Abstract: This invention relates to altered forms of members of the RNase A superfamily. An RNase A can be modified to be cytotoxic by altering its amino acid sequence so that it is not bound easily by the ribonuclease inhibitor while still retaining catalytic properties. While earlier work had identified some modifications to RNase A that would result in cytotoxicity, the use of the FADE algorithm for molecular interaction analysis has led to several other locations that were candidates for modification. Some of those modifications did result in RNase A variants with increase cytotoxicity.

Abstract: Methods and reagents for site-selective functionalization of peptides and proteins. The methods most generally involve the reaction of a thioester with hydrazine. Reagents include bifunctional reagents of formula: H2N—NH—CH2-M-L-FG and salts thereof where M is a single bond or a chemical group carrying a non-bonding electron pair, such as —C(O)NR?—, where R? is H, or an alkyl or aryl group; L is an optional linker group as described above; and FG is a functional group having reactivity that is orthongonal to that of the hydrazine group. FG can, among others, be an azide, alkenyl, alkynyl, nitrile (—CN) or triazole group and is preferably an azide group (—N3). Methods and reagents can, for example, be combined with intein-mediated protein splicing to link proteins or fragments thereof to various chemical species or to a surface.

Abstract: The present invention provides improved methods for synthesis of phosphinothiol reagents, as well as novel protected reagents, for use in formation of amide bonds, and particularly, for peptide ligation. The invention provides phosphine-borane complexes useful as reagents in the formation of amide bonds, particularly for the formation of an amide bond between any two of an amino acid, a peptide, or a protein.

Abstract: The present invention is a method for a covalent ligation of one or more molecules to one or more surfaces, that is site-specific and both rapid and high yielding. The covalent ligation to the surface is based on the reaction of an azide and a phosphinothioester to form an amide bond. The method of the invention is particularly well-suited to the immobilization of peptides, proteins or protein fragments to surfaces.

Abstract: A novel collagen mimic comprising a tripeptide unit having the formula (flpYaaGly)n, where flp is 4(S)-fluoro-L-proline, is disclosed. The collagen mimic has increased stability relative to the collagen-related triple helices (ProYaaGly)n, (hypYaaGly)n, and (HypYaaGly)n.

Abstract: An enzyme is re-engineered to be a zymogen, an enzyme precursor which is converted into an enzyme by protease cleavage. In the example described here, an RNase A enzyme is converted into a zymogen by adding to the enzyme a bridge of amino acids linking the amino and carboxyl termini of the enzyme. The bridge has built in it a protease cleavage site for a specific protease, for example the protease plasmepsin II, produced by the malaria parasite. Since RNase A can be made cytotoxic, this permits a cytotoxic enzyme to be made in the form of a zymogen that becomes active only when it is acted on by a protease only present in a particular target cell such as a pathogen.

Abstract: The present invention provides improved methods for synthesis of phosphinothiol reagents, as well as novel protected reagents, for use in formation of amide bonds, and particularly for peptide ligation. The invention provides phosphine-borane complexes useful as reagents in the formation of amide bonds, particularly for the formation of an amide bond between any two of an amino acid, a peptide, or a protein.

Abstract: Methods and reagents for the formation of amide bonds between an activated carboxylic acid derivative and an azide useful in the synthesis of peptides, proteins and derivatized or labeled amino acids, peptide or proteins. The method involves the formation of a phosphinothioester which reacts with an azide resulting in amide formation. The invention provides phosphinothiol reagents which convert activated carboxylic acid derivatives to phosphinothioesters which then react with azides to form an amide bond. The methods and reagents of the invention can be used for stepwise synthesis of peptides on solid supports or for the ligation to two or more amino acids, two or more peptide or two or more protein fragments.

Abstract: Disclosed are ?-peptides and ?-peptide conjugates that are capable of diffusing or otherwise being transported across the cell membranes of living cells. The ?-peptides contain at least six ?-amino acid residues, at leastsix of which are preferably ?3-homoarginine residues. It has been found that when pharmacologically-active agents are conjugated to these types of ?-peptides, the resulting conjugates (also disclosed herein) are also capable of diffusing or otherwise being transported across the cell membranes of living cells, including mammalian cells.

Abstract: A method for evaluating a test compound's ability to modulate prolyl 4-hydroxylase is disclosed. In one embodiment, the method comprises the steps of introducing a test compound into a test chimeric, P4H-gene modified, or a wild-type nematode, wherein the test chimeric nematode has a complemented prolyl-4-hydroxylase gene mutation, and observing the effect of the test compound on the prolyl 4-hydroxylase activity of the progeny of the test chimeric, P4H-gene modified, or the wild-type nematode, wherein a dpy or embryonic lethal phenotype indicates prolyl-4-hydroxylase inhibition.

