent conjugates.
The peptides of the present disclosure can further comprise negative amino acid residues. In some cases, the peptide has 2 or fewer negative amino acid residues. In other cases, the peptide has 4 or fewer negative amino acid residues, 3 or fewer negative amino acid residues, or 1 or fewer negative amino acid residues. The negative amino acid residues can be selected from any negative charged amino acid residues. The negative amino acid residues can selected from either E or D, or a combination of both E and D.
The peptides of the present disclosure can further comprise basic amino acid residues. In some embodiments, basic residues are added to the peptide sequence to increase the charge at physiological pH. The added basic residues can be any basic amino acid. The added basic residues can be selected from K or R, or a combination of K or R.
In some embodiments, the peptide has a charge distribution comprising an acidic region and a basic region. An acidic region can be a nub. A nub is a portion of a peptide extending out of the peptide’s three-dimensional structure. A basic region can be a patch. A patch is a portion of a peptide that does not designate any specific topology characteristic of the peptide’s three-dimensional structure. In further embodiments, a knotted peptide can be 6 or more basic residues and 2 or fewer acidic residues.
The peptides of the present disclosure can further comprise positively charged amino acid residues. In some cases, the peptide has at least 2 positively charged residues. In other cases, the peptide has at least 3 positively charged residues, at least 4 positively charged residues, at least 5 positively charged residues, at least 6 positively charged residues, at least 7 positively charged residues, at least 8 positively charged residues or at least 9 positively charged residues. The positively charged residues can be selected from any positively charged amino acid residues. The positively charged residues can be selected from either K or R, or a combination of K and R.
In addition, the peptides herein can comprise a 4-19 amino acid residue fragment of any of the above sequences containing at least 2 cysteine residues, and at least 2 or 3 positively charged amino acid residues (for example, arginine, lysine or histidine, or any combination of arginine, lysine or histidine). In other embodiments, the peptides herein is a 20-70 amino acid residue fragment of any of the above sequences containing at least 2 cysteine residues, no more than 2 basic residues, and at least 2 or 3 positively charged amino acid residues (for example, arginine, lysine or histidine, or any combination of arginine, lysine or histidine). In some embodiments, such peptide fragments contact the cartilage and exhibit properties of those described herein for peptide and peptide-active agent conjugates.
In some embodiments, the peptide contains one or more disulfide bonds and has a positive net charge at neutral pH. At physiological pH, peptides can have a net charge, for example, of -5, -4, -3, -2, -1, 0, +1, +2, +3, +4, or +5. When the net charge is zero, the peptide can be uncharged or zwitterionic. In some instances, the peptide can have a positive charge at physiological pH. In some instances, the peptide can have a charge ≥ +2 at physiological pH, ≥ +3.5 at physiological pH, ≥ +4.5 at physiological pH. In some embodiments, the peptide contains one or more disulfide bonds and has a positive net charge at neutral pH where the net charge can be +0.5 or less than +0.5, +1 or less than +1, + 1.5 or less than +1.5, +2 or less than +2, +2.5 or less than +2.5, +3 or less than +3, +3.5 or less than +3.5, +4 or less than +4, +4.5 or less than +4.5, +5 or less than +5, +5.5 or less than +5.5, +6 or less than +6, +6.5 or less than +6.5, +7 or less than +7, +7.5 or less than +7.5, +8 or less than +8, +8.5 or less than +8.5, +9 or less than +9.5, + 10 or less than + 10. In some embodiments, the peptide has a negative net charge at physiological pH where the net charge can be -0.5 or less than -0.5, -1 or less than -1, -1.5 or less than -1.5, -2 or less than -2, -2.5 or less than -2.5, -3 or less than -3, -3.5 or less than -3.5, -4 or less than -4, -4.5 or less than -4.5, -5 or less than -5, -5.5 or less than -5.5, -6 or less than -6, -6.5 or less than -6.5, -7 or less than -7, -7.5 or less than -7.5, -8 or less than -8, -8.5 or less than -8.5, -9 or less than -9.5, -10 or less than -10. In some cases, the engineering of one or more mutations within a peptide yields a peptide with an altered isoelectric point, charge, surface charge, or rheology at physiological pH. Such engineering of a mutation to a peptide derived from a scorpion or spider can change the net charge of the complex, for example, by decreasing the net charge by 1, 2, 3, 4, or 5, or by increasing the net charge by 1, 2, 3, 4, or 5. In such cases, the engineered mutation may facilitate the ability of the peptide to contact the cartilage. Suitable amino acid modifications for improving the rheology and potency of a peptide can include conservative or non-conservative mutations. A peptide can comprises at most 1 amino acid mutation, at most 2 amino acid mutations, at most 3 amino acid mutations, at most 4 amino acid mutations, at most 5 amino acid mutations, at most 6 amino acid mutations, at most 7 amino acid mutations, at most 8 amino acid mutations, at most 9 amino acid mutations, at most 10 amino acid mutations, or another suitable number as compared to the sequence of the venom or toxin that the peptide is derived from. In other cases, a peptide, or a functional fragment thereof, comprises at least 1 amino acid mutation, at least 2 amino acid mutations, at least 3 amino acid mutations, at least 4 amino acid mutations, at least 5 amino acid mutations, at least 6 amino acid mutations, at least 7 amino acid mutations, at least 8 amino acid mutations, at least 9 amino acid mutations, at least 10 amino acid mutations, or another suitable number as compared to the sequence of the venom or toxin that the peptide is derived from. In some embodiments, mutations can be engineered within a peptide to provide a peptide that has a desired charge or stability at physiological pH.
In some embodiments, charge can play a role in cartilage homing. The interaction of a peptide of this disclosure in solution and in vivo can be influenced by the isoelectric point (pI) of the knottin peptide and/or the pH of the solution or the local environment it is in. The charge of a peptide in solution can impact the solubility of the protein as well as parameters such as biodistribution, bioavailability, and overall pharmacokinetics. Additionally, positively charged molecules can interact with negatively charged molecules. Positively charged molecules such as the peptides disclosed herein can interact and bind with negatively charged molecules such as the negatively charged extracellular matrix molecules in the cartilage including hyaluranon and aggrecan. Positively charged residues can also interact with specific regions of other proteins and molecules, such as negatively charged residues of receptors or electronegative regions of an ion channel pore on cell surfaces. As such, the pI of a peptide can influence whether a peptide of this disclosure can efficiently home to cartilage. Identifying a correlation between pI and cartilage homing can be an important strategy in identifying lead peptide candidates of the present disclosure. The pI of a peptide can be calculated using a number of different methods including the Expasy pI calculator and the Sillero method. The Expasy pI can be determined by calculating pKa values of amino acids as described in Bjellqvist et al., which were defined by examining polypeptide migration between pH 4.5 to pH 7.3 in an immobilized pH gradient gel environment with 9.2 M and 9.8 M urea at 15° C. or 25° C. (Bjellqvist et al. Electrophoresis. 14(10):1023-31 (1993)). The Sillero method of calculating pI can involve the solution of a polynomial equation and the individual pKas of each amino acid. This method does not use denaturing conditions (urea) (Sillero et al. 179(2): 319-35 (1989)) Using these pI calculation methods and quantifying the cartilage to blood ratio of peptide signal after administration to a subject can be a strategy for identifying a trend or correlation in charge and cartilage homing. In some embodiments, a peptide with a pI above biological pH (~pH 7.4) can exhibit efficient homing to cartilage. In some embodiments, a peptide with a pI of at least 8, at least 9, at least 10, or at least 11 can efficiently home to cartilage. In other embodiments, a peptide with a pI of 11 - 12 can home most efficiently to cartilage. In certain embodiments, a peptide can have a pI of about 9. In other embodiments, a peptide can have a pI of 8 - 10. In some embodiments, more basic peptides can home more efficiently to cartilage. In other embodiments, a high pI alone may not be sufficient to cause cartilage homing of a peptides.
In some embodiments, the tertiary structure and electrostatics of a peptide of the disclosure can impact cartilage homing. Structural analysis or analysis of charge distribution can be a strategy to predict residues important in biological function, such as cartilage homing. For example, several peptides of this disclosure that home to cartilage can be grouped into a structural class defined herein as “hitchins,” and can share the properties of disulfide linkages between C1-C4, C2-C5, and C3-C6. The folding topologies of peptides knotted through three disulfide linkages (C1-C4, C2-C5, and C3-C6), can be broken down into structural families based on the three-dimensional arrangement of the disulfides. Knottins have the C3-C6 disulfide linkage passing through the macrocycle formed by the C1-C4 and C2-C5 disulfide linkages, hitchins have the C2-C5 disulfide linkage passing through the macrocycle formed by the C1-C4 and C3-C6 disulfide linkages, and yet other structural families have the C1-C4 disulfide linkage passing through the macrocycle formed by the C2-C5 and C3-C6 disulfide linkages. Variants of “hitchin” class peptides with preserved disulfide linkages at these cysteine residues, primary sequence identity, and/or structural homology can be a method of identifying or predicting other potential knottin peptide candidates that can home to cartilage. Additionally, members and related members of the calcin family of peptides can also home to cartilage, despite having a distinct tertiary structure from the “hitchin” class of peptides. Calcin peptides are structurally a subset of the knottin peptides, with knottin disulfide connectivity and topology, but are further classified on the basis of functioning to bind and activate ryanodine receptors (RyRs). These receptors are calcium channels that act to regulate the influx and efflux of calcium in muscle (Schwartz et al. Br J Pharmacol 157(3):392-403. (2009)). Variants of the calcin family of peptides with preserved key residues can be one way to predict promising candidates that can home to cartilage. In some embodiments, structural analysis of a peptide of this disclosure can be determined by evaluating peptides for resistance to degradation in buffers with various proteases or reducing agents. Structural analysis of the distribution of charge density on the surface of a peptide can also be a strategy for predicting promising candidates that can home to cartilage. Peptides with large patches of positive surface charge (when at pH 7.5) can home to cartilage.
The NMR solution structures, x-ray crystallography, or crystal structures of related structural homologs can be used to inform mutational strategies that can improve the folding, stability, and manufacturability, while maintaining the ability of a peptide to home to cartilage. They can be used to predict the 3D pharmacophore of a group of structurally homologous scaffolds, as well as to predict possible graft regions of related proteins to create chimeras with improved properties. For example, this strategy can be used to identify critical amino acid positions and loops that can be used to design drugs with improved properties or to correct deleterious mutations that complicate folding and manufacturability for the peptides. These key amino acid positions and loops can be retained while other residues in the peptide sequences can be mutated to improve, change, remove, or otherwise modify function, homing, and activity of the peptide.
Additionally, the comparison of the primary sequences and the tertiary sequences of two or more peptides can be used to reveal sequence and 3D folding patterns that can be leveraged to improve the peptides and parse out the biological activity of these peptides. For example, comparing two different peptide scaffolds that home to cartilage can lead to the identification of conserved pharmacophores that can guide engineering strategies, such as designing variants with improved folding properties. Important pharmacophore, for example, can comprise aromatic residues or basic residues, which can be important for binding.
Improved peptides can also be engineered based upon immungenicity information, such as immunogenicity information predicted by TEPITOPE and TEPITOPEpan. TEPITOPE is a computational approach which uses position specific scoring matrix to provide prediction rules for whether a peptide will bind to 51 different HLA-DR alleles, and TEPITOPEpan is method that uses TEPITOPE to extrapolate from HLA-DR molecules with known binding specificities to HLA-DR molecules with unknown binding specificities based on pocket similarity. For example, TEPITOPE and TEPITOPEpan can be used to determine immunogenicity of peptides that home to cartilage. Comparison of peptides with high immunogenecity to peptides with low immunogenicity can guide engineering strategies for designing variants with decreased immunogenicity.
A peptide of this disclosure can bind to sodium channels. The peptide can bind to calcium channels. The peptide can block potassium channels and/or sodium channels. The peptide can block calcium channels. In some embodiments, the peptide can activate potassium channels and/or sodium channels. In other embodiments, the peptide can activate calcium channels. In still other embodiments, the peptide can be a potassium channel agonist, a potassium channel antagonist, a portion of a potassium channel, a sodium channel agonist, a sodium channel antagonist, a calcium channel agonist, a calcium channel antagonist, a hadrucalcin, a theraphotoxin, a huwentoxin, a kaliotoxin, a cobatoxin or a lectin. In some embodiments, the lectin can be SHL-Ib2. In some embodiments, the peptide can interact with, binds, inhibits, inactivates, or alters expression of ion channels or chloride channels. In some embodiments, the peptide can interact with an Nav1.7 ion channel. In some embodiments, the peptide can interact with a Kv 1.3 ion channel. In still other embodiments, the peptide interacts with proteases, matrix metalloproteinase, inhibits cancer cell migration or metastases, has antimicrobial activity, or has antitumor activity. In addition to acting on matrix metalloproteinases, the peptide can interact with other possible proteases (e.g., elastases).
In some embodiments, the peptide has other therapeutic effects on the cartilage or structures thereof or nearby. Beta defensin expression in articular cartilage can be correlated with immunomodulatory functions as we well as osteoarthritis, autoimmune rheumatic disorders such as systemic lupus erythematosus and rheumatoid arthritis (Vordenbäumen and Schneider 2011, Varoga 2004 and Varoga 2005). In some embodiments, the peptides or their mutants inhibit beta defensins, supplement beta defensins, are competitive inhibitors of beta defensins, active or block activation of beta defensin targets, and are used as immune modulators, or to treat autoimmune, arthritis, infections, and other articular disorders.
The present disclosure can also encompass multimers of the various peptides described herein. Examples of multimers include dimers, trimers, tetramers, pentamers, hexamers, heptamers, and so on. A multimer can be a homomer formed from a plurality of identical subunits or a heteromer formed from a plurality of different subunits. In some embodiments, a peptide of the present disclosure is arranged in a multimeric structure with at least one other peptide,or two, three, four, five, six, seven, eight, nine, ten, or more other peptides. In certain embodiments, the peptides of a multimeric structure each have the same sequence. In alternative embodiments, some or all of the peptides of a multimeric structure have different sequences.
The present disclosure further includes peptide scaffolds that, e.g., can be used as a starting point for generating additional peptides. In some embodiments, these scaffolds can be derived from a variety of knotted peptides or knottins. Some suitable peptides for scaffolds can include, but are not limited to, chlorotoxin, brazzein, circulin, stecrisp, hanatoxin, midkine, hefutoxin, potato carboxypeptidase inhibitor, bubble protein, attractin, α-GI, α-GID, µ-PIIIA, ω-MVIIA, ω-CVID, χ-MrIA, ρ-TIA, conantokin G, contulakin G, GsMTx4, margatoxin, shK, toxin K, chymotrypsin inhibitor (CTI), and EGF epiregulin core.
In some embodiments, the peptide sequences of the disclosure are flanked by additional amino acids. One or more additional amino acids can, for example, confer a desired in vivo charge, isoelectric point, chemical conjugation site, stability, or physiologic property to a peptide.
Identifying sequence homology can be important for determining key residues that preserve cartilage homing function. For example, in some embodiments identification of conserved positively charged residues can be important in preserving cartilage homing in any homologous variants that are made. In other embodiments, identification of basic or aromatic dyads, can be important in preserving interaction and activity with Kv ion channels in homologous variants.
Two or more peptides can share a degree of homology and share similar properties in vivo. For instance, a peptide can share a degree of homology with a peptide of the present disclosure. In some cases, a peptide of the disclosure can have up to about 20% pairwise homology, up to about 25% pairwise homology, up to about 30% pairwise homology, up to about 35% pairwise homology, up to about 40% pairwise homology, up to about 45% pairwise homology, up to about 50% pairwise homology, up to about 55% pairwise homology, up to about 60% pairwise homology, up to about 65% pairwise homology, up to about 70% pairwise homology, up to about 75% pairwise homology, up to about 80% pairwise homology, up to about 85% pairwise homology, up to about 90% pairwise homology, up to about 95% pairwise homology, up to about 96% pairwise homology, up to about 97% pairwise homology, up to about 98% pairwise homology, up to about 99% pairwise homology, up to about 99.5% pairwise homology, or up to about 99.9% pairwise homology with a second peptide. In some cases, a peptide of the disclosure can have at least about 20% pairwise homology, at least about 25% pairwise homology, at least about 30% pairwise homology, at least about 35% pairwise homology, at least about 40% pairwise homology, at least about 45% pairwise homology, at least about 50% pairwise homology, at least about 55% pairwise homology, at least about 60% pairwise homology, at least about 65% pairwise homology, at least about 70% pairwise homology, at least about 75% pairwise homology, at least about 80% pairwise homology, at least about 85% pairwise homology, at least about 90% pairwise homology, at least about 95% pairwise homology, at least about 96% pairwise homology, at least about 97% pairwise homology, at least about 98% pairwise homology, at least about 99% pairwise homology, at least about 99.5% pairwise homology, at least about 99.9% pairwise homology with a second peptide. Various methods and software programs can be used to determine the homology between two or more peptides, such as NCBI BLAST, Clustal W, MAFFT, Clustal Omega, AlignMe, Praline, or another suitable method or algorithm.
In still other instances, the variant nucleic acid molecules of a peptide of any one of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198-216, SEQ ID NO: 237 -SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432 can be identified by either a determination of the sequence identity or homology of the encoded peptide amino acid sequence with the amino acid sequence of any one of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198-216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432, or by a nucleic acid hybridization assay. Such peptide variants can include nucleic acid molecules (1) that remain hybridized with a nucleic acid molecule having the nucleotide sequence of any one of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198-216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432 (or any complement of the previous sequences) under stringent washing conditions, in which the wash stringency is equivalent to 0.5 × -2 × SSC with 0.1% SDS at 55-65° C., and (2) that encode a peptide having at least 70%, at least 80%, at least 90%, at least 95% or greater than 95% sequence identity or homology to the amino acid sequence of any one SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198-216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432. Alternatively, peptide variants of any one SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198-216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432 can be characterized as nucleic acid molecules (1) that remain hybridized with a nucleic acid molecule having the nucleotide sequence of any one SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198-216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432 (or any complement of the previous sequences) under highly stringent washing conditions, in which the wash stringency is equivalent to 0.1 × -0.2 × SSC with 0.1% SDS at 50-65° C., and (2) that encode a peptide having at least 70%, at least 80%, at least 90%, at least 95% or greater than 95% sequence identity or homology to the amino acid sequence of any one of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198-216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432.
Percent sequence identity or homology can be determined by conventional methods. See, for example, Altschul et al., Bull. Math. Bio. 48:603 (1986), and Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1992). Briefly, two amino acid sequences are aligned to optimize the alignment scores using a gap opening penalty of 10, a gap extension penalty of 1, and the “BLOSUM62” scoring matrix of Henikoff and Henikoff (Id.). The sequence identity or homology is then calculated as: ([Total number of identical matches]/[length of the longer sequence plus the number of gaps introduced into the longer sequence in order to align the two sequences])(100).
