Mirac proteins
This disclosure relates to a method of generating conditionally active biologic proteins from wild type proteins, in particular therapeutic proteins, which are reversibly or irreversibly inactivated at the wild type normal physiological conditions. For example, evolved proteins are virtually inactive at body temperature, but are active at lower temperatures.
1. A method of preparing a conditionally active biologic protein, the method comprising steps of
i. selecting the wild-type mammalian biologic protein;
ii. evolving the DNA which encodes the wild-type mammalian biologic protein using one or more evolutionary techniques to create at least one mutant DNA;
iii. expressing the at least one mutant DNA to obtain at least one mutant protein; and
iv. modifying at least one of the peptide backbone, the amino acid side-chains and the amino or carboxyl termini of the at least one mutant protein by a chemical process or a natural process to introduce at least one modification selected from the group consisting of acetylation, acylation, PEGylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a home moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of a phosphatidylinositol, cross-linking cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristolyation, oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, and transfer-RNA mediated addition of amino acids to protein to obtain at least one modified mutant protein which exhibits both (a) a decrease in activity in an assay at normal physiological condition that is within a normal range of the physiological condition at a site of administration of the conditionally active protein to a subject, or at a tissue or organ at a site of action of the conditionally active protein of a subject, when compared to the activity of the wild-type protein in the assay at the same normal physiological condition, and (b) an increase in activity in an assay under aberrant condition that deviates from the normal range of the physiological condition at the site of administration of the conditionally active protein, or at the tissue or organ at the site of action of the conditionally active protein, when compared to the activity of the wild-type protein in the assay at the same aberrant condition; and
wherein the normal physiological condition and aberrant condition are the same condition selected from the group consisting of temperature, pH, osmotic pressure, osmolality, oxidation and electrolyte concentration.
2. The method of claim 1 , wherein the condition is temperature; and
wherein the conditionally active biologic protein is inactive at the normal physiological temperature, and is active at the aberrant temperature.
3. A method of preparing a conditionally active biological response modifier, the method comprising steps of:
a. selecting an inflammatory response mediator;
b. identifying a wild-type antibody to the selected mediator;
c. evolving the wild-type antibody to obtain one or more mutant antibodies;
d. screening the one or more mutant antibodies differentially for mutants that exhibit a decreased binding affinity to the mediator in an assay at a normal physiological condition that is within a normal range of the physiological condition at a site of administration of the conditionally active protein to a subject, or at a tissue or organ at a site of action of the conditionally active protein of a subject, when compared to the binding affinity of the wild-type antibody in the assay at the same normal physiological condition, and exhibit an increased binding affinity to the mediator in an assay at an aberrant condition that deviates from the normal range of the physiological condition at the site of administration of the conditionally active protein, or at the tissue or organ at the site of action of the conditionally active protein, when compared to the binding affinity of the wild-type antibody in the assay at the same aberrant condition to identify at least one up mutant antibody; and
e. modifying at least one of the peptide backbone, the amino acid side-chain and the amino or carboxyl termini of the at least one up-mutant antibody by a chemical process or a natural process introduce at least one modification selected from the group consisting of acetylation, acylation, PEGylation, ADP-ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of a phosphatidylinositol, cross-linking cyclization, disulfide bond formation, demethylation, formation of covalent cross-links, formation of cysteine, formation of pyroglutamate, formylation, gamma-carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristolyation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, and transfer-RNA mediated addition of amino acids to the at least on recombined up-mutant antibody to obtain the conditionally active biological response modifier that exhibits both a decrease in binding affinity to the mediator in the assay at the same normal physiological condition, when compared to the binding affinity of the wild-type antibody in the assay at the same normal physiological condition, and an increase in binding affinity to the mediator in the assay at the same aberrant condition when compared to the binding affinity of the wild-type antibody in the assay at the same aberrant condition and
wherein the normal physiological condition and aberrant condition are the same condition selected from the group consisting of temperature, pH, osmotic pressure, osmolality, oxidation and electrolyte concentration.
4. The method of claim 1 , wherein the modification comprises disulfide bond formation.
5. The method of claim 1 , wherein the modification comprises covalent attachment.
6. The method of claim 1 , wherein the modification is selected from the group consisting of phosphorylation and acetylation.
