ALBUMIN VARIANTS
The present invention relates to variants of a parent albumin having altered plasma half-life compared with the parent albumin. The present invention also relates to fusion polypeptides and conjugates comprising said variant albumin.
This application is a division of U.S. application Ser. No. 14/863,685, filed Sep. 24, 2015, pending, which is a division of U.S. application Ser. No. 14/262,244 filed Apr. 25, 2014, now abandoned, which is a division of U.S. application Ser. No. 13/504,326 filed Apr. 26, 2012 (issued as U.S. Pat. No. 8,748,380), which is a 35 U.S.C. 371 national application of PCT/EP2010/066572 filed Nov. 1, 2010, which claims priority or the benefit under 35 U.S.C. 119 of European application nos. 10174162.7 and 09174698.2 filed Aug. 26, 2010 and Oct. 30, 2009, respectively, and U.S. provisional application Nos. 61/348,001 and 61/327,171 filed May 25, 2010 and Apr. 23, 2010, respectively, the contents of which are fully incorporated herein by reference.
REFERENCE TO A SEQUENCE LISTINGThis application contains a Sequence Listing in computer readable form, which is incorporated herein by reference.
BACKGROUND OF THE INVENTION Field of the InventionThe present invention relates to variants of albumin or fragments thereof or fusion polypeptides comprising variant albumin or fragments thereof having a change in half-life compared to the albumin, fragment thereof or fusion polypeptide comprising albumin or a fragment thereof.
Description of the Related ArtAlbumin is a protein naturally found in the blood plasma of mammals where it is the most abundant protein. It has important roles in maintaining the desired osmotic pressure of the blood and also in transport of various substances in the blood stream.
Albumins have been characterized from many species including human, pig, mouse, rat, rabbit and goat and they share a high degree of sequence and structural homology.
Albumin binds in vivo to its receptor, the neonatal Fc receptor (FcRn) “Brambell” and this interaction is known to be important for the plasma half-life of albumin. FcRn is a membrane bound protein, expressed in many cell and tissue types. FcRn has been found to salvage albumin from intracellular degradation (Roopenian D. C. and Akilesh, S. (2007), Nat. Rev. Immunol 7, 715-725.). FcRn is a bifunctional molecule that contributes to maintaining a high level of IgGs and albumin in serum in mammals such as human beings.
Whilst the FcRn-immunoglobulin (IgG) interaction has been characterized in the prior art, the FcRn-albumin interaction is less well characterized. The major FcRn binding site is localized within DIII (381-585). Andersen et al (2010). Clinical Biochemistry 43, 367-372. Data indicates that IgG and albumin bind non-cooperatively to distinct sites on FcRn (Andersen et al. (2006), Eur. J. Immunol 36, 3044-3051; Chaudhury et al. (2006), Biochemistry 45, 4983-4990.).
It is known that mouse FcRn binds IgG from mice and humans whereas human FcRn appears to be more discriminating (Ober et al. (2001) Int. Immunol 13, 1551-1559). Andersen et al. (2010). Journal of Biological Chemistry 285(7):4826-36, describes the affinity of human and mouse FcRn for each mouse and human albumin (all possible combinations). No binding of albumin from either species was observed at physiological pH to either receptor. At acidic pH, a 100-fold difference in binding affinity was observed. In all cases, binding of albumin and IgG from either species to both receptors were additive.
Human serum albumin (HSA) has been well characterized as a polypeptide of 585 amino acids, the sequence of which can be found in Peters, T., Jr. (1996) All about Albumin: Biochemistry, Genetics and Medical, Applications pp10, Academic Press, Inc., Orlando (ISBN 0-12-552110-3). It has a characteristic binding to its receptor FcRn, where it binds at pH 6.0 but not at pH 7.4.
The plasma half-life of HSA has been found to be approximately 19 days. A natural variant having lower plasma half-life has been identified (Peach, R. J. and Brennan, S. 0., (1991) Biochim Biophys Acta. 1097:49-54) having the substitution D494N. This substitution generated an N-glycosylation site in this variant, which is not present in the wild-type albumin. It is not known whether the glycosylation or the amino acid change is responsible for the change in plasma half-life.
Albumin has a long plasma half-life and because of this property it has been suggested for use in drug delivery. Albumin has been conjugated to pharmaceutically beneficial compounds (WO 2000/69902A), and it was found that the conjugate—maintained the long plasma half-life of albumin. The resulting plasma half-life of the conjugate was generally considerably longer than the plasma half-life of the beneficial therapeutic compound alone.
Further, albumin has been fused to therapeutically beneficial peptides (WO 2001/79271 A and WO 2003/59934 A) with the typical result that the fusion has the activity of the therapeutically beneficial peptide and a considerably longer plasma half-life than the plasma half-life of the therapeutically beneficial peptides alone.
Otagiri et al (2009), Biol. Pharm, Bull. 32(4), 527-534, discloses that 77 albumin variant are know, of these 25 are found in domain III. A natural variant lacking the last 175 amino acids at the carboxy termini has been shown to have reduced half-life (Andersen et al (2010), Clinical Biochemistry 43, 367-372). Iwao et al. (2007) studied the half-life of naturally accuring human albumin variants using a mouse model, and found that K541E and K560E had reduced half-life, E501K and E570K had increased half-life and K573E had almost no effect on half-life (Iwao, et. al. (2007) B.B.A. Proteins and Proteomics 1774, 1582-1590).
Galliano et al (1993) Biochim. Biophys. Acta 1225, 27-32 discloses a natural variant E505K. Minchiotti et al. (1990) discloses a natural variant K536E. Minchiotti et al (1987) Biochim. Biophys. Acta 916, 411-418 discloses a natural variant K574N. Takahashi et al (1987) Proc. Natl. Acad. Sci. USA 84, 4413-4417, discloses a natural variant D550G. Carlson et al (1992). Proc. Nat. Acad. Sci. USA 89, 8225-8229, discloses a natural variant D550A.
Albumin has the ability to bind a number of ligands and these become associated (associates) with albumin. This property has been utilized to extend the plasma half-life of drugs having the ability to noncovalently bind to albumin. This can also be achieved by binding a pharmaceutical beneficial compound, which has little or no albumin binding properties, to a moiety having albumin binding properties. See review article and reference therein, Kratz (2008). Journal of Controlled Release 132, 171-183.
Albumin is used in preparations of pharmaceutically beneficial compounds, in which such a preparation maybe for example, but not limited to, a nano particle or micro particle of albumin. In these examples the delivery of a pharmaceutically beneficial compound or mixture of compounds may benefit from alteration in the albumins affinity to its receptor where the beneficial compound has been shown to associate with albumin for the means of delivery.
It is not clear what determines the plasma half-life of the formed associates (for example but not limited to Levemir®, Kurtzhals P et al. Biochem. J. 1995; 312:725-731) conjugates or fusion polypeptides but it appears to be a result of the combination of the albumin and the selected pharmaceutically beneficial compound/polypeptide. It would be desirable to be able to control the plasma half-life of given albumin conjugates, associates or albumin fusion polypeptides so that a longer or shorter plasma half-life can be achieved than given by the components of the association, conjugation or fusion, in order to be able to design a particular drug according to the particulars of the indication intended to be treated.
Albumin is known to accumulate and be catabolised in tumours, it has also been shown to accumulate in inflamed joints of rheumatoid arthritis sufferers. See review article and reference therein, Kratz (2008). Journal of Controlled Release 132, 171-183. It is envisaged that HSA variants with increased affinity for FcRn would be advantageous for the delivery of pharmaceutically beneficial compounds.
It may even be desirable to have variants of albumin that have little or no binding to FcRn in order to provide shorter half-lives or controlled serum pharmacokinetics as described by Kenanova et al (2009) J. Nucl. Med.; 50 (Supplement 2):1582).
SUMMARY OF THE INVENTIONThe present invention provides variants of a parent albumin with improved properties compared to its parent. In particular the invention provides variants of a parent albumin having altered plasma half-life compare to its parent.
The present invention relates to isolated variants of albumin or fragments thereof, or fusion polypeptides comprising variant albumin or fragments thereof, of a parent albumin, comprising an alteration at one or more (several) positions corresponding to positions 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584 of the mature polypeptide of SEQ ID NO: 2, wherein the variant is not the variant consisting of SEQ ID NO: 2 with the substitution D494N, E501K, K541E, D550G,A, K573E or K574N.
The alteration at one or more position may independently be selected among substitutions, insertions and deletions, where substitution are preferred.
The present invention also relates to isolated polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of producing the variants.
The present invention also relates to conjugates or associates comprising the variant albumin or fragment thereof according to the invention and a beneficial therapeutic moiety or to a fusion polypeptide comprising a variant albumin or fragment thereof of the invention and a fusion partner polypeptide.
The invention further relates to compositions comprising the variant albumin, fragment thereof, fusion polypeptide comprising variant albumin or fragment thereof or conjugates comprising the variant albumin or fragment thereof, according to the invention or associates comprising the variant albumin or fragment thereof, according to the invention. The compositions are preferably pharmaceutical compositions.
The invention further relates to a pharmaceutical composition comprising a variant albumin, fragment thereof, fusion polypeptide comprising variant albumin or fragment thereof or conjugates comprising the variant albumin or fragment thereof, or associates comprising the variant albumin or fragment thereof, wherein said variant albumin, fragment thereof, fusion polypeptide comprising variant albumin or fragment thereof or conjugates comprising the variant albumin or fragment or associates of variant albumin or fragment thereof has altered plasma half-life compared to the corresponding plasma half-life of the HSA or fragment thereof, fusion polypeptide comprising HSA or fragment thereof or conjugates or associates of HSA or, fragment thereof, comprising HSA or fragment thereof.
The present invention relates to isolated variants of albumin or fragments thereof, or fusion polypeptides comprising variant albumin or fragments thereof, of a parent albumin, comprising an alteration at one or more (several) positions corresponding to positions 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584 of the mature polypeptide of SEQ ID NO: 2, wherein the variant is not the variant consisting of SEQ ID NO: 2 with the substitution D494N, E501K, K541E, D550G,A, K573E or K574N.
The alteration at one or more position may independently be selected among substitutions, insertions and deletions, where substitution are preferred.
DefinitionsVariant: The term “variant” means a polypeptide derived from a parent albumin by one or more alteration(s), i.e., a substitution, insertion, and/or deletion, at one or more (several) positions. A substitution means a replacement of an amino acid occupying a position with a different amino acid; a deletion means removal of an amino acid occupying a position; and an insertion means adding 1 or more, preferably 1-3 amino acids immediately adjacent to an amino acid occupying a position.
Mutant: The term “mutant” means a polynucleotide encoding a variant.
Wild-Type Albumin: The term “wild-type” (WT) albumin means albumin having the same amino acid sequence as naturally found in an animal or in a human being.
Parent or Parent albumin The term “parent” or “parent albumin” means an albumin to which an alteration is made by the hand of man to produce the albumin variants of the present invention. The parent may be a naturally occurring (wild-type) polypeptide or an allele thereof, or even a variant thereof.
FcRn and shFcRn: The term “FcRn” means the human neonatal Fc receptor (FcRn). shFcRn is a soluble recombinant form of FcRn.
smFcRn: The term “smFcRn” is a soluble recombinant form of the mouse neonatal Fc Receptor.
Isolated variant: The term “isolated variant” means a variant that is modified by the hand of man and separated completely or partially from at least one component with which it naturally occurs. In one aspect, the variant is at least 1% pure, e.g., at least 5% pure, at least 10% pure, at least 20% pure, at least 40% pure, at least 60% pure, at least 80% pure, and at least 90% pure, as determined by SDS-PAGE or GP-HPLC.
Substantially pure variant: The term “substantially pure variant” means a preparation that contains at most 10%, at most 8%, at most 6%, at most 5%, at most 4%, at most 3%, at most 2%, at most 1%, and at most 0.5% by weight of other polypeptide material with which it is natively or recombinantly associated. Preferably, the variant is at least 92% pure, e.g., at least 94% pure, at least 95% pure, at least 96% pure, at least 97% pure, at least 98% pure, at least 99%, at least 99.5% pure, and 100% pure by weight of the total polypeptide material present in the preparation. The variants of the present invention are preferably in a substantially pure form. This can be accomplished, for example, by preparing the variant by well known recombinant methods and by purification methods.
Mature polypeptide: The term “mature polypeptide” means a polypeptide in its final form following translation and any post-translational modifications, such as N-terminal processing, C-terminal truncation, glycosylation, phosphorylation, etc. In one aspect, the mature polypeptide is amino acids 1 to 585 of SEQ ID NO: 2, with the inclusion of any post-translational modifications.
Mature polypeptide coding sequence: The term “mature polypeptide coding sequence” means a polynucleotide that encodes a mature albumin polypeptide. In one aspect, the mature polypeptide coding sequence is nucleotides 1 to 1758 of SEQ ID NO: 1.
Sequence Identity: The relatedness between two amino acid sequences or between two nucleotide sequences is described by the parameter “sequence identity”.
For purposes of the present invention, the degree of sequence identity between two amino acid sequences is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, J. Mol. Biol. 48: 443-453) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, Trends Genet. 16: 276-277), preferably version 3.0.0 or later. The optional parameters used are gap open penalty of 10, gap extension penalty of 0.5, and the EBLOSUM62 (EMBOSS version of BLOSUM62) substitution matrix. The output of Needle labelled “longest identity” (obtained using the −nobrief option) is used as the percent identity and is calculated as follows:
(Identical Residues×100)/(Length of Alignment−Total Number of Gaps in Alignment)
For purposes of the present invention, the degree of sequence identity between two deoxyribonucleotide sequences is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, supra) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, supra), preferably version 3.0.0 or later. The optional parameters used are gap open penalty of 10, gap extension penalty of 0.5, and the EDNAFULL (EMBOSS version of NCBI NUC4.4) substitution matrix. The output of Needle labeled “longest identity” (obtained using the −nobrief option) is used as the percent identity and is calculated as follows:
(Identical Deoxyribonucleotides×100)/(Length of Alignment−Total Number of Gaps in Alignment)
Fragment: The term “fragment” means a polypeptide having one or more (several) amino acids deleted from the amino and/or carboxyl terminus of an albumin and/or an internal region of albumin that has retained the ability to bind to FcRn. Fragments may consist of one uninterrupted sequence derived from HSA or it may comprise two or more sequences derived from HSA. The fragments according to the invention have a size of more than approximately 20 amino acid residues, preferably more than 30 amino acid residues, more preferred more than 40 amino acid residues, more preferred more than 50 amino acid residues, more preferred more than 75 amino acid residues, more preferred more than 100 amino acid residues, more preferred more than 200 amino acid residues, more preferred more than 300 amino acid residues, even more preferred more than 400 amino acid residues and most preferred more than 500 amino acid residues.
Allelic variant: The term “allelic variant” means any of two or more alternative forms of a gene occupying the same chromosomal locus. Allelic variation arises naturally through mutation, and may result in polymorphism within populations. Gene mutations can be silent (no change in the encoded polypeptide) or may encode polypeptides having altered amino acid sequences. An allelic variant of a polypeptide is a polypeptide encoded by an allelic variant of a gene.