Additionally, there are many established algorithms available to align two amino acid sequences. For example, the “FASTA” similarity search algorithm of Pearson and Lipman is a suitable protein alignment method for examining the level of sequence identity or homology shared by an amino acid sequence of a peptide disclosed herein and the amino acid sequence of a peptide variant. The FASTA algorithm is described by Pearson and Lipman, Proc. Nat′l Acad. Sci. USA 85:2444 (1988), and by Pearson, Meth. Enzymol. 183:63 (1990). Briefly, FASTA first characterizes sequence similarity by identifying regions shared by the query sequence (e.g., SEQ ID NO: 1) and a test sequence that has either the highest density of identities (if the ktup variable is 1) or pairs of identities (if ktup=2), without considering conservative amino acid substitutions, insertions, or deletions. The ten regions with the highest density of identities are then rescored by comparing the similarity of all paired amino acids using an amino acid substitution matrix, and the ends of the regions are “trimmed” to include only those residues that contribute to the highest score. If there are several regions with scores greater than the “cutoff” value (calculated by a predetermined formula based upon the length of the sequence and the ktup value), then the trimmed initial regions are examined to determine whether the regions can be joined to form an approximate alignment with gaps. Finally, the highest scoring regions of the two amino acid sequences are aligned using a modification of the Needleman-Wunsch-Sellers algorithm (Needleman and Wunsch, J. Mol. Biol. 48:444 (1970); Sellers, Siam J. Appl. Math. 26:787 (1974)), which allows for amino acid insertions and deletions. Illustrative parameters for FASTA analysis are: ktup=1, gap opening penalty=10, gap extension penalty=1, and substitution matrix=BLOSUM62. These parameters can be introduced into a FASTA program by modifying the scoring matrix file (“SMATRIX”), as explained in Appendix 2 of Pearson, Meth. Enzymol. 183:63 (1990).
FASTA can also be used to determine the sequence identity or homology of nucleic acid molecules using a ratio as disclosed above. For nucleotide sequence comparisons, the ktup value can range between one to six, preferably from three to six, most preferably three, with other parameters set as described above.
Some examples of common amino acids that are a “conservative amino acid substitution” are illustrated by a substitution among amino acids within each of the following groups: (1) glycine, alanine, valine, leucine, and isoleucine, (2) phenylalanine, tyrosine, and tryptophan, (3) serine and threonine, (4) aspartate and glutamate, (5) glutamine and asparagine, and (6) lysine, arginine and histidine. The BLOSUM62 table is an amino acid substitution matrix derived from about 2,000 local multiple alignments of protein sequence segments, representing highly conserved regions of more than 500 groups of related proteins (Henikoff and Henikoff, Proc. Nat′l Acad. Sci. USA 89:10915 (1992)). Accordingly, the BLOSUM62 substitution frequencies can be used to define conservative amino acid substitutions that may be introduced into the amino acid sequences of the present invention. Although it is possible to design amino acid substitutions based solely upon chemical properties (as discussed above), the language “conservative amino acid substitution” preferably refers to a substitution represented by a BLOSUM62 value of greater than -1. For example, an amino acid substitution is conservative if the substitution is characterized by a BLOSUM62 value of 0, 1, 2, or 3. According to this system, preferred conservative amino acid substitutions are characterized by a BLOSUM62 value of at least 1 (e.g., 1, 2 or 3), while more preferred conservative amino acid substitutions are characterized by a BLOSUM62 value of at least 2 (e.g., 2 or 3).
Determination of amino acid residues that are within regions or domains that are critical to maintaining structural integrity can be determined. Within these regions one can determine specific residues that can be more or less tolerant of change and maintain the overall tertiary structure of the molecule. Methods for analyzing sequence structure include, but are not limited to, alignment of multiple sequences with high amino acid or nucleotide identity or homology and computer analysis using available software (e.g., the Insight II.RTM. viewer and homology modeling tools; MSI, San Diego, Calif.), secondary structure propensities, binary patterns, complementary packing and buried polar interactions (Barton, G.J., Current Opin. Struct. Biol. 5:372-6 (1995) and Cordes, M.H. et al., Current Opin. Struct. Biol. 6:3-10 (1996)). In general, when designing modifications to molecules or identifying specific fragments determination of structure can typically be accompanied by evaluating activity of modified molecules.
Pairwise sequence alignment is used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid). By contrast, multiple sequence alignment (MSA) is the alignment of three or more biological sequences. From the output of MSA applications, homology can be inferred and the evolutionary relationship between the sequences assessed. One of skill in the art would recognize as used herein, “sequence homology” and “sequence identity” and “percent (%) sequence identity” and “percent (%) sequence homology” have been used interchangeably to mean the sequence relatedness or variation, as appropriate, to a reference polynucleotide or amino acid sequence.
Chemical ModificationsA peptide can be chemically modified one or more of a variety of ways. In some embodiments, the peptide can be mutated to add function, delete function, or modify the in vivo behavior. One or more loops between the disulfide linkages can be modified or replaced to include active elements from other peptides (such as described in Moore and Cochran, Methods in Enzymology, 503, p.223-251, 2012). Amino acids can also be mutated, such as to increase half-life, modify, add or delete binding behavior in vivo, add new targeting function, modify surface charge and hydrophobicity, or allow conjugation sites. N-methylation is one example of methylation that can occur in a peptide of the disclosure. In some embodiments, the peptide can be modified by methylation on free amines. For example, full methylation can be accomplished through the use of reductive methylation with formaldehyde and sodium cyanoborohydride.
A chemical modification can, for instance, extend the half-life of a peptide or change the biodistribution or pharmacokinetic profile. A chemical modification can comprise a polymer, a polyether, polyethylene glycol, a biopolymer, a polyamino acid, a fatty acid, a dendrimer, an Fc region, a simple saturated carbon chain such as palmitate or myristolate, or albumin. The chemical modification of a peptide with an Fc region can be a fusion Fc-peptide. A polyamino acid can include, for example, a polyamino acid sequence with repeated single amino acids (e.g., polyglycine), and a polyamino acid sequence with mixed polyamino acid sequences (e.g., gly-ala-gly-ala) that can or can not follow a pattern, or any combination of the foregoing.
In some embodiments, the peptides of the present disclosure may be modified such that the modification increases the stability and/or the half-life of the peptides. In some embodiments, the attachment of a hydrophobic moiety, such as to the N-terminus, the C-terminus, or an internal amino acid, can be used to extend half-life of a peptide of the present disclosure. In other embodiments, the peptide of the present disclosure can include post-translational modifications (e.g., methylation and/or amidation), which can affect, e.g., serum half-life. In some embodiments, simple carbon chains (e.g., by myristoylation and/or palmitylation) can be conjugated to the fusion proteins or peptides. In some embodiments, the simple carbon chains may render the fusion proteins or peptides easily separable from the unconjugated material. For example, methods that may be used to separate the fusion proteins or peptides from the unconjugated material include, but are not limited to, solvent extraction and reverse phase chromatography. The lipophilic moieties can extend half-life through reversible binding to serum albumin. The conjugated moieties can, e.g., be lipophilic moieties that extend half-life of the peptides through reversible binding to serum albumin. In some embodiments, the lipophilic moiety can be cholesterol or a cholesterol derivative including cholestenes, cholestanes, cholestadienes and oxysterols. In some embodiments, the peptides can be conjugated to myristic acid (tetradecanoic acid) or a derivative thereof. In other embodiments, the peptides of the present disclosure are coupled (e.g., conjugated) to a half-life modifying agent. Examples of half-life modifying agents include but are not limited to: a polymer, a polyethylene glycol (PEG), a hydroxyethyl starch, polyvinyl alcohol, a water soluble polymer, a zwitterionic water soluble polymer, a water soluble poly(amino acid), a water soluble polymer of proline, alanine and serine, a water soluble polymer containing glycine, glutamic acid, and serine, an Fc region, a fatty acid, palmitic acid, or a molecule that binds to albumin.
In some embodiments, the first two N-terminal amino acids (GS) of SEQ ID NO: 1 -SEQ ID NO: 194, SEQ ID NO: 196, or SEQ ID NO: 198 - SEQ ID NO: 216 can serve as a spacer or linker in order to facilitate conjugation or fusion to another molecule, as well as to facilitate cleavage of the peptide from such conjugated or fused molecules. In some embodiments, the fusion proteins or peptides of the present disclosure can be conjugated to other moieties that, e.g., can modify or effect changes to the properties of the peptides.
Active Agent ConjugatesPeptides according to the present disclosure can be conjugated or fused to an agent for use in the treatment of cartilage diseases, disorders, or injuries. For example, in certain embodiments, a peptide as described herein can be fused to another molecule, such as an active agent that provides a functional capability. A peptide can be fused with an active agent through expression of a vector containing the sequence of the peptide with the sequence of the active agent. In various embodiments, the sequence of the peptide and the sequence of the active agent are expressed from the same Open Reading Frame (ORF). In various embodiments, the sequence of the peptide and the sequence of the active agent can comprise a contiguous sequence. The peptide and the active agent can each retain similar functional capabilities in the fusion peptide compared with their functional capabilities when expressed separately.
Furthermore, for example, in certain embodiments, the peptides described herein are attached to another molecule, such as an active agent that provides a functional capability. In some embodiments, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 active agents can be linked to a peptide. Multiple active agents can be attached by methods such as conjugating to multiple lysine residues and/or the N-terminus, or by linking the multiple active agents to a scaffold, such as a polymer or dendrimer and then attaching that agent-scaffold to the peptide (such as described in Yurkovetskiy, A. V., Cancer Res 75(16): 3365-72 (2015). Examples of active agents include but are not limited to: a peptide, an oligopeptide, a polypeptide, a peptidomimetic, a polynucleotide, a polyribonucleotide, a DNA, a cDNA, a ssDNA, a RNA, a dsRNA, a micro RNA, an oligonucleotide, an antibody, a single chain variable fragment (scFv), an antibody fragment, an aptamer, a cytokine, an interferon, a hormone, an enzyme, a growth factor, a checkpoint inhibitor, a PD-1 inhibitor, a PD-L1 inhibitor, a CTLA4 inhibitor, a CD antigen, aa chemokine, a neurotransmitter, an ion channel inhibitor, a G-protein coupled receptor inhibitor, a G-protein coupled receptor activator, a chemical agent, a radiosensitizer, a radioprotectant, a radionuclide, a therapeutic small molecule, a steroid, a corticosteroid, an anti-inflammatory agent, an immune modulator, a complement fixing peptide or protein, a tumor necrosis factor inhibitor, a tumor necrosis factor activator, a tumor necrosis factor receptor family agonist, a tumor necrosis receptor antagonist,, a tumor necrosis factor (TNF) soluble receptor or antibody, caspase protease activator or inhibitor, an NF-κB a RIPK1 and/or RIPK3 inhibitor or activator (e.g., through Toll-like receptors (TLRs) TLR-3 and/or TLR-4, or T-cell receptor (TCR) and the like), a death-receptor ligand (E.g., Fas ligand) activator or inhibitor, TNF receptor family (e.g., TNFR1, TNFR2, lymphotoxin β receptor/TNFRS3, OX40/TNFRSF4, CD40/TNFRSF5, Fas/TNFRSF6, decoy receptor 3/TNFRSF6B, CD27/TNFRSF7, CD30/TNFRSF8, 4-1BB/TNFRSF9, DR4 (death receptor 4/TNFRS10A), DR5 (death receptor 5/TNFRSF10B), decoy receptor ⅟TNFRSF10C, decoy receptor 2/TNFRSF10D, RANK (receptor activator of NF-kappa B/TNFRSF11A), OPG (osteoprotegerin/TNFRSF11B), DR3 (death receptor 3/TNFRSF25), TWEAK receptor/TNFRSF12A, TAC1/TNFRSF13B, BAFF-R (BAFF receptor/TNFRSF13C), HVEM (herpes virus entry mediator/TNFRSF14), nerve growth factor receptor/TNFRSF16, BCMA (B cell maturation antigen/TNFRSF17), GITR (glucocorticoid-induced TNF receptor/TNFRSF18), TAJ (toxicity and JNK inducer/TNFRSF19), RELT/TNFRSF19L, DR6 (death receptor 6/TNFRSF21), TNFRSF22, TNFRSF23, ectodysplasin A2 isoform receptor/TNFRS27, ectodysplasin 1, and anhidrotic receptor, a TNF receptor superfamily ligand including - TNF alpha, lymphotoxin-α, tumor necrosis factor membrane form, tumor necrosis factor shed form, LIGHT, lymphotoxin β2α1 heterotrimer, OX-40 ligand, compound 1 [PMID: 24930776], CD40 ligand, Fas ligand, TL1A, CD70, CD30 ligand, TRAF1, TRAF2, TRAF3, TRAIL, RANK ligand, APRIL, BAFF, B and T lymphocyte attenuator, NGF, BDNF, neurotrophin-3, neurotrophin-4, TL6, ectodysplasin A2, ectodysplasin A1 - a TIMP-3 inhibitor, a BCL-2 family inhibitor, an IAP disruptor, a protease inhibitor, an amino sugar, a chemotherapeutic (whether acting through an apoptotic or non-apoptotic pathway) (Ricci et al. Oncologist 11(4):342-57 (2006)), a cytotoxic chemical, a toxin, a tyrosine kinase inhibitor (e.g. imatinib mesylate), protons, bevacuzimab (antivascular agent), erlotinib (EGFR inhibitor), an anti-infective agent, an antibiotic, an anti-viral agent, an anti-fungal agent, an aminoglycoside, a nonsteroidal anti-inflammatory drug (NSAID), a statin, a nanoparticle, a liposome, a polymer, a biopolymer, a polysaccharide, a proteoglycan, a glycosaminoglycan, polyethylene glycol, a lipid, a dendrimer, a fatty acid, or an Fc domain or an Fc region, or an active fragment or a modification thereof. Any combination of the above active agents can be co-delivered with peptides or peptide conjugates of this disclosure. Additionally, in some embodiments, other co-therapies such as proton therapy or ablative radiotherapy can be administered to a subject in need thereof along with peptides or peptide conjugates of this disclosure. In some embodiments, the peptide is covalently or non-covalently linked to an active agent, e.g., directly or via a linker. TNF blockers suppress the immune system by blocking the activity of TNF, a substance in the body that can cause inflammation and lead to immune-system diseases, such as Crohn’s disease, ulcerative colitis, rheumatoid arthritis, ankylosing spondylitis, psoriatic arthritis and plaque psoriasis. The drugs in this class include Remicade (infliximab), Enbrel (etanercept), Humira (adalimumab), Cimzia (certolizumab pegol) and Simponi (golimumab). The peptide disclosed herein can be used to home, distribute to, target, directed to, is retained by, accumulate in, migrate to, and/or bind to cartilage, and thus also be used for localizing the attached or fused active agent. Furthermore, knotted chlorotoxin peptide can be internalized in cells (Wiranowska, M., Cancer Cell Int., 11: 27 (2011)). Therefore, cellular internalization, subcellular localization, and intracellular trafficking after internalization of the active agent peptide conjugate or fusion peptide can be important factors in the efficacy of an active agent conjugate or fusion. (Ducry, L., Antibody Drug Conjugates (2013); and Singh, S. K., Pharm Res. 32(11): 3541-3571 (2015)). Exemplary linkers suitable for use with the embodiments herein are discussed in further detail below.
The peptides or fusion peptides of the present disclosure can also be conjugated to other moieties that can serve other roles, such as providing an affinity handle (e.g., biotin) for retrieval of the peptides from tissues or fluids. For example, peptides or fusion peptides of the present disclosure can also be conjugated to biotin. In addition to extension of half-life, biotin could also act as an affinity handle for retrieval of peptides or fusion peptides from tissues or other locations. In some embodiments, fluorescent biotin conjugates that can act both as a detectable label and an affinity handle can be used. Non limiting examples of commercially available fluorescent biotin conjugates include Atto 425-Biotin, Atto 488-Biotin, Atto 520-Biotin, Atto-550 Biotin, Atto 565-Biotin, Atto 590-Biotin, Atto 610-Biotin, Atto 620-Biotin, Atto 655-Biotin, Atto 680-Biotin, Atto 700-Biotin, Atto 725-Biotin, Atto 740-Biotin, fluorescein biotin, biotin-4-fluorescein, biotin-(5-fluorescein) conjugate, and biotin-B-phycoerythrin, Alexa fluor 488 biocytin, Alexa flour 546, Alexa Fluor 549, lucifer yellow cadaverine biotin-X, Lucifer yellow biocytin, Oregon green 488 biocytin, biotin-rhodamine and tetramethylrhodamine biocytin. In some other examples, the conjugates could include chemiluminescent compounds, colloidal metals, luminescent compounds, enzymes, radioisotopes, and paramagnetic labels. In some embodiments, the peptide described herein can be attached to another molecule. For example, the peptide sequence also can be attached to another active agent (e.g., small molecule, peptide, polypeptide, polynucleotide, antibody, aptamer, cytokine, growth factor, neurotransmitter, an active fragment or modification of any of the preceding, fluorophore, radioisotope, radionuclide chelator, acyl adduct, chemical linker, or sugar, etc.). In some embodiments, the peptide can be fused with, or covalently or non-covalently linked to an active agent.
Additionally, more than one peptide sequence derived from a toxin or venom can be present on or fused with a particular peptide. A peptide can be incorporated into a biomolecule by various techniques. A peptide can be incorporated by a chemical transformation, such as the formation of a covalent bond, such as an amide bond. A peptide can be incorporated, for example, by solid phase or solution phase peptide synthesis. A peptide can be incorporated by preparing a nucleic acid sequence encoding the biomolecule, wherein the nucleic acid sequence includes a subsequence that encodes the peptide. The subsequence can be in addition to the sequence that encodes the biomolecule, or can substitute for a subsequence of the sequence that encodes the biomolecule.