7. The method of claim 1 , wherein the evolving step comprises a process selected from the group consisting of substituting one or more nucleotides in the DNA for a different nucleotide, deleting one or more nucleotides from the DNA, and adding one or more nucleotides to the DNA.
8. The method of claim 1 , wherein the evolving step comprises a technique selected from the group consisting of PCR, error-prone PCR, shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursive ensemble mutagenesis, exponential ensemble mutagenesis, site-specific mutagenesis, gene reassembly, gene site saturated mutagenesis, ligase chain reaction, in vitro mutagenesis, ligase chain reaction, oligonucleotide synthesis, and combinations thereof.
9. The method of claim 1 , wherein the expression step comprises expressing the mutant DNA in an expression vector selected from the group consisting of viral particles, baculovirus, phage, plasmids, phagemids, cosmids, fosmids, bacterial artificial chromosomes, viral DNA, P1-based artificial chromosomes, yeast plasmids, yeast artificial chromosomes, and combinations thereof.
10. The method of claim 9 , wherein the expression vector comprises an expression control sequence to direct RNA synthesis.
11. The method of claim 1 , wherein the expression step comprises expressing the mutant DNA in a host cell selected from the group consisting of bacterial cells, fungal cells, insect cells, mammalian cells, adenoviruses, and plant cells.
12. The method of claim 3 , wherein the modification comprises covalent attachment.
13. The method of claim 3 , wherein the modification comprises disulfide bond formation.
14. The method of claim 3 , wherein the modification is selected from the group consisting of phosphorylation and acetylation.
15. The method of claim 1 , wherein said at least one mutant protein obtained in step iii) is a mimetic.
16. The method of claim 1 , wherein at least two said modified mutant proteins are produced by said modifying step, which at least two said modified mutant proteins exhibit both: (a) a decrease in activity in the assay at the normal physiological condition when compared to the wild-type protein at the normal physiological condition, and (b) an increase in activity in the assay at the aberrant condition when compared to the wild-type protein at the aberrant condition, and further comprising the step of selecting one said modified mutant protein which exhibits both: (a) a decrease in activity in the assay at the normal physiological condition when compared to the activity of the wild-type protein in the assay at the same normal physiological condition, and (b) an increase in activity in the assay under the aberrant condition when compared to the activity of the wild-type protein in the assay at the same aberrant condition and has a largest ratio of the activity in assay under the aberrant condition to the activity in the assay under the normal physiological condition.
17. The method of claim 1 , further comprising
v. repeating steps ii-iv, as necessary, to obtain at least two said conditionally active biologic proteins which exhibit both:(a) a decrease in activity in the assay at the normal physiological condition when compared to the activity of the wild-type protein in the assay at the same normal physiological condition, and (b) an increase in activity in the assay under the aberrant condition when compared to the activity of the wild-type protein in the assay at the same aberrant condition.
18. The method of claim 17 , wherein the modification is selected from disulfide bond formation and covalent attachment.
19. The method of claim 17 , wherein the modification is selected from the group consisting of phosphorylation and acetylation.
20. The method of claim 1 , wherein the conditionally active biologic protein has a length shorter than the wild-type mammalian biologic protein.
21. The method of claim 3 , wherein the conditionally active biological response modifier has a length shorter than the wild-type antibody.
22. The method of claim 17 , wherein the conditionally active biologic protein has a length shorter than the wild-type mammalian biologic protein.
23. The method of claim 1 , wherein the condition is pH.
24. The method of claim 1 , wherein the condition is temperature.
25. The method of claim 1 , wherein the condition is electrolyte concentration.
26. The method of claim 3 , wherein the condition is pH.
27. The method of claim 3 , wherein the condition is temperature.
28. The method of claim 3 , wherein the condition is electrolyte concentration.
29. The method of claim 3 , wherein at least two up-mutant antibodies are identified in step (d), further comprising the step of recombining at least one heavy chain and at least one light chain of the at least two up-mutant antibodies to create at least one recombined up-mutant antibody between steps (d) and (e) and wherein step (e) is carried out on the recombined up-mutant antibody.
30. The method of claim 1 , wherein the activity is selected from the group consisting of enzyme activity, and binding activity.
31. The method of claim 30 , wherein the activity is binding activity and the binding activity is binding to an antigen.