Coding sequence: The term “coding sequence” means a polynucleotide, which directly specifies the amino acid sequence of its translated polypeptide product. The boundaries of the coding sequence are generally determined by an open reading frame, which usually begins with the ATG start codon or alternative start codons such as GTG and TTG and ends with a stop codon such as TAA, TAG, and TGA. The coding sequence may be a DNA, cDNA, synthetic, or recombinant polynucleotide.
cDNA: The term “cDNA” means a DNA molecule that can be prepared by reverse transcription from a mature, spliced, mRNA molecule obtained from a eukaryotic cell. cDNA lacks intron sequences that may be present in the corresponding genomic DNA. The initial, primary RNA transcript is a precursor to mRNA that is processed through a series of steps, including splicing, before appearing as mature spliced mRNA.
Nucleic acid construct: The term “nucleic acid construct” means a nucleic acid molecule, either single- or double-stranded, which is isolated from a naturally occurring gene or is modified to contain segments of nucleic acids in a manner that would not otherwise exist in nature or which is synthetic. The term nucleic acid construct is synonymous with the term “expression cassette” when the nucleic acid construct contains the control sequences required for expression of a coding sequence of the present invention.
Control sequences: The term “control sequences” means all components necessary for the expression of a polynucleotide encoding a variant of the present invention. Each control sequence may be native or foreign to the polynucleotide encoding the variant or native or foreign to each other. Such control sequences include, but are not limited to, a leader, polyadenylation sequence, propeptide sequence, promoter, signal peptide sequence, and transcription terminator. At a minimum, the control sequences include a promoter, and transcriptional and translational stop signals. The control sequences may be provided with linkers for the purpose of introducing specific restriction sites facilitating ligation of the control sequences within the coding region of the polynucleotide encoding a variant.
Operably linked: The term “operably linked” means a configuration in which a control sequence is placed at an appropriate position relative to the coding sequence of a polynucleotide such that the control sequence directs the expression of the coding sequence.
Expression: The term “expression” includes any step involved in the production of the variant including, but not limited to, transcription, post-transcriptional modification, translation, post-translational modification, and secretion.
Expression vector: The term “expression vector” means a linear or circular DNA molecule that comprises a polynucleotide encoding a variant and is operably linked to additional nucleotides that provide for its expression.
Host cell: The term “host cell” means any cell type that is susceptible to transformation, transfection, transduction, and the like with a nucleic acid construct or expression vector comprising a polynucleotide of the present invention. The term “host cell” encompasses any progeny of a parent cell that is not identical to the parent cell due to mutations that occur during replication.
Plasma half-life: Plasma half-life is ideally determined in vivo in suitable individuals. However, since it is time consuming and expensive and there inevitable are ethical concerns connected with doing experiments in animals or man it is desirable to use an in vitro assay for determining whether plasma half-life is extended or reduced. It is known that the binding of albumin to its receptor FcRn is important for plasma half-life and the correlation between receptor binding and plasma half-life is that a higher affinity of albumin to its receptor leads to longer plasma half-life. Thus for the present invention a higher affinity of albumin to FcRn is considered indicative of an increased plasma half-life and a lower affinity of albumin to its receptor is considered indicative of a reduced plasma half-life.
In this application and claims the binding of albumin to its receptor FcRn is described using the term affinity and the expressions “stronger” or “weaker”. Thus, it should be understood that a molecule having a higher affinity to FcRn than HSA is considered to bind stronger to FcRn than HSA and a molecule having a lower affinity to FcRn than HSA is considered to bind weaker to FcRn than HSA.
The terms “longer plasma half-life” or “shorter plasma half-life” and similar expressions are understood to be in relationship to the corresponding parent albumin molecule. Thus, a longer plasma half-life with respect to a variant albumin of the invention means that the variant has longer plasma half-life than the corresponding albumin having the same sequences except for the alteration(s) in positions corresponding to 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584 in SEQ ID NO: 2.
Conventions for Designation of VariantsFor purposes of the present invention, the mature polypeptide disclosed in SEQ ID NO: 2 is used to determine the corresponding amino acid residue in another albumin. The amino acid sequence of another albumin is aligned with the mature polypeptide disclosed in SEQ ID NO: 2, and based on the alignment, the amino acid position number corresponding to any amino acid residue in the mature polypeptide disclosed in SEQ ID NO: 2 is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, J. Mol. Biol. 48: 443-453) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, Trends Genet. 16: 276-277), preferably version 3.0.0 or later.
Identification of the corresponding amino acid residue in another albumin can be confirmed by an alignment of multiple polypeptide sequences using “ClustalW” (Larkin et al., 2007, Bioinformatics 23: 2947-2948).
When the other polypeptide (or protein) has diverged from the mature polypeptide of SEQ ID NO: 2 such that traditional sequence-based comparison fails to detect their relationship (Lindahl and Elofsson, 2000, J. Mol. Biol. 295: 613-615), other pairwise sequence comparison algorithms can be used. Greater sensitivity in sequence-based searching can be attained using search programs that utilize probabilistic representations of polypeptide families (profiles) to search databases. For example, the PSI-BLAST program generates profiles through an iterative database search process and is capable of detecting remote homologs (Atschul et al., 1997, Nucleic Acids Res. 25: 3389-3402). Even greater sensitivity can be achieved if the family or superfamily for the polypeptide has one or more representatives in the protein structure databases. Programs such as GenTHREADER (Jones, 1999, J. Mol. Biol. 287: 797-815; McGuffin and Jones, 2003, Bioinformatics 19: 874-881) utilize information from a variety of sources (PSI-BLAST, secondary structure prediction, structural alignment profiles, and solvation potentials) as inputs to a neural network that predicts the structural fold for a query sequence. Similarly, the method of Gough et al., 2000, J. Mol. Biol. 313: 903-919, can be used to align a sequence of unknown structure within the superfamily models present in the SCOP database. These alignments can in turn be used to generate homology models for the polypeptide, and such models can be assessed for accuracy using a variety of tools developed for that purpose.
For proteins of known structure, several tools and resources are available for retrieving and generating structural alignments. For example the SCOP superfamilies of proteins have been structurally aligned, and those alignments are accessible and downloadable. Two or more protein structures can be aligned using a variety of algorithms such as the distance alignment matrix (Holm and Sander, 1998, Proteins 33: 88-96) or combinatorial extension (Shindyalov and Bourne, 1998, Protein Engineering 11: 739-747), and implementations of these algorithms can additionally be utilized to query structure databases with a structure of interest in order to discover possible structural homologs (e.g., Holm and Park, 2000, Bioinformatics 16: 566-567).
In describing the albumin variants of the present invention, the nomenclature described below is adapted for ease of reference. The accepted IUPAC single letter or three letter amino acid abbreviation is employed.
Substitutions.
For an amino acid substitution, the following nomenclature is used: Original amino acid, position, substituted amino acid. Accordingly, for example the substitution of threonine with alanine at position 226 is designated as “Thr226Ala” or “T226A”. Multiple mutations are separated by addition marks (“+”), e.g., “Gly205Arg+Ser411Phe” or “G205R+S411F”, representing substitutions at positions 205 and 411 of glycine (G) with arginine (R) and serine (S) with phenylalanine (F), respectively. The Figures also use (“/”), e.g., “E492T/N503D” this should be viewed as interchangeable with (“+”).
Deletions.
For an amino acid deletion, the following nomenclature is used: Original amino acid, position*. Accordingly, the deletion of glycine at position 195 is designated as “Gly195*” or “G195*”. Multiple deletions are separated by addition marks (“+”), e.g., “Gly195*+Ser411*” or
“G195*+S411*”.
Insertions.
For an amino acid insertion, the following nomenclature is used: Original amino acid, position, original amino acid, inserted amino acid. Accordingly the insertion of lysine after glycine at position 195 is designated “Gly195GlyLys” or “G195GK”. An insertion of multiple amino acids is designated [Original amino acid, position, original amino acid, inserted amino acid #1, inserted amino acid #2; etc.]. For example, the insertion of lysine and alanine after glycine at position 195 is indicated as “Gly195GlyLysAla” or “G195GKA”.
In such cases the inserted amino acid residue(s) are numbered by the addition of lower case letters to the position number of the amino acid residue preceding the inserted amino acid residue(s). In the above example, the sequence would thus be:
Multiple Alterations.
Variants comprising multiple alterations are separated by addition marks (“+”), e.g., “Arg170Tyr+Gly195Glu” or “R170Y+G195E” representing a substitution of tyrosine and glutamic acid for arginine and glycine at positions 170 and 195, respectively.
Different Substitutions.
Where different substitutions can be introduced at a position, the different substitutions are separated by a comma, e.g., “Arg170Tyr,Glu” represents a substitution of arginine with tyrosine or glutamic acid at position 170. Thus, “Tyr167Gly,Ala+Arg170Gly,Ala” designates the following variants:
“Tyr167Gly+Arg170Gly”, “Tyr167Gly+Arg170Ala”, “Tyr167Ala+Arg170Gly”, and “Tyr167Ala+Arg170Ala”.
Parent AlbuminAlbumins are proteins and constitute the most abundant protein in plasma in mammals and albumins from a long number of mammals have been characterized by biochemical methods and/or by sequence information. Several albumins, e.g., human serum albumin (HSA), have also been characterized crystallographically and the structure determined.
HSA is a preferred albumin according to the invention and is a protein consisting of 585 amino acid residues and has a molecular weight of 67 kDa. In its natural form it is not glycosylated. The amino acid sequence of HSA is shown in SEQ ID NO: 2. The skilled person will appreciate that natural alleles may exist having essentially the same properties as HSA but having one or more amino acid changes compared to SEQ ID NO: 2, and the inventors also contemplate the use of such natural alleles as parent albumin according to the invention.
Albumins have generally a long plasma half-life of approximately 20 days or longer, e.g., HSA has a plasma half-life of 19 days. It is known that the long plasma half-life of HSA is mediated via interaction with its receptor FcRn, however, an understanding or knowledge of the exact mechanism behind the long half-life of HSA is not essential for the present invention.
According to the invention the term “albumin” means a protein having the same, or very similar three dimensional structure as HSA and having a long plasma half-life. As examples of albumin proteins according to the invention can be mentioned human serum albumin, primate serum albumin, (such as chimpanzee serum albumin, gorilla serum albumin), rodent serum albumin (such as hamster serum albumin, guinea pig serum albumin, mouse albumin and rat serum albumin), bovine serum albumin, equine serum albumin, donkey serum albumin, rabbit serum albumin, goat serum albumin, sheep serum albumin, dog serum albumin, chicken serum albumin and pig serum albumin. HSA as disclosed in SEQ ID NO: 2 or any naturally occurring allele thereof, is the preferred albumin according to the invention.
The parent albumin, a fragment thereof, or albumin part of a fusion polypeptide comprising albumin or a fragment thereof according to the invention has generally a sequence identity to the sequence of HSA shown in SEQ ID NO: 2 of at least 60%, preferably at least 70%, preferably at least 80%, preferably at least 85%, preferably at least 86%, preferably at least 87%, preferably at least 88%, preferably at least 89%, preferably at least 90%, preferably at least 91%, preferably at least 92%, preferably at least 93%, preferably at least 94%, preferably at least 95%, more preferred at least 96%, more preferred at least 97%, more preferred at least 98% and most preferred at least 99%.
The parent preferably comprises or consists of the amino acid sequence of SEQ ID NO: 2. In another aspect, the parent comprises or consists of the mature polypeptide of SEQ ID NO: 2.
In another embodiment, the parent is an allelic variant of the mature polypeptide of SEQ ID NO: 2.
In a second aspect, the parent is encoded by a polynucleotide that hybridizes under very low stringency conditions, low stringency conditions, medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with (i) the mature polypeptide coding sequence of SEQ ID NO: 1, (ii) the mature polypeptide coding sequence of SEQ ID NO: 1, or (iii) the full-length complementary strand of (i) or (ii) (J. Sambrook, E. F. Fritsch, and T. Maniatis, 1989, Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor, New York).
The polynucleotide of SEQ ID NO: 1 or a subsequence thereof, as well as the amino acid sequence of SEQ ID NO: 2 or a fragment thereof, may be used to design nucleic acid probes to identify and clone DNA encoding a parent from strains of different genera or species according to methods well known in the art. In particular, such probes can be used for hybridization with the genomic or cDNA of the genus or species of interest, following standard Southern blotting procedures, in order to identify and isolate the corresponding gene therein. Such probes can be considerably shorter than the entire sequence, but should be at least 14, e.g., at least 25, at least 35, or at least 70 nucleotides in length. Preferably, the nucleic acid probe is at least 100 nucleotides in length, e.g., at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, at least 500 nucleotides, at least 600 nucleotides, at least 700 nucleotides, at least 800 nucleotides, or at least 900 nucleotides in length. Both DNA and RNA probes can be used. The probes are typically labelled for detecting the corresponding gene (for example, with 32P, 3H, 355, biotin, or avidin). Such probes are encompassed by the present invention.
A genomic DNA or cDNA library prepared from such other organisms may be screened for DNA that hybridizes with the probes described above and encodes a parent. Genomic or other DNA from such other organisms may be separated by agarose or polyacrylamide gel electrophoresis, or other separation techniques. DNA from the libraries or the separated DNA may be transferred to and immobilized on nitrocellulose or other suitable carrier material. In order to identify a clone or DNA that is homologous with SEQ ID NO: 1 or a subsequence thereof, the carrier material is used in a Southern blot.
For purposes of the present invention, hybridization indicates that the polynucleotide hybridizes to a labelled nucleotide probe corresponding to the polynucleotide shown in SEQ ID NO: 1, its complementary strand, or a subsequence thereof, under low to very high stringency conditions. Molecules to which the probe hybridizes can be detected using, for example, X-ray film or any other detection means known in the art.
In one aspect, the nucleic acid probe is the mature polypeptide coding sequence of SEQ ID NO: 1. In another aspect, the nucleic acid probe is nucleotides 1 to 1785 of SEQ ID NO: 1. In another aspect, the nucleic acid probe is a polynucleotide that encodes the polypeptide of SEQ ID NO: 2 or a fragment thereof. In another aspect, the nucleic acid probe is SEQ ID NO: 1.
For long probes of at least 100 nucleotides in length, very low to very high stringency conditions are defined as prehybridization and hybridization at 42° C. in 5×SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and either 25% formamide for very low and low stringencies, 35% formamide for medium and medium-high stringencies, or 50% formamide for high and very high stringencies, following standard Southern blotting procedures for 12 to 24 hours optimally. The carrier material is finally washed three times each for 15 minutes using 2×SSC, 0.2% SDS at 45° C. (very low stringency), 50° C. (low stringency), 55° C. (medium stringency), 60° C. (medium-high stringency), 65° C. (high stringency), or 70° C. (very high stringency).