Detectable Agent ConjugatesA peptide can be conjugated to an agent used in imaging, research, therapeutics, theranostics, pharmaceuticals, chemotherapy, chelation therapy, targeted drug delivery, and radiotherapy. The agent can be a detectable agent. In some embodiments, a knottin peptide is conjugated to detectble agents, such as a metal, a radioisotope, a dye, fluorophore, or another suitable material that can be used in imaging. Non-limiting examples of radioisotopes include alpha emitters, beta emitters, positron emitters, and gamma emitters. In some embodiments, the metal or radioisotope is selected from the group consisting of actinium, americium, bismuth, cadmium, cesium, cobalt, europium, gadolinium, iridium, lead, lutetium, manganese, palladium, polonium, radium, ruthenium, samarium, strontium, technetium, thallium, and yttrium. In some embodiments, the metal is actinium, bismuth, lead, radium, strontium, samarium, or yttrium. In some embodiments, the radioisotope is actinium-225 or lead-212. In some embodiments, the fluorophore is a fluorescent agent emitting electromagnetic radiation at a wavelength between 650 nm and 4000 nm, such emissions being used to detect such agent. In some embodiments the fluorophore is a fluorescent agent is selected from the group consisting of Non-limiting examples of fluorescent dyes that could be used as a conjugating molecule in the present disclosure include DyLight-680, DyLight-750, VivoTag-750, DyLight-800, IRDye-800, VivoTag-680, Cy5.5, or indocyanine green (ICG). In some embodiments, near infrared dyes often include cyanine dyes. Additional non-limiting examples of fluorescent dyes for use as a conjugating molecule in the present disclosure include acradine orange or yellow, Alexa Fluors and any derivative thereof, 7-actinomycin D, 8-anilinonaphthalene-1-sulfonic acid, ATTO dye and any derivative thereof, auramine-rhodamine stain and any derivative thereof, bensantrhone, bimane, 9-10-bis(phenylethynyl)anthracene, 5,12 - bis(phenylethynyl)naththacene, bisbenzimide, brainbow, calcein, carbodyfluorescein and any derivative thereof, 1-chloro-9,10-bis(phenylethynyl)anthracene and any derivative thereof, DAPI, DiOC6, DyLight Fluors and any derivative thereof, epicocconone, ethidium bromide, FlAsH-EDT2, Fluo dye and any derivative thereof, FluoProbe and any derivative thereof, Fluorescein and any derivative thereof, Fura and any derivative thereof, GelGreen and any derivative thereof, GelRed and any derivative thereof, fluorescent proteins and any derivative thereof, m isoform proteins and any derivative thereof such as for example mCherry, hetamethine dye and any derivative thereof, hoeschst stain, iminocoumarin, indian yellow, indo-1 and any derivative thereof, laurdan, lucifer yellow and any derivative thereof, luciferin and any derivative thereof, luciferase and any derivative thereof, mercocyanine and any derivative thereof, nile dyes and any derivative thereof, perylene, phloxine, phyco dye and any derivative thereof, propium iodide, pyranine, rhodamine and any derivative thereof, ribogreen, RoGFP, rubrene, stilbene and any derivative thereof, sulforhodamine and any derivative thereof, SYBR and any derivative thereof, synapto-pHluorin, tetraphenyl butadiene, tetrasodium tris, Texas Red, Titan Yellow, TSQ, umbelliferone, violanthrone, yellow fluroescent protein and YOYO-1. Other Suitable fluorescent dyes include, but are not limited to, fluorescein and fluorescein dyes (e.g., fluorescein isothiocyanine or FITC, naphthofluorescein, 4′, 5′-dichloro-2’, 7‘-dimethoxyfluorescein, 6-carboxyfluorescein or FAM, etc.), carbocyanine, merocyanine, styryl dyes, oxonol dyes, phycoerythrin, erythrosin, eosin, rhodamine dyes (e.g., carboxytetramethyl-rhodamine or TAMRA, carboxyrhodamine 6G, carboxy-X-rhodamine (ROX), lissamine rhodamine B, rhodamine 6G, rhodamine Green, rhodamine Red, tetramethylrhodamine (TMR), etc.), coumarin and coumarin dyes (e.g., methoxycoumarin, dialkylaminocoumarin, hydroxycoumarin, aminomethylcoumarin (AMCA), etc.), Oregon Green Dyes (e.g., Oregon Green 488, Oregon Green 500, Oregon Green 514., etc.), Texas Red, Texas Red-X, SPECTRUM RED, SPECTRUM GREEN, cyanine dyes (e.g., CY-3, Cy-5, CY-3.5, CY-5.5, etc.), ALEXA FLUOR dyes (e.g., ALEXA FLUOR 350, ALEXA FLUOR 488, ALEXA FLUOR 532, ALEXA FLUOR 546, ALEXA FLUOR 568, ALEXA FLUOR 594, ALEXA FLUOR 633, ALEXA FLUOR 660, ALEXA FLUOR 680, etc.), BODIPY dyes (e.g., BODIPY FL, BODIPY R6G, BODIPY TMR, BODIPY TR, BODIPY 530/550, BODIPY 558/568, BODIPY 564/570, BODIPY 576/589, BODIPY 581/591, BODIPY 630/650, BODIPY 650/665, etc.), IRDyes (e.g., IRD40, IRD 700, IRD 800, etc.), and the like. Additional suitable detectable agents are described in PCT/US14/56177. Non-limiting examples of radioisotopes include alpha emitters, beta emitters, positron emitters, and gamma emitters. In some embodiments, the metal or radioisotope is selected from the group consisting of actinium, americium, bismuth, cadmium, cesium, cobalt, europium, gadolinium, iridium, lead, lutetium, manganese, palladium, polonium, radium, ruthenium, samarium, strontium, technetium, thallium, and yttrium. In some embodiments, the metal is actinium, bismuth, lead, radium, strontium, samarium, or yttrium. In some embodiments, the radioisotope is actinium-225 or lead-212.
Other embodiments of the present disclosure provide peptides conjugated to a radiosensitizer or photosensitizer. Examples of radiosensitizers include but are not limited to: ABT-263, ABT-199, WEHI-539, paclitaxel, carboplatin, cisplatin, oxaliplatin, gemcitabine, etanidazole, misonidazole, tirapazamine, and nucleic acid base derivatives (e.g., halogenated purines or pyrimidines, such as 5-fluorodeoxyuridine). Examples of photosensitizers include but are not limited to: fluorescent molecules or beads that generate heat when illuminated, porphyrins and porphyrin derivatives (e.g., chlorins, bacteriochlorins, isobacteriochlorins, phthalocyanines, and naphthalocyanines), metalloporphyrins, metallophthalocyanines, angelicins, chalcogenapyrrillium dyes, chlorophylls, coumarins, flavins and related compounds such as alloxazine and riboflavin, fullerenes, pheophorbides, pyropheophorbides, cyanines (e.g., merocyanine 540), pheophytins, sapphyrins, texaphyrins, purpurins, porphycenes, phenothiaziniums, methylene blue derivatives, naphthalimides, nile blue derivatives, quinones, perylenequinones (e.g., hypericins, hypocrellins, and cercosporins), psoralens, quinones, retinoids, rhodamines, thiophenes, verdins, xanthene dyes (e.g., eosins, erythrosins, rose bengals), dimeric and oligomeric forms of porphyrins, and prodrugs such as 5-aminolevulinic acid. Advantageously, this approach allows for highly specific targeting of diseased cells (e.g., cancer cells) using both a therapeutic agent (e.g., drug) and electromagnetic energy (e.g., radiation or light) concurrently. In some embodiments, the peptide is covalently or non-covalently linked to the agent, e.g., directly or via a linker. Exemplary linkers suitable for use with the embodiments herein are discussed in further detail below
LinkersPeptides according to the present disclosure that home, target, migrate to, are retained by, accumulate in, and/or bind to, or are directed to the cartilage can be attached to another moiety (e.g., an active agent), such as a small molecule, a second peptide, a protein, an antibody, an antibody fragment, an aptamer, polypeptide, polynucleotide, a fluorophore, a radioisotope, a radionuclide chelator, a polymer, a biopolymer, a fatty acid, an acyl adduct, a chemical linker, or sugar or other active agent described herein through a linker, or directly in the absence of a linker.
A peptide can be directly attached to another molecule by a covalent attachment. For example, the peptide is attached to a terminus of the amino acid sequence of a larger polypeptide or peptide molecule, or is attached to a side chain, such as the side chain of a lysine, serine, threonine, cysteine, tyrosine, aspartic acid, a non-natural amino acid residue, or glutamic acid residue. The attachment can be via an amide bond, an ester bond, an ether bond, a carbamate bond, a carbon-nitrogen bond, a triazole, a macrocycle, an oxime bond, a hydrazone bond, a carbon-carbon single double or triple bond, a disulfide bond, or a thioether bond. In some embodiments, similar regions of the disclosed peptide(s) itself (such as a terminus of the amino acid sequence, an amino acid side chain, such as the side chain of a lysine, serine, threonine, cysteine, tyrosine, aspartic acid, a non-natural amino acid residue, or glutamic acid residue, via an amide bond, an ester bond, an ether bond, a carbamate bond, a carbon-nitrogen bond, a triazole, a macrocycle, an oxime bond, a hydrazone bond, a carbon-carbon single double or triple bond, a disulfide bond, or a thioether bond, or linker as described herein) can be used to link other molecules.
Attachment via a linker can involve incorporation of a linker moiety between the other molecule and the peptide. The peptide and the other molecule can both be covalently attached to the linker. The linker can be cleavable, non-cleavable, self-immolating, hydrophilic, or hydrophobic. The linker can have at least two functional groups with one bonded to the peptide, the other bonded to the other molecule, and a linking portion between the two functional groups.
Non-limiting examples of the functional groups for attachment can include functional groups capable of forming an amide bond, an ester bond, an ether bond, a carbonate bond, a carbamate bond, or a thioether bond. Non-limiting examples of functional groups capable of forming such bonds can include amino groups; carboxyl groups; hydroxyl groups; aldehyde groups; azide groups; alkyne and alkene groups; ketones; hydrazides; acid halides such as acid fluorides, chlorides, bromides, and iodides; acid anhydrides, including symmetrical, mixed, and cyclic anhydrides; carbonates; carbonyl functionalities bonded to leaving groups such as cyano, succinimidyl, and N-hydroxysuccinimidyl; hydroxyl groups; sulfhydryl groups; and molecules possessing, for example, alkyl, alkenyl, alkynyl, allylic, or benzylic leaving groups, such as halides, mesylates, tosylates, triflates, epoxides, phosphate esters, sulfate esters, and besylates.
Non-limiting examples of the linking portion can include alkylene, alkenylene, alkynylene, polyether, such as polyethylene glycol (PEG), hydroxy carboxylic acids, polyester, polyamide, polyamino acids, polypeptides, cleavable peptides, valine-citrulline, aminobenzylcarbamates, D-amino acids, and polyamine, any of which being unsubstituted or substituted with any number of substituents, such as halogens, hydroxyl groups, sulfhydryl groups, amino groups, nitro groups, nitroso groups, cyano groups, azido groups, sulfoxide groups, sulfone groups, sulfonamide groups, carboxyl groups, carboxaldehyde groups, imine groups, alkyl groups, halo-alkyl groups, alkenyl groups, halo-alkenyl groups, alkynyl groups, halo-alkynyl groups, alkoxy groups, aryl groups, aryloxy groups, aralkyl groups, arylalkoxy groups, heterocyclyl groups, acyl groups, acyloxy groups, carbamate groups, amide groups, urethane groups, epoxides, and ester groups.
Non-limiting examples of linkers include:
wherein each n is independently 0 to about 1,000; 1 to about 1,000; 0 to about 500; 1 to about 500; 0 to about 250; 1 to about 250; 0 to about 200; 1 to about 200; 0 to about 150; 1 to about 150; 0 to about 100; 1 to about 100; 0 to about 50; 1 to about 50; 0 to about 40; 1 to about 40; 0 to about 30; 1 to about 30; 0 to about 25; 1 to about 25; 0 to about 20; 1 to about 20; 0 to about 15; 1 to about 15; 0 to about 10; 1 to about 10; 0 to about 5; or 1 to about 5. In some embodiments, each n is independently 0, about 1, about 2, about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34, about 35, about 36, about 37, about 38, about 39, about 40, about 41, about 42, about 43, about 44, about 45, about 46, about 47, about 48, about 49, or about 50. In some embodiments, m is 1 to about 1,000; 1 to about 500; 1 to about 250; 1 to about 200; 1 to about 150; 1 to about 100; 1 to about 50; 1 to about 40; 1 to about 30; 1 to about 25; 1 to about 20; 1 to about 15; 1 to about 10; or 1 to about 5. In some embodiments, m is 0, about 1, about 2, about 3,about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34, about 35, about 36, about 37, about 38, about 39, about 40, about 41, about 42, about 43, about 44, about 45, about 46, about 47, about 48, about 49, or about 50.
In some cases a linker can be a succinic linker, and a drug can be attached to a peptide via an ester bond or an amide bond with two methylene carbons in between. In other cases, a linker can be any linker with both a hydroxyl group and a carboxylic acid, such as hydroxy hexanoic acid or lactic acid.
The linker can be a cleavable or a noncleavable linker. The use of a cleavable linker permits release of the conjugated moiety (e.g., a therapeutic agent) from the peptide, e.g., after targeting to the cartilage. In some cases the linker is enzyme cleavable, e.g., a valine-citrulline linker. In some embodiments, the linker contains a self-immolating portion. In other embodiments, the linker includes one or more cleavage sites for a specific protease, such as a cleavage site for matrix metalloproteases (MMPs), thrombin, or cathepsin. Alternatively or in combination, the linker is cleavable by other mechanisms, such as via pH, reduction, or hydrolysis. A hydrolytically labile linker, (amongst other cleavable linkers described herein) can be advantageous in terms of releasing active agents from the peptide. For example, an active agent in a conjugate form with the peptide may not be active, but upon release from the conjugate after targeting to the cartilage, the active agent is active.
The rate of hydrolysis of the linker can be tuned. For example, the rate of hydrolysis of linkers with unhindered esters is faster compared to the hydrolysis of linkers with bulky groups next an ester carbonyl. A bulky group can be a methyl group, an ethyl group, a phenyl group, a ring, or an isopropyl group, or any group that provides steric bulk. In some cases, the steric bulk can be provided by the drug itself, such as by ketorolac when conjugated via its carboxylic acid. The rate of hydrolysis of the linker can be tuned according to the residency time of the conjugate in the cartilage. For example, when a peptide is cleared from the cartilage relatively quickly, the linker can be tuned to rapidly hydrolyze. In contrast, for example, when a peptide has a longer residence time in the cartilage, a slower hydrolysis rate can allow for extended delivery of an active agent. This can be important when the peptide is used to deliver a drug to the cartilage. “Programmed hydrolysis in designing paclitaxel prodrug for nanocarrier assembly” Sci Rep 2015, 5, 12023 Fu et al., provides an example of modified hydrolysis rates.
Peptide StabilityA peptide of the present disclosure can be stable in various biological conditions. For example, any peptide of SEQ ID NO: 1 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 can exhibit resistance to reducing agents, proteases, oxidative conditions, or acidic conditions.
In some cases, biologic molecules (such as peptides and proteins) can provide therapeutic functions, but such therapeutic functions are decreased or impeded by instability caused by the in vivo environment. (Moroz et al. Adv Drug Deliv Rev 101: 108-21 (2016), Mitragotri et al. Nat Rev Drug Discov 13(9):655-72 (2014), Bruno et al. Ther Deliv (11):1443-67 (2013), Sinha et al. Crit Rev Ther Drug Carrier Syst. 24(1):63-92 (2007), Hamman et al. BioDrugs 19(3):165-77 (2005)). For instance, the GI tract can contain a region of low pH (e.g. pH ~1), a reducing environment, or a protease-rich environment that can degrade peptides and proteins. Proteolytic activity in other areas of the body, such as the mouth, eye, lung, intranasal cavity, joint, skin, vaginal tract, mucous membranes, and serum, can also be an obstacle to the delivery of functionally active peptides and polypeptides. Additionally, the half-life of peptides in serum can be very short, in part due to proteases, such that the peptide can be degraded too quickly to have a lasting therapeutic effect when administering reasonable dosing regimens. Likewise, proteolytic activity in cellular compartments such as lysosomes and reduction activity in lysosomes and the cytosol can degrade peptides and proteins such that they may be unable to provide a therapeutic function on intracellular targets. Therefore, peptides that are resistant to reducing agents, proteases, and low pH may be able to provide enhanced therapeutic effects or enhance the therapeutic efficacy of co-formulated or conjugated active agents in vivo.
Additionally, oral delivery of drugs can be desirable in order to target certain areas of the body (e.g., disease in the GI tract such as colon cancer, irritable bowel disorder, infections, metabolic disorders, and constipation) despite the obstacles to the delivery of functionally active peptides and polypeptides presented by this method of administration. For example, oral delivery of drugs can increase compliance by providing a dosage form that is more convenient for patients to take as compared to parenteral delivery. Oral delivery can be useful in treatment regimens that have a large therapeutic window. Therefore, peptides that are resistant to reducing agents, proteases, and low pH can allow for oral delivery of peptides without nullifying their therapeutic function.
Peptide Resistance to Reducing AgentsPeptides of this disclosure can contain one or more cysteines, which can participate in disulfide bridges that can be integral to preserving the folded state of the peptide. Exposure of peptides to biological environments with reducing agents can result in unfolding of the peptide and loss of functionality and bioactivity. For example, glutathione (GSH) is a reducing agent that can be present in many areas of the body and in cells, and can reduce disulfide bonds. As another example, a peptide can become reduced upon cellular internalization during trafficking of a peptide across the gastrointestinal epithelium after oral administration A peptide can become reduced upon exposure to various parts of the GI tract. The GI tract can be a reducing environment, which can inhibit the ability of therapeutic molecules with disulfide bonds to have optimal therapeutic efficacy, due to reduction of the disulfide bonds. A peptide can also be reduced upon entry into a cell, such as after internalization by endosomes or lysosomes or into the cytosol, or other cellular compartments. Reduction of the disulfide bonds and unfolding of the peptide can lead to loss of functionality or affect key pharmacokinetic parameters such as bioavailability, peak plasma concentration, bioactivity, and half-life. Reduction of the disulfide bonds can also lead to increased susceptibility of the peptide to subsequent degradation by proteases, resulting in rapid loss of intact peptide after administration. In some embodiments, a peptide that is resistant to reduction can remain intact and can impart a functional activity for a longer period of time in various compartments of the body and in cells, as compared to a peptide that is more readily reduced..
In certain embodiments, the peptides of this disclosure can be analyzed for the characteristic of resistance to reducing agents to identify stable peptides. In some embodiments, the peptides of this disclosure can remain intact after being exposed to different molarities of reducing agents such as 0.00001 M - 0.0001 M, 0.0001 M - 0.001 M, 0.001 M - 0.01 M, 0.01 M -0.05 M, 0.05 M - 0.1 M, for greater 15 minutes or more. In some embodiments, the reducing agent used to determine peptide stability can be dithiothreitol (DTT), Tris(2-carboxyethyl)phosphine HCl (TCEP), 2-Mercaptoethanol, (reduced) glutathione (GSH), or any combination thereof. In some embodiments, at least 5%-10%, at least 10%-20%, at least 20%-30%, at least 30%-40%, at least 40%-50%, at least 50%-60%, at least 60%-70%, at least 70%-80%, at least 80%-90%, or at least 90%-100% of the peptide remains intact after exposure to a reducing agent.
Peptide Resistance to ProteasesThe stability of peptides of this disclosure can be determined by resistance to degradation by proteases. Proteases, also referred to as peptidases or proteinases, can be enzymes that can degrade peptides and proteins by breaking bonds between adjacent amino acids. Families of proteases with specificity for targeting specific amino acids can include serine proteases, cysteine proteases, threonine proteases, aspartic proteases, glutamic proteases, esterases, serum proteases, and asparagine proteases. Additionally, metalloproteases, matrix metalloproteases, elastase, carboxypeptidases, Cytochrome P450 enzymes, and cathepsins can also digest peptides and proteins. Proteases can be present at high concentration in blood, in mucous membranes, lungs, skin, the GI tract, the mouth, nose, eye, and in compartments of the cell. Misregulation of proteases can also be present in various diseases such as rheumatoid arthritis and other immune disorders. Degradation by proteases can reduce bioavailability, biodistribution, half-life, and bioactivity of therapeutic molecules such that they are unable to perform their therapeutic function. In some embodiments, peptides that are resistant to proteases can better provide therapeutic activity at reasonably tolerated concentrations in vivo.
