In silico Driven Redesign of a Clinically Relevant Antibody for the Treatment of GD2 Positive Tumors

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Ahmed, Mahiuddin ^a   Goldgur, Yehuda ^a   Hu, Jian ^a   Guo, Hong Fen ^a   Cheung, Nai Kong V ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ARGININE; GANGLIOSIDE GD2; GANGLIOSIDE GD2 ANTIBODY; GLYCINE; HU 3F8; ISOLEUCINE; MONOCLONAL ANTIBODY; PENTASACCHARIDE; RITUXIMAB; SIALIC ACID; TUMOR ANTIGEN; UNCLASSIFIED DRUG;

ANTIBODY DEPENDENT CELLULAR CYTOTOXICITY; ANTIBODY ENGINEERING; ANTIGEN EXPRESSION; ARTICLE; BRAIN TUMOR; CANCER CELL; CANCER CELL CULTURE; CANCER IMMUNOTHERAPY; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG EFFICACY; DRUG TARGETING; HUMAN; HUMAN CELL; HYDROGEN BOND; IN SILICO SCANNING MUTAGENESIS; LUNG SMALL CELL CANCER; MELANOMA; MOLECULAR DOCKING; MOLECULAR INTERACTION; MUTAGENESIS; NEUROBLASTOMA; NEUROECTODERM; POINT MUTATION; RETINOBLASTOMA; SARCOMA; STRUCTURE ANALYSIS;

ANTIBODIES, MONOCLONAL; ANTIBODY-DEPENDENT CELL CYTOTOXICITY; CRYSTALLOGRAPHY, X-RAY; FLOW CYTOMETRY; GANGLIOSIDES; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MOLECULAR STRUCTURE; NEOPLASMS;

EID: 84877805975     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0063359     Document Type: Article

References (37)