For short probes that are about 15 nucleotides to about 70 nucleotides in length, stringency conditions are defined as prehybridization and hybridization at about 5° C. to about 10° C. below the calculated T, using the calculation according to Bolton and McCarthy (1962, Proc. Natl. Acad. Sci. USA 48: 1390) in 0.9 M NaCl, 0.09 M Tris-HCl pH 7.6, 6 mM EDTA, 0.5% NP-40, 1×Denhardt's solution, 1 mM sodium pyrophosphate, 1 mM sodium monobasic phosphate, 0.1 mM ATP, and 0.2 mg of yeast RNA per ml following standard Southern blotting procedures for 12 to 24 hours optimally. The carrier material is finally washed once in 6×SCC plus 0.1% SDS for 15 minutes and twice each for 15 minutes using 6×SSC at 5° C. to 10° C. below the calculated Tm.
In a third aspect, the parent is encoded by a polynucleotide with a sequence identity to the mature polypeptide coding sequence of SEQ ID NO: 1 of at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100%, which encodes a polypeptide which is able to function as an albumin. In an embodiment, the parent is encoded by a polynucleotide comprising or consisting of SEQ ID NO: 1.
Preparation of VariantsIn a further aspect the invention relates to a method for preparing a variant albumin, fragment thereof, or fusion polypeptide comprising variant albumin or a fragment thereof comprising the steps of:
-
- a. Identifying one or more amino acid residue positions being important for the binding of albumin to FcRn, in an albumin or a fragment thereof or the albumin part of a fusion polypeptide comprising albumin or a fragment thereof;
- b. Providing a nucleic acid encoding said albumin, the fragment thereof or the albumin part of a fusion polypeptide comprising albumin or the fragment thereof;
- c. Modifying the nucleic acid provided in b., so that the one or more (several) amino acid residue located at the positions identified in a., are deleted or substituted or inserted with a different amino acid;
- d. Expressing the modified nucleic acid in a suitable host cell; and
- e. Recovering the variant albumin, the fragment thereof or the fusion polypeptide comprising variant albumin or the fragment thereof.
The identification of one or more amino acid residue positions being important for the binding of albumin to FcRn, in albumin, fragment thereof or the albumin part of a fusion polypeptide can be done in several ways including, but not limited to, random mutagenesis followed by analysis of the generated mutants and comparison with the non-mutated parent molecule, and identification based on structural considerations optionally followed by generation of variants having the identified alterations and comparison with the non-mutated patent molecule.
A preferred method for identification of one or more amino acid residue positions to be changed to in order to prepare a variant HSA having an altered binding to FcRn compared with natural HSA, comprises the following steps:
-
- i) Identifying a non-human albumin having a different binding property to FcRn;
- ii) Identifying the amino acid residues of the human serum albumin interacting with FcRn;
- iii) Comparing the primary and/or the tertiary structure of the identified non-human albumin and human serum albumin with respect to the amino acid residues identified in step ii) and identifying the amino acid residues that differ between said non-human albumin and human serum albumin as being responsible for the observed binding difference; and
- iv) Optionally preparing variants of HSA at the positions identified in step iii) and confirming that the prepared variants have altered binding to FcRn compared with HSA.
Step i) above may be done using the SPR assay described below. However, the skilled person will appreciate that other methods may be used to identify non-human albumins having different binding properties to FcRn than HSA, and that the method is not dependent on how the non-human albumin, having different binding properties to FcRn, has been identified.
In one preferred embodiment the identified non-human albumin has a stronger binding to FcRn than HSA. Examples of non-human albumins having stronger binding to FcRn than HSA include donkey serum albumin, rabbit serum albumin, dog serum albumin, hamster serum albumin, guinea pig serum albumin, mouse serum albumin and rat serum albumin. Step ii) may be accomplished by considering the structure of FcRn, HSA and the binding complex of these two. In the absence of an available structure of the binding complex it is possible to use a model where the HSA structure is docked into the structure of the FcRn structure and thereby identify amino acid residues of HSA interacting with FcRn.
In another preferred embodiment the identified non-human albumin has a weaker binding to FcRn than HSA. Examples of non-human albumins having weaker binding to FcRn than HSA include bovine serum albumin, goat serum albumin, sheep serum albumin and chicken serum albumin. Step ii) may be accomplished by considering the structure of FcRn, HSA and the binding complex of these two. In absence of an available structure of the binding complex it is possible to use a model where the HSA structure is docked into the structure of the FcRn structure and thereby identify residues of HSA interacting with FcRn.
In this invention and claims, an amino acid residues of HSA interacting with FcRn is considered any amino acid residues of HSA being located less than 10A from an amino acid in the FcRn or any amino acid residue that is involved in a hydrogen bond, a salt bridge or a polar or nonpolar interaction with an amino acid residue that is located less than 10A from an amino acid in the FcRn. Preferably the amino acid in HSA residues are located less than 10A from amino acids in the FcRn, more preferred less than 6A from amino acids in the FcRn and most preferred less than 3A from amino acids in the FcRn.
Step iii) and iv) can be done using techniques well known to the skilled person.
The present invention also relates to methods for obtaining a variant albumin or fragments thereof, or fusion polypeptides comprising the variant albumin or fragments thereof, or associates of variant albumin or fragment thereof comprising: (a) introducing into a parent albumin or fragments thereof, or fusion polypeptides comprising the parent albumin or fragments thereof an alteration at one or more (several) positions corresponding to positions 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584 of the mature polypeptide of SEQ ID NO: 2; and (b) recovering the variant albumin or fragments thereof, or fusion polypeptides comprising the variant albumin or fragments thereof.
The variants can be prepared by those skilled persons using any mutagenesis procedure known in the art, such as site-directed mutagenesis, synthetic gene construction, semi-synthetic gene construction, random mutagenesis, shuffling, etc.
Site-directed mutagenesis is a technique in which one or more (several) mutations are created at one or more defined sites in a polynucleotide encoding the parent.
Site-directed mutagenesis can be accomplished in vitro by PCR involving the use of oligonucleotide primers containing the desired mutation. Site-directed mutagenesis can also be performed in vitro by cassette mutagenesis involving the cleavage by a restriction enzyme at a site in the plasmid comprising a polynucleotide encoding the parent and subsequent ligation of an oligonucleotide containing the mutation in the polynucleotide. Usually the restriction enzyme that digests at the plasmid and the oligonucleotide is the same, permitting ligation of the plasmid and insert to one another. See, e.g., Scherer and Davis, 1979, Proc. Natl. Acad. Sci. USA 76: 4949-4955; and Barton et al., 1990, Nucleic Acids Res. 18: 7349-4966.
Site-directed mutagenesis can also be accomplished in vivo by methods known in the art. See, e.g., U.S. Patent Application Publication No. 2004/0171154; Storici et al., 2001, Nature Biotechnol. 19: 773-776; Kren et al., 1998, Nat. Med. 4: 285-290; and Calissano and Macino, 1996, Fungal Genet. Newslett. 43: 15-16.
Any site-directed mutagenesis procedure can be used in the present invention. There are many commercial kits available that can be used to prepare variants.
Synthetic gene construction entails in vitro synthesis of a designed polynucleotide molecule to encode a polypeptide of interest. Gene synthesis can be performed utilizing a number of techniques, such as the multiplex microchip-based technology described by Tian et al. (2004, Nature 432: 1050-1054) and similar technologies wherein olgionucleotides are synthesized and assembled upon photo-programable microfluidic chips.
Single or multiple amino acid substitutions, deletions, and/or insertions can be made and tested using known methods of mutagenesis, recombination, and/or shuffling, followed by a relevant screening procedure, such as those disclosed by Reidhaar-Olson and Sauer, 1988, Science 241: 53-57; Bowie and Sauer, 1989, Proc. Natl. Acad. Sci. USA 86: 2152-2156; WO 95/17413; or WO 95/22625. Other methods that can be used include error-prone PCR, phage display (e.g., Lowman et al., 1991, Biochemistry 30: 10832-10837; U.S. Pat. No. 5,223,409; WO 92/06204) and region-directed mutagenesis (Derbyshire et al., 1986, Gene 46: 145; Ner et al., 1988, DNA 7: 127).
Mutagenesis/shuffling methods can be combined with high-throughput, automated screening methods to detect activity of cloned, mutagenized polypeptides expressed by host cells (Ness et al., 1999, Nature Biotechnology 17: 893-896). Mutagenized DNA molecules that encode active polypeptides can be recovered from the host cells and rapidly sequenced using standard methods in the art. These methods allow the rapid determination of the importance of individual amino acid residues in a polypeptide.
Semi-synthetic gene construction is accomplished by combining aspects of synthetic gene construction, and/or site-directed mutagenesis, and/or random mutagenesis, and/or shuffling. Semi-synthetic construction is typified by a process utilizing polynucleotide fragments that are synthesized, in combination with PCR techniques. Defined regions of genes may thus be synthesized de novo, while other regions may be amplified using site-specific mutagenic primers, while yet other regions may be subjected to error-prone PCR or non-error prone PCR amplification. Polynucleotide sub sequences may then be shuffled.
VariantsThe present invention also provides variant albumins or fragments thereof, or fusion polypeptides comprising the variant albumin or fragments thereof, of a parent albumin, comprising an alteration at one or more (several) positions corresponding to positions 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584 in SEQ ID NO: 2, wherein each alteration is independently a substitution, insertion or deletion with the provision that the and the variant is not SEQ ID NO: 2 having the substitution D494N, E501K, K541E, D550G,A, K573E or K574N.
The variant albumin, a fragment thereof, or albumin part of a fusion polypeptide comprising variant albumin or a fragment thereof according to the invention has generally a sequence identity the sequence of HSA shown in SEQ ID NO: 2 of at least 60%, preferably at least 70%, preferably at least 80%, preferably at least 85%, preferably at least 90%, more preferred at least 95%, more preferred at least 96%, more preferred at least 97%, more preferred at least 98% and most preferred at least 99%.
In one aspect, the number of alterations in the variants of the present invention is 1-20, e.g., 1-10 and 1-5, such as 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 alterations.
The variant albumin, a fragment thereof or fusion polypeptide comprising the variant albumin or fragment thereof has altered plasma half-life compared with the corresponding parent albumin, fragment thereof, or fusion polypeptide comprising the variant albumin or fragment thereof.
In a particular preferred embodiment the parent albumin is HSA and the variant albumin, a fragment thereof or fusion polypeptide comprising the variant albumin or fragment thereof has altered plasma half-life compared with the HSA, the corresponding fragment or fusion polypeptide comprising HSA or fragment thereof.
The correlation between binding of albumin to its receptor and plasma half-life has been realized by the present inventors based on the natural occurring allele of HSA D494N. The inventors have analyzed this allele and found that it has a lower affinity to its receptor FcRn.
Further, it has been disclosed that a transgenic mouse having the natural mouse FcRn replaced with human FcRn has a higher serum albumin level than normal mouse; see (J Exp Med. (2003) 197(3):315-22). The inventors have discovered that human FcRn has a higher affinity to mouse serum albumin than mouse FcRn has to mouse serum albumin and, therefore, the observed increase in serum albumin in the transgenic mice corresponds with a higher affinity between serum albumin and its receptor, confirming the correlation between albumin binding to FcRn and plasma half-life. In addition, variants of albumin that have little or no binding to FcRn have been shown to have reduced half-life in a mouse model, Kenanova et al (2009) J. Nucl. Med.; 50 (Supplement 2): 1582).
One way to determine whether the affinity of a variant albumin to FcRn is higher or lower than the parent albumin is to use the Surface Plasmon Resonance assay (SPR) as described below. The skilled person will understand that other methods might be useful to determine whether the affinity of a variant albumin to FcRn is higher or lower than the affinity of the parent albumin to FcRn, e.g., determination and comparison of the binding constants KD. Thus, according to the invention variant albumins having a KD that is lower than the KD for natural HSA is considered to have a higher plasma half-life than HSA and variant albumins having a KD that is higher than the KD for natural HSA is considered to have a lower plasma half-life than HSA.
The variants of albumin or fragments thereof or fusion polypeptides comprising albumin or fragments thereof comprise one or more alterations, such as substitutions, deletions or insertions at one or more (several) positions corresponding to the positions in HSA selected from the group consisting of 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584. The substitution may be any substitution where the amino acid in the natural albumin sequence is substituted with a different amino acid selected among the remaining 19 natural occurring amino acids.
In one aspect, a variant comprises an alteration at one or more (several) positions corresponding to positions 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584 in SEQ ID NO: 2. In another aspect, a variant comprises an alteration at two positions corresponding to any of 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584 in SEQ ID NO: 2. In another aspect, a variant comprises an alteration at three positions corresponding to any of positions 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584 in SEQ ID NO: 2. In another aspect, a variant comprises an alteration at each position corresponding to positions 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584 in SEQ ID NO: 2.
In another aspect, the variant comprises the substitution Q417A,H of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution H440Q of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution H464Q of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution A490D of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution E492G, T,P,H of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution V493P,L of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution D494N,Q,A,E,P of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution E495Q,A of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution T496A of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution P499A of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution K500E,G,D,A,S,C,P,H,F,N,W,T,M,Y,V,Q,L,I,R of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution E501A,P,Q of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution N503K,D,H of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution A504E of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution E505K, D of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution T506F, S of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution H510Q of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution H535Q of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution K536A of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution P537A of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution K538A,H of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution T540S of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution K541A,D,G,N,E of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution E542P,D of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution D550N of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution K573Y,W,P,H,F,V,I,T,N,S,G,M,C,A,E,Q,R,L,D of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution K574N of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution Q580K of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution L575F of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution A577T,E of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution A578R,S of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution S579C,T of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution Q580K of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution A581D of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution A582T of the mature polypeptide of SEQ ID NO: 2. In another aspect, the variant comprises the substitution G584A of the mature polypeptide of SEQ ID NO: 2.