In some embodiments, peptides of this disclosure can resist degradation by any class of protease. In certain embodiments, peptides of this disclosure resist degradation by pepsin (which can be found in the stomach), trypsin (which can be found in the duodenum), serum proteases, or any combination thereof. In certain embodiments, peptides of this disclosure can resist degradation by lung proteases (e.g., serine, cysteinyl, and aspartyl proteases, metalloproteases, neutrophil elastase, alpha-1 antitrypsin, secretory leucoprotease inhibitor, elafin), or any combination thereof. In some embodiments, the proteases used to determine peptide stability can be pepsin, trypsin, chymotrypsin, or any combination thereof. In some embodiments, at least 5%-10%, at least 10%-20%, at least 20%-30%, at least 30%-40%, at least 40%-50%, at least 50%-60%, at least 60%-70%, at least 70%-80%, at least 80%-90%, or at least 90%-100% of the peptide remains intact after exposure to a protease. Peptides of SEQ ID NO: 212, SEQ ID NO: 24, and SEQ ID NO: 111 can have particular structural qualities, which make them more resistant to protease degradation. For example, peptide of SEQ ID NO: 24 and SEQ ID NO: 112 exhibit the “hitchin” topology as described previously, which can be associated with resistance to protease and chemical degradation.
Peptide Stability in Acidic ConditionsPeptides of this disclosure can be administered in biological environments that are acidic. For example, after oral administration, peptides can experience acidic environmental conditions in the gastric fluids of the stomach and gastrointestinal (GI) tract. The pH of the stomach can range from ~1-4 and the pH of the GI tract ranges from acidic to normal physiological pH descending from the upper GI tract to the colon. In addition, the vagina, late endosomes, and lysosomes can also hav acidic pH values, such as less than pH 7. These acidic conditions can lead to denaturation of peptides and proteins into unfolded states. Unfolding of peptides and proteins can lead to increased susceptibility to subsequent digestion by other enzymes as well as loss of biological activity of the peptide.
In certain embodiments, the peptides of this disclosure can resist denaturation and degradation in acidic conditions and in buffers, which simulate acidic conditions. In certain embodiments, peptides of this disclosure can resist denaturation or degradation in buffer with a pH less than 1, a pH less than 2, a pH less than 3, a pH less than 4, a pH less than 5, a pH less than 6, a pH less than 7, or a pH less than 8. In some embodiments, peptides of this disclosure remain intact at a pH of 1-3. In certain embodiments, at least 5%-10%, at least 10%-20%, at least 20%-30%, at least 30%-40%, at least 40%-50%, at least 50%-60%, at least 60%-70%, at least 70%-80%, at least 80%-90%, or at least 90%-100% of the peptide remains intact after exposure to a buffer with a pH less than 1, a pH less than 2, a pH less than 3, a pH less than 4, a pH less than 5, a pH less than 6, a pH less than 7, or a pH less than 8. In other embodiments, at least 5%-10%, at least 10%-20%, at least 20%-30%, at least 30%-40%, at least 40%-50%, at least 50%-60%, at least 60%-70%, at least 70%-80%, at least 80%-90%, or at least 90%-100% of the peptide remains intact after exposure to a buffer with a pH of 1-3. In other embodiments, the peptides of this disclosure can be resistant to denaturation or degradation in simulated gastric fluid (pH 1-2). In some embodiments, at least 5-10%, at least 10%-20%, at least 20%-30%, at least 30%-40%, at least 40%-50%, at least 50%-60%, at least 60%-70%, at least 70%-80%, at least 80%-90%, or at least 90-100% of the peptide remains intact after exposure to simulated gastric fluid. In some embodiments, low pH solutions such as simulated gastric fluid or citrate buffers can be used to determine peptide stability.
Peptide Stability at High TemperaturesPeptides of this disclosure can be administered in biological environments with high temperatures. For example, after oral administration, peptides can experience high temperatures in the body. Body temperature can range from 36° C. to 40° C. High temperatures can lead to denaturation of peptides and proteins into unfolded states. Unfolding of peptides and proteins can lead to increased susceptibility to subsequent digestion by other enzymes as well as loss of biological activity of the peptide. In some embodiments, a peptide of this disclosure can remain intact at temperatures from 25° C. to 100° C. High temperatures can lead to faster degradation of peptides. Stability at a higher temperature can allow for storage of the peptide in tropical environments or areas where access to refrigeration is limited. In certain embodiments, 5%-100% of the peptide can remain intact after exposure to 25° C. for 6 months to 5 years. 5%-100% of a peptide can remain intact after exposure to 70° C. for 15 minutes to 1 hour. 5%-100% of a peptide can remain intact after exposure to 100° C. for 15 minutes to 1 hour. In other embodiments, at least 5%-10%, at least 10%-20%, at least 20%-30%, at least 30%-40%, at least 40%-50%, at least 50%-60%, at least 60%-70%, at least 70%-80%, at least 80%-90%, or at least 90%-100% of the peptide remains intact after exposure to 25° C. for 6 months to 5 years. In other embodiments, at least 5%-10%, at least 10%-20%, at least 20%-30%, at least 30%-40%, at least 40%-50%, at least 50%-60%, at least 60%-70%, at least 70%-80%, at least 80%-90%, or at least 90%-100% of the peptide remains intact after exposure to 70° C. for 15 minutes to 1 hour. In other embodiments, at least 5%-10%, at least 10%-20%, at least 20%-30%, at least 30%-40%, at least 40%-50%, at least 50%-60%, at least 60%-70%, at least 70%-80%, at least 80%-90%, or at least 90%-100% of the peptide remains intact after exposure to 100° C. for 15 minutes to 1 hour.
Pharmacokinetics of PeptidesThe pharmacokinetics of any of the peptides of this disclosure can be determined after administration of the peptide via different routes of administration. For example, the pharmacokinetic parameters of a peptide of this disclosure can be quantified after intravenous, subcutaneous, intramuscular, rectal, aerosol, parenteral, ophthalmic, pulmonary, transdermal, vaginal, optic, nasal, oral, sublingual, inhalation, dermal, intrathecal, intranasal, intra-articular, peritoneal, buccal, synovial, or topical administration. Peptides of the present disclosure can be analyzed by using tracking agents such as radiolabels or fluorophores. For example, a radiolabeled peptides of this disclosure can be administered via various routes of administration. Peptide concentration or dose recovery in various biological samples such as plasma, urine, feces, any organ, skin, muscle, and other tissues can be determined using a range of methods including HPLC, fluorescence detection techniques (TECAN quantification, flow cytometry, iVIS), or liquid scintillation counting.
The methods and compositions described herein can relate to pharmacokinetics of peptide administration via any route to a subject. Pharmacokinetics can be described using methods and models, for example, compartmental models or noncompartmental methods. Compartmental models include but are not limited to monocompartmental model, the two compartmental model, the multicompartmental model or the like. Models can be divided into different compartments and can be described by the corresponding scheme. For example, one scheme is the absorption, distribution, metabolism and excretion (ADME) scheme. For another example, another scheme is the liberation, absorption, distribution, metabolism and excretion (LADME) scheme. In some aspects, metabolism and excretion can be grouped into one compartment referred to as the elimination compartment. For example, liberation can include liberation of the active portion of the composition from the delivery system, absorption includes absorption of the active portion of the composition by the subject, distribution includes distribution of the composition through the blood plasma and to different tissues, metabolism, which includes metabolism or inactivation of the composition and finally excretion, which includes excretion or elimination of the composition or the products of metabolism of the composition. Compositions administered intravenously to a subject can be subject to multiphasic pharmacokinetic profiles, which can include but are not limited to aspects of tissue distribution and metabolism/excretion. As such, the decrease in plasma or serum concentration of the composition is often biphasic, including, for example an alpha phase and a beta phase, occasionally a gamma, delta or other phase is observed
Pharmacokinetics includes determining at least one parameter associated with administration of a peptide to a subject. In some aspects, parameters include at least the dose (D), dosing interval (τ), area under curve (AUC), maximum concentration (Cmax), minimum concentration reached before a subsequent dose is administered (Cmin), minimum time (Tmin), maximum time to reach Cmax (Tmax), volume of distribution (Vd), steady-state volume of distribution (Vss), back-extrapolated concentration at time 0 (C0), steady state concentration (Css), elimination rate constant (ke), infusion rate (kin), clearance (CL), bioavailability (f), fluctuation (%PTF) and elimination half-life (t½).
In certain embodiments, the peptides of any of SEQ ID NO: 1 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 exhibit optimal pharmacokinetic parameters after oral administration. In other embodiments, the peptides of any of SEQ ID NO: 1 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 exhibit optimal pharmacokinetic parameters after any route of administration, such as oral administration, inhalation, intranasal administration, topical administration, intravenous administration, subcutaneous administration, intra-articular administration, intramuscular administration, intraperitoneal administration, or any combination thereof.
In some embodiments any peptide of SEQ ID NO: 1 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 exhibits an average Tmax of 0.5 - 12 hours, or 1-48 hours at which the Cmax is reached, an average bioavailability in serum of 0.1% - 10% in the subject after administering the peptide to the subject by an oral route, an average bioavailability in serum of less than 0.1% after oral administration to a subject for delivery to the GI tract, an average bioavailability in serum of 10-100% after parenteral administration, an average t½ of 0.1 hours - 168 hours, or 0.25 hours - 48 hours in a subject after administering the peptide to the subject, an average clearance (CL) of 0.5-100 L/hour or 0.5 - 50 L/hour of the peptide after administering the peptide to a subject, an average volume of distribution (V d) of 200 - 20,000 mL in the subject after systemically administering the peptide to the subject, or optionally no systemic uptake, any combination thereof.
Methods of ManufactureVarious expression vector/host systems can be utilized for the production of the recombinant expression of peptides described herein. Non-limiting examples of such systems include microorganisms such as bacteria transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing a nucleic acid sequence encoding peptides or peptide fusion proteins/chimeric proteins described herein, yeast transformed with recombinant yeast expression vectors containing the aforementioned nucleic acid sequence, insect cell systems infected with recombinant virus expression vectors (e.g., baculovirus) containing the aforementioned nucleic acid sequence, plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus (CaMV), tobacco mosaic virus (TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing the aforementioned nucleic acid sequence, or animal cell systems infected with recombinant virus expression vectors (e.g., adenovirus, vaccinia virus) including cell lines engineered to contain multiple copies of the aforementioned nucleic acid sequence, either stably amplified (e.g., CHO/dhfr, CHO/glutamine synthetase) or unstably amplified in double-minute chromosomes (e.g., murine cell lines). Disulfide bond formation and folding of the peptide could occur during expression or after expression or both.
A host cell can be adapted to express one or more peptides described herein. The host cells can be prokaryotic, eukaryotic, or insect cells. In some cases, host cells are capable of modulating the expression of the inserted sequences, or modifying and processing the gene or protein product in the specific fashion desired. For example, expression from certain promoters can be elevated in the presence of certain inducers (e.g., zinc and cadmium ions for metallothionine promoters). In some cases, modifications (e.g., phosphorylation) and processing (e.g., cleavage) of peptide products can be important for the function of the peptide. Host cells can have characteristic and specific mechanisms for the post-translational processing and modification of a peptide. In some cases, the host cells used to express the peptides secretes minimal amounts of proteolytic enzymes.
In the case of cell- or viral-based samples, organisms can be treated prior to purification to preserve and/or release a target polypeptide. In some embodiments, the cells are fixed using a fixing agent. In some embodiments, the cells are lysed. The cellular material can be treated in a manner that does not disrupt a significant proportion of cells, but which removes proteins from the surface of the cellular material, and/or from the interstices between cells. For example, cellular material can be soaked in a liquid buffer or, in the case of plant material, can be subjected to a vacuum, in order to remove proteins located in the intercellular spaces and/or in the plant cell wall. If the cellular material is a microorganism, proteins can be extracted from the microorganism culture medium. Alternatively, the peptides can be packed in inclusion bodies. The inclusion bodies can further be separated from the cellular components in the medium. In some embodiments, the cells are not disrupted. A cellular or viral peptide that is presented by a cell or virus can be used for the attachment and/or purification of intact cells or viral particles. In addition to recombinant systems, Peptides can also be synthesized in a cell-free system using a variety of known techniques employed in protein and peptide synthesis.
In some cases, a host cell produces a peptide that has an attachment point for a drug. An attachment point could comprise a lysine residue, an N-terminus, a cysteine residue, a cysteine disulfide bond, or a non-natural amino acid. The peptide could also be produced synthetically, such as by solid-phase peptide synthesis, or solution-phase peptide synthesis. The peptide could be folded (formation of disulfide bonds) during synthesis or after synthesis or both. Peptide fragments could be produced synthetically or recombinantly and then joined together synthetically, recombinantly, or via an enzyme.
In other aspects, the peptides of the present disclosure can be prepared by conventional solid phase chemical synthesis techniques, for example according to the Fmoc solid phase peptide synthesis method (“Fmoc solid phase peptide synthesis, a practical approach,” edited by W. C. Chan and P. D. White, Oxford University Press, 2000).
Pharmaceutical Compositions of PeptidesA pharmaceutical composition of the disclosure can be a combination of any peptide described herein with other chemical components, such as carriers, stabilizers, diluents, dispersing agents, suspending agents, thickening agents, antioxidants, solubilizers, buffers, osmolytes, salts, surfactants, amino acids, encapsulating agents, bulking agents, cryoprotectants, and/or excipients. The pharmaceutical composition facilitates administration of a peptide described herein to an organism. Pharmaceutical compositions can be administered in therapeutically-effective amounts as pharmaceutical compositions by various forms and routes including, for example, intravenous, subcutaneous, intramuscular, rectal, aerosol, parenteral, ophthalmic, pulmonary, transdermal, vaginal, optic, nasal, oral, sublingual, inhalation, dermal, intrathecal, intranasal, and topical administration. A pharmaceutical composition can be administered in a local or systemic manner, for example, via injection of the peptide described herein directly into an organ, optionally in a depot.
Parenteral injections can be formulated for bolus injection or continuous infusion. The pharmaceutical compositions can be in a form suitable for parenteral injection as a sterile suspension, solution or emulsion in oily or aqueous vehicles, and can contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Pharmaceutical formulations for parenteral administration include aqueous solutions of a peptide described herein in water soluble form. Suspensions of peptides described herein can be prepared as oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions can contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. The suspension can also contain suitable stabilizers or agents which increase the solubility and/or reduces the aggregation of such peptides described herein to allow for the preparation of highly concentrated solutions. Alternatively, the peptides described herein can be lyophilized or in powder form for re-constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use. In some embodiments, a purified peptide is administered intravenously.
A peptide of the disclosure can be applied directly to an organ, or an organ tissue or cells, such as brain or brain tissue or cancer cells, during a surgical procedure. The recombinant peptides described herein can be administered topically and can be formulated into a variety of topically administrable compositions, such as solutions, suspensions, lotions, gels, pastes, medicated sticks, balms, creams, and ointments. Such pharmaceutical compositions can contain solubilizers, stabilizers, tonicity enhancing agents, buffers and preservatives.
In practicing the methods of treatment or use provided herein, therapeutically-effective amounts of the peptide described herein described herein can be administered in pharmaceutical compositions to a subject suffering from a condition that affects the immune system. In some embodiments, the subject is a mammal such as a human. A therapeutically-effective amount can vary widely depending on the severity of the disease, the age and relative health of the subject, the potency of the compounds used, and other factors.
Pharmaceutical compositions can be formulated using one or more physiologically-acceptable carriers comprising excipients and auxiliaries, which facilitate processing of the active compounds into preparations that can be used pharmaceutically. Formulation can be modified depending upon the route of administration chosen. Pharmaceutical compositions comprising a peptide described herein can be manufactured, for example, by expressing the peptide in a recombinant system, purifying the peptide, lyophilizing the peptide, mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or compression processes. The pharmaceutical compositions can include at least one pharmaceutically acceptable carrier, diluent, or excipient and compounds described herein as free-base or pharmaceutically-acceptable salt form.
Methods for the preparation of peptides described herein comprising the compounds described herein include formulating the peptide described herein with one or more inert, pharmaceutically-acceptable excipients or carriers to form a solid, semi-solid, or liquid composition. Solid compositions include, for example, powders, tablets, dispersible granules, capsules, cachets, and suppositories. These compositions can also contain minor amounts of nontoxic, auxiliary substances, such as wetting or emulsifying agents, pH buffering agents, and other pharmaceutically-acceptable additives.
Non-limiting examples of pharmaceutically-acceptable excipients can be found, for example, in Remington: The Science and Practice of Pharmacy, Nineteenth Ed (Easton, Pa.: Mack Publishing Company, 1995); Hoover, John E., Remington’s Pharmaceutical Sciences, Mack Publishing Co., Easton, Pennsylvania 1975; Liberman, H.A. and Lachman, L., Eds., Pharmaceutical Dosage Forms, Marcel Decker, New York, N.Y., 1980; and Pharmaceutical Dosage Forms and Drug Delivery Systems, Seventh Ed. (Lippincott Williams & Wilkins1999), each of which is incorporated by reference in its entirety.
Administration of Pharmaceutical CompositionsA pharmaceutical composition of the disclosure can be a combination of any venom or toxin derived peptide described herein with other chemical components, such as carriers, stabilizers, diluents, dispersing agents, suspending agents, thickening agents, and/or excipients. The pharmaceutical composition facilitates administration of a peptide described herein to an organism. Pharmaceutical compositions can be administered in therapeutically-effective amounts as pharmaceutical compositions by various forms and routes including, for example, intravenous, subcutaneous, intramuscular, rectal, aerosol, parenteral, ophthalmic, pulmonary, transdermal, vaginal, optic, nasal, oral, inhalation, dermal, intra-articular, intrathecal, intranasal, and topical administration. A pharmaceutical composition can be administered in a local or systemic manner, for example, via injection of the peptide described herein directly into an organ, optionally in a depot.
Parenteral injections can be formulated for bolus injection or continuous infusion. The pharmaceutical compositions can be in a form suitable for parenteral injection as a sterile suspension, solution or emulsion in oily or aqueous vehicles, and can contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Pharmaceutical formulations for parenteral administration include aqueous solutions of a peptide described herein in water-soluble form. Suspensions of peptides described herein can be prepared as oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions can contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. The suspension can also contain suitable stabilizers or agents which increase the solubility and/or reduces the aggregation of such peptides described herein to allow for the preparation of highly concentrated solutions. Alternatively, the peptides described herein can be lyophilized or in powder form for re-constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use. In some embodiments, a purified peptide is administered intravenously. A peptide described herein can be administered to a subject, home, target, migrates to, is retained by, and/or binds to, or be directed to an organ, e.g., the cartilage.
A peptide of the disclosure can be applied directly to an organ, or an organ tissue or cells, such as cartilage or cartilage tissue or cells, during a surgical procedure. The recombinant peptides described herein can be administered topically and can be formulated into a variety of topically administrable compositions, such as solutions, suspensions, lotions, gels, pastes, medicated sticks, balms, creams, and ointments. Such pharmaceutical compositions can contain solubilizers, stabilizers, tonicity enhancing agents, buffers and preservatives.
In practicing the methods of treatment or use provided herein, therapeutically-effective amounts of the peptide described herein described herein are administered in pharmaceutical compositions to a subject suffering from a condition. In some instances the pharmaceutical composition will affect the physiology of the animal, such as the immune system, inflammatory response, or other physiologic affect. In some embodiments, the subject is a mammal such as a human. A therapeutically-effective amount can vary widely depending on the severity of the disease, the age and relative health of the subject, the potency of the compounds used, and other factors.
