A novel antibody humanization method based on epitopes scanning and molecular dynamics simulation

PLoS ONE

Volumn 8, Issue 11, 2013, Pages

  Zhang, Ding ^a   Chen, Cai Feng ^a   Zhao, Bin Bin ^a   Gong, Lu Lu ^a   Jin, Wen Jing ^a   Liu, Jing Jun ^a   Wang, Jing Fei ^b   Wang, Tian Tian ^d   Yuan, Xiao Hui ^a   He, You Wen ^a,c  

^a INSTITUTE OF PATHOGEN BIOLOGY   (China)

^b INSTITUTE OF PLANT PROTECTION   (China)

^c DUKE UNIVERSITY MEDICAL CENTER   (United States)

^d GENERAL HOSPITAL OF CHINESE PEOPLE'S ARMED POLICE FORCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; BASE SEQUENCE; COMPLEMENTARITY DETERMINING REGIONS; DNA PRIMERS; EPITOPES; HUMANS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; MUTATION; SEQUENCE HOMOLOGY, AMINO ACID; SURFACE PLASMON RESONANCE;

EID: 84894379331     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0080636     Document Type: Article

References (52)

1. Swann PG, Tolnay M, Muthukkumar S, Shapiro MA, Rellahan BL, et al. (2008) Considerations for the development of therapeutic monoclonal antibodies. Curr Opin Immunol 20: 493-499.
2. Reichert JM (2012) Marketed therapeutic antibodies compendium. MAbs 4: 413-415.
3. Jiang W, Swiggard WJ, Heufler C, Peng M, Mirza A, et al. (1995) The receptor DEC-205 expressed by dendritic cells and thymic epithelial cells is involved in antigen processing. Nature 375: 151-155.
4. Figdor CG, van Kooyk Y, Adema GJ (2002) C-type lectin receptors on dendritic cells and Langerhans cells. Nat Rev Immunol 2: 77-84.
5. Lahoud MH AF, Zhang JG, Meuter S, Policheni AN, Kitsoulis S, et al. (2012) DEC-205 is a cell surface receptor for CpG oligonucleotides. Proc Natl Acad Sci U S A 109: 16270-16275.
6. Bonifaz LC, Bonnyay DP, Charalambous A, Darguste DI, Fujii S, et al. (2004) In vivo targeting of antigens to maturing dendritic cells via the DEC-205 receptor improves T cell vaccination. J Exp Med 199: 815-824.
7. Presta LG (2006) Engineering of therapeutic antibodies to minimize immunogenicity and optimize function. Adv Drug Deliv Rev 58: 640-656.
8. Nelson AL, Dhimolea E, Reichert JM (2010) Development trends for human monoclonal antibody therapeutics. Nat Rev Drug Discov 9: 767-774.
9. Calvo B, Zuniga L (2012) Therapeutic monoclonal antibodies: strategies and challenges for biosimilars development. Curr Med Chem 19: 4445-4450.
10. Almagro JC, Fransson J (2008) Humanization of antibodies. Front Biosci 13: 1619-1633.
11. Hackett J, Jr., Hoff-Velk J, Golden A, Brashear J, Robinson J, et al. (1998) Recombinant mouse-human chimeric antibodies as calibrators in immunoassays that measure antibodies to Toxoplasma gondii. J Clin Microbiol 36: 1277-1284.
12. Tjandra JJ, Ramadi L, McKenzie IF (1990) Development of human anti-murine antibody (HAMA) response in patients. Immunol Cell Biol 68 (Pt 6): 367-376.
13. Jones PT, Dear PH, Foote J, Neuberger MS, Winter G (1986) Replacing the complementarity-determining regions in a human antibody with those from a mouse. Nature 321: 522-525.
14. Verhoeyen M, Milstein C, Winter G (1988) Reshaping human antibodies: grafting an antilysozyme activity. Science 239: 1534-1536.
15. Kennedy GA, Tey SK, Cobcroft R, Marlton P, Cull G, et al. (2002) Incidence and nature of CD20-negative relapses following rituximab therapy in aggressive B-cell non-Hodgkin's lymphoma: a retrospective review. Br J Haematol 119: 412-416.
16. Lazar GA, Desjarlais JR, Jacinto J, Karki S, Hammond PW (2007) A molecular immunology approach to antibody humanization and functional optimization. Mol Immunol 44: 1986-1998.
17. Chaudhary VK, Queen C, Junghans RP, Waldmann TA, FitzGerald DJ, et al. (1989) A recombinant immunotoxin consisting of two antibody variable domains fused to Pseudomonas exotoxin. Nature 339: 394-397.
18. Kettleborough CA, Saldanha J, Heath VJ, Morrison CJ, Bendig MM (1991) Humanization of a mouse monoclonal antibody by CDR-grafting: the importance of framework residues on loop conformation. Protein Eng 4: 773-783.
19. Padlan EA (1991) A possible procedure for reducing the immunogenicity of antibody variable domains while preserving their ligand-binding properties. Mol Immunol 28: 489-498.
20. Pedersen JT, Henry AH, Searle SJ, Guild BC, Roguska M, et al. (1994) Comparison of surface accessible residues in human and murine immunoglobulin Fv domains. Implication for humanization of murine antibodies. J Mol Biol 235: 959-973.
21. Roguska MA, Pedersen JT, Henry AH, Searle SM, Roja CM, et al. (1996) A comparison of two murine monoclonal antibodies humanized by CDR-grafting and variable domain resurfacing. Protein Eng 9: 895-904.