In one aspect, the variant comprises an alteration at a position corresponding to position 417. In another aspect, the amino acid at a position corresponding to position 417 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Ala or His. In another aspect, the variant comprises the substitution Q417A, H of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 440. In another aspect, the amino acid at a position corresponding to position 440 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Ala. In another aspect, the variant comprises the substitution H440Q of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 464. In another aspect, the amino acid at a position corresponding to position 464 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Ala. In another aspect, the variant comprises the substitution H464Q of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 490 In another aspect, the amino acid at a position corresponding to position 490 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val. In another aspect, the variant comprises the substitution A490G of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 492. In another aspect, the amino acid at a position corresponding to position 492 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Gly. In another aspect, the variant comprises the substitution E492G of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 493. In another aspect, the amino acid at a position corresponding to position 493 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Pro. In another aspect, the variant comprises the substitution V493P of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 494. In another aspect, the amino acid at a position corresponding to position 494 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Asn, Gln or Ala. In another aspect, the variant comprises the substitution D494N,Q, A of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 495. In another aspect, the amino acid at a position corresponding to position 495 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Gln or Ala. In another aspect, the variant comprises the substitution E495Q or A of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 496. In another aspect, the amino acid at a position corresponding to position 496 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Ala. In another aspect, the variant comprises the substitution T496A of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 499. In another aspect, the amino acid at a position corresponding to position 499 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Ala. In another aspect, the variant comprises the substitution P499A of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 500. In another aspect, the amino acid at a position corresponding to position 500 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Ala. In another aspect, the variant comprises the substitution K500E,G,D,A,S,C,P,H,F,N,W,T,M,Y,V,Q,L,I,R of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 501. In another aspect, the amino acid at a position corresponding to position 501 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Ala or Gln to reduce affinity and Pro to increase affinity. In another aspect, the variant comprises the substitution E501A, Q, P of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 503. In another aspect, the amino acid at a position corresponding to position 503 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Asp or Lys or His. In another aspect, the variant comprises the substitution N503D, K, H of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 504. In another aspect, the amino acid at a position corresponding to position 504 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val. In another aspect, the variant comprises the substitution A504 of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 505. In another aspect, the amino acid at a position corresponding to position 505 is substituted with Ala, Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val. In another aspect, the variant comprises the substitution E505D of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 506. In another aspect, the amino acid at a position corresponding to position 506 is substituted with Ala, Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val. In another aspect, the variant comprises the substitution T506S,F of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 510. In another aspect, the amino acid at a position corresponding to position 510 is substituted with Ala, Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Gin. In another aspect, the variant comprises the substitution H510Q of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 535. In another aspect, the amino acid at a position corresponding to position 535 is substituted with Ala, Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Gin. In another aspect, the variant comprises the substitution H535Q of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 536. In another aspect, the amino acid at a position corresponding to position 536 is substituted with Ala, Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Ala. In another aspect, the variant comprises the substitution K536A of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 537. In another aspect, the amino acid at a position corresponding to position 537 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Ala. In another aspect, the variant comprises the substitution P537A of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 538. In another aspect, the amino acid at a position corresponding to position 538 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Ala. In another aspect, the variant comprises the substitution K538H, A of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 540. In another aspect, the amino acid at a position corresponding to position 540 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val. In another aspect, the variant comprises the substitution T540S of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 541. In another aspect, the amino acid at a position corresponding to position 541 is substituted with Ala, Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Gly, Asp or Ala. In another aspect, the variant comprises the substitution K541G, D A, N of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 542. In another aspect, the amino acid at a position corresponding to position 542 is substituted with Ala, Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Asp or Pro. In another aspect, the variant comprises the substitution E542D, P of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 550. In another aspect, the amino acid at a position corresponding to position 550 is substituted with Ala, Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Asn to reduce affinity, preferably with Glu to increase affinity.
In another aspect, the variant comprises an alteration at a position corresponding to position 573. In another aspect, the amino acid at a position corresponding to position 573 is substituted with Ala, Arg, Asn, Asp, Cys, Gin, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Tyr, Trp, Pro, His. Phe, Val, Ile, Thr, Asn, Ser, Gly, Met, Cys, Ala, Glu, Gin, Arg, Leu, Asp. In another aspect, the variant comprises the substitution K573Y,W,P,H,F,V,I,T,N,S,G,M,C,A,E,Q,R,L,D of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 574. In another aspect, the amino acid at a position corresponding to position 574 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Asn. In another aspect, the variant comprises the substitution K574N of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 575. In another aspect, the amino acid at a position corresponding to position 575 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Phe. In another aspect, the variant comprises the substitution L575F of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 577. In another aspect, the amino acid at a position corresponding to position 577 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Thr or Glu. In another aspect, the variant comprises the substitution A577TE of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 578. In another aspect, the amino acid at a position corresponding to position 578 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Arg or Ser. In another aspect, the variant comprises the substitution A578R,S of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 579. In another aspect, the amino acid at a position corresponding to position 579 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Cys or Thr. In another aspect, the variant comprises the substitution S579C,T of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 580. In another aspect, the amino acid at a position corresponding to position 580 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Lys. In another aspect, the variant comprises the substitution Q580K of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 581. In another aspect, the amino acid at a position corresponding to position 581 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Asp. In another aspect, the variant comprises the substitution A581D of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 582. In another aspect, the amino acid at a position corresponding to position 582 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Thr. In another aspect, the variant comprises the substitution A582T of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at a position corresponding to position 584. In another aspect, the amino acid at a position corresponding to position 584 is substituted with Ala, Arg, Asn, Asp, Cys, Gln, Glu, Gly, His, Ile, Leu, Lys, Met, Phe, Pro, Ser, Thr, Trp, Tyr, or Val, preferably with Ala. In another aspect, the variant comprises the substitution G584A of the mature polypeptide of SEQ ID NO: 2.
In another aspect, the variant comprises an alteration at positions corresponding to positions 494 and 496 in SEQ ID NO: 2, such as those described above.
In another aspect, the variant comprises alterations at positions corresponding to positions 492 and 493 in SEQ ID NO: 2, such as those described above.
In another aspect, the variant comprises alterations at positions corresponding to positions 494 and 417 in SEQ ID NO: 2, such as those described above.
In another aspect, the variant comprises alterations at positions corresponding to positions 492 and 503 in SEQ ID NO: 2, such as those described above.
In another aspect, the variant comprises alterations at positions corresponding to positions 492 and 573 in SEQ ID NO: 2, such as those described above.
In another aspect, the variant comprises alterations at positions corresponding to positions 492, 503, and 573 in SEQ ID NO: 2, such as those described above.
In one embodiment the variant albumin or fragments thereof, or fusion polypeptides comprising the variant albumin or fragments thereof according to the invention contains one substitution at a position corresponding to a position in HSA selected from the group consisting of 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584 in SEQ ID NO: 2 provided that the variant albumin is not the variant consisting of SEQ ID NO: 2 with the substitution D494N, E501K, K541E, D550G,A, K573E or K574N. The variant albumin, fragment thereof or fusion polypeptides comprising variant albumin or a fragment thereof according to the invention may comprise additional substitutions, insertions or deletions at one or more (several) positions corresponding to other positions in HSA.
In another embodiment the variant albumin or fragments thereof, or fusion polypeptides comprising variant albumin or fragments thereof according to the invention contains two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen fifteen, sixteen, seventeen, eighteen, nineteen twenty or even more substitutions at positions corresponding to positions in HSA selected from the group consisting of 417, 440, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 575, 577, 578, 579, 580, 581, 582 and 584 of SEQ ID NO: 2. The variant albumin or fragments thereof, or fusion polypeptides comprising variant albumin or fragments thereof according to the invention may comprise additional substitutions, insertions or deletions at positions corresponding to other positions in HSA.
In a further embodiment the variants of albumin or fragments thereof, or fusion polypeptides comprising variant albumin or a fragment thereof according to the invention have a plasma half-life that is longer than the plasma half-life of the parent albumin fragment thereof or fusion polypeptide comprising the parent albumin or a fragment thereof. Examples according to this embodiment include variants of albumin or fragments thereof, or fusion polypeptides comprising variant albumin or a fragment thereof comprising a substitution in the position corresponding to 492, 503, 542, 550, 573, 574, 580, 581, 582 or 584 in SEQ ID NO: 2. Preferred substitutions according to this embodiment of the invention include the substitution of the amino acid residue in the position corresponding to 492 in SEQ ID NO: 2 with a G residue, substitution of the amino acid residue in the position corresponding to 503 in SEQ ID NO: 2 with a H or a K residue, substitution of the amino acid residue in the position corresponding to 550 in SEQ ID NO: 2 with an E residue, the substitution of the amino acid residue in a position corresponding to 573 in SEQ ID NO: 2 with an Y,W,P,H,F,V,I,T,N,S,G,M,C,A,E,Q,R,L or a D, the substitution of the amino acid residue in a position corresponding to 574 in SEQ ID NO: 2 with an N residue, or the substitution of the amino acid residue in the position corresponding to 580 in SEQ ID NO: 2 with an K residue. Other preferred variants have a substitution in the position corresponding to 492 in SEQ ID NO: 2 with a G residue and a substitution in the position corresponding to 573 in SEQ ID NO: 2 with an A or a P residue. Other preferred variant has a number of substitutions corresponding to position 492 in SEQ ID NO: 2 with an H residue in position 503 in SEQ ID NO: 2.
Other preferred variants have a substitution in the position corresponding to 492 in SEQ ID NO: 2 with a G residue and a substitution in the position corresponding to position 503 in SEQ ID NO: 2 corresponding to a H or a K and a substitution in position 573 in SEQ ID NO: 2 with an A or a P residue.
In a further embodiment the variants of albumin or fragments thereof, or fusion polypeptides comprising variant albumin or fragments thereof according to the invention have a plasma half-life that is shorter than the plasma half-life of the parent albumin fragment thereof or fusion polypeptide comprising the parent albumin or a fragment thereof. Examples according to this embodiment include variants of albumin or fragments thereof, or fusion polypeptides comprising variant albumin or a fragment thereof comprising a substitution in the position corresponding to 417, 440, 494, 495, 496, 499, 500, 501, 536, 537, 538, 541, 494+496 or 492+493 in SEQ ID NO: 2. Preferred substitutions include the substitutions corresponding to Q417A, H440Q, D494E+Q417H, D494N,Q,A, E495Q,A, T496A, D494N+T496A or, P499A, K500A, E501A, E501Q, K536A, P537A, K538A, K541G, K541A K541D or D550N in SEQ ID NO: 2.
In another embodiment of the invention the variants of albumin or fragments thereof, or fusion polypeptides comprising variant albumin or a fragment thereof according to the invention have lost their ability to bind FcRn. In this connection variants of albumin or fragments thereof, or fusion polypeptides comprising variant albumin or fragments thereof is considered to have lost the ability to bind FcRn if the measured resonance units for the variant in the SPR assay described below is less than 10% of the measured resonance units for the corresponding parent albumin or fragment thereof. Examples according to this embodiment include variants of albumin or fragments thereof, or fusion polypeptides comprising variant albumin or fragments thereof comprising a substitution at a position corresponding to 464, 500, 510 or 535 in SEQ ID NO: 2. Preferred substitutions include the substitutions corresponding to H464Q, K500A,P,C,S,A,D.G H510Q or H535Q in SEQ ID NO: 2.
In addition to the one or more substitutions at one or more positions corresponding to positions 417, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574, 580 581, 582 and 584 in SEQ ID NO: 2 the variant albumin or fragments thereof, or fusion polypeptides comprising variant albumin or fragments thereof according to the invention may contain additional substitutions, deletions or insertions in other positions of the molecules. Such additional substitutions, deletions or insertions may be useful in order to alter other properties of the molecules such as but not limited to altered glycosylation; introduction of reactive groups of the surface such a thiol groups, removing/generating a carbamoylation site; etc.
Residues that might be altered in order to provide reactive residues on the surface and which advantageously could be applied to the present invention has been disclosed in the unpublished patent application WO 2010/092135 (Included by reference). Particular preferred residues include the positions corresponding to positions in SEQ ID NO: 2.
As examples of alterations that can be made in SEQ ID NO: 2 or in corresponding positions in other albumins in order to provide a reactive thiol group on the surface includes alterations corresponding to following alterations in SEQ ID NO: 2: L585C, D1C, A2C, D562C, A364C, A504C, E5050, T79C, E86C, D129C, D549C, A581C, D121C, E82C, S270C, A578C, L595LC, D1DC, A2AC, D562DC, A364AC, A504AC, E505EC, T79TC, E86EC, D129DC, D549DC, A581AC, A581AC, D121DC, E82EC, S270SC, A579AC, C360*, C316*, C75*, C168*, C558*, C361*, C91*, C124*, C169* and C567*. Alternatively a cysteine residue may be added to the N or C terminal of albumin.
PolynucleotidesThe present invention also relates to isolated polynucleotides that encode any of the variants of the present invention.
Nucleic Acid ConstructsThe present invention also relates to nucleic acid constructs comprising a polynucleotide encoding a variant of the present invention operably linked to one or more (several) control sequences that direct the expression of the coding sequence in a suitable host cell under conditions compatible with the control sequences.
A polynucleotide may be manipulated in a variety of ways to provide for expression of a variant. Manipulation of the polynucleotide prior to its insertion into a vector may be desirable or necessary depending on the expression vector. The techniques for modifying polynucleotides utilizing recombinant DNA methods are well known in the art.
The control sequence may be a promoter sequence, which is recognized by a host cell for expression of the polynucleotide. The promoter sequence contains transcriptional control sequences that mediate the expression of the variant. The promoter may be any nucleic acid sequence that shows transcriptional activity in the host cell including mutant, truncated, and hybrid promoters, and may be obtained from genes encoding extracellular or intracellular polypeptides either homologous or heterologous to the host cell.
In a yeast host, useful promoters are obtained from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae protease A (PRA1), Saccharomyces cerevisiae protease B (PRB1), Saccharomyces cerevisiae translation elongation factor (TEF1), Saccharomyces cerevisiae translation elongation factor (TEF2), Saccharomyces cerevisiae galactokinase (GAL1), Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH1, ADH2/GAP), Saccharomyces cerevisiae triose phosphate isomerase (TPI), Saccharomyces cerevisiae metallothionein (CUP1), and Saccharomyces cerevisiae 3-phosphoglycerate kinase. Other useful promoters for yeast host cells are described by Romanos et al., 1992, Yeast 8: 423-488.
The control sequence may also be a suitable transcription terminator sequence, which is recognized by a host cell to terminate transcription. The terminator sequence is operably linked to the 3′-terminus of the polynucleotide encoding the variant. Any terminator that is functional in the host cell may be used.
Preferred terminators for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C (CYC1), Saccharomyces cerevisiae alcohol dehydrogenase (ADH1) and Saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators for yeast host cells are described by Romanos et al., 1992, supra.
The control sequence may also be a suitable leader sequence, a nontranslated region of an mRNA that is important for translation by the host cell. The leader sequence is operably linked to the 5′-terminus of the polynucleotide encoding the variant. Any leader sequence that is functional in the host cell may be used.
Suitable leaders for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae 3-phosphoglycerate kinase, Saccharomyces cerevisiae alpha-factor, and Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP).
The control sequence may also be a polyadenylation sequence, a sequence operably linked to the 3′-terminus of the variant-encoding sequence and, when transcribed, is recognized by the host cell as a signal to add polyadenosine residues to transcribed mRNA. Any polyadenylation sequence that is functional in the host cell may be used.
Useful polyadenylation sequences for yeast host cells are described by Guo and Sherman, 1995, Mol. Cellular Biol. 15: 5983-5990.
The control sequence may also be a signal peptide coding region that encodes a signal peptide linked to the N-terminus of a variant and directs the variant into the cell's secretory pathway. The 5′-end of the coding sequence of the polynucleotide may inherently contain a signal peptide coding region naturally linked in translation reading frame with the segment of the coding region that encodes the variant. Alternatively, the 5′-end of the coding sequence may contain a signal peptide coding region that is foreign to the coding sequence. The foreign signal peptide coding region may be required where the coding sequence does not naturally contain a signal peptide coding region. Alternatively, the foreign signal peptide coding region may simply replace the natural signal peptide coding region in order to enhance secretion of the variant. However, any signal peptide coding region that directs the expressed variant into the secretory pathway of a host cell may be used.