Pharmaceutical compositions can be formulated using one or more physiologically-acceptable carriers comprising excipients and auxiliaries, which facilitate processing of the active compounds into preparations that can be used pharmaceutically. Formulation can be modified depending upon the route of administration chosen. Pharmaceutical compositions comprising a peptide described herein can be manufactured, for example, by expressing the peptide in a recombinant system, purifying the peptide, lyophilizing the peptide, mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or compression processes. The pharmaceutical compositions can include at least one pharmaceutically acceptable carrier, diluent, or excipient and compounds described herein as free-base or pharmaceutically-acceptable salt form.
Methods for the preparation of peptides described herein comprising the compounds described herein include formulating the peptide described herein with one or more inert, pharmaceutically-acceptable excipients or carriers to form a solid, semi-solid, or liquid composition. Solid compositions include, for example, powders, tablets, dispersible granules, capsules, cachets, and suppositories. These compositions can also contain minor amounts of nontoxic, auxiliary substances, such as wetting or emulsifying agents, pH buffering agents, and other pharmaceutically-acceptable additives.
Non-limiting examples of pharmaceutically-acceptable excipients can be found, for example, in Remington: The Science and Practice of Pharmacy, Nineteenth Ed (Easton, Pa.: Mack Publishing Company, 1995); Hoover, John E., Remington’s Pharmaceutical Sciences, Mack Publishing Co., Easton, Pennsylvania 1975; Liberman, H.A. and Lachman, L., Eds., Pharmaceutical Dosage Forms, Marcel Decker, New York, N.Y., 1980; and Pharmaceutical Dosage Forms and Drug Delivery Systems, Seventh Ed. (Lippincott Williams & Wilkins1999), each of which is incorporated by reference in its entirety.
Use of Peptide in Imaging and Surgical MethodsThe present disclosure generally relates to peptides that home, target, migrate to, are retained by, accumulate in, and/or bind to, or are directed to specific regions, tissues, structures, or cells within the body and methods of using such peptides. These peptides have the ability to contact the cartilage, which makes them useful for a variety of applications. In particular, the peptides can have applications in site-specific modulation of biomolecules to which the peptides are directed to. End uses of such peptides can include, for example, imaging, research, therapeutics, theranostics, pharmaceuticals, chemotherapy, chelation therapy, targeted drug delivery, and radiotherapy. Some uses can include targeted drug delivery and imaging.
In some embodiments, the present disclosure provides a method for detecting a cancer, cancerous tissue, or tumor tissue, the method comprising the steps of contacting a tissue of interest with a peptide of the present disclosure, wherein the peptide is conjugated to a detectable agent and measuring the level of binding of the peptide, wherein an elevated level of binding, relative to normal tissue, is indicative that the tissue is a cancer, cancerous tissue or tumor tissue.
In some embodiments, the disclosure provides a method of imaging an organ or body region or region, tissue or structure of a subject, the method comprising administrating to the subject the peptide or a pharmaceutical composition disclosed herein and imaging the subject. In some embodiments such imaging is used to detect a condition associated with a function of the cartilage. In some cases the condition is an inflammation, a cancer, a degradation, a growth disturbance, genetic, a tear or an injury, or another suitable condition. In some cases the condition is a chondrodystrophy, a traumatic rupture or detachment, pain following surgery in regions of the body containing cartilage, costochondritis, herniation, polychondritis, arthritis, osteoarthritis, rheumatoid arthritis, ankylosing spondylitis (AS), Systemic Lupus Erythematosus (SLE or “Lupus”), Psoriatic Arthritis (PsA), gout, achondroplasia, or another suitable condition. In some case the condition is associated with a cancer or tumor of the cartilage. In some cases the condition is a type of chondroma or chondrosarcoma, whether metastatic or not, or another suitable condition. In some embodiments, such as those associated with cancers, the imaging may be associated with surgical removal of the diseased region, tissue, structure or cell of a subject.
Furthermore, the present disclosure provides methods for intraoperative imaging and resection of a diseased or inflamed tissue, cancer, cancerous tissue, or tumor tissue using a peptide of the present disclosure conjugated with a detectable agent. In some embodiments, the diseased or inflamed tissue, cancer, cancerous tissue, or tumor tissue is detectable by fluorescence imaging that allows for intraoperative visualization of the cancer, cancerous tissue, or tumor tissue using a peptide of the present disclosure. In some embodiments, the peptide of the present disclosure is conjugated to one or more detectable agents. In a further embodiment, the detectable agent comprises a fluorescent moiety coupled to the peptide. In another embodiment, the detectable agent comprises a radionuclide. In some embodiments, imaging is achieved during open surgery. In further embodiments, imaging is accomplished using endoscopy or other non-invasive surgical techniques.
Treatment of Cartilage DisordersThe term “effective amount,” as used herein, can refer to a sufficient amount of an agent or a compound being administered which will relieve to some extent one or more of the symptoms of the disease or condition being treated. The result can be reduction and/or alleviation of the signs, symptoms, or causes of a disease, or any other desired alteration of a biological system. Compositions containing such agents or compounds can be administered for prophylactic, enhancing, and/or therapeutic treatments. An appropriate “effective” amount in any individual case can be determined using techniques, such as a dose escalation study.
The methods, compositions, and kits of this disclosure can comprise a method to prevent, treat, arrest, reverse, or ameliorate the symptoms of a condition. The treatment can comprise treating a subject (e.g., an individual, a domestic animal, a wild animal or a lab animal afflicted with a disease or condition) with a peptide of the disclosure. In treating a disease, the peptide can contact the cartilage of a subject. The subject can be a human. A subject can be a human; a non-human primate such as a chimpanzee, or other ape or monkey species; a farm animal such as a cattle, horse, sheep, goat, swine; a domestic animal such as a rabbit, dog, and cat; a laboratory animal including a rodent, such as a rat, mouse and guinea pig, or the like. A subject can be of any age. A subject can be, for example, an elderly adult, adult, adolescent, pre-adolescens, child, toddler, infant, or fetus in utero.
Treatment can be provided to the subject before clinical onset of disease. Treatment can be provided to the subject after clinical onset of disease. Treatment can be provided to the subject after 1 day, 1 week, 6 months, 12 months, or 2 years or more after clinical onset of the disease. Treatment may be provided to the subject for more than 1 day, 1 week, 1 month, 6 months, 12 months, 2 years or more after clinical onset of disease. Treatment may be provided to the subject for less than 1 day, 1 week, 1 month, 6 months, 12 months, or 2 years after clinical onset of the disease. Treatment can also include treating a human in a clinical trial. A treatment can comprise administering to a subject a pharmaceutical composition, such as one or more of the pharmaceutical compositions described throughout the disclosure. A treatment can comprise a once daily dosing. A treatment can comprise delivering a peptide of the disclosure to a subject, either intravenously, subcutaneously, intramuscularly, by inhalation, dermally, intra-articular injection, orally, intrathecally, transdermally, intranasally, via a peritoneal route, or directly onto or into a j oint, e.g., via topical, intra-articular injection route or injection route of application. A treatment can comprise administering a peptide-active agent complex to a subject, either intravenously, intra-articular injection, parenterally, orally, via a peritoneal route, or directly onto, near or into the cartilage.
Types of cartilage diseases or conditions that can be treated with a peptide of the disclosure can include inflammation, pain management, anti-infective, pain relief, anti-cytokine, cancer, injury, degradation, genetic basis, remodeling, hyperplasia, surgical injury/trauma, or the like. Examples of cartilage diseases or conditions that can be treated with a peptide of the disclosure include Costochondritis, Spinal disc herniation, Relapsing polychondritis, Injury to the articular cartilage, any manner of rheumatic disease (e.g., Rheumatoid Arthritis (RA), ankylosing spondylitis (AS), Systemic Lupus Erythematosus (SLE or “Lupus”), Psoriatic Arthritis (PsA), Osteoarthritis, Gout, and the like), Herniation, Achondroplasia, Benign or non-cancerous chondroma, Malignant or cancerous chondrosarcoma, Chondriodystrophies, Chondromalacia patella, Costochondritis, Halus rigidus, Hip labral tear, Osteochondritis dssecans, Osteochondrodysplasias, Torn meniscus, Pectus carinatum, Pectus excavatum, Chondropathy, Chondromalacia, Polychondritis, Relapsing Polychondritis, Slipped epiphysis, Osteochondritis Dissecans, Chondrodysplasia, Costochondritis, Perichondritis, Osteochondroma, Knee osteoarthritis, Finger osteoarthritis, Wrist osteoarthritis, Hip osteoarthritis, Spine osteoarthritis, Chondromalacia, Osteoarthritis Susceptibility, Ankle Osteoarthritis, Spondylosis, Secondary chondrosarcoma, Small and unstable nodules as seen in osteoarthritis, Osteochondroses, Primary chondrosarcoma, Cartilage disorders, scleroderma, collagen disorders, Chondrodysplasia, Tietze syndrome, Dermochondrocorneal dystrophy of Francois, Epiphyseal dysplasia multiple 1, Epiphyseal dysplasia multiple 2, Epiphyseal dysplasia multiple 3, Epiphyseal dysplasia multiple 4, Epiphyseal dysplasia multiple 5, Ossified Ear cartilages with Mental deficiency, Muscle Wasting and Bony Changes, Periosteal chondrosarcoma, Carpotarsal osteochondromatosis, Achondroplasia, Genochondromatosis II, Genochondromatosis, Chondrodysplasia -- disorder of sex development, Chondroma, Chordoma, Atelosteogenesis, type 1, Atelosteogenesis Type III, Atelosteogenesis, type 2, Pyknoachondrogenesis, Osteoarthropathy of fingers familial, Dyschondrosteosis - nephritis, Coloboma of Alar-nasal cartilages with telecanthus, Alar cartilages hypoplasia - coloboma - telecanthus, Pierre Robin syndrome - fetal chondrodysplasia, Dysspondyloenchondromatosis, Achondroplasia regional -dysplasia abdominal muscle, Osteochondritis Dissecans, Familial Articular Chondrocalcinosis, Tracheobronchomalacia, Chondritis, Dyschondrosteosis, Jequier-Kozlowski-skeletal dysplasia, Chondrodystrophy, Cranio osteoarthropathy, Tietze’s syndrome, Hip dysplasia - ecchondromata, Bessel-Hagen disease, Chondromatosis (benign), Enchondromatosis (benign), Chondrocalcinosis due to apatite crystal deposition, Meyenburg-Altherr-Uehlinger syndrome, Enchondromatosis-dwarfism-deafness, premature growth plate closure (e.g., due to dwarfism, injury, therapy such as retinoid therapy for adolescent acne, or ACL repair), Astley-Kendall syndrome, Synovial osteochondromatosis, Severe achondroplasia with developmental delay and acanthosis nigricans, Chondrocalcinosis, Stanescu syndrome, Familial osteochondritis dissecans, Achondrogenesis type 1A, Achondrogenesis type 2, Achondrogenesis, Langer-Saldino Type, Achondrogenesis type 1B, Achondrogenesis type 1A and 1B, Type II Achondrogenesis-Hypochondrogenesis, Achondrogenesis, Achondrogenesis type 3, Achondrogenesis type 4, Chondrocalcinosis 1, Chondrocalcinosis 2, Chondrocalcinosis familial articular, Diastrophic dysplasia, Fibrochondrogenesis, Hypochondroplasia, Keutel syndrome, Maffucci Syndrome, Osteoarthritis Susceptibility 6, Osteoarthritis Susceptibility 5, Osteoarthritis Susceptibility 4, Osteoarthritis Susceptibility 3, Osteoarthritis Susceptibility 2, Osteoarthritis Susceptibility 1, Pseudoachondroplasia, Cauliflower ear, Costochondritis, Growth plate fractures, Pectus excavatum, septic arthritis, gout, pseudogout (calcium pyrophosphate deposition disease or CPPD), gouty arthritis, bacterial, viral, or fungal infections in or near the j oint, bursitis, tendinitis, arthropathies, or another cartilage or joint disease or condition.
In some embodiments, a peptide or peptide conjugate of this disclosure can be administered to a subject in order to target,an arthritic joint. In other embodiments, a peptide or peptide conjugate of this disclosure can be administered to a subject in order to treat an arthritic joint.
In some embodiments, the present disclosure provides a method for treating a cancer, the method comprising administering to a subject in need thereof an effective amount of a peptide of the present disclosure.
In some embodiments, the present disclosure provides a method for treating a cancer, the method comprising administering to a patient in need thereof an effective amount of a pharmaceutical composition comprising a peptide of the present disclosure and a pharmaceutically acceptable carrier.
In some embodiments, the peptides of the present disclosure can be used to treat chondrosarcoma. Chondrosarcoma is a cancer of cartilage producing cells and is often found in bones and joints. It falls within the family of bone and soft-tissue sarcomas. In certain embodiments, administration of a peptide or peptide conjugate of the present disclosure can be used to image and diagnose or target and treat a subject with chondrosarcoma. The adminstration of a peptide or peptide conjugate of the present disclosure can be used in combination with ablative radiotherapy or proton therapy to treat chondrosarcoma. The subject can be a human or an animal.
In some embodiments, a peptide or peptide conjugate of this disclosure can be used to treat Chordoma. In certain embodiments, administration of a peptide or peptide conjugate of the present disclosure can be used to image and diagnose or target and treat a subject with chordoma. The adminstration of a peptide or peptide conjugate of the present disclosure can be used in combination with a tyrosine kinase inhibitor, such as imatinib mesylate, and ablative radiotherapy or proton therapy to treat chordoma. The adminstration of a peptide or peptide conjugate of the present disclosure can be used in combination with an antivascular agent such as bevacizumab and an epidermal growth factor receptor inhibitor such as erlotinib to treat chordoma. The subject can be a human or an animal.
In some embodiments, the present disclosure provides a method for inhibiting invasive activity of cells, the method comprising administering an effective amount of a peptide of the present disclosure to a subject.
In some embodiments, the peptides of the present disclosure are conjugated to one or more therapeutic agents. In further embodiments, the therapeutic agent is a chemotherapeutic, anti-cancer drug, or anti-cancer agent selected from, but are not limited to: anti-inflammatories, such as for example a glucocorticoid, a corticosteroid, a protease inhibitor, such as for example collagenase inhibitor or a matrix metalloprotease inhibitor (i.e., MMP-13 inhibitor), an amino sugar, vitamin (e.g., Vitamin D), and antibiotics, antiviral, or antifungal, a statin, an immune modulator, radioisotopes, toxins, enzymes, sensitizing drugs, nucleic acids, including interfering RNAs, antibodies, anti-angiogenic agents, cisplatin, anti-metabolites, mitotic inhibitors, growth factor inhibitors, paclitaxel, temozolomide, topotecan, fluorouracil, vincristine, vinblastine, procarbazine, decarbazine, altretamine, methotrexate, mercaptopurine, thioguanine, fludarabine phosphate, cladribine, pentostatin, cytarabine, azacitidine, etoposide, teniposide, irinotecan, docetaxel, doxorubicin, daunorubicin, dactinomycin, idarubicin, plicamycin, mitomycin, bleomycin, tamoxifen, flutamide, leuprolide, goserelin, aminogluthimide, anastrozole, amsacrine, asparaginase, mitoxantrone, mitotane and amifostine, and their equivalents, as well as photo-ablation. Some of these active agents induce programmed cell death such as apoptosis in target cells and thereby improve symptoms or ameliorate disease. Apoptosis can be induced by many active agents, including, for example, chemotherapeutics, anti-inflammatories, corticosteroids, NSAIDS, tumor necrosis factor alpha (TNF-α) modulators, tumor necrosis factor receptor (TNFR) family modulators. In some embodiments, peptides of this disclosure can be used to target active agents to pathways of cell death or cell killing, such as caspases, apoptsis activators and inhibitors, XBP-1, Bcl-2, Bcl-Xl, Bcl-w, and other disclosed herein. In other embodiments, the therapeutic agent is any nonsteroidal anti-inflammatory drug (NSAID). The NSAID can be any heterocyclic acetic acid derivatives such as ketorolac, indomethacin, etodolac, or tolemetin, any propionic acid derivatives such as naproxen, any enolic acid derivatives, any anthranilic acid derivatives, any selective COX-2 inhibitors such as celecoxib, any sulfonanilides, any salicylates, aceclofenac, nabumetone, sulindac, diclofenac, or ibuprofen. In other embodiments, the therapeutic agent is any steroid, such as dexamethasone, budesonide, triamcinolone, cortisone, prednisone, rednisolone, triamcinolone hexacetonide, or methylprednisolone. In other embodiments, the therapeutic agent is a pain reliever, such as acetaminophen, opioids, local anesthetics, anti-depressants, glutamate receptor anatagonists, adenosine, or neuropetides. In some embodiments, a treatment consists of administering a combination of any of the above therapeutic agents and a peptide conjugate, such as a treatment in which both a dexamethasone-peptide conjugate and an NSAID are administered to a patient. Peptides of the current disclosure that target the cartilage can be used to treat the diseases conditions as described herein, for example, any diseases or conditions including tears, injuries (i.e., sports injuries), genetic factors, degradation, thinning, inflammation, cancer or any other disease or condition of the cartilage or to target therapeutically-active substances to treat these diseases amongst others. In other cases, a peptide of the disclosure can be used to treat traumatic rupture, detachment, chostochondritis, spinal disc herniation, relapsing and non-relapsing polychondritis, injury to the articular cartilage, osteoarthritis, arthritis or achondroplasia. In some cases, the peptide or peptide-active agent can be used to target cancer in the cartilage, for example benign chondroma or malignant chondrosarcoma, by contacting the cartilage by diffusion into chondrocytes and then having antitumor function, targeted toxicity, inhibiting metastases, etc. As well, such peptide or peptide-active agent can be used to label, detect, or image such cartilage lesions, including tumors and metastases amongst other lesions, which may be removed through various surgical techniques or by targeting with peptide-active agents that induce programmed cell death or kill cells.
Venom or toxin derived peptide(s), peptides, modified peptides, labeled peptides, peptide-active agent conjugates and pharmaceutical compositions described herein can be administered for prophylactic and/or therapeutic treatments. In therapeutic applications, the composition can be administered to a subject already suffering from a disease or condition, in an amount sufficient to cure or at least partially arrest the symptoms of the disease or condition, or to cure, heal, improve, or ameliorate the condition. Such peptides described herein can also be administered to prevent (either in whole or in part), lessen a likelihood of developing, contracting, or worsening a condition. Amounts effective for this use can vary based on the severity and course of the disease or condition, previous therapy, the subject’s health status, weight, response to the drugs, and the judgment of the treating physician. Venom or toxin derived peptide(s), peptides, modified peptides, labeled peptides, peptide-active agent conjugates and pharmaceutical compositions described herein can allow for targeted homing of the peptide and local delivery of any conjugate. For example, a peptide conjugated to a steroid allows for local delivery of the steroid, which is significantly more effective and less toxic than traditional systemic steroids. A peptide conjugated to an NSAID is another example. In this case, the peptide conjugated to an NSAID allows for local delivery of the NSAID, which allows for administration of a lower NSAID dose and is subsequently less toxic. By delivering an active agent to the joint, pain relief can be more rapid, may be more long lasting, and can be obtained with a lower systemic dose and off-site undesired effects than with systemic dosing without targeting.
