Structure-guided deimmunization of therapeutic proteins

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 7262 LNBI, Issue , 2012, Pages 184-198

  Parker, Andrew S ^a   Griswold, Karl E ^b   Bailey Kellogg, Chris ^a  

^a Dartmouth College   (United States)

^b DARTMOUTH COLLEGE   (United States)

Author keywords

deimmunization; experiment planning; multi objective optimization; sequence based protein design; structure based protein design; therapeutic proteints

Indexed keywords

DEIMMUNIZATION; EXPERIMENT PLANNING; MULTI OBJECTIVE OPTIMIZATIONS (MOO); PROTEIN DESIGN; THERAPEUTIC PROTEINTS;

ALGORITHMS; AMINO ACIDS; ANTIGENS; INTEGER PROGRAMMING; MOLECULAR BIOLOGY; MOLECULAR RECOGNITION; MOLECULAR STRUCTURE; MULTIOBJECTIVE OPTIMIZATION; PEPTIDES;

DESIGN;

EID: 84860790543     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-29627-7_19     Document Type: Conference Paper

References (35)

1. Chen, C.Y., Georgiev, I., Anderson, A.C., Donald, B.R.: Computational structurebased redesign of enzyme activity. PNAS 106, 3764-3769 (2009)
2. Dahiyat, B., Mayo, S.: De novo protein design: Fully automated sequence selection. Science 278, 82-87 (1997)
3. De Groot, A.S., Knopp, P.M., Martin, W.: De-immunization of therapeutic proteins by T-cell epitope modification. Dev. Biol (Basel) 122, 171-194 (2005)
4. De Groot, A.S., Martin, W.: Reducing risk, improving outcomes: Bioengineering less immunogenic protein therapeutics. Clinical Immunology 131, 189-201 (2009)
5. De Groot, A.S., Moise, L.: Prediction of immunogenicity for therapeutic proteins: State of the art. Curr. Opin. Drug Discov. Devel. 10, 332-340 (2007)
6. Desmet, J., De Maeyer, M., Hazes, B., Lasters, I.: The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356, 539-542 (1992)
7. Dinglasan, R.R., Kalume, D.E., Kanzok, S.M., Ghosh, A.K., Muratova, O., Pandey, A., Jacobs-Lorena, M.: Disruption of Plasmodium falciparum development by antibodies against a conserved mosquito midgut antigen. PNAS 104, 13461-13466 (2007)
8. Georgiev, I., Lilien, R.H., Donald, B.R.: A Novel Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions overMolecular Ensembles. In: Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2006. LNCS (LNBI), vol. 3909, pp. 530-545. Springer, Heidelberg (2006)
9. Goldstein, R.F.: Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophysical J. 66, 1335-1340 (1994)
10. Grigoryan, G., Reinke, A., Keating, A.: Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature 458, 859-864 (2009)
11. He, L., Friedman, A.M., Bailey-Kellogg, C.: A divide and conquer approach to determine the pareto frontier for optimization of protein engineering experiments proteins. Proteins (2011)
12. Hwang, W.Y.K., Foote, J.: Immunogenicity of engineered antibodies. Methods 36, 3-10 (2005)
13. Indiveri, F., Murdaca, G.: Immunogenicity of erythropoietin and other growth factors. Rev. Clin. Exp. Hematol. 1, 7-11 (2002)
14. Jones, P.T., Dear, P.H., Foote, J., Neuberger, M.S., Winter, G.: Replacing the complementarity-determining regions in a human antibody with those from a mouse. Nature 321, 522-525 (1986)
15. Jones, T.D., Phillips, W.J., Smith, B.J., Bamford, C.A., Nayee, P.D., Baglin, T.P., Gaston, J.S.H., Baker, M.P.: Identification and removal of a promiscuous CD4+ T cell epitope from the C1 domain of factor VIII. J. Thromb. Haemost. 3, 991-1000 (2005)
16. Kessler, M., Goldsmith, D., Schellekens, H.: Immunogenicity of biopharmaceuticals. Nephrology, Dialysis, Transplantation 21, v9-v12 (2006)
17. Kingsford, C., Chazelle, B., Singh, M.: Solving and analyzing side-chain positioning problems using linear and integer programming. Bioinf. 21, 1028-1036 (2005)