Useful signal peptides for yeast host cells are obtained from the genes for Saccharomyces cerevisiae alpha-factor and Saccharomyces cerevisiae invertase. Other useful signal peptide coding sequences are described by Romanos et al., 1992, supra.
Where both signal peptide and propeptide regions are present at the N-terminus of a variant, the propeptide region is positioned next to the N-terminus of the variant and the signal peptide region is positioned next to the N-terminus of the propeptide region.
Methods of ProductionThe variants of the present invention can be prepared using techniques well known to the skilled person. One convenient way is by cloning nucleic acid encoding the parent albumin or a fragment thereof or fusion polypeptide comprising albumin or a fragment thereof, modifying said nucleic acid to introduce the desired substitution(s) at one or more (several) positions corresponding to positions 417, 464, 490, 492, 493, 494, 495, 496, 499, 500, 501, 503, 504, 505, 506, 510, 535, 536, 537, 538, 540, 541, 542, 550, 573, 574 and 580 in SEQ ID NO: 2, where the variant is not the variant consisting of SEQ ID NO:2 with the substitution D494N, E501K, K541E, D550G,A, K573E or K574N., preparing a suitable genetic construct where the modified nucleic acid is placed in operative connection with suitable regulatory genetic elements, such as promoter, terminator, activation sites, ribosome binding sites etc., introducing the genetic construct into a suitable host organism, culturing the transformed host organism under conditions leading to expression of the variant and recovering the variant. All these techniques are known in the art and it is within the skills of the average practitioner to design a suitable method for preparing a particular variant according to the invention.
The variant polypeptide of the invention may also be connected to a signal sequence in order to have the variant polypeptide secreted into the growth medium during culturing of the transformed host organism. It is generally advantageous to have the variant polypeptide secreted into the growth medium in order to ease recovery and purification.
Techniques for preparing variant polypeptides have also been disclosed in WO 2009019314 (included by reference) and these techniques may also be applied to the present invention.
Albumins have been successfully expressed as recombinant proteins in a range of hosts including fungi (including but not limited to Aspergillus (WO06066595), Kluyveromyces (Fleer 1991, Bio/technology 9, 968-975), Pichia (Kobayashi 1998 Therapeutic Apheresis 2, 257-262) and Saccharomyces (Sleep 1990, Bio/technology 8, 42-46)), bacteria (Pandjaitab 2000, J. Allergy Clin. Immunol. 105, 279-285)), animals (Barash 1993, Transgenic Research 2, 266-276) and plants (including but not limited to potato and tobacco (Sijmons 1990, Bio/technology 8, 217 and Farran 2002, Transgenic Research 11, 337-346). The variant polypeptide of the invention is preferably produced recombinantly in a suitable host cell. In principle any host cell capable of producing a polypeptide in suitable amounts may be used and it is within the skills of the average practitioner to select a suitable host cell according to the invention. A preferred host organism is yeast, preferably selected among Saccharomycacae, more preferred Saccharomyces cerevisiae.
The variant polypeptides of the invention may be recovered and purified from the growth medium using a combination of known separation techniques such as filtration, centrifugation, chromatography, and affinity separation techniques etc. It is within the skills of the average practitioner to purify the variants of the invention using a particular combination of such known separation steps. As an example of purification techniques that may be applied to the variants of the present invention can be mentioned the teaching of WO0044772.
The variant polypeptides of the invention may be used for delivering a therapeutically beneficial compound to an animal or a human individual in need thereof. Such therapeutically beneficial compounds include, but are not limited, to labels and readily detectable compounds for use in diagnostics, such as various imaging techniques; pharmaceutical active compounds such as drugs, or specifically binding moieties such as antibodies. The variants of the invention may even be connected to two or more different therapeutically beneficial compounds, e.g., an antibody and a drug, which gives the combined molecule the ability to bind specifically to a desired target and thereby provide a high concentration of the connected drug at that particular target.
Fusion PolypeptidesThe variants of albumin or fragments thereof according to the invention may also be fused with a non-albumin polypeptide fusion partner. The fusion partner may in principle be any polypeptide but generally it is preferred that the fusion partner is a polypeptide having therapeutic or diagnostic properties. Fusion polypeptides comprising albumin or fragments thereof are known in the art. It has been found that such fusion polypeptide comprising albumin or a fragment thereof and a fusion partner polypeptide have a longer plasma half-life compared to the unfused fusion partner polypeptide. According to the invention it is possible to alter the plasma half-life of the fusion polypeptides according to the invention compared to the corresponding fusion polypeptides of the prior art.
One or more therapeutic polypeptides may be fused to the N-terminus, the C-terminus of albumin, inserted into a loop in the albumin structure or any combination thereof. It may or it may not comprise linker sequences separating the various components of the fusion polypeptide.
Teachings relating to fusions of albumin or a fragment thereof are known in the art and the skilled person will appreciate that such teachings can also be applied to the present invention. WO 2001/79271 A and WO 2003/59934 A also contain examples of therapeutic polypeptides that may be fused to albumin or fragments thereof, and these examples apply also to the present invention.
ConjugatesThe variants of albumin or fragments thereof according to the invention may be conjugated to a second molecule using techniques known within the art. Said second molecule may comprise a diagnostic moiety, and in this embodiment the conjugate may be useful as a diagnostic tool such as in imaging; or the second molecule may be a therapeutic compound and in this embodiment the conjugate may be used for therapeutic purposes where the conjugate will have the therapeutic properties of the therapeutic compound as well as the long plasma half-life of the albumin. Conjugates of albumin and a therapeutic molecule are known in the art and it has been verified that such conjugates have long plasma half-life compared with the non-conjugated, free therapeutic molecule as such. The conjugates may conveniently be linked via a free thio group present on the surface of HSA (amino acid residue 34 of mature HSA) using well known chemistry.
In one particular preferred aspect the variant albumin or fragment thereof is conjugated to a beneficial therapeutic compound and the conjugate is used for treatment of a condition in a patient in need thereof, which condition is responsive to the particular selected therapeutic compound. Techniques for conjugating such a therapeutically compound to the variant albumin or fragment thereof are known in the art. WO 2009/019314 discloses examples of techniques suitable for conjugating a therapeutically compound to a polypeptide which techniques can also be applied to the present invention. Further WO 2009/019314 discloses examples of compounds and moieties that may be conjugated to substituted transferrin and these examples may also be applied to the present invention. The teaching of WO 2009/019314 is included herein by reference.
HSA contains in its natural form one free thiol group that conveniently may be used for conjugation. As a particular embodiment within this aspect the variant albumin or fragment thereof may comprise further modifications provided to generate additional free thiol groups on the surface. This has the benefit that the payload of the variant albumin or fragment thereof is increased so that more than one molecule of the therapeutic compound can be conjugated to each molecule of variant albumin or fragment thereof, or two or more different therapeutic compounds may be conjugated to each molecule of variant albumin or fragment thereof, e.g., a compound having targeting properties such as an antibody specific for example a tumour; and a cytotoxic drug conjugated to the variant albumin or fragment thereof thereby creating a highly specific drug against a tumour. Teaching of particular residues that may be modified to provide for further free thiol groups on the surface can be found in copending patent application WO 2010/092135, which is incorporated by reference.
AssociatesThe variants of albumin or fragments thereof may further be used in form of “associates”. In this connection the term “associate” is intended to mean a compound comprising a variant of albumin or a fragment thereof and another compound bound or associated to the variant albumin or fragment thereof by non-covalent binding. As an example of such an associate can be mentioned an associate consisting variant albumin and a lipid associated to albumin by a hydrophobic interaction. Such associates are known in the art and they may be prepared using well known techniques. As an example of a preferred associate according to the invention can be mentioned an associate comprising variant albumin and paclitaxel.
Other UsesThe variant albumin or fragments thereof or fusion polypeptides comprising variant albumin or fragments thereof according to the invention have the benefit that their plasma half-life is altered compared to the parent albumin or fragments thereof or fusion polypeptides comprising parent albumin or fragments thereof. This has the advantage that the plasma half-life of conjugates comprising variant albumin or a fragment thereof or fusion polypeptide comprising variant albumin or a fragment thereof, or an associate comprising variant albumin or a fragment thereof according to the invention can be selected in accordance with the particular therapeutic purpose.
For example for a conjugate, associate or fusion polypeptide used for imaging purposes in animals or human beings, where the imaging moiety has an very short half-life and a conjugate or a fusion polypeptide comprising HSA has a plasma half-life that is far longer than needed for the imaging purposes it would be advantageous to use a variant albumin or fragment thereof of the invention having a shorter plasma half-life than the parent albumin or fragment thereof, to provide conjugates of fusion polypeptides having a plasma half-life that is sufficiently long for the imaging purpose but sufficiently short to be cleared form the body of the particular patient on which it is applied.
In another example for a conjugate, an associate or fusion polypeptide comprising a therapeutic compound effective to treat or alleviate a particular condition in a patient in need for such a treatment it would be advantageous to use the variant albumin or fragment thereof having a longer plasma half-life than the parent albumin or fragment thereof, to provide associates or conjugates or fusion polypeptides having longer plasma half-lives which would have the benefit that the administration of the associate or conjugate or fusion polypeptide of the invention would be needed less frequently or reduced dose with less side affects compared to the situation where the parent albumin or associates thereof or fragment thereof was used.
In a further aspect the invention relates to compositions comprising the variant albumin, associates thereof or fragment thereof, variant albumin fragment or associates thereof or fusion polypeptide comprising variant albumin or fragment thereof according to the invention. The compositions are preferably pharmaceutical compositions. The composition may be prepared using techniques known in the area such as disclosed in recognized handbooks within the pharmaceutical field.
In a particular embodiment the compositions comprise a variant albumin or a fragment thereof according to the invention and a compound comprising a pharmaceutically beneficial moiety and an albumin binding domain (ABD). According to the invention ABD means a site, moiety or domain capable of binding to circulating albumin in vivo and thereby conferring transport in the circulation of the ABD and any compound or moiety bound to said ABD. ABD's are known in the art and have been shown to bind very tight to albumin so a compound comprising an ABD bound to albumin will to a certain extent behave as a single molecule. The inventors have realized by using the variant albumin or fragment thereof according to the invention together with a compound comprising a pharmaceutically beneficial moiety and an ABD makes it possible to alter the plasma half-life of the compound comprising a pharmaceutically beneficial moiety and an ABD compared to the situation where said compound were injected as such in a patient having need thereof or administered in a formulation comprising natural albumin or a fragment thereof.
The variant albumin or fragments thereof, conjugates comprising variant albumin or a fragment thereof or fusion polypeptide comprising variant albumin or a fragment thereof, or an associate comprising variant albumin or a fragment thereof according to the invention may also be incorporated into nano- or microparticles using techniques well known within the art. A preferred method for preparing nano- or microparticles that may be applied to the variant albumins or fragments thereof according to the invention is disclosed in WO 2004/071536, which is incorporated herein by reference.
CompositionsThe present invention is also directed to the use of a variant of albumin or a fragment thereof or fusion polypeptides comprising variant albumin or fragments thereof, or a conjugate comprising a variant of albumin or a fragment thereof, or an associate comprising a variant of albumin or a fragment thereof for the manufacture of a pharmaceutical composition, where in the variant of albumin or a fragment thereof or fusion polypeptides comprising variant albumin or fragments thereof, or a conjugate comprising a variant of albumin or a fragment thereof, or an associate comprising a variant of albumin or a fragment thereof has an altered plasma half-life compared with HSA or the corresponding fragment thereof or fusion polypeptide comprising HSA or fragment thereof or conjugate comprising HSA.
In this connection the corresponding fragment of HSA is intended to mean a fragment of HSA that aligns with and has same number of amino acids as the fragment of the variant albumin with which it is compared. Similarly the corresponding fusion polypeptide comprising HSA or conjugate comprising HSA is intended to mean molecules having same size and amino acid sequence as the fusion polypeptide of conjugate comprising variant albumin, with which it is compared.
Preferably the variant of albumin or a fragment thereof or fusion polypeptides comprising variant albumin or fragments thereof, fragment thereof, or a conjugate comprising a variant of albumin or a fragment thereof has a plasma half-life that is higher than the plasma half-life of HSA or the corresponding fragment thereof or fusion polypeptide comprising HSA or fragment thereof.
Alternatively, this may be expressed as the variant of albumin or a fragment thereof or fusion polypeptides comprising variant albumin or fragments thereof, fragment thereof, or a conjugate comprising a variant of albumin or a fragment thereof has a KD to FcRn that is lower that the corresponding KD for HSA or the corresponding fragment thereof or fusion polypeptide comprising HSA or fragment thereof. Preferably, is KD for the variant of albumin or a fragment thereof or fusion polypeptides comprising variant albumin or fragments thereof, fragment thereof, or a conjugate comprising a variant of albumin or a fragment thereof less than 0.9×KD for HSA, more preferred less than 0.5×KD for HSA, more preferred less than 0.1×KD for HSA, even more preferred less than 0.05×KD for HSA, even more preferred less than 0.02×KD for HSA and most preferred less than 0.01×KD for HSA.
The variant of albumin or a fragment thereof or fusion polypeptides comprising variant albumin or fragments thereof, fragment thereof, or a conjugate comprising a variant of albumin or a fragment thereof is preferably the variant of albumin or a fragment thereof or fusion polypeptides comprising variant albumin or fragments thereof, fragment thereof, or a conjugate comprising a variant of albumin or a fragment thereof according to the invention.
The present invention is further described by the following examples that should not be construed as limiting the scope of the invention.
Examples Materials and MethodsELISA:
Wells were coated with wild-type HSA or variants diluted in phosphate buffered saline (PBS) to stated concentrations, incubated overnight at 4 C and then blocked with 4% skimmed milk (Acumedia) for 1 hour at room temperature. The wells were then washed four times with PBS/0.005% TWEEN® 20 (PBS/T) pH 6.0 before glutathione-S-transferase (GST)-fused ( )hFcRn (0.5 μg/ml) as described in FEBS J. 2008 August; 275(16):4097-110. pre-incubated with an horseradish peroxidase (HRP)-conjugated polyclonal anti-GST from goat (1:5000; GE Healthcare), diluted in 4% skimmed milk PBS/0.005% TWEEN® 20 (PBS/T) pH 6.0 was added to each well and incubated for 1.5 h at room temperature followed by washing four times with PBS/T pH 6.0. One hundred μl of the substrate tetramethylbenzidine (TMB) (Calbiochem) was added to each well and incubated for 45 min before 100 μl of 0.25 M HCl was added. The absorbance was measured at 450 nm using a Sunrise TECAN spectrophotometer (TECAN, Maennedorf, Switzerland). The same ELISA was repeated with PBS/T pH 7.4.