Peptides of the current disclosure that target the cartilage can be used to treat or manage pain associated with a cartilage injury or disorder, or any other cartilage or joint condition as described herein. The peptides can be used either directly or as carriers of active drugs, peptides, or molecules. For example, since ion channels can be associated with pain and can be activated in disease states such as arthritis, peptides that interact with ion channels can be used directly to reduce pain. In another embodiment, the peptide is conjugated to an active agent with anti-inflammatory activity, in which the peptide acts as a carrier for the local delivery of the active agent to reduce pain.
In some embodiments, the peptides described herein provide a method of treating a cartilage condition of a subject, the method comprising administering to the subject a therapeutically-effective amount of a peptide comprising the sequence SEQ ID NO: 1 or fragment thereof. In some embodiments, the peptides described herein provide a method of treating a cartilage condition of a subject, the method comprising administering to the subject a peptide of any one of SEQ ID NO: 2 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 -SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 or fragment thereof.
Multiple peptides described herein can be administered in any order or simultaneously. In some cases, multiple functional fragments of peptides derived from toxins or venom can be administered in any order or simultaneously. If simultaneously, the multiple peptides described herein can be provided in a single, unified form, such as an intravenous injection, or in multiple forms, such as subsequent intravenous dosages.
Peptides can be packaged as a kit. In some embodiments, a kit includes written instructions on the use or administration of the peptides.
EXAMPLESThe following examples are included to further describe some embodiments of the present disclosure, and should not be used to limit the scope of the disclosure.
Example 1 Manufacture of PeptidesThis example provides a method for generating knottin peptides. Peptides derived from knottin peptides of scorpions and spiders were generated in mammalian cell culture using a published methodology. (A.D. Bandaranayke, C. Correnti, B.Y. Ryu, M. Brault, R.K. Strong, D. Rawlings. 2011. Daedalus: a robust, turnkey platform for rapid production of decigram quantities of active recombinant proteins in human cell lines using novel lentiviral vectors. Nucleic Acids Research. (39)21, e143).
The peptide sequence was reverse-translated into DNA, synthesized, and cloned in-frame with siderocalin using standard molecular biology techniques. (M.R. Green, Joseph Sambrook. Molecular Cloning. 2012 Cold Spring Harbor Press.). The resulting construct was packaged into a lentivirus, transfected into HEK293 cells, expanded, isolated by immobilized metal affinity chromatography (IMAC), cleaved with tobacco etch virus protease, and purified to homogeneity by reverse-phase chromatography. Following purification, each peptide was lyophilized and stored frozen.
Example 2 Radiolabeling of PeptideThis example describes radiolabelling of knottin peptides. Several knottins (some sequences derived from spiders and scorpions) were radiolabeled by reductive methylation with 14C formaldehyde and sodium cyanoborohydride with standard techniques. See J Biol Chem. 254(11):4359-65 (1979). The sequences were engineered to have the amino acids, “G” and “S” at the N terminus. See Methods in Enzymology V91:1983 p.570 and Journal of Biological Chemistry 254(11):1979 p. 4359. An excess of formaldehyde was used to ensure complete methylation (dimethylation of every free amine). The labeled peptides were isolated via solid-phase extraction on Strata-X columns (Phenomenex 8B-S100-AAK), rinsed with water with 5% methanol, and recovered in methanol with 2% formic acid. Solvent was subsequently removed in a blowdown evaporator with gentle heat and a stream of nitrogen gas.
Example 3 Dosing of Peptide With Kidney LigationThis example describes a dosing scheme for administering knottin peptides to mice in conjunction with kidney ligation. Different dosages of the peptides were administered to Female Harlan athymic nude mice, weighing 20 g - 25 g, via tail vein injection (n = 2 mice per knottin). The sequence of thirteen cartilage homing peptides of SEQ ID NO: 21 - SEQ ID NO: 33 are shown in TABLE 1. The experiment was done in duplicates. The kidneys were ligated to prevent renal filtration of the peptides. Each peptide was radiolabeled by methylating lysines and the N-terminus, so the actual binding agent may contain methyl or dimethyl lysine(s) and a methylated or dimethylated amino terminus.
A target dosage of 50-100 nmol of each peptide carrying 10-25 uCi of 14C was administered to Female Harlan athymic nude mice while anesthetized. Each peptide was allowed to freely circulate within the animal before the animals were euthanized and sectioned.
Example 4 Peptide Homing With Kidney LigationThis example illustrates peptide homing to cartilage of mice with kidneys that were ligated prior to peptide administration. At the end of the dosing period in EXAMPLE 3, mice were frozen in a hexane/dry ice bath and then frozen in a block of carboxymethylcellulose. Whole animal sagittal slices were prepared that resulted in thin frozen sections being available for imaging. Thin, frozen sections of animal including imaging of tissues such as brain, tumor, liver, kidney, lung, heart, spleen, pancreas, muscle, adipose, gall bladder, upper gastrointestinal tract, lower gastrointestinal tract, bone, bone marrow, reproductive track, eye, cartilage, stomach, skin, spinal cord, bladder, salivary gland, and other types of tissues were obtained with a microtome, allowed to desiccate in a freezer, and exposed to phosphoimager plates for about ten days.
These plates were developed, and the signal (densitometry) from each organ was normalized to the signal found in the heart blood of each animal. A signal in tissue darker than the signal expected from blood in that tissue indicates peptide accumulation in a region, tissue, structure or cell. For instance, the cartilage is avascular and contains minute amounts of blood. A ratio of at least 170% signal in the cartilage versus heart ventricle was chosen as a reference level for significant targeting to cartilage, which also correlated with clear accumulation in cartilaginous tissues in the images of the slices.
Additionally, the peptide can be retained in cartilage for hours after treatment. The SEQ ID NO: 24 peptide was radiolabeled as in Example 3 and 100 nmol of peptide was injected into a mouse with intact kidneys.
TABLE 2 summarizes the net charge at neutral pH and migration of the peptides of SEQ ID NO: 21 - SEQ ID NO: 33 to the cartilage (C) and muscle (M) compared to the level in the blood 3 hours after administration. The “cartilage” entries reflect the percentage of signal in the cartilage compared to the blood signal in the heart ventricle within the tissue slices. Peptides that are cartilage homers have a cartilage signal of >170%, peptides that are efficient cartilage homers can have a cartilage signal of >300%, and peptides that are strong cartilage homers have a cartilage signal of >500%. SEQ ID NO: 484 corresponds to an amino acid sequence of GSECLGFGKGCNPSNDQCCKSSNLVCSRKHRWCKYEIGK.
As shown in TABLE 2, sequences with significant positive charge at physiological pH exhibited higher accumulation in cartilage. Many of these sequences share common elements. These common elements may represent parts of the sequence that confer cartilage homing to the peptide by locating positive charge or other binding elements into certain parts of the three dimensional structure of the folded peptide. For instance, K or R residues might be preferentially located in certain parts of the sequence in order to locate positive charge on the correct surface areas for homing, especially with respect to the C residues which determine folding and loop location of the folded peptide. However, only parts of these sequences may be important for homing or other aspects of the sequences may be important for homing.
Two example sequences containing common elements are
and
where X can independently be any number of any amino acid or no amino acid.
is a sequence based on the most common elements found in the following sequences:
and
. Sequence
is a sequence based on the most common elements found in the following sequences:
and
. A dash, “-,” indicates that no amino acid is in that position. The following residues may be independently interchanged in SEQ ID NO: 9 or SEQ ID NO: 10: any K and any R; any M, any I, any L, and any V; any G and any A; any S and any T; and any Q and any N. These sets of interchangeable amino acids have similarities in properties that can allow for them to be interchangeable without inhibiting homing to cartilage. For example, any K can be interchanged with any R because K and R both provide a positive charge at physiological pH and thus may provide necessary charge for homing to cartilage, and any S can be interchanged with any T because S and T both have ahydroxyl group available for hydrogen bonding. The N-terminal GS sequence may or may not be included between the peptides of the present disclosure.
Particular fragments with common elements were also noted, such as the GKCINKKCKC (SEQ ID NO: 316) fragment with the internal fragments KCIN (SEQ ID NO: 317) and KKCK (SEQ ID NO: 318), PCKR (SEQ ID NO: 319), KRCSRR (SEQ ID NO: 320), and KQC (SEQ ID NO: 321). The following residues may be independently interchanged in SEQ ID NO: 101 - SEQ ID NO: 105 or SEQ ID NO: 316 - SEQ ID NO: 321: any K and any R; any M, any I, any L, and any V; and G and any A; any S and any T; and any Q and any N.
A predominance of R and K residues were noted in the C-terminal parts of the peptides as well as in the fragments, correlating with the high positive charge of the peptides.
The peptides of SEQ ID NO: 21 and SEQ ID NO: 33 in TABLE 1 are derived from a scorpion toxin (e.g., Buthus martensii Karsh) that was found to migrate specifically to a region, tissue, structure or cells in the cartilage, potentially by diffusion.
This example describes certain exemplary therapeutic agents that are conjugated to a knottin peptide. A peptide of the disclosure is expressed recombinantly or chemically synthesized and then is conjugated to an exemplary drug, such as paclitaxel or triamcinolone acetonide using techniques known in the art, such as those described in Bioconjugate Techniques by Greg Hermanson. One or more drugs is conjugated per peptide, or an average of less than one drug is conjugated per peptide.
Coupling of these drugs to a peptide of any of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 or SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 targets the drug to the cartilage of the subject. One or more drug-peptide conjugates are administered to a human or animal.
Example 6 Treatment of OsteoarthritisThis example describes a method for treating osteoarthritis using peptides of the present disclosure. This method is used as a treatment for acute and/or chronic symptoms associated with osteoarthritis. A peptide of the present disclosure is expressed recombinantly or chemically synthesized and then is used directly or conjugated to an anti-inflammatory compound, such as triamcinolone acetonide and dexamethasone. The resulting peptide or peptide-drug conjugate is administered in a pharmaceutical composition subcutaneously, intravenously, or orally, or is injected directly into a joint of a patient and targeted to cartilage. The formulation can be modified physically or chemically to increase the time of exposure in the cartilage. The peptide is selected from SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 or SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432. One or more anti-inflammatory peptide conjugates are administered to a human or animal.
Example 7 Treatment of Cartilage DegradationThis example describes a method for treating and/or preventing cartilage degradation using a peptide of the present disclosure. This method is used as a treatment for acute and/or chronic symptoms associated with cartilage degradation. Progressive degradation or thinning of the cartilage is difficult to treat in part because molecules such as small molecule drugs and antibodies typically do not reach the avascular cartilage. A peptide of the present disclosure is used for its homing and/or native activity, or is mutated to generate activity such as MMP protease inhibition. It is expressed recombinantly or chemically synthesized and then is used directly or conjugated to an extracellular matrix targeting compound, such as an inhibitor of MMP activity (e.g., MMP13, collagenase (MMP-1), or other agent as described herein). The resulting peptide or peptide-drug conjugate is administered in a pharmaceutical composition subcutaneously, intravenously, or orally, or is injected directly into a joint of a patient and targeted to extracellular matrix. The peptide is selected from SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 or SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432. One or more extracellular matrix targeting conjugates are administered to a human or animal.
Example 8 Treatment of a Cartilage InjuryThis example describes a method for treating a cartilage injury using a peptide of the present disclosure. A peptide of the present disclosure is expressed recombinantly or chemically synthesized and then is used directly or conjugated to a therapeutic compound, such as those described herein, including, but not limited to triamcinolone and dexamethasone. The resulting peptide or peptide-drug conjugate is administered in a pharmaceutical composition to a patient and targeted to cartilage. The peptide is selected from S SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 or SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432. One or more therapeutic compound-peptide conjugates are administered to a human or animal.
Example 9 Treatment of Rheumatoid ArthritisThis example describes a method for treating rheumatoid arthritis. This method is used as a treatment for acute and/or chronic symptoms associated with rheumatoid arthritis. A peptide of the present disclosure is expressed recombinantly or chemically synthesized and then is used directly, or is conjugated to an anti-inflammatory compound, such as triamcinolone and dexamethasone. When the peptide is used directly, the peptide can, for example, bind or inhibit ion channels such as Kv 1.3. The resulting peptide or peptide-drug conjugate is administered in a pharmaceutical composition to a patient and is targeted to cartilage. The peptide is selected from SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 or SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432. One or more anti-inflammatory compound-peptide conjugates are administered to a human or animal subcutaneously, intravenously, or orally, or is injected directly into a joint
Example 10 Treatment of GoutThis example describes a method for treating gout using peptides of the present disclosure. This method is used as a treatment for acute and/or chronic symptoms associated with gout. A peptide of the present disclosure is expressed and administered in a pharmaceutical composition to a patient as a therapeutic for gout. A peptide of the disclosure is recombinantly or chemically synthesized and then is used directly or conjugated to a nonsteroidal anti-inflammatory drugs, colchicine, a steroid, or uricase. The peptide selected from SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 or SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 is administered in a pharmaceutical composition to a patient and the peptide is targeted to the cartilage affected by gout. One or more peptides are administered to a human or animal subcutaneously, intravenously, or orally, or is injected directly into a joint.
Example 11 Treatment or Management of PainThis example describes a method for treating or managing pain associated with a cartilage injury or disorder. This method is used as a treatment for acute and/or chronic symptoms associated with a cartilage injury or disorder. A peptide of the disclosure is expressed and administered in a pharmaceutical composition to a patient as a therapeutic for pain as a result of injury or other cartilage or joint condition as described herein. The peptide of the present disclosure inhibits ion channels, such as Nav 1.7. The peptide is expressed recombinantly or chemically synthesized, wherein the peptide selected from SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 or SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432. Alternatively, the peptides of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 or SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432 are mutated to maintain the cartilage homing function, but to add or increase ion channel inhibition, such as to Nav 1.7. Following expression or synthesis, the peptide is used directly or conjugated to an NSAID. Following administration of the peptide, the peptide targets to the cartilage affected by pain. One or more peptides are administered to a human or animal subcutaneously, intravenously, or orally, or is injected directly into a joint.
Example 12 Immunogenicity of PeptidesThis example describes the evaluation of immunogenicity for certain peptides of the present disclosure. Immunogenicity was predicted using the network-based alignment algorithm (“NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide biding prediction”, Nielsen et. al. BMC Bioinformatics 2009 Vol 10, p296). The algorithm was applied to intact knottin proteins with sequences SEQ ID NO: 21 - SEQ ID NO: 33 against 24 alleles of HLA-DR, HLA-DP, HLA-DQ and H2-IAb MHCII classes.
Immunogenicity was evaluated in silico for additional intact cartilage homing peptides. TABLE 3 illustrates the MHC class II peptide binding prediction of intact cartilage homing peptides sequences. The prediction values were obtained using network-based alignment algorithm. The algorithm was run using intact knottin peptides against 28 alleles of HLA-DR, HLA-DP, DLA-DQ, and H2-IAb MHC II classes. Some of the intact knottin peptides were predicted to be strong binders of MHC class II, however excluding certain sequences known to have high immunogenicity such as C-terminal proline in a peptide of SEQ ID NO: 111 or glycine in a peptide of SEQ ID NO: 199 reduced binding to MHC II alleles. As an example, peptides of SEQ ID NO: 209 - SEQ ID NO: 210 have 90% homology to a peptide of SEQ ID NO: 111 and SEQ ID NO: 110, respectively, and are less immunogenic due to reduced binding to MHC II alleles. In another example, a peptide of SEQ ID NO: 211 has 83% homology to a peptide of SEQ ID NO: 114 and is less immunogenic due to reduced binding to MHC II alleles.
This example describes the conjugation of ketorolac to a knottin peptide using a lactic acid linker. As shown below in reaction scheme (I), a conjugate is produced from a mixture of (R,S)-ketorolac, lactic acid, and a knottin peptide:
The ketorolac-lactic acid linker conjugate depicted above is then reacted with a lysine or the N-terminus of a knottin peptide to create a ketorolac-lactic acid- peptide conjugate. The knottin peptide is selected from the peptides of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432.
Ketorolac is currently dosed as an enantiomeric mixture, in which enantiomers with a single racemic stereocenter are very difficult to separate. As in the reaction scheme (I), a diastereomer with two chiral centers is created by the addition of a chiral linker such as L-lactic acid. Since diastereomers are easily separated, the active enantiomer of ketorolac conjugated to the lactic acid linker can be purified prior to conjugation to a knottin peptide. The chemical synthesis can use any conjugation techniques known in the art, such as described in Bioconjugate Techniques by Greg Hermanson and in “Ketorolac-dextran conjugates: synthesis, in vitro, and in vivo evaluation:” Acta Pharm. 57 (2007) 441-450, Vyas, Trivedi, and Chaturvedi. The conjugate can display anti-inflammatory activity, or free ketorolac is released from the conjugate to provide anti-inflammatory activity. The free ketorolac can result from hydrolysis that occurs after administration, such as hydrolysis at the ester bond. By dosing the conjugate containing the cartilage homing peptide, a higher AUC of ketorolac delivery to the joint may be achieved than would be achieved by systemic dosing of ketorolac alone.
Example 14 Ibuprofen Peptide ConjugateThis example describes the conjugation of ibuprofen to a knottin peptide using a PEG linker. A conjugate is produced using ibuprofen and a PEG linker, which forms an ester bond that can hydrolyze as described in “In vitro and in vivo study of poly(ethylene glycol) conjugated ibuprofen to extend the duration of action,” Scientia Pharmaceutica, 2011, 79:359-373, Nayak and Jain. Fischer esterification is used to conjugate ibuprofen with a short PEG, e.g., with triethylene glycol, to yield ibuprofen-ester-PEG-OH.
Following preparation of the PEG-ibuprofen conjugate as shown above, the hydroxyl moiety of PEG is activated with N,N′-disuccinimidyl carbonate (DSC) to form ibuprofen-ester-PEG-succinimidyl carbonate, which is then reacted with a lysine or the N-terminus of a knottin peptide to form an ibuprofen-ester-PEG-peptide conjugate. The knottin peptide is selected from any one of the peptides of sequence SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432. The conjugate can display anti-inflammatory activity, or free ibuprofen is released from the conjugate to provide anti-inflammatory activity. The free ibuprofen can result from hydrolysis that occurs after administration, such as hydrolysis at the ester bond.
Ibuprofen-peptide conjugates are administered to a subject in need thereof. The subject can be a human or a non-human animal.
Example 15 Dexamethasone Peptide ConjugateThis example describes different methods of conjugating dexamethasone with a peptide of this disclosure. A peptide of SEQ ID NO: 111 was recombinantly expressed. Dexamethasone was readily conjugated to a peptide of this disclosure using a dicarboxylic acid linker. The peptide-dexamethasone conjugate was made by first converting dexamethasone to a hemisuccinate by reacting it with succinic anhydride. The hemisuccinate was then converted to a succinate carboxylic acid containing an active ester, using dicyclohexyl carbodiimide (DCC) or 1-ethyl-3-(3-dimethylamninopropyl)carbodiimide (EDC) in the presence of N-hydroxy succinimide (NHS). This active ester was then reacted with a lysine or the N-terminus of a knottin peptide to create a dexamethasone-carboxylic acid-peptide conjugate. Methods such as those described in “Functionalized derivatives of hyaluronic acid oligosaccharides: drug carriers and novel biomaterials” Bioconjugate Chemistry 1994, 5, 339-347, Pouyani and Prestwich, and Bioconjugate Techniques by Greg Hermanson can be used.