18. Klyushnenkova, E.N., Kouiavskaia, D.V., Kodak, J.A., Vandenbark, A.A., Alexander, R.B.: Identification of HLA-DRB1*1501-restricted T-cell epitopes from human prostatic acid phosphatase. Prostate 67, 1019-1028 (2007)
19. Leader, B., Baca, Q.J., Golan, D.E.: Protein therapeutics: A summary and pharmacological classification. Nat. Rev. Drug Disc. 7, 21-39 (2008)
20. Lilien, R., Stevens, B., Anderson, A., Donald, B.: A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase A phenylalanine adenlytaion enzyme. In: Proc. RECOMB, pp. 46-57 (2004)
21. McCaldon, P., Argos, P.: Oligopeptide biases in protein sequences and their use in predicting protein coding regions in nucleotide sequences. Proteins: Structure, Function and Genetics 4, 99-122 (1988)
22. Mustafa, A.S., Shaban, F.A.: Propred analysis and experimental evaluation of promiscuous T-cell epitopes of three major secreted antigens of Mycobacterium tuberculosis. Tuberculosis 86, 115-124 (2006)
23. Osipovitch, D.C., Parker, A.S., Makokha, C.D., Desrosiers, J., DeGroot, A.S., Baiely-Kellogg, C., Griswold, K.E.: Computational design of immune-evading enzymes for ADEPT therapy (in preperation)
24. Parker, A.S., Griswold, K.E., Bailey-Kellogg, C.: Optimization of combinatorial mutagenesis. J. Comput. Biol. 18, 1743-1756 (2011); In: Bafna, V., Sahinalp, S.C. (eds.) RECOMB 2011. LNCS, vol. 6577, pp. 321-335. Springer, Heidelberg (2011)
25. Parker, A.S., Griswold, K.E., Bailey-Kellogg, C.: Optimization of therapeutic proteins to delete t-cell epitopes while maintaining beneficial residue interactions. J. Bioinf. Comput. Biol. 9, 207-229 (2011); conf. ver: Proc CSB, pp.100-113 (2010)
26. Parker, A.S., Zheng, W., Griswold, K.E., Bailey-Kellogg, C.: Optimization algorithms for functional deimmunization of therapeutic proteins. BMC Bioinf. 11, 180 (2010)
27. Pierce, N., Winfree, E.: Protein design is NP-hard. Protein Eng. 15, 779-782 (2002)
28. Schellekens, H.: Bioequivalence and the immunogenicity of biopharmaceuticals. Nature Reviews Drug Discovery 1, 457-462 (2002)
29. Singh, H., Raghava, G.: ProPred: Prediction of HLA-DR binding sites. Bioinformatics 17, 1236-1237 (2001)
30. Southwood, S., Sidney, J., Kondo, A., del Guercio, M.F., Appella, E., Hoffman, S., Kubo, R.T., Chesnut,R.W., Grey,H.M., Sette, A.: Several common HLA-DRtypes share largely overlapping peptide binding repertoires. J. Immunol. 160, 3363-3373 (1998)
31. Sturniolo, T., Bono, E., Ding, J., Raddrizzani, L., Tuereci, O., Sahin, U., Braxenthaler, M., Gallazzi, F., Protti, M.P., Sinigaglia, F., Hammer, J.: Generation of tissue-specific and promiscuous HLA ligand database using DNA microarrays and virtual HLA class II matrices. Nature Biotechnol. 17, 555-561 (1999)
32. Tangri, S., Mothe, B.R., Eisenbraun, J., Sidney, J., Southwood, S., Briggs, K., Zinckgraf, J., Bilsel, P., Newman, M., Chesnut, R., LiCalsi, C., Sette, A.: Rationally engineered therapeutic proteins with reduced immunogenicity. J. Immunol. 174, 3187-3196 (2005)
33. Wang, P., Sidney, J., Dow, C., Mothe, B., Sette, A., Peters, B.: A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comp. Biol. 4, e1000048 (2008)
34. Warmerdam, P.A.M., Plaisance, S., Vanderlick, K., Vandervoort, P., Brepoels, K., Collen, D., Maeyer, M.D.: Elimination of a human T-cell region in staphylokinase by T-cell screening and computer modeling. J. Thromb. Haemost. 87, 666-673 (2002)
35. Zheng, W., Friedman, A.M., Bailey-Kellogg, C.: Algorithms for joint optimization of stability and diversity in planning combinatorial libraries of chimeric proteins. J. Comput. Biol. 16, 1151-1168 (2009); In: Vingron, M., Wong, L. (eds.) RECOMB 2008. LNCS (LNBI), vol. 4955, pp. 300-314. Springer, Heidelberg (2008)