Surface Plasmon Resonance (SPR):SPR experiments were carried out using a Biacore 3000 instrument (GE Healthcare). Flow cells of CM5 sensor chips were coupled with shFcRn-GST (1400-5000 RU) using amine coupling chemistry as described in the protocol provided by the manufacturer. The coupling was performed by injecting 10 μg/ml of the protein in 10 mM sodium acetate pH 5.0 (GE healthcare). Phosphate buffer (67 mM phosphate buffer, 0.15M NaCl, 0.005% TWEEN® 20) at pH 6.0) was used as running buffer and dilution buffer. Regeneration of the surfaces were achieved using injections of HBS-EP buffer (0.01M HEPES, 0.15M NaCl, 3 mM EDTA, 0.005% surfactant P20) at pH 7.4 (Biacore AB). For binding to immobilized shFcRn-GST, 1.0-0.5 μM of each HSA variant was injected over the surface at constant flow rate (40 μl/ml) at 25 C. In all experiments, data was zero adjusted and the reference cell subtracted. Data evaluation was performed using BIAevaluation 4.1 software (BIAcore AB).
The same SPR assay was repeated with HBS-EP buffer pH 7.4.
For the purposes of this patent unless otherwise stated HSA, WT HSA, rHA refer to Recombinant human serum albumin commercially available under the registered tradename RECOMBUMIN (available from Novozymes Biopharma UK Ltd, Nottingham UK) was used for the examples.
Serum albumin from other species: The albumins were recombinant wheres stated, produced using sequences provided from publicly available databases. Or purchased from commercial suppliers.
FcRn Expression and purification of soluble Human (shFcRn) and Mouse (smFcRn) FcRn: Methods for the generation of shFcRn and smFcRn expression plasmids, expression and purification of each heterodimer can be found in Berntzen et al. (2005) J. Immunol. Methods 298:93-104). Alternatively shFcRn FcRn heterodimer was produced by GeneArt AG (Germany). Sequences for the two sub units of the heterodimer can be found in SEQ ID NO: 3 and SEQ ID NO: 4. The soluble receptor was expressed in HEK293 cells and purified from culture supernatant using Ni-HiTrap chromatography columns.
Example 1. Preparation of Variants Preparation of Specific HSA Mutein Expression PlasmidsMethods for the expression of HSA mutant variants and HSA fusion variants were produced using several techniques. Standard molecular biology techniques were employed throughout such as described in Sambrook, J. and D. W. Russell, 2001. Molecular Cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
Method 1. Amino Acid Substitutions in HSA Detailed in Table1Synthetic DNA NcoI/SacI fragments (859 bp) were generated by gene assembly (GeneArt AG, Germany) containing point mutations within the HSA-encoding gene (SEQ ID NO: 1) to introduce the desired amino acid substitution in the translated protein. Table 2 details the codons used to introduce the amino acid substitutions into the HSA-encoding gene. The nucleotide sequence of the synthetic fragment encoding unchanged amino acids (i.e. wild type) was identical to that in pDB2243 (described in WO 00/44772). The synthetic nucleotide fragments were ligated into NcoI/SacI-digested pDB2243 to produce plasmids pDB3876-pDB3886 (Table 1). For the production of expression plasmids, pDB3876-pDB3886 (see Table 1) were each digested with NotI and PvuI, the DNA fragments were separated through a 0.7% (w/v) TAE gel, and 2992 bp fragments (‘NotI’ cassettes' including PRB1 promoter, DNA encoding the fusion leader (FL) sequence (disclosed in WO 2010/092135), nucleotide sequence encoding HSA and ADH1 terminator; see
A PCR-based method, using a QuickChange Lightening Kit (Statagene), was employed to introduce point mutations into HSA. Oligonucleotide pairs xAP094 (SEQ ID NO: 5)/xAP095 (SEQ ID NO: 6) and xAP096 (SEQ ID NO: 7)/xAP097 (SEQ ID NO: 8) were used to generate two HSA variants (D494N+E495Q+T496A and E495Q+T496A, respectively). Plasmid pDB3927(disclosed in WO 2010/092135) was used as template DNA and the methodology recommended by the manufacturer of the kit was followed. The resulting plasmids were named pDB3995 and pDB3996 (contain HSA D494N+E495Q+T496A and E495Q+T496A expression cassettes, respectively). pDB3995 and pDB3996 were digested with BstEII/BsrBI and the linearised DNA molecules were purified using standard techniques. One hundred ng of each BstEII/BsrBI digested DNA, purified using a Qiagen PCR-Purification kit following the manufacturer's instructions, was mixed individually with 100 ng Acc65I/BamHI-digested pDB3936) (disclosed in WO 2010/092135) and used to directly transform S. cerevisiae BXP10cir0 using the Sigma Yeast Transformation kit described below.
Method 3. Amino Acid Substitutions in HSA Detailed in Table 3Plasmid pDB3927 (disclosed in WO 2010/092135) (containing an identical nucleotide sequence encoding HSA as in pDB2243) was manipulated to amino acid substitutions within the mature HSA protein. Synthetic DNA fragments were generated (GeneArt AG, Germany or DNA2.0 Inc, USA) (NcoI/Bsu36I, AvrII/SphI or SacI/SphI fragments), containing point mutations within the HSA-encoding gene to introduce the desired amino acid substitution(s) into the translated protein sequence. Table 2 details the codons used to introduce the amino acid substitutions into the HSA-encoding gene. The nucleotide sequence of the synthetic fragment encoding unchanged amino acids (i.e. wild type) was identical to those in pDB3927. Synthetic DNA fragments were sub-cloned into NcoI/Bsu361, AvrII/SphI-, SacI/Sph-digested pDB3927 (described in PCT 11527.204-WO) to generate pDB4006-pDB4010, pDB4083-pDB4101 and pDB4103-pDB4111 and pDB4194, pDB4200,pDB4202 (see Table 3).
Similarly, BamHI/SalI fragments containing point mutations in the nucleotide sequence encoding HSA were generated by gene assembly (DNA2.0 Inc, USA) and ligated into BamHI/SalI-digested pDB3964 (described in WO 2010/092135) to produce plasmids pDB3986-pDB3989 (Table 3).
The C-terminal string of amino acids from position 573-585 (KKLVAASQAALGL) (SEQ ID NO: 9) in HSA were mutated to those in macaque (PKFVAASQAALA) (SEQ ID NO: 10), mouse (PNLVTRCKDALA) (SEQ ID NO: 11), rabbit (PKLVESSKATLG) (SEQ ID NO: 12) and sheep (PKLVASTQAALA) (SEQ ID NO: 13) serum albumin. The codons used to introduce each amino acid substitution are given in Table 2. Synthetic DNA fragments (SacI/SphI) were generated (DNA2.0 Inc, USA) by gene assembly (the nucleotide sequence of the synthetic fragment encoding unchanged amino acids (i.e. wild type) was identical to that in pDB3927) and were sub-cloned into SacI/SphI-digested pDB3927 to produce plasmids pDB4114-4117 (Table 3).
Plasmids pDB3883 (Table 1), pDB4094 and pDB4095 (Table 3) were digested with NcoI/SacI and 857 bp fragments from each digest were purified before being ligated into NcoI/SacI-digested pDB4006 or pDB4110 (8.688 kb) (Table 3) to produce pDB4156-pDB4161.
Expression plasmids were generated in vivo (i.e. via homologous recombination in S. cerevisiae; a technique referred to as gap repair or in vivo cloning-see Orr-Weaver & Szostak. 1983. Proc. Natl. Acad. Sci. USA. 80:4417-4421). Modified plasmids listed in Table 3 were digested with BstEII/BsrBI and the linearised DNA molecules were purified using standard techniques. One hundred ng of each BstEII/BsrBI digested DNA, purified using a Qiagen PCR-Purification kit following the manufacturer's instructions, was mixed individually with 100 ng Acc65I/BamHI-digested pDB3936 (disclosed in WO 2010/092135) and used to directly transform S. cerevisiae BXP10cir0 using the Sigma Yeast Transformation kit described below.
PCR was used to produce two permutation libraries in which the codons encoding amino acid 500 or 573 of mature HSA were changed (mutated) to alternative non-wild type amino acids and a termination codons (K5XXSTOP). Mutagenic oligonucletides (Table 4 and Table 5), were designed to amplify HSA-encoding DNA and incorporate the desired changes. That is, for the changes at position 500, pDB4082 (
For the permutation library for position 500 of HSA, the nucleotide sequence encoding HSA corresponding to that between the SalI/HindIII sites (see plasmid map pDB4082,
The permutation library at amino acid position 573 in HSA was generated using pDB3927 as template DNA and involved amplifying the albumin-encoding DNA corresponding to that between the NcoI and Bsu361 sites using oligonucleotides detailed in Table 5.
For the albumin variants based at positions 500 and 573, each PCR-product was purified using a Qiagen PCR-clean up kit (according to the manufactures instructions), digested with SalI/HindIII (position 500 library) or NcoI/Bsu361 (position 573 library). The digested DNAs were then purified using a Qiagen PCR-clean up kit and ligated into SalI/HindIII—or NcoI/Bsu361-digested pDB4082 or pDB3927, respectively, replacing the equivalent native sequence. Ligations were transformed into E. coli DH5α, subsequent plasmids isolated from transformants using a Qiagen miniprep kit (according to the manufacturer's instructions) and the correct constructs identified by restriction analysis. This produced a collection of plasmids, pDB4204-pDB4222 (position 500 library) pDB4173 to pDB4190 (position 573 library), containing albumin genes which differed only in their sequence corresponding to the codon for the amino acid at position 500 or 573 Table 4 and 5, respectively). The specific changes in each plasmid were confirmed by sequencing.
The resultants plasmids were used to generate expression plasmids and albumin fusion producing yeast by in vivo cloning as described above. That is, S. cerevisiae was transformed using the Sigma Yeast Transformation kit (described below), using a mixture of a 100 ng BstEII/BsrBI-digeste HSA variant containing plasmid and 100 ng Acc65I/BamHI digested pDB3936.
Transformation of S. cerevisiae
S. cerevisiae BXP10 cir0 (as previously described WO/2001/079480) or Strain A cir0 (described in WO/2005/061718) was streaked on to YEPD plates (1% (w/v) yeast extract, 2% (w/v) Bactopeptone, 2% (w/v) glucose), 1.5% agar) and allowed to grow for 4 days at 30° C. prior to transformation. One μg of whole plasmid (i.e. circular plasmids) or, for gap repair, 100 ng BstEII/BsrBI- or NsiI/PvuI-digested HSA variant or HSA variant fusion containing plasmid and 100 ng Acc65I/BamHI digested pDB3936 were used to transform S. cerevisiae using a Sigma Yeast Transformation kit using a modified lithium acetate method (Sigma yeast transformation kit, YEAST-1, protocol 2; Ito et al. (1983) J. Bacteriol., 153, 16; Elble, (1992) Biotechniques, 13, 18). The protocol was amended slightly by incubating the transformation at room temperature for 4 h prior to heat shock. Following heat shock, the cells were briefly centrifuged before being resuspended in 200 μl 1M sorbitol then spread over BMMD agar plates, the composition of BMMD is described by Sleep et al., (2001), Yeast, 18, 403. Plates were incubated at 30° C. for 4 days before individual colonies were patched on to fresh BMMD plates. Yeast strain numbers are detailed in Table 1.
Stocks were prepared for each yeast strain as follows: BMMD broth was inoculated with a heavy loop of each yeast patch and grown for 24 h at 30° C. with orbital shaking at 200 rpm. Cells were harvested by centrifugation at 1900×g for 5 min in a Sorval RT600 centrifuge, 15 mL supernatant was removed and replaced by trehalose 40% (w/v). The cells were resuspended and transferred to cyrovials (1 mL) for storage at −80° C.
Shake Flask Growth of S. cerevisiae
BMMD (recipe 0.17% (w/v) yeast nitrogen base without amino acid and ammonium sulphate (Difco), 37.8 mM ammonium sulphate, 29 mM citric acid, 142 mM disodium hydrogen orthophosphate dehydrate pH6.5, 2% (w/v) glucose) media (10 mL) was inoculated with each yeast strain and grown for 12 h at 30° C. with orbital shaking at 200 rpm. An aliquot of each starter culture (4 mL) was used to inoculate 2×200 mL BMMD media and grown for 36 h at 30° C. with orbital shaking at 200 rpm. Cells were harvested by filtration through 0.2 μm vacuum filter membranes (Stericup, Millipore) including a GF-D prefilter (Whatman) and the supernatant retained for purification.
Primary Concentration
Retained culture supernatant was concentrated using Tangential Flow Filtration using a Pall Filtron LV system fitted with a Omega 10KD (0.093 sq·m2) filter (LV Centramate™ cassette, Pall Filtron) with a transmembrane pressure of 20 psi and a recirculation rate of 180 mL·min−1.
FermentationFed-batch fermentations were carried out in a 10 L Sartorius Biostat C fermenter at 30° C.; pH was monitored and adjusted by the addition of ammonia or sulphuric acid as appropriate. The ammonia also provided the nitrogen source for the cultures. The level of dissolved oxygen was monitored and linked to the stirrer speed, to maintain the level at >20% of saturation. Inocula were grown in shake flasks in buffered minimal media (recipe). For the batch-phase the cultures was inoculated into fermenter media (approximately 50% of the fermenter volume) containing 2% (w/v) sucrose. The feed stage was automatically triggered by a sharp rise in the level of dissolved oxygen. Sucrose was kept at growth-limiting concentrations by controlling the rate of feed to a set nominal growth rate. The feed consisted of fermentation media containing 50% (w/v) sucrose, all essentially as described by Collins. (Collins, S. H., (1990) Production of secreted proteins in yeast, in: T. J. R. Harris (Ed.) Protein production by biotechnology, Elsevier, London, pp. 61-77).
GP-HPLC Quantitation
Purified albumin variants, fusions and conjugates were analysed by GP-HPLC and quantification as follows. Injections of 25 μL were made onto a 7.8 mm id×300 mm length TSK G3000SWXL column (Tosoh Bioscience), with a 6.0 mm id×40 mm length TSK SW guard column (Tosoh Bioscience). Samples were chromatographed in 25 mM sodium phosphate, 100 mM sodium sulphate, 0.05% (w/v) sodium azide, pH 7.0 at 1 mL/min, Samples were quantified by UV detection at 280 nm, by peak area, relative to a recombinant human albumin standard of known concentration (10 mg/mL) and corrected for their relative extinction coefficients.
Purification of Albumin Variants from Shake Flask
Albumin variants were purified from shake flask (either culture supernatant or concentrated culture supernatant) using a single chromatographic step using an albumin affinity matrix (AlbuPure™—ProMetic BioSciences, Inc.). Chromatography was performed at a constant linear velocity of 240 cm/h throughout. Culture supernatant was applied to a 6 cm bed height, 2.0 mL packed bed pre-equilibrated with 50 mM sodium acetate pH5.3. Following load the column was washed with 10 column volume (CV) of equilibration buffer, then 50 mM ammonium acetate pH8.0 (10CV). Product was eluted with either 50 mM ammonium acetate 10 mM octanoate pH8.0, 50 mM Ammonium Acetate 30 mM Sodium Octanoate 200 mM Sodium Chloride pH7.0 or 200 mM Potassium thiocyanate. The column was cleaned with 0.5M NaOH (3cv) and 20 mM NaOH (3.5cv). Eluate fraction from each albumin variant were concentrated and diafiltered against 10 volumes of 50 mM sodium chloride (Vivaspin20 10,000 MWCO PES with optional diafiltration cups, Sartorius). Purified albumin variants were quantified by GP-HPLC as described above.