Peptide-dexamethasone conjugates were prepared by coupling dexamethasone to the peptides of this disclosure using standard coupling-reagent chemistry. For example, dexamethasone conjugates were made by reacting dexamethasone hemigluterate with 1.05 molar equivalents of 1,1′-carbonyldiimidazole in anhydrous DMSO in an inert atmosphere. After 30 minutes, excess dexamethasone in anhydrous DMSO was added along with two molar equivalents of anhydrous trimethylamine. The N-hydroxysuccinimide ester of the peptide-dexamethasone conjugate was generated to form a shelf-stable intermediate for later reaction with an amine-containing carrier. The N-terminal dexamethasone-peptide conjugate (SEQ ID NO: 111B) was verified by electrospray mass spectrometry (ES-MS) within a 10 ppm error.
A knottin peptide of any of the sequences of this disclosure including SEQ ID NO: 21 -SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216, SEQ ID NO: 237 -SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432, are conjugated to dexamethasone using the methods described above.
Example 16 Peptide Conjugate HydrolysisThis example describes preparation of knottin peptide conjugates having tunable hydrolysis rates. The dexamethasone conjugate described in EXAMPLE 15 is synthesized with the modification that instead of using succinic anhydride, other molecules are used to provide steric hindrance to hydrolysis at the carbon adjacent to the final hydrolyzable ester. In one exemplary conjugate, the dexamethasone conjugate is synthesized with tetramethyl succinic anhydride to generate hindered esters, which causes a decreased rate of hydrolysis. In another exemplary conjugate, one methyl group is present at the adjacent carbon. In another exemplary conjugate, two methyl groups are present at the adjacent carbon. In another exemplary conjugate, one ethyl group is present at the adjacent carbon. In another exemplary conjugate, two ethyl groups are present at the adjacent carbon. The rate of hydrolysis in these exemplary conjugates is therefore adjusted as compared to the conjugates in EXAMPLE 15, preventing premature cleavage and ensuring that the majority of peptide-dexamethasone conjugates accumulate in cartilage.
The resulting peptide conjugates are administered to a human or animal subcutaneously, intravenously, orally, or injected directly into a joint to treat disease.
Example 17 Effects of Peptide on Ion ChannelsThis example describes the interaction between knottin peptides of the present disclosure and ion channels. Ion channels can be associated with pain and can be activated in disease states such as arthritis. A peptide of the disclosure is expressed and administered in a pharmaceutical composition to a patient to treat a joint condition or disease associated with an ion channel and treatable by binding, blocking, or interacting with the ion channel. Ion channels, such as Nav 1.7, are inhibited by peptides of the present disclosure. A given peptide is expressed recombinantly or chemically synthesized, wherein the peptide selected from SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432. Following expression or synthesis, the peptide is used directly or conjugated to a therapeutic compound, such as those described herein. A peptide of the present disclosure selectively interacts with ion channels, or is mutated in order to interact with ion channels. For example, a peptide of this disclosure is bound to Nav 1.7 or Nav 1.7 is blocked by a peptide of this disclosure. When the peptide is administered to a human subject, Nav 1.7 signaling is reduced in the tissues in proximity to the joints, and pain relief is thereby provided.
Example 18 Dosing of Peptide Without Kidney LigationThis example describes a dosing scheme for administering knottin peptides to mice without kidney ligation. The peptide administered had the sequence of SEQ ID NO: 24 as shown in TABLE 1. The peptide was radiolabeled by methylating lysines and the N-terminus, so the actual binding agent may contain methyl or dimethyl lysine(s) and a methylated or dimethylated amino terminus.
A target dosage of 100 nmol of each peptide carrying 10-25 µCi of 14C was administered to Female Harlan athymic nude mice by a tail vein injection. Each peptide was allowed to freely circulate within the animal for either 4 hours or 24 hours before the animals were euthanized and sectioned.
Example 19 Peptide Homing With Intact KidneysThis example illustrates peptide homing to cartilage in animals with intact kidneys. At the end of the 4 hour or 24 hour dosing periods in Example 18, mice were frozen in a hexane/dry ice bath and then frozen in a block of carboxymethylcellulose. Whole animal sagittal slices were prepared that resulted in thin frozen sections being available for imaging. Thin, frozen sections of animal including imaging of tissues such as brain, tumor, liver, kidney, lung, heart, spleen, pancreas, muscle, adipose, gall bladder, upper gastrointestinal track, lower gastrointestinal track, bone, bone marrow, reproductive track, eye, cartilage, stomach, skin, spinal cord, bladder, salivary gland, and other types of tissues were obtained with a microtome, allowed to desiccate in a freezer, and exposed to phosphoimager plates for about ten days.
These plates were developed. A signal in tissue darker than the signal expected from blood in that tissue indicates peptide accumulation in a region, tissue, structure or cell. For instance, the cartilage is avascular and contains minute amounts of blood.
This example illustrates peptide homing to cartilage mice after administration of a peptide fluorophore conjugate. A peptide of SEQ ID NO: 111 was chemically conjugated to one molecule of Cyanine 5.5, a near infrared fluorophore, at the N-terminus of the peptide via an active NHS ester on the dye. A dose of 10 nmol of each peptide of SEQ ID NO: 111 conjugated to a Cy5.5 fluorophore (SEQ ID NO: 111A) was administered to Female Haland athymic nude mice, weighing 20-25 g, and was administered via tail vein injection. Each experiment was done in duplicate (n=2 mice per group). The peptide of SEQ ID NO: 111 conjugated to a Cy5.5 fluorophore (SEQ ID NO: 111A) was allowed to freely circulate for the described time period before the mice were euthanized at various time points. Mice were evaluated for peptide distribution of the peptide of SEQ ID NO: 111 conjugated to a Cy5.5 fluorophore (SEQ ID NO: 111A) fluorescence in whole body imaging and in isolated hind limb imaging.
For Whole body fluorescence (WBF), at the end of the dosing period, mice were frozen in a hexane/dry ice bath and then embedded in a frozen block of carboxymethylcellulose. Whole animal sagittal slices were prepared that resulted in thin frozen sections for imaging. Thin frozen sections were obtained using a microtome and allowed visualization of tissues. Sections were allowed to dessicate in a freezer prior to imaging. WBF was then performed on fluorescent sections, which were scanned on a Li-Cor Odyssey scanner at a setting of 169 µm resolution, medium quality, 700 channel, L-2.0 intensity.
For isolated hind limb fluorescence studies, mice were euthanized by CO2 asphyxiation at the end of the dosing period. The right hind limb was removed at the hip joint and imaged on a Sepctrum IVIS imager (ex/em: 675 nm.720 nm) with a 1 second exposure length and a focal height of 0.5 cm. Limbs were imaged with skin removed and with muscle removed.
TABLE 4 summarizes fluorescence signal in IVD cartilage, at various time points after administration of SEQ ID NO: 111 peptide conjugated to a Cy5.5 fluorophore (SEQ ID NO: 111A) in mice.
This example illustrates peptide homing to cartilage mice 5 minutes to 48 hours after administration of a radiolabeled peptide. Signal from the radiolabeled peptides was found in all types of cartilage at each time point examined. Each peptide was radiolabeled by methylating lysines at the N-terminus as described in EXAMPLE 2. As such, the peptide may contain methyl or dimethyl lysines and a methylated or dimethlyated amino terminus. A dose of 100 nmol radiolabeled peptide was administered via tail vein injection in Female Harlan athymic nude mice, weighing 20-25 g. The experiment was done in duplicate (n=2 animals per group). In some animals, kidneys were ligated to prevent renal filtration of the radiolabled peptides and extend plasma half-life. Each radiolabeled peptide was allowed to freely circulate within the animal for the described time period before the animals were euthanized and sectioned.
Whole body autoradiography (WBA) sagittal sectioning was performed as follows. At the end of the dosing period, mice were frozen in a hexane/dry ice bath and then embedded in a frozen block of carboxymethylcellulose. Whole animal sagittal slices were prepared that resulted in thin frozen sections for imaging. Thin frozen sections were obtained using a microtome and allowed visualization of tissues such as brain, tumor, liver, kidney, lung, heart, spleen, pancreas, muscle, adipose, gall bladder, upper gastrointestinal tract, lower gastrointestinal tract, bone, bone marrow, reproductive tract, eye, cartilage, stomach, skin, spinal cord, bladder, salivary gland, and more. Sections were allowed to dessicate in a freezer prior to imaging.
For the autoradiography imaging, tape mounted thin sections were freeze dried and radioactive samples were exposed to phophoimager plates for 7 days. These plates were developed and the signal (densitometry) from each organ was normalized to the signal found in the cardiac blood of each animal. A signal in tissue darker than the signal expected from blood in that tissue indicates accumulation in a region, tissue, structure, or cell.
TABLE 5 shows the signal of radiolabeled peptides of SEQ ID NO: 24 and SEQ ID NO: 111 in IVD and knee joints as a percentage of the blood. Because the peptides may arrive at the joint within five minutes, a therapeutic effect from the peptide or a conjugated active agent may begin quickly. A therapeutic effect could be long lasting, due to continued presence of detected agents at 48 hours and/or due to long lasting pharmacodynamics effects.
A radiolabeled peptide of SEQ ID NO: 111 was observed in the intervertebral disc (IVD) and synovial joints at all time points (5 minutes - 48 hours). The signal to background ratio in IVD peaked at 24 hours. The signal to background ratio in knee joints peaked at 8 hours. Signal in IVD was observed to progress from the periphery of the cartilage adjacent to the bone inwards.
TABLE 6 shows the signal, as a percentage of signal in blood, of radiolabeled peptides of SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 114, and SEQ ID NO: 200in synovial joints.
TABLE 7 shows the signal of radiolabeled peptides of SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 114, and SEQ ID NO: 200 in the intervertebral disc (IVD).
Peptides signal for SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 114, and SEQ ID NO: 200 all showed signal in cartilage and exhibited cartilage homing properties. All peptides shown in TABLE 6 and TABLE 7 were variants of other peptides of this disclosure in which all lysine (K) residues were mutated to arginine (R)_residues. The peptide of SEQ ID NO: 109 is a K to R variant of a peptide of SEQ ID NO: 22, the peptide of SEQ ID NO: 110 is a K to R variant of a peptide of SEQ ID NO: 23, the peptide of SEQ ID NO: 114 is a K to R variant of a peptide of SEQ ID NO: 27, and the peptide of SEQ ID NO: 200 is a K to R variant of a peptide of SEQ ID NO: 86. These data show that K to R variants of cartilage homing peptides retain their cartilage homing properties. Radiolabeled peptide signals of SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 114, and SEQ ID NO: 200 exhibited accumulation in the IVD and joint cartilage at 3 hours after radiolabeled peptide administration. Radiolabeled peptide signals from SEQ ID NO: 109 and SEQ ID NO: 200 were maintained or increased in IVD and joint cartilage between 3 and 24 hours. Radiolabeled peptide signal from SEQ ID NO: 110 decreased in joint and IVD cartilage between 3 and 24 hours. Radiolabeled peptide of SEQ ID NO: 114 exhibited reduced residence time with a signal near the limit of detection by 24 hours. SEQ ID NO: 110 was also present in the joint and IVD cartilage at 24 hours. SEQ ID NO: 109 exhibited the highest signal in cartilage, followed by SEQ ID NO: 200, SEQ ID NO: 110, and then SEQ ID NO: 114. The signal as a percentage of blood of a peptide of SEQ ID NO: 111 in the synovial joint (TABLE 5) at 3 hours and 24 hours ranked in intensity between peptides of SEQ ID NO: 200 and SEQ ID NO: 110 (TABLE 6). The signal as a percentage of blood of a peptide of SEQ ID NO: 111 in IVD (TABLE 5) at 3 hours and 24 hours was higher than any of the peptides of SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 114, and SEQ ID NO: 200 (TABLE 7).
SEQ ID NO: 434 is a linearized version of SEQ ID NO: 111, where the knotted scaffold of the peptide has been removed by mutating out the cysteine residues that form the disulfide bonds of the peptide to serine residues, but retaining the rest of the sequence.
TABLE 8 shows quantification of signal as a percentage of signal in blood from a linearized radiolabeled SEQ ID NO: 434 peptide in intervertebral discs (IVD).
The peptide of SEQ ID NO: 434, a linearized version of the peptide of SEQ ID NO: 111, homed to cartilage to a much lesser extent than the folded knotted peptide (SEQ ID NO: 111). The signal of the folded knotted peptide of SEQ ID NO: 111 was ~20-fold greater at 3 hours and ~50-fold greater at 24 hours (TABLE 5) as compared to the linearized peptide of SEQ ID NO: 434 (TABLE 8). These results indicate that in addition to changes in primary sequence or peptide charge, homing to cartilage can also be related to changes in conformation, or tertiary structure. Namely, in some cases, folded knottin peptides can be exemplary cartilage homers in comparison to unfolded, linearized peptides of the same primary sequence (except for the mutated cysteine residues).
Example 22 Budesonide Peptide ConjugatesThis example describes conjugation of a peptide of this disclosure to budesonide. Budesonide is readily conjugated to any peptide disclosed herein via a dicarboxylic acid linker. The dicarboxylic acid linker is a linear dicarboxylic acid, such as succinic acid, or a related cyclic anhydride, such as succinic anhydride. Reactions with anhydrides can proceed under simple conditions. For example, the reaction of budesonide with five molar equivalents of glutaric anhydride is carried out in anhydrous pyridine at room temperature. Reactions with dicarboxylic acids can occur using standard carbodiimide coupling methods. For example, budesonide is reacted with one molar equivalent dimethylsuccinic acid, one molar equivalent 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (or another carbodiimide), and 0.2 molar equivalents of 40-dimethylamino pyridine.
The same methods as described in EXAMPLE 16 are used to adjust the rate of hydrolysis of peptide-budesonide conjugates, preventing premature cleavage and ensuring that the majority of peptide-budesonide conjugates accumulate in cartilage.
Peptide-budesonide conjugates are prepared by coupling budesonide to the peptides of this disclosure using standard coupling-reagent chemistry. The protocol for making the NHS succinic ester of budesonide is similar to that of dexamethasone, as described in EXAMPLE 15. The N-hydroxysuccinimide ester of the peptide-budesonide conjugate is generated to form a shelf-stable intermediate for later reaction with an amine-containing carrier.
The knottin peptide can be any peptide with the sequence selected from SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216 SEQ ID NO: 237 -SEQ ID NO: 410, SEQ ID NO: 412, or SEQ ID NO: 414 - SEQ ID NO: 432.
Example 23 Peptide Charge and Cartilage HomingThis example describes the charge of peptides of this disclosure and how it correlates to cartilage homing. TABLE 9 shows the number of lysines, and pI as calculated by various methods including Expasy pI and MYpI in peptides of this disclosure. The pI refers to the isoelectric point and is the pH at which the net charge of the peptide is zero.
A structure-based 3D modeling approach using a Poisson-Boltzmann distribution was also taken to identify the pI of various peptides of this disclosure. This approach identified the charge at biological pH (pH 7) and the overall pI, as summarized in TABLE 10, of peptides in their unfolded and folded state. The 3D structures of verified cartilage homers were determined by x-ray crystallography or modeled using various homolog-based approaches. The structures were analyzed using the PDB2PQR package (1) and the Adaptive Posisson-Boltzmann Solver software package (2). These structures are shown in
This example describes structural features and electrostatics of the cartilage homing peptides of this disclosure. Analysis of the primary sequences and predicted tertiary structure of multiple cartilage homing candidates (for example, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 27, and SEQ ID NO: 28) revealed interesting aspects of their structures that may be important for preserving biological function. Several cartilage homing candidates were grouped into a structural class identified herein as “hitchins.”
Upon further structural analysis, it was identified that many of the cartilage homing proteins have a contiguous surface of positive charge that accounts for most of the solvent accessible surface area as shown in
Other peptides that share the “hitchins” or calcin topology, that have large contiguous areas of positive surface charge, and/or that have pI values similar to other cartilage homing peptides as shown in EXAMPLE 24, may also be predicted to home to cartilage. For example, in some cases these include peptides of SEQ ID NO: 72 - SEQ ID NO: 75, SEQ ID NO: 206, SEQ ID NO: 208 - SEQ ID NO: 213, SEQ ID NO: 288 - SEQ ID NO: 291, SEQ ID NO: 422, or SEQ ID NO: 424 - SEQ ID NO: 429.
The structure of known cartilage homing peptides was also used to systematically vary key parameters and identify homologous sequences that are predicted to have cartilage homing properties using NCBI BLAST. Three criteria were modulated in NCBI BLAST to identify potential new sequences including setting the percentage of overall sequence identity, conservation of cysteines for preservation of disulfide bridges, and conservation of positively and/or negatively charged residues. Peptides of SEQ ID NO: 208 - SEQ ID NO: 213 were identified as homologous to SEQ ID NO: 24 and are predicted to have cartilage homing properties.
Example 25 Peptide Localization in ChondrocytesThis example illustrates binding of peptides of this disclosure to chondrocytes within cartilage in animals with intact kidneys. In one embodiment, animals are dosed and are processed as described in EXAMPLE 20 and EXAMPLE 21. Whole animal sagittal slices are prepared that result in thin frozen sections being available for staining and imaging. At the end of the dosing period, animals are euthanized and cartilage is removed for use in staining and imaging procedures. One or more of the following cartilage components are identified in thin frozen sections or live cartilage explants using standard staining techniques: collagen fibrils, glycosaminoglycans, or chondrocytes. A peptide of this disclosure is found to localize to chondrocytes in cartilage. Localization is visualized and confirmed by microscopy.
In another embodiment, peptides or peptide-drug conjugates of this disclosure are administered in humans and are localized in chondrocytes in cartilage.
Example 26 Peptide Localization in Cartilage Extracellular MatrixThis example illustrates localization of peptides of this disclosure in cartilage extracellular matrix. Peptides of this disclosure are bound to extracellular matrix within cartilage in animals with intact kidneys. Thin frozen sections or live cartilage explants are acquired, stained, and visualized as described in EXAMPLE 25. A peptide of the present disclosure is found to localize to the extracellular matrix in cartilage. Localization is visualized and confirmed by microscopy.
In another embodiment, peptides or peptide-drug conjugates of this disclosure are administered in humans and are localized in cartilage extracellular matrix.
Example 27 Peptide Binding to Cartilage ExplantsThis example illustrates a peptide or peptide conjugation of this disclosure binding to human and animal cartilage explants in culture. A peptide is selected from any one of the peptides of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432. Peptides are recombinantly expressed or chemically synthesized and are used directly, after radiolabeling, or after conjugation to a fluorophore or therapeutic compound. A peptide of peptide conjugate of this disclosure is incubated with cartilage explants derived from humans or animals. Peptides of peptide conjugate are found to bind to cartilage explants. Binding is confirmed using various methods that include but are not limited to liquid scintillation counting, confocal microscopy, immunohistochemistry, HPLC, or LC/MS.
Example 28 Peptide Homing to an Arthritic JointThis example illustrates peptide homing to cartilage in humans or animals with arthritis. A peptide of the present disclosure is expressed recombinantly or chemically synthesized and is used directly, after radiolabeling, or after conjugation to a fluorophore or therapeutic compound. A peptide is selected from any one of the peptides of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432. The peptide or peptide conjugate is administered to a human or animal subcutaneously, intravenously, or orally, or is injected directly into a joint. The peptide or peptide conjugate homes to cartilage.