Abstract: Methods and reagents for the formation of amide bonds between an activated carboxylic acid derivative and an azide useful in the synthesis of peptides, proteins and derivatized or labeled amino acids, peptide or proteins. The method involves the formation of a phosphinothioester which reacts with an azide resulting in amide formation. The invention provides phosphinothiol reagents which convert activated carboxylic acid derivatives to phosphinothioesters which then react with azides to form an amide bond. The methods and reagents of the invention can be used for stepwise synthesis of peptides on solid supports or for the ligation to two or more amino acids, two or more peptide or two or more protein fragments.

Abstract: An enzyme is re-engineered to be a zymogen, an enzyme precursor which is converted into an enzyme by protease cleavage. In the example described here, an RNase A enzyme is converted into a zymogen by adding to the enzyme a bridge of amino acids linking the amino and carboxyl termini of the enzyme. The bridge has built in it a protease cleavage site for a specific protease, for example the protease plasmepsin II, produced by the malaria parasite. Since RNase A can be made cytotoxic, this permits a cytotoxic enzyme to be made in the form of a zymogen that becomes active only when it is acted on by a protease only present in a particular target cell such as a pathogen.

Abstract: The present invention provides improved methods for synthesis of phosphinothiol reagents, as well as novel protected reagents, for use in formation of amide bonds, and particularly for peptide ligation. The invention provides phosphine-borane complexes useful as reagents in the formation of amide bonds, particularly for the formation of an amide bond between any two of an amino acid, a peptide, or a protein.

Abstract: Disclosed are &bgr;-peptides and &bgr;-peptide conjugates that are capable of diffusing or otherwise being transported across the cell membranes of living cells. The &bgr;-peptides contain at least six &bgr;-amino acid residues, at leastsix of which are preferably &bgr;3-homoarginine residues. It has been found that when pharmacologically-active agents are conjugated to these types of &bgr;-peptides, the resulting conjugates (also disclosed herein) are also capable of diffusing or otherwise being transported across the cell membranes of living cells, including mammalian cells.

Abstract: Modified ribonucleases belonging to the RNase A superfamily of ribonucleases is disclosed. Each modified ribonuclease has a steric hindrance moiety added to it in the loop region corresponding to amino acids 85-94 of bovine pancreatic RNase A. Such a modified ribonuclease has reduced binding affinity for ribonuclease inhibitor (RI), exhibits wild-type ribonuclease activity, and exhibits enhanced cytotoxicity toward tumor cells, relative to the wild-type ribonuclease.

Abstract: A novel collagen mimic comprising a tripeptide unit having the formula (XaaFlpGly).sub.n, where Flp is 4(R)-fluoro-L-proline, is disclosed. The collagen mimic has increased stability relative to the collagen-related triple helices (ProProGly).sub.n and (ProHypGly).sub.n.

Abstract: An analysis of the protein folding characteristics of the eukaryotic protein folding enzyme protein disulfide isomerase (PDI) led to a study of the minimally sufficient motif for catalytic activity of that enzyme as well as the prokaryotic enzyme thioredoxin. Based on such study, a model for this catalytic activity was developed which was used to predict what non-protein catalysts might substitute for this enzymatic activity. Based on this analysis, it was predicted that a small molecular weight dithiol molecule having a pK.sub.a of less than about 8.0 and an E.degree.' of more than about -0.25 V could catalyze the formation of proper disulfide bonds in a eukaryotic protein. Subsequently, it was verified that such a dithiol, such as the exemplary molecule N,N'-bis(2-mercaptoacetyl)-1,2-diaminocyclohexane (BMC), is capable of catalyzing the proper formation of disulfide bonds, and the proper folding of proteins, both in vivo and in vitro.

Abstract: Modified ribonucleases belonging to the RNase A superfamily of ribonucleases is disclosed. Each modified ribonuclease has a mutation in the loop region corresponding to amino acids 85-94 of bovine pancreatic RNase A. Each modified ribonuclease has reduced binding affinity for ribonuclease inhibitor (RI), wild-type ribonuclease activity, and exhibits enhanced cytotoxicity toward tumor cells, relative to the wild-type ribonuclease. Also disclosed is a method for obtaining a modified ribonuclease having reduced binding affinity for RI, wild-type ribonuclease activity, and enhanced cytotoxicity.

Abstract: A method for inactivating, at a desired stage of an in vitro process, a target enzyme having coupled thereto a biotin molecule, includes adding to a reaction mix an inactivating protein having an affinity for the biotin molecule that is sufficient to inhibit the activity of the target enzyme.The method is embodied in the ribonuclease activity of the enzyme RNase S, which can be active in a form composed of an S peptide and an S protein, not covalently bound together, which associate to form the catalytic molecule. By adding an affinity moeity to the S peptide, it is possible to a second, inactivating protein having affinity for the affinity moeity to disassociate the S peptide from the S protein, and thereby terminate catalytic activity of RNase S at a desired point in any reaction.

Abstract: A ribonuclease molecule altered at a single amino acid, relative to its wild-type form, displays altered substrate specificity and substrate binding mechanism. The altered protein cleaves RNA efficiently after C, U and A residues, whereas the wild-type protein cannot cleave efficiently after A. The change that alters the specificity also permits the protein to cleave poly (A) portions of an RNA molecule processively.