Purification of Albumin-Fusion Variants from Shake Flask
Albumin-fusion variants were purified from shake flask culture supernatant using a single chromatographic step using an albumin affinity matrix (AlbuPure™—ProMetic BioSciences, Inc.). Chromatography was performed at a constant linear velocity of 240 cm/h throughout. Culture supernatant or concentrated culture supernatant was applied to a 6 cm bed height, 2.0 mL packed bed pre-equilibrated with 50 mM sodium acetate pH5.3. Following load the column was washed with 10 column volume (cv) equilibration buffer then 50 mM ammonium acetate pH8.0 (10cv). Product was eluted with either 50 mM ammonium acetate 10 mM octanoate pH8.0, 50 mM Ammonium Acetate 30 mM Sodium Octanoate 200 mM Sodium Chloride pH7.0, 50 mM Ammonium Acetate 100 mM Sodium Octanoate pH9.0 or 200 mM Potassium thiocyanate. The column was cleaned with 0.5M NaOH (3cv) and 20 mM NaOH (3.5cv). Eluate fraction from each albumin variant-fusion were concentrated and diafiltered against 10 volumes of 25 mM Tris, 150 mM NaCl, 2 mM KCl, pH 7.4 (Vivaspin20 10,000 MWCO PES with optional diafiltration cups, Sartorius). Purified albumin-fusion variants were quantified by GP-HPLC as described above.
Purification of Albumin Variants from Fermentation
Albumin variants were purified from high cell density fed batch fermentation supernatants after separation by centrifugation, using a Sorvall RC 3C centrifuge (DuPont). Culture supernatant was chromatographed through an 11 cm bed height column 8.6 mL packed bed packed with a custom synthesised albumin affinity matrix (AlbuPure™—ProMetic BioSciences, Inc.) as described above. Product was eluted using elution buffers describe above at a flow rate of 120 cm/h. The eluate fraction(s) was analysed by GP-HPLC. (above). and reducing SDS-PAGE for purity and if required concentrated (Vivaspin20 10,000 MWCO PES) and applied to a 2.4×96 cm column packed with Superdex 75 run at a flow rate of 39 cm/h in 25 mM Tris, 150 mM NaCl, 2 mM KCl, pH 7.4. The peak was fractionated, assayed by GP-HPLC and pooled in order to generate the monomeric protein of interest. Pooled fractions were concentrated (Vivaspin20 10,000 MWCO PES, Sartorius).
All proteins to be assayed for receptor (FcRn) binding properties and or other analysis were quantified by GP-HPLC as described above corrected for their relative extinction coefficients.
Example 2. Determination of Receptor (shFcRn) Binding Properties of Blood Derived HSA and Recombinant Human AlbuminEssentially fatty acid-free HSA (Sigma-Aldrich) was further purified by size exclusion chromatography as described in Andersen et al (2010). J. Biol. Chem. 285, (7), 4826-4836. Ten μM of monomeric HSA and rHA were analysed using SPR as described above and the data presented in
Direct comparison of HSA (blood derived) with recombinant human albumin (Recombumin) at the same concentration (10 μM) (
Two established FcRn binding assays were used, ELISA and SPR. There are major differences between the assays: In the ELISA system HSA is coated directly in wells and shFcRn-GST is added in solution whereas in the SPR assay shFcRn-GST is immobilized to a CM5 chip and HSA injected in solution. The pH can be varied in both systems.
The variants were analysed using ELISA at pH 6.0 and pH 7.4. Results are disclosed in
The variants were analysed using SPR analysis at pH 6.0 and pH 7.4. Results are disclosed for a representative number of variants in
The SPR data disclosed in
The conclusions of the analysis are that all tested variants have the characteristic binding to the receptor at pH 6.0 but no binding at pH 7.4. The variants D494N,Q,A, E495Q,A, T496A, and D494N+T496A show reduced binding to the receptor compared to HSA.
Example 4. Determination of Receptor (shFcRn/smFcRn) Binding Properties of Albumin VariantsUsing the SPR analysis method below the association constant Ka, the dissociation constant Kd and the binding constant KD calculated for HSA and mouse serum albumin (MSA) binding to human and mouse FcRn (Table 8).
SPR analyses-SPR analyses were performed on a BIAcore 3000 instrument (GE Healthcare) using CM5 chips and immobilization of smFcRn-GST and shFcRn-GST variants or smFcRn was performed using the amine coupling kit (GE Healthcare). Protein samples (10 μg/ml) were injected in 10 mM sodium acetate at pH 4.5 (GE Healthcare), all as described by the manufacturer. Unreacted moieties on the surface were blocked with 1 M ethanolamine. For all experiments, phosphate buffer (67 mM phosphate buffer, 0.15 M NaCl, 0.005% TWEEN® 20) at pH 6.0 or pH 7.4, or HBS-P buffer (0.01 M HEPES, 0.15 M NaCl, 0.005% surfactant P20) at pH 7.4 were used as running buffer or dilution buffer. Kinetic measurements were performed using a low density immobilized surface (100-200 resonance units (RU)). Serial dilutions of hIgG1 (2000.0-31.2 nM), mIgG1 (1000.0-15.6 nM), MSA (20.0-0.3 μM) and HSA (200.0-3.1 μM) were injected at pH 6.0 or pH 7.4, at a flow rate 50 μl/minute at 25° C. Additive binding was recorded by injecting HSA (10 01), MSA (5 01), hIgG1 (100 nM) or mIgG1 (100 nM) alone or two at a time at 25° C. at 20 μl/minute at pH 6.0 over immobilized shFcRn (˜600 RU) or smFcRn (˜600 RU). Competitive binding was measured by injecting shFcRn (50 nM) or smFcRn (100 nM) alone or together with different amounts of HSA or MSA (10.0-0.05 μM) over immobilized HSA (˜2600 RU) or MSA (˜2000 RU). In all cases, to correct for nonspecific binding and bulk buffer effects, responses obtained from the control surfaces and blank injections were subtracted from each interaction curve. Kinetic rate values were calculated using predefined models (Langmuir 1:1 ligand model, heterogeneous ligand model and steady state affinity model) provided by the BIAevaluation 4.1 software. The closeness of the fit, described by the statistical value χ2 that represents the mean square, was lower than 2.0 in all affinity estimations.
Commercially available animal albumin (either Sigma-Aldrich or Calbiochem) were further purified as described in Andersen et al (2010). J. Biol. Chem. 285, (7), 4826-4836. The binding of donkey serum albumin, bovine serum albumin, goat serum albumin, sheep serum albumin, rabbit serum albumin, dog serum albumin, hamster serum albumin, guinea pig albumin, rat serum albumin and chicken serum albumin to shFcRn was determined using the techniques described in Materials and Methods. The ELISA results are disclosed in
The SPR results are shown in
A hierarchy ranging from strongest to weakest binding is as follows; guinea pig=1>rabbit>hamster/dog>rat/mouse>donkey>human>bovine>goat/sheep>chicken. This data shows that animal albumins have different affinities for shFcRn.
Example 6. Kinetics of the HSA Variant for shFcRnThe binding constants for variants according to the invention were determined according to the methods described in Materials and Methods.
The results correspond with the conclusions made in Example 3 based on SPR and ELISA data but in addition shows that E492G has increased affinity to its receptor,
Example 7. Competitive Analysis of the HSA VariantsCompetitive analysis of the HSA variants prepared in example 1 and WT HSA was performed using the methods described in example 4. Results are shown in
Using the method of Example 1 variants of HSA having the substitutions Q417A and D494E+Q417H were constructed. The kinetic properties of these variants were tested using the methods in Materials and Methods and are shown in Table 12.
The data show that variants Q417A and D494E+Q417H bind weaker to the receptor than the wild-type HSA.
Example 9. Analysis of HSA Variants in Position 499, 500, 536, 537, 538 and 573Using the method of Example 1 variants of HSA having the substitutions P499A, K500A, K536A, P537A, K538A and K573A were constructed. The receptor binding properties of these variants were tested as described in Materials and Methods. Results are shown in
The data demonstrated that variants P499A, K536A, P537A and K538A had a reduced binding affinity to shFcRn relative to HSA. Variant K500A had almost completely lost its ability to bind to shFcRn and K573A had an increased binding affinity to shFcRn both relative to HSA.
Example 10. Analysis of Variants in Position 501 of HSAUsing the method of Example 1 variants of HSA having the substitutions E501A and E501Q were constructed. The kinetic properties of these variants were tested as described in Materials and Methods.
The data shows that variants E501A and E501Q have a slightly decreased binding affinity to shFcRn relative to HSA.
Example 11. Analysis of HSA Variants in Position 573Using the method of Example 1 variants of HSA having a substitution at position 573 were constructed. All variants at position 573 were generated and the receptor binding properties of these variants were tested as described in Materials and Methods but with SPR analysis performed at pH5.5. Results are shown in the table 14 below and
The results show that all variants having substitution in position 573 have improved binding to shFcRn compared with WT HSA. In particular the variants K573F, K573H, K573P, K573W and K573Y have more than 10 fold lower KD to shFcRn than the parent HSA. The variant K573STOP is a truncated albumin having a stop codon in position 573. The sensorgram for the K573STOP variant show significantly reduced binding compare to the WT HSA and generated a high KD. The increased affinity that we have shown for the variant K573E, a natural variant characterized by Otagiri (2009). Biol. Pharm. Bull. 32(4) 527-534, is predicted to have increased half-life in vivo.
Example 12. Analysis of Further HSA VariantsUsing the method of Example 1 variants of HSA having the substitutions E492G, E492G+N503H, N503H, D550E, E492G+N503K, E542P, H440Q, K541G, K541D, D550N E492G+K538H+K541N+E542D, E492T+N503K+K541A, E492P+N503K+K541G+E542P, E492H+E501P+N503H+E505D+T506S+T540S+K541E, A490D+E492T+V493L+E501P+N503D+A504E+E505K+T506F+K541D, E492G+V493P+K538H+K541N+E542D were constructed. The receptor binding properties of these variants were tested as described in Materials and Methods, and the results are shown in Table 15 and
The results show that for position 550, a substitution to E results in an increased affinity whilst a substitution to N resulted in reduced affinity for shFcRn at pH6.0. When this analysis was repeated for the D550E substitution at pH5.5 however no observable increase in affinity was seen. The substituted for an acid amino acid (E) maintains and improves the binding. However the substitution for an uncharged amide amino acid reduces binding at pH6.0. Based on this observation, we would predict for this position that substitutions to basic amino acids (H, K and R) would result in further reductions in binding.
Example 13. Mutations in his ResiduesThe following variants were generated using the methods described in Example 1: H440Q, H464Q, H510Q and H535Q.
It was found that the variant H440Q bound with comparable affinity as HSA. In contrast H464Q, H510Q and H535Q had significantly reduced affinity to shFcRn. This supports the previously published observations that mutagenesis of these Histidine residues significantly reduced HSA binding to shFcRn (Wu et al (2010). PEDS, 23(10)789-798). Wu et al show a reduced half-life for a diabody fusion proteins (scFv-DIII)2 in mice with an order of removal from slowest to fastest: Db-DIII WT>H535A>H510A>H464A>Db. Based on affinity to shFcRn and when compared to smFcRn (example 5) we would predict the clearance order in humans to be (for glutamine (Q) substitutions) WT>H440Q>H510Q>H464Q>H535Q.
Example 14. Further VariantsThe following variants were generated using the methods described in Example 1: K574N and Q580K in HSA. Binding of the variants to FcRn was tested using the SPR assay as described in Materials and Methods and the results are shown in Table 16.
The results show that variants K574N and Q580K bound stronger to shFcRn.
Using the method of Example 1 variants of HSA having a substitution at position 500 were constructed. All variants at position 500 were generated and the receptor binding properties of these variants were tested. Biacore X, Biacore X100 and Sensor Chip CM5 were used for all analyses, both supplied by G E Healthcare. shFcRn produced by GeneArt AG (Germany) (diluted to 10 μg/mL in 10 mM sodium acetate pH5.0 (G E Healthcare)) was immobilised on flow cell 2 (FC2) to levels between 1600-2200 response units (RU) via standard amine coupling as per manufacturers instructions (G E Healthcare). A blank immobilisation was performed on flow cell 1 (FC1) for it to serve as a reference cell. To stabilise the assay, 3-5 start up cycles were run first, with running buffer (67 mM phosphate buffer, 0.15M NaCl, 0.005% Tween 20 at pH5.75±0.25) only, followed by regeneration. WT rHA and K500 library variants were injected at various concentrations (1 μM-150 μM) for 90 s at a constant flow rate of (30 μl/min) at 25° C. followed by regeneration of the surface using HBS-EP buffer pH7.4 (G E Healthcare) until approximate initial baseline RU was restored (usually 12 s pulse would suffice).
Results are shown in the Table 17 and
The results show for variants K500R and K5001 have increased and comparable affinity for shFcRn compared to WT HSA respectively. Variant K500E bound tightly to immobilised shFcRn but still demonstrated the characteristic pH-dependency of the FcRn interaction. This complex was very stable, such that kinetic analysis was not possible (
All variants bound to shFcRn (to some extent) at pH5.5. No binding of K500 library variants to shFcRn was detectable at pH7.4.
Example 16. Fusion PolypeptidesThe generation of albumin fusions containing albumin muteins
Plasmids containing expression cassettes for the production of scFv (vHvL) genetically-fused to HSA, at either the N- or C-terminus or both, (described in, Evans et al., 2010. Protein Expression and Purification. 73, 113-124) were modified to allow the production of albumin fusions using in vivo cloning (describe above). That is, pDB3017 (
Similarly, pDB3165 (containing the bivalent fusion) (
Synthetic SalI/Bsu361 DNA fragments (269 bp), which contain point mutations within the albumin encoding nucleotide sequence to introduce amino acid substitutions corresponding to K500A, or D550N or K573P into the translated albumin protein sequence, were generated by gene assembly (GeneArt AG, Germany). The SalI/Bsu361 fragments were individually ligated into Sa/l/Bsu361-digested pDB4168-pDB4170 and pDB4172 and used to transform chemically competent E. coli DH5α using standard techniques to generate plasmids pDB4265-pDB4276 (Table 18).
Similarly, a DNA fragment was generated by PCR (using standard techniques), to introduce a K573A substitution in the translated albumin protein sequence. PCR was performed using the New England Biolabs Phusion kit using pDB4267 (
Table 19 describes PCR cycling.
The PCR-product was purified, digested with SalI/Bsu361, and the fragment (269 bp) isolated was ligated into Sa/l/Bsu361-digested pDB4168-pDB4170 and pDB4172 and used to transform chemically competent E. coli DH5α. Resulting plasmids (pDB4277-pDB4280) are listed in Table 18.