Example 29 Peptide Homing to Cartilage in Non-Human AnimalsThis example illustrates a peptide or peptide conjugate of this disclosure homing to cartilage in non-human animals. Non-human animals include but are not limited to guinea pigs, rabbits, dog, cats, horses, and other non-human animals. A peptide of the present disclosure is recombinantly expressed or chemically synthesized and are used directly, after radiolabeling, or after conjugation to a fluorophore or therapeutic compound. The peptide is selected from any one of the peptides of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 -SEQ ID NO: 216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 -SEQ ID NO: 432. The resulting peptide or peptide conjugate is administered to a non-human animal subcutaneously, intravenously, or orally, or is injected directly into a joint. Biodistribution is assessed by LC/MS, autoradiography, positron emission tomography (PET), or fluorescence imaging. A peptide or peptide conjugate is homed to cartilage in non-human animals.
Example 30 Treatment of ChondrosarcomaThis example illustrates treatment of chondrosarcoma using peptides of the present disclosure. A peptide of the present disclosure is recombinantly expressed or chemically synthesized and are used directly, after radiolabeling, or after conjugation to a fluorophore or therapeutic compound, such as paclitaxel or monomethyl auristatin E. The peptide or peptide conjugate is administered in a pharmaceutical composition to a subject as a therapeutic for chondrosarcoma. The peptide is selected from any one of the peptides of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432. One or more peptides or peptide conjugates of the present disclosure are administered to a subject. A subject can be a human or an animal. The pharmaceutical composition is administered subcutaneously, intravenously, orally, or injected directly into a joint. The peptides or peptide conjugates target cartilage affected by chondrosarcoma.
Example 31 Method to Determine Improved Peptide VariantsThis example shows a method for determining ways to improve peptide variants by comparing and analyzing the primary sequences and tertiary structures of scaffold peptides.
Many cartilage homing peptides that come from scorpions are predicted to modulate Kv ion channels.
This example illustrates making and using peptide-Fc protein fusions. A peptide of SEQ ID NO: 111 was recombinantly expressed with the sequence for the human IgG1 Fc protein in HEK293 cells to yield a sequence of SEQ ID NO: 435 (METDTLLLWVLLLWVPGSTGGSGVPINVRCRGSRDCLDPCRRAGMRFGRCINSRCHCT PGGSGGSDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEV KFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALP APIEKTISKAKGQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPEN NYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK)
The sequence of any peptide of this disclosure is expressed as a fusion protein with either murine or human Fc by adding a secretion signal sequence to the N-terminus and an Fc sequence to the C-terminus. This creates a bivalent molecule with improved secretion properties. The larger peptide-Fc fusion is expressed in different mammalian or insect cell lines and is useful as a research reagent and a therapeutic.
Fc fusion to a peptide of SEQ ID NO: 111 to yield a sequence of SEQ ID NO: 435 extends half-life and improves biodistribution of the peptide to cartilage. Any peptide of this disclosure is co-expressed with Fc protein to yield Fc-fusion peptides with longer half-life and improved homing to cartilage. In SEQ ID NO: 435, the secretion signal sequence METDTLLLWVLLLWVPGSTG (SEQ ID NO: 485) is followed by the peptide of SEQ ID NO: 111, and is followed by the sequence for Fc protein. Cleaving can be imprecise, resulting in cleavage at position 20 or position 21 of SEQ ID NO: 435.
Example 33 Treatment of ChordomaThis example illustrates treatment of chordoma using peptides of the present disclosure. A peptide of the present disclosure is recombinantly expressed or chemically synthesized and are used directly, after radiolabeling, or after conjugation to a fluorophore or therapeutic compound, such as paclitaxel or monomethyl auristatin E. The peptide or peptide conjugate is administered in a pharmaceutical composition to a subject as a therapeutic for chordoma. The peptide is selected from any one of the peptides of SEQ ID NO: 21 - SEQ ID NO: 194, SEQ ID NO: 196, SEQ ID NO: 198 - SEQ ID NO: 216, SEQ ID NO: 237 - SEQ ID NO: 410, SEQ ID NO: 412, SEQ ID NO: 414 - SEQ ID NO: 432. One or more peptides or peptide conjugates of the present disclosure are administered to a subject. A subject can be a human or an animal. The pharmaceutical composition is administered subcutaneously, intravenously, orally, or injected directly into a joint. The peptides or peptide conjugates target cartilage affected by chordoma.
Example 34 Peptide Detectable Agent ConjugatesThis example describes the dye labeling of peptides. A peptide of the disclosure is expressed recombinantly or chemically synthesized, and then the N-terminus of the peptide is conjugated to an detectable agent via an NHS ester using DCC or EDC to produce a peptide-detectable agent conjugate. The detectable agent is the fluorophore dye is a cyanine dye, such as Cy5.5 or an Alexa fluorophore, such as Alexa647.
The peptide detectable agent conjugates are administered to a subject. The subject can be a human or a non-human animal. After administration, the peptide detectable agent conjugates home to cartilage. The subject, or a biopsy from the subject, can be imaged to visualize localization of the peptide detectable agent conjugates to cartilage. In some aspects, visualization of the peptide detectable agent conjugates in cartilage after administration results in diagnosis of arthritis, cartilage damage, or any cartilage disorder.
Example 35 Peptide Conjugates With Cleavable LinkersThis example describes preparation of knottin peptide conjugates having cleavable linkers. A peptide of the disclosure is expressed recombinantly or chemically synthesized. The peptide is conjugated to a detectable agent or an active agent via a cleavable linker, such as an ester bond using standard 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) or dicylcohexylcarbodiimide (DCC) based chemistry or thionyl chloride or phosphorous chloride-based bioconjugation chemistries. The linker is cleaved by esterases, MMP, cathepsin B, a protease, or thrombin.
The resulting peptide conjugates are administered to a human or animal subcutaneously, intravenously, orally, or injected directly into a joint to treat disease. The peptide is cleaved from the detectable agent or active agent only by digestion by a cleaving agent.
Example 36 Intra-articular Administration of Peptides and Peptide ConjugatesThis example illustrates intra-articular administration of peptides or peptide conjugates of this disclosure. A peptide of this disclosure is expressed recombinantly or chemically synthesized. In some cases, the peptide is subsequently conjugated to a detectable agent or an active agent. The peptide or peptide conjugate is administered to a subject in need thereof via intra-articular administration. The cartilage is penetrated by the peptide or peptide conjugate due to the small size of the peptide or peptide conjugate, and due to binding of cartilage components by the peptide or peptide conjugate. The peptide or peptide conjugate is bound to cartilage and the residence time in the cartilage is longer due to this binding. Optionally, the injected material is aggregated, is crystallized, or complexes are formed, further extending the depot effect and contributing to longer residence time.
Example 37 Treatment for Rapid Pain ReliefThis example illustrates rapid pain relief in patients treated for rheumatoid arthritis or osteoarthritis with the peptides or peptide conjugates of this disclosure. A peptide of this disclosure is expressed recombinantly or chemically synthesized, and then the N-terminus of the peptide is conjugated to an active agent via an NHS ester to produce a peptide-active agent conjugate. In some aspects the active agent is lidocaine. In some cases, the peptide alone is administered to the subject.
The peptide or peptide-active agent conjugate is administered to a subject in need thereof. The subject is a human or non-human animal. The subject in need thereof has rheumatoid arthritis or osteoarthritis. The peptide or peptide conjugate is delivered via intravenous administration. Upon administration, the peptide or peptide conjugate rapidly homes to cartilage. Rapid pain relief within five minutes to an hour is experienced by the subject, and pain relieve can last as long as over 3 hours.
Example 38 Selective Mutation of Residues to Produce Stable PeptidesThis example illustrates selective mutations of residues to produce peptides with enhanced stability, such as enhanced stability during manufacturing or storage. A peptide of this disclosure is expressed recombinantly or chemically synthesized. Met residues are mutated to valine, Ala, Leu, or Ile to prevent oxidation. Asn-Pro sequences are mutated to any other residue (except cysteine) to avoid cleavage reactions. Asn-Gly or Asn-Ser, and/or Asn-Pro are replaced with any other residue (except cysteine) to reduce deamidation. Asp-Gly, Asp-Ser, or Asp-Pro are replaced with any other residue (except cysteine) to reduce cleavage reactions.
The above mutations in the primary sequence of peptides of this disclosure result in enhanced peptide stability during manufacturing, storage, and after administration to a subject in need thereof.
Example 39 Peptide Resistance to Pepsin DigestionThis example shows peptide resistance to pepsin. SEQ ID NO: 24 peptide and SEQ ID NO: 111 peptide were suspended in 500 µl of ddH2O at a stock concentration of 2 mg/ml. Reactions were prepared with 12.5 µg peptide and 20 µg pepsin in simulated gastric fluid (pH 1.05) and incubated for 30 minutes at 37.5° C. Reactions were quenched with a final concentration of 100 mM Tris base and 10 mM dithiothreitol (DTT). Reversed phase HPLC (RP-HPLC) was run on samples using an Agilent 1260 HPLC equipped with a C-18 Poroshell 120B column. Sample were analyzed by a gradient method with a mobile phase of Solvent A (water with 0.1% TFA) and Solvent B (acetonitrile with 0.1% TFA). Solvent B was ramped up from 5%-45% of the mobile phase over a period of 10 minutes. Peptides were detected at an absorbance of 214 nm and 280 nm.
This example shows peptide resistance to trypsin digestion. Various peptides were suspended in 500 µl of ddH2O at a stock concentration of 2 mg/ml. Reactions were prepared with 12.5 µg peptide and 5 µg trypsin in 25 mM Tris/75 mM NaCl buffer (pH 7.0) and incubated for 30 minutes at 37.5° C. Reactions were quenched with 5 µg of soybean trypsin inhibitor and 10 mM dithiothreitol (DTT). Reversed phase HPLC (RP-HPLC) was run on samples using an Agilent 1260 HPLC equipped with a C-18 Poroshell 120B column. Sample were analyzed by a gradient method with a mobile phase of Solvent A (water with 0.1% TFA) and Solvent B (acetonitrile with 0.1% TFA). Solvent B was ramped up from 5%-45% of the mobile phase over a period of 10 minutes.
This example shows of peptide resistance to reducing agents. Several peptides were suspended in 500 µl of ddH2O to a stock concentration of 2 mg/ml. Reactions were prepared by adding 12.5 µg peptide from the stock solution to a 10 mM solution of DTT in PBS and allowed to incubate at room temperature for 30 minutes. RP-HPLC was run on samples using an Agilent 1260 HPLC equipped with a C-18 Poroshell 120B column. Samples were analyzed by a gradient method with a mobile phase of Solvent A (water with 0.1% TFA) and Solvent B (acetonitrile with 0.1% TFA). Solvent B was ramped up from 5%-45% of the mobile phase over a period of 10 minutes.
This example describes intravenous and oral administration of peptides of this disclosure, including transit of the intact peptide through the GI tract and to the feces after oral administration. A radiolabeled peptide of SEQ ID NO: 24 was administered intravenously or orally to female Harlan athymic nude mice, 6-8 weeks of age. Radiolabeled peptides of SEQ ID NO: 24was administered intravenously (IV) at a dose of 4.8 µCi / 20 nmol. Radiolabeled peptide of SEQ ID NO: 24 was administered orally (PO) at a dose of 24 µCi / 100 nmol. Mice were euthanized at various time points by CO2 asphyxiation and biological fluids were collected, including blood, urine, and feces. Urine was collected be abdominal palpitation immediately before CO2 asphyxiation. Blood was collected by cardiac puncture immediately after CO2 asphyxiation and centrifuged to separate plasma. Feces was collected either before or after CO2 asphyxiation by palpitation of the colon. Samples were analyzed by HPLC to quantify the concentration or dose of intact peptide recovered in plasma, urine, and feces. For HPLC analysis, urine samples were first diluted at a 1:20 ratio in water and plasma samples were diluted at a 1:5 ratio in water. Feces samples were dissolved in Tris buffer, centrifuged to remove the insoluble fraction, and supernatants were diluted at a 1:1 ratio in water.
TABLE 11 shows a summary of the study design.
This example describes a method for identifying new cartilage homing peptides by sequence alignment to the pFam00451:toxin_2 structural class family. The pFam00451:toxin_2 structural class is a family of peptides related by similarities in sequence identity.
The pFam00451:toxin_2 structural class family is used as a scaffold to identify variant peptides that have cartilage homing properties. Any member of the pFam00451:toxin_2 structural class family is used to predict new cartilage homing peptides based on homology, preserved residues, or a preserved cysteine residue.
Example 44 Temperature Stable PeptidesThis example illustrates peptide stability at high temperatures. Peptides were first suspended in 500 µl of ddH2O to a stock concentration of 2 mg/ml. Reactions were prepared by adding 6.25 µl of peptide from the stock solution with 95 µl ddH2O and incubated at room temperature, 70° C., or 100° C. for one hour in a Thermocycler. RP-HPLC was then run on samples using an Agilent 1260 HPLC equipped with a C-18 Poroshell 120B column. Sample were analyzed by a gradient method with a mobile phase of Solvent A (water with 0.1% TFA) and Solvent B (acetonitrile with 0.1% TFA). Solvent B was ramped up from 5%-45% of the mobile phase over a period of 10 minutes.
Peptides of SEQ ID NO: 28 and SEQ ID NO: 483 were analyzed by HPLC after incubation at room temperature (25° C.), 70° C., or 100° C. for one hour. After incubation at 70° C. for 1 hour, peptides of SEQ ID NO: 483 and SEQ ID NO: 28 showed approximately the same HPLC elution time and peak height as the samples incubated at room temperature, indicating the peptides were resistant to heat-induced degradation. After incubation at 100° C. for 1 hour, peptides of SEQ ID NO: 483 and SEQ ID NO: 28 underwent various degrees of degradation as evidenced by the reduced amount of peptide eluting at the original elution time.
While preferred embodiments of the present disclosure have been shown and described herein, it will be apparent to those skilled in the art that such embodiments are provided by way of example only. It is not intended that the disclosure be limited by the specific examples provided within the specification. While the disclosure has been described with reference to the aforementioned specification, the descriptions and illustrations of the embodiments herein are not meant to be construed in a limiting sense. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. Furthermore, it shall be understood that all embodiments of the disclosure are not limited to the specific depictions, configurations or relative proportions set forth herein which depend upon a variety of conditions and variables. It should be understood that various alternatives to the embodiments of the disclosure described herein may be employed in practicing the disclosure. It is therefore contemplated that the disclosure shall also cover any such alternatives, modifications, variations or equivalents. It is intended that the following claims define the scope of the disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby.
Claims
1-118. (canceled)
119. A method of delivering a composition to a cartilage of a subject, the method comprising administering the composition to the subject, wherein the composition comprises a peptide having:
- (a) at least 90% sequence identity to SEQ ID NO: 327 or SEQ ID NO: 240,
- (b) at least 90% sequence identity to SEQ ID NO: 325 or SEQ ID NO: 238, or
- (c) at least 90% sequence identity to SEQ ID NO: 416 or SEQ ID NO: 421;
- wherein the peptide homes, targets, or migrates to the cartilage of the subject following administration.
120. The method of claim 119, wherein the composition further comprises an active agent linked to the peptide.
121. The method of claim 120, wherein the active agent comprises a therapeutic agent, a detectable agent, or a combination thereof.
122. The method of claim 121, wherein the therapeutic agent comprises a therapeutic small molecule.
123. The method of claim 121, wherein the therapeutic agent comprises an antibiotic, an anti-viral agent, an anti-fungal agent, an anti-inflammatory agent, a protease inhibitor, an immune modulator, an anti-cytokine agent, a tyrosine kinase inhibitor, a growth factor, a cytotoxic T-lymphocyte-associated protein 4 (CTLA4) inhibitor, a B-cell lymphoma 2 (BCL-2) family inhibitor, a tumor necrosis factor alpha (TNF-α) modulator, a tumor necrosis factor receptor (TNFR) family modulator, or any combination thereof.
124. The method of claim 123, wherein the anti-inflammatory agent comprises a steroid or a nonsteroidal anti-inflammatory drug (NSAID).
125. The method of claim 124, wherein the steroid is a corticosteroid or a glucocorticoid.
126. The method of claim 124, wherein the steroid is triamcinolone acetonide, dexamethasone, budesonide, triamcinolone, cortisone, prednisone, prednisolone, triamcinolone hexacetonide, or methylprednisolone.
127. The method of claim 124, wherein the NSAID is ibuprofen, naproxen, ketorolac, indomethacin, etodolac, tolemetin, celecoxib, aceclofenac, nabumetone, sulindac, or diclofenac.
128. The method of claim 123, wherein the protease inhibitor is a matrix metalloprotease 13 (MMP13) inhibitor.
129. The method of claim 121, wherein the therapeutic agent comprises imatinib mesylate or methotrexate.
130. The method of claim 121, wherein the therapeutic agent comprises a therapeutic peptide.
131. The method of claim 130, wherein the therapeutic peptide is a cytokine, an enzyme, a growth factor, a chemokine, a neurotransmitter, an Fc region, or any combination thereof.
132. The method of claim 121, wherein the therapeutic agent comprises an antibody or an antibody fragment.
133. The method of claim 121, wherein the detectable agent comprises a fluorophore, a metal, a metal chelate, an X-ray contrast agent, a PET agent, a radioisotope, a photosensitizer, a radiosensitizer, a radionuclide chelator, or any combination thereof.
134. The method of claim 119, wherein the peptide comprises 4 or more cysteine residues and a plurality of disulfide bridges formed between cysteine residues.
135. The method of claim 119, wherein the peptide comprises a sequence of SEQ ID NO: 327, SEQ ID NO: 325, SEQ ID NO: 240, SEQ ID NO: 238, SEQ ID NO: 416, or SEQ ID NO: 421.
136. The method of claim 119, comprising administering the composition by inhalation, intranasally, orally, topically, intravenously, subcutaneously, intra-articularly, intramuscularly, intraperitoneally, or a combination thereof.
137. The method of claim 119, further comprising treating a condition in the subject.
138. The method of claim 137, wherein the condition is associated with the cartilage.
139. The method of claim 137, wherein the condition is a type of arthritis or lupus.
140. The method of claim 137, wherein the condition is rheumatoid arthritis, osteoarthritis, gout, pseudogout, ankylosing spondylitis, or psoriatic arthritis.
141. The method of claim 119, further comprising detecting a condition in the cartilage.
142. The method of claim 141, wherein the condition comprises a lesion, a degradation, a growth disturbance, a tear, an infection, an inflammation, or an injury.
143. The method of claim 142, wherein the lesion comprises a tumor or a metastasis.
144. The method of claim 142, further comprising surgically removing the lesion.
Type: Application
Filed: Mar 2, 2023
Publication Date: Nov 16, 2023
Inventors: James OLSON (Seattle, WA), Andrew David Strand (Seattle, WA), Emily June Girard (Renton, WA), Roland Strong (Seattle, WA), Christopher Mehlin (Seattle, WA), Colin Correnti (Seattle, WA), Natalie Nairn (Seattle, WA)
Application Number: 18/177,642