22. Sivasubramanian A, Sircar A, Chaudhury S, Gray JJ (2009) Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins 74: 497-514.
23. Caravella JA, Wang D, Glaser SM, Lugovskoy A (2010) Structure-Guided Design of Antibodies. Curr Comput Aided Drug Des.
24. Vyas VK, Ukawala RD, Ghate M, Chintha C (2012) Homology modeling a fast tool for drug discovery: current perspectives. Indian J Pharm Sci 74: 1-17.
25. Mo SL, Liu WF, Li CG, Zhou ZW, Luo HB, et al. (2012) Pharmacophore, QSAR, and binding mode studies of substrates of human cytochrome P450 2D6 (CYP2D6) using molecular docking and virtual mutations and an application to chinese herbal medicine screening. Curr Pharm Biotechnol 13: 1640-1704.
26. Cheng X, Ivanov I (2012) Molecular dynamics. Methods Mol Biol 929: 243-285.
27. Coutsias EA, Seok C, Dill KA (2004) Using quaternions to calculate RMSD. J Comput Chem 25: 1849-1857.
28. Lefranc MP, Pommie C, Ruiz M, Giudicelli V, Foulquier E, et al. (2003) IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol 27: 55-77.
29. Yuan XH, Qu ZY, Wu XM, Wang YC, Wei FX, et al. (2009) Homology Modeling and Evolution Trace Analysis of Human Adenovirus Type 3 Hexon. Chem J Chinese Universities 30: 1636.
30. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, et al. (2007) Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci Chapter 2: Unit 2 9.
31. Spassov VZ, Flook PK, Yan L (2008) LOOPER: a molecular mechanics-based algorithm for protein loop prediction. Protein Eng Des Sel 21: 91-100.
32. MacKerell AD, Jr., Banavali N, Foloppe N (2000) Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56: 257-265.
33. Yuan XH, WANG Y-C, QU ZY, REN JY, WANG JF, et al. (2011) Novel Rapid Molecular Modeling Method Based on Evolutional Tree for Human Adenovirus Hexon Proteins Family. Chem J Chinese Universities 32: 1838.
34. Yuan XH, Wang YC, Jin WJ, Zhao BB, Chen CF, et al. (2012) Structure-based high-throughput epitope analysis of hexon proteins in B and C species human adenoviruses (HAdVs). PLoS One 7: e32938.
35. Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8: 477-486.
36. Suyama M, Matsuo Y, Nishikawa K (1997) Comparison of protein structures using 3D profile alignment. J Mol Evol 44 Suppl 1: S163-173.
37. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
38. Yuan X, Qu Z, Wu X, Wang Y, Liu L, et al. (2009) Molecular modeling and epitopes mapping of human adenovirus type 3 hexon protein. Vaccine 27: 5103-5110.
39. Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, et al. (2005) GROMACS: fast, flexible, and free. J Comput Chem 26: 1701-1718.
40. Chatterjee S, Debenedetti PG, Stillinger FH, Lynden-Bell RM (2008) A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modified water models. J Chem Phys 128: 124511.
41. Cheatham TE, Miller JL, Fox T, Darden TA, Kollman PA (1995) Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins. J Am Chem Soc 117: 4193.
42. Coutsias EA, Seok C, Dill KA (2004) Using quaternions to calculate RMSD. J Comput Chem 25: 1849.
43. Zhou LJ, Tedder TF (1996) CD14+ blood monocytes can differentiate into functionally mature CD83+ dendritic cells. Proc Natl Acad Sci U S A 93: 2588-2592.
44. Brady JL, Corbett AJ, McKenzie BS, Lew AM (2006) Rapid specific amplification of rat antibody cDNA from nine hybridomas in the presence of myeloma light chains. J Immunol Methods 315: 61-67.
45. Poljak RJ, Amzel LM, Chen BL, Phizackerley RP, Saul F (1974) The three-dimensional structure of the fab' fragment of a human myeloma immunoglobulin at 2.0-angstrom resolution. Proc Natl Acad Sci U S A 71: 3440-3444.
46. Morrison SL, Johnson MJ, Herzenberg LA, Oi VT (1984) Chimeric human antibody molecules: mouse antigen-binding domains with human constant region domains. Proc Natl Acad Sci U S A 81: 6851-6855.
47. Carter P, Presta L, Gorman CM, Ridgway JB, Henner D, et al. (1992) Humanization of an anti-p185HER2 antibody for human cancer therapy. Proc Natl Acad Sci U S A 89: 4285-4289.
48. Nurisso A, Daina A, Walker RC (2012) A practical introduction to molecular dynamics simulations: applications to homology modeling. Methods Mol Biol 857: 137-173.
49. Friedman R, Boye K, Flatmark K (2013) Molecular modelling and simulations in cancer research. Biochim Biophys Acta.
50. Wang P, Sidney J, Dow C, Mothe B, Sette A, et al. (2008) A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PloS Comput Biol. 4(4):e1000048.
51. Wang P, Sidney J, Kim Y, Sette A, Lund O, et al. (2010) Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics. 11:568.
52. Southwood S, Sidney J, Kondo A, Guercio del MF, Appella E, et al. (1998) Several common HLA-DR types share largely overlapping peptide binding repertoires. J. Immunol. 160:3363-3373.