The nucleotide sequence encoding the FLAG tag was removed from plasmids pDB4168 and pDB4268-4270 (plasmids for the expression of scFv N-terminally fused to HSA and HSA muteins K500A, D550N and K573P, respectively. pDB4168 and pDB4268-4270 (Table 18) were digested with Bsu361/SphI to remove a 231 bp product comprising 3′ region of HSA-encoding gene, nucleotide sequence encoding FLAG tag and 5′ region of ADH1 terminator. A Bsu361/SphI fragment (207 bp), comprising 3′ region of HSA-encoding gene and 5′ region of mADH1 terminator (SEQ ID1) from pDB4181 was ligated into Bsu361/SphI-digested pDB4168 and pDB4268-pDB4270 using standard techniques. Ligation mixtures were used to transform chemically competent E. coli DH5α using standard techniques to generate plasmids pDB4281-pDB4284 (Table 18)
pDB4265-pDB4284 were digested with BstEII/BsrBI and the linearised DNA molecules were purified using standard techniques. One hundred ng BstEII/BsrBI DNA samples were mixed with 100 ng Acc65I/BamHI-digested pDB3936 and used to transform S. cerevisiae BXP10cir0 using the Sigma Yeast Transformation kit described below. In each case the expression plasmid was generated in the yeast by homologous recombination (in vivo cloning) between the albumin-fusion containing plasmid (pDB4265-pDB4280) (Table 18) and pDB3936.
Plasmids pDB3017, pDB3021, pDB3056 and pDB3165 (wild type HSA fusions, described by Evans et al., 2010. Protein Expression and Purification. 73, 113-124) were used to transform S. cerevisiae Strain Acir0 (described in WO/2005/061718) using the Sigma Yeast Transformation kit described below.
The nucleotide sequence encoding human IL-1RA (interleukin-1 receptor antagonist) (accession number: CAA59087) could be synthetically generated by gene assembly. The nucleotide sequence of the 708 bp synthetic fragment (Bsu361/SphI fragment) is given in SEQ ID NO: 55 and includes the 3′ region of the gene encoding HSA, the nucleotide sequence encoding a GS linker, the nucleotide sequence encoding human IL-1RA (N84Q to abolish the N-linked glycosylation motif) and the 5′ region of the ADH1 terminator. The synthetic DNA fragment could be ligated into Bsu361/SphI-digested pDB3927 to produce pDB2588.
Plasmids containing the expression cassettes for the production of IL-1RA genetically fused to the C-terminus of HSA and the HSA variants K500A, D550N, K573A and K573P were prepared as follows. pDB2588 was digested with Bsu361/SphI and a 705 bp fragment containing the ‘3 region of the HSA encoding gene, nucleotide sequence encoding a GS linker, nucleotide sequence encoding human IL1-RA (N84Q) and the 5’ region of a modified S. cerevisiae ADH1 terminator (SEQ 1D3) was purified using standard techniques then ligated into Bsu361/SphI-digested pDB4006 (containing HSA K573A expression cassette), pDB4010 (containing HSA D550N expression cassette), pDB4086 (containing HSA K500A expression cassette), pDB4110 (containing HSA K573P expression cassette) to generate pDB4287, pDB4286, pDB4285 and pDB4288, respectively (for an example, see
Preparation of an S. cerevisiae strain expressing wild type HSA genetically fused to a GS linker and IL1-RA (N84Q) (see Table 18) could also be generated following the methods described above.
The fusion polypeptides were analysed for their binding to FcRn using the SPR method described above and following results were obtained:
In example 8 it was shown that the K500A variant did not significantly bind shFcRn, in Example 10 it was shown that the K573P and K573A variants bind shFcRn stronger than HSA and in Example 11 it was shown that the D550N variant binds FcRn weaker than HSA.
In the present example it is shown that these observed difference in binding properties also are reflected in fusion polypeptides in different configurations: C-terminal fusions with a small moiety (HSA-FLAG), C-terminal fusions with a larger polypeptide (HSA-IL1RA); N-terminal fusions with polypeptide (scFv-HSA); N- and C-terminal fusions (scFv-HSA-FLAG and scFv-HSA-scFv-FLAG).
Example 17. Conjugation of Horseradish Peroxidase Protein to Albumin and the K573P VariantFor conjugation analysis, commercially available recombinant albumin (Recombumin™) was used as a control molecule. For this example, a final 200 mg/mL albumin K573P variant of the invention was purified from a fed batch fermentation by means described in Material and Methods. A two step purification was carried out;
The first step used a column (bed volume approximately 400 mL, bed height 11 cm) packed with AlbuPure™ matrix (ProMetic). This was equilibrated with 50 mM sodium acetate, pH 5.3 and loaded with neat culture supernatant, at approximately pH 5.5-6.5, to approximately 20 mg/mL matrix. The column was then washed with approximately 5 column volumes each of 50 mM sodium acetate, pH 5.3, 50 mM sodium phosphate, pH 6.0, 50 mM sodium phosphate, pH 7.0 and 50 mM ammonium acetate, pH 8.0, respectively. Bound protein was eluted using approximately two column volumes of 50 mM ammonium acetate, 10 mM octanoate, pH 7.0. The flow rate for the entire purification was 154 mL/min.
For the second step, the eluate from the first step was diluted approximately two fold with water to give a conductivity of 2.5±0.5 mS/cm after adjustment to pH 5.5±0.3 with acetic acid. This was loaded onto a DEAE-Sepharose Fast Flow (GE Healthcare) column (bed volume approximately 400 mL, bed height 11 cm), equilibrated with 80 mM sodium acetate, 5 mM octanoate, pH 5.5. Loading was approximately 30 mg protein/mL matrix. The column was washed with approximately 5 column volumes of 80 mM sodium acetate, 5 mM octanoate, pH 5.5. Followed by approximately 10 column volumes of 15.7 mM potassium tetraborate, pH 9.2. The bound protein was eluted using two column volumes of 110 mM potassium tetraborate, 200 mM sodium chloride, approximately pH 9.0. The flow rate was 183 mL/min during the load and wash steps, and 169 mL/min during the elution step.
The eluate was concentrated and diafiltered against 145 mM NaCl, using a Pall Centramate Omega 10,000 Nominal MWCO membrane, to give a final protein concentration of approximately 200 mg/mL.
Both 200 mg/mL stock solutions of the rHA and K573P variant albumin were diluted down to 5 mg/mL, using phosphate buffer saline (PBS), pH adjusted to pH 6.5-6.7. This ensured a favourable pH environment for the maleimide reactive group of the EZ-Link® Maleimide Activated Horseradish Peroxidase (Thermo Scientific) to react with the free sulphydryl, to form a stable thioester bond. 2 mg of the EZ-Link® Maleimide Activated Horseradish Peroxidase (HRP) was mixed with either 1 mL of the 5 mg/ML rHA or K573P variant albumin. This mixture ensured an approximate 2 fold molar excess of the albumin, or K573P variant albumin. This mixture was minimally incubated at 4° C., for 24 hours. The reaction mixtures were then checked for conjugation, using GP-HPLC.
To separate unconjugated species (rHA, or Albumin variant K573P and unreacted HRP) from the corresponding conjugated species the samples were first concentrated (Vivaspin20, 10,000 MWCO PES, Sartorius), and then individually applied to a Tricorn Superdex™ 200, 10/300 GL column (GE Healthcare), run at a flow rate of 45 cm/hr in PBS. The elution peak was fractionated and GP-HPLC analysed. Fractions containing the conjugated species were pooled, concentrated and diafiltered against 50 mM NaCl and analysed by GP-HPLC to demonstrate (
These samples were then assayed using the Biacore method described herein (Table 21). This example demonstrates that the K573P maintains its increased affinity for shFcRn compared the the WT HSA.
Example 18. Conjugation of Fluorescein to Albumin and the K573P VariantThe two same albumin samples used in Example 17, were also the start materials for this example. I.e. Approximately 200 mg/mL rHA or the K573P albumin variant.
Fluorescein-5-Maleimide, Thermo Scientific (F5M) was dissolved in dimethylformamide, to give a final concentration of 25 mg/mL. This was then further diluted into 18 mls of PBS, pH adjusted to approximately pH 6.5. To this solution either 1 ml of 200 mg/mL rHA or 1 mL of 200 mg/mL K573P variant was added. This gave an approximate 20 fold final molar excess of F5M. These samples were incubated and allowed to conjugate overnight at 4° C., in the dark, to allow the maleimide groups on the F5M to react with predominantly the free sulfhydryl, present in both albumin species.
Following overnight incubation aliquots of the reaction mixtures were extensively diafiltered against 50 mM NaCl to remove unconjugated FSM, (Vivaspin20, 10,000 MWCO PES, Sartorius). Conjugation was confirmed by ultraviolet visualization of conjugated Fluorescein:Albumins Following standard SDS-PAGE (
These diafiltered samples were then assayed using the Biacore method described herein (Table 21). This example demonstrates that the conjugation of a small molecule to either rHA or a variant, e.g. K573P does not affect the trend in binding affinities to shFcRn.
The following variants were generated using the methods described in Example 1 E492T, N503D, E492T+N503D, K538H, E542D, D494N+E495Q+T496A, E495Q+T496A, N403K, K541A and K541N. SPR analysis was carried out as described in Example 15 and the results presented in
Substitutions N503D, D494N+E495Q+T496A E492T+N503D, E495Q+T496A within HSA had a negative inpact on binding to shFcRn at pH5.5.
The following variants were generated using the methods described in Example 1. Binding to the shFcRn was determined as described in Materials and Methods and the results are presented in Table 22.
This example demonstrates that for all C-terminal swaps to human albumin tested an increase in binding over the donor albumin was observed. All donor sequences contain the K573P substitution shown to significantly increase binding but less that the K573P alone (Table 20).
Example 21. Competitive Binding Analysis of Variant Albumin FusionsCompetitive binding studies, using variant albumin fusions and a selection of variant albumins prepared as described in Example 1, were performed as described in Example 4. Results are presented in
The competitive binding hierarchy was identical for the variants fusions of HSA-FLAG and, N+C-terminal scFv HSA-FLAG to the hierarchy of the individual HSA variants (unfused and fused) affinity data. For the IL1Ra variants K573P, K573A, and the K500A were as predicted, however the D550N appears to inhibit more efficiently than the WT fusion.
Example 22. Further HSA VariantsThe following variants were generated using methods described in Example 1: HSA E492G+K573A, HSA E492G+N503K+K573A, HSA E492G+N503H+K573A, HSA E492G+K573P, HSA E492G+N503K+K573P, HSA E492G+N503H+K573P. SPR analysis was performed as described in Materials and Methods. Results (
HSA E492G+K573A, HSA E492G+N503K+K573A, unlike HSA E492G+N503H+K573A, had marginally improved binding beyond that of HSA K573A. The combination variants containing K573P did not show improved binding over the K573P single variant.
Claims
1. (canceled)
2. A method of preparing a variant albumin comprising:
- providing to a host cell, a nucleic acid encoding a variant albumin having at least 90% sequence identity to SEQ ID NO: 2 along the length of said variant albumin; wherein said variant albumin has a substitution corresponding to substitutions in SEQ ID NO: 2 selected from K573A,C,D,F,G,H,I,L,M,N,P, R,S,V,W, or Y; and
- generating said variant albumin from said nucleic acid.
3. The method of claim 2, wherein said nucleic acid encodes a variant albumin having at least 95% sequence identity to SEQ ID NO: 2.
4. The method of claim 2, wherein said nucleic acid encodes a variant albumin having at least 98% sequence identity to SEQ ID NO: 2.
5. The method of claim 2, further comprising isolating the variant albumin from said host cell or from a media for said host cell.
6. The method of claim 2, wherein said variant of albumin has a longer serum half-life than an albumin having the sequence of SEQ ID NO: 2.
7. The method of claim 2, wherein said variant of albumin has an enhanced binding to FcRn relative to an albumin having the sequence of SEQ ID NO: 2.
8. The method of claim 2, further comprising modifying said nucleic acid to include one or more alterations, which generate a thiol group on said variant albumin.
9. The method of claim 2, wherein said variant albumin has a sequence identity to SEQ ID NO: 2 of more than 90% along the length of said variant albumin, and wherein said variant albumin is at least 100 amino acids in length.
10. A nucleic acid encoding a variant albumin having at least 90% sequence identity to SEQ ID NO: 2 along the length of said variant albumin, wherein said variant albumin has a substitution corresponding to K573A,C,D,F,G,H,I,L,M,N,P, R,S, V,W, or Y.
11. The nucleic acid of claim 10, wherein said nucleic acid encodes a variant albumin having at least 95% sequence identity to SEQ ID NO: 2.
12. The nucleic acid of claim 10, wherein said nucleic acid encodes a variant albumin having at least 98% sequence identity to SEQ ID NO: 2.
13. A method of preparing a fusion polypeptide comprising a variant albumin, the method comprising:
- providing to a host cell, a nucleic acid encoding a fusion polypeptide comprising a variant albumin having at least 90% sequence identity to SEQ ID NO: 2 along the length of said variant albumin and a second polypeptide; wherein said variant albumin has a substitution corresponding to the substitutions in SEQ ID NO: 2 selected from K573A,C,D,F,G,H,I,L,M,N,P,Q,R,S,T,V,W, or Y; and
- generating said fusion polypeptide from said nucleic acid.
14. The method of claim 13, further comprising isolating the fusion polypeptide from said host cell or from a media for said host cell.
15. The method of claim 13, wherein said fusion polypeptide has a longer serum half-life than a fusion polypeptide comprising an albumin having the sequence of SEQ ID NO: 2.
16. The method of claim 13, wherein said variant of albumin has enhanced binding to FcRn relative to an albumin having the sequence of SEQ ID NO: 2.
17. The method of claim 13, further comprising modifying said nucleic acid to further comprise one or more alterations that generate a thiol group on said variant albumin.
18. The method of claim 13, wherein said variant albumin has a sequence identity to SEQ ID NO: 2 of more than 90% along the length of said variant albumin, and wherein said variant albumin is at least 100 amino acids in length.
19. The method of claim 13, wherein said nucleic acid encodes a variant albumin having at least 95% sequence identity to SEQ ID NO: 2.
20. A nucleic acid encoding a fusion polypeptide comprising a variant albumin having at least 90% sequence identity to SEQ ID NO: 2, wherein said variant albumin has a substitution corresponding to K573A,C,D,F,G,H,I,L,M,N,P,Q,R,S,T,V,W, or Y, and a second polypeptide.
21. The nucleic acid of claim 19, wherein said nucleic acid encodes a variant albumin having at least 95% sequence identity to SEQ ID NO: 2.
Type: Application
Filed: Jan 12, 2018
Publication Date: Jun 14, 2018
Inventors: Darrell Sleep (Nottingham), Andrew Plumridge (Derbyshire), Jason Cameron (Nottingham), Inger Sandlie (Oslo), Jan Terje Andersen (Oslo), Esben Peter Friis (Herlev)
Application Number: 15/870,349