1. Hakomori S (1994) Role of gangliosides in tumor progression. In: Svennerholm L, Asbury AK, Reisfeld RA, Sandhoff K, Suzuki K et al., editors. Progress in Brain Research: Elsevier Science BV. 241-250.
2. Modak S, Cheung NK, (2007) Disialoganglioside directed immunotherapy of neuroblastoma. Cancer Invest 25: 67-77.
3. Yu AL, Gilman AL, Ozkaynak MF, London WB, Kreissman SG, et al. (2010) Anti-GD2 antibody with GM-CSF, interleukin-2, and isotretinoin for neuroblastoma. N Engl J Med 363: 1324-1334.
4. Ladisch S, Li R, Olson E, (1994) Ceramide structure predicts tumor ganglioside immunosuppressive activity. Proc Natl Acad Sci, USA 91: 1974-1978.
5. Lammie GA, Cheung NKV, Gerald W, Rosenblum M, Cordon-Cardo C, (1993) Ganglioside GD2 expression in the human nervous system and in neuroblastomas- an immunohistochemical study. International Journal of Oncology 3: 909-915.
6. Cheung NK, Lazarus H, Miraldi FD, Abramowsky CR, Kallick S, et al. (1987) Ganglioside GD2 specific monoclonal antibody 3F8: a phase I study in patients with neuroblastoma and malignant melanoma. J Clin Oncol 5: 1430-1440.
7. Cheung NK, Guo H, Hu J, Tassev DV, Cheung IY, (2012) Humanizing murine IgG3 anti-GD2 antibody m3F8 substantially improves antibody-dependent cell-mediated cytotoxicity while retaining targeting in vivo. Oncoimmunology 1: 477-486.
8. Cheung NK, Cheung IY, Kushner BH, Ostrovnaya I, Chamberlain E, et al. (2012) Murine Anti-GD2 Monoclonal Antibody 3F8 Combined With Granulocyte-Macrophage Colony-Stimulating Factor and 13-Cis-Retinoic Acid in High-Risk Patients With Stage 4 Neuroblastoma in First Remission. J Clin Oncol.
9. Kushner B, Kramer K, Modak S, Cheung NK, (2007) Anti-GD2 anitbody 3F8 plus granulocyte-macrophage colony stimulating factor (GM-CSF) for primary refractory neuroblastoma (NB) in the bone marrow (BM). Proc Amer Soc Clin Oncol 25: 526s.
10. Cheung NK, Cheung IY, Kushner BH, Ostrovnaya I, Chamberlain E, et al. (2012) Murine anti-GD2 monoclonal antibody 3F8 combined with granulocyte-macrophage colony-stimulating factor and 13-cis-retinoic acid in high-risk patients with stage 4 neuroblastoma in first remission. J Clin Oncol 30: 3264-3270.
11. Natali PG, Bigotti A, Nicotra MR, Nardi RM, Delovu A, et al. (1989) Analysis of the antigenic profile of uveal melanoma lesions with anti-cutaneous melanoma-associated antigen and anti-HLA monoclonal antibodies. Cancer Res 49: 1269-1274.
12. Mujoo K, Kipps TJ, Yang HM, Cheresh DA, Wargalla U, et al. (1989) Functional properties and effect on growth suppression of human neuroblastoma tumors by isotype switch variants of monoclonal antiganglioside GD2 antibody 14.18. Cancer Res 49: 2857-2861.
13. Gillies SD, Lo KM, Wesolowski J, (1989) High-level expression of chimeric antibodies using adapted cDNA variable region cassettes. J Immunol Methods 125: 191-202.
14. Mujoo K, Reisfeld RA, Cheung L, Rosenblum MG, (1991) A potent and specific immunotoxin for tumor cells expressing disialoganglioside GD2. Cancer Immunol Immunother 34: 198-204.
15. Brignole C, Marimpietri D, Pagnan G, Di Paolo D, Zancolli M, et al. (2005) Neuroblastoma targeting by c-myb-selective antisense oligonucleotides entrapped in anti-GD2 immunoliposome: immune cell-mediated anti-tumor activities. Cancer Lett 228: 181-186.
16. Cheung NK, Modak S, Lin Y, Guo H, Zanzonico P, et al. (2004) Single-chain Fv-streptavidin substantially improved therapeutic index in multistep targeting directed at disialoganglioside GD2. J Nucl Med 45: 867-877.
17. Pule MA, Savoldo B, Myers GD, Rossig C, Russell HV, et al. (2008) Virus-specific T cells engineered to coexpress tumor-specific receptors: presistence and antitumor activity in individuals with neuroblastoma. Nature 14: 1264-1270.
18. Agostino M, Jene C, Boyle T, Ramsland PA, Yuriev E, (2009) Molecular Docking of Carbohydrate Ligands to Antibodies: Structural Validation against Crystal Structures. Journal of Chemical Information and Modeling 49: 2749-2760.
19. Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil CR, (2008) Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br J Pharmacol 153Suppl 1: S7-26.
20. Wu G, Robertson DH, Brooks CL 3rd, Vieth M (2003) Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm. J Comput Chem 24: 1549-1562.
21. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47: 1739-1749.
22. Erickson JA, Jalaie M, Robertson DH, Lewis RA, Vieth M, (2004) Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J Med Chem 47: 45-55.
23. Momany FA, Rone R, (1992) Validation of the General Purpose QUANTA 3.2/CHARMm Force Field. J Comp Chem 13: 888-900.
24. Barderas R, Desmet J, Timmerman P, Meloen R, Casal JI, (2008) Affinity maturation of antibodies assisted by in silico modeling. Proc Natl Acad Sci U S A 105: 9029-9034.
25. Stanfield RL, Fieser TM, Lerner RA, Wilson IA, (1990) Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A. Science 248: 712-719.
26. Pokkuluri PR, Bouthillier F, Li Y, Kuderova A, Lee J, et al. (1994) Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes. J Mol Biol 243: 283-297.
27. Cheung NK, Landmeier B, Neely J, Nelson AD, Abramowsky C, et al. (1986) Complete tumor ablation with iodine 131-radiolabeled disialoganglioside GD2-specific monoclonal antibody against human neuroblastoma xenografted in nude mice. J Natl Cancer Inst 77: 739-745.
28. Heimburg-Molinaro J, Rittenhouse-Olson K, (2009) Development and characterization of antibodies to carbohydrate antigens. Methods Mol Biol 534: 341-357.
29. Cheung NK, Saarinen UM, Neely JE, Landmeier B, Donovan D, et al. (1985) Monoclonal antibodies to a glycolipid antigen on human neuroblastoma cells. Cancer Res 45: 2642-2649.
30. Mccoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, et al. (2007) Phaser crystallographic software. Journal of Applied Crystallography 40: 658-674.
31. Murshudov GN, Vagin AA, Dodson EJ, (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallographica Section D-Biological Crystallography 53: 240-255.
32. Bailey S, (1994) The Ccp4 Suite- Programs for Protein Crystallography. Acta Crystallographica Section D-Biological Crystallography 50: 760-763.
33. Lamzin VS, Wilson KS, (1993) Automated Refinement of Protein Models. Acta Crystallographica Section D-Biological Crystallography 49: 129-147.
34. Chennamsetty N, Voynov V, Kayser V, Helk B, Trout BL, (2009) Design of therapeutic proteins with enhanced stability. Proc Natl Acad Sci U S A 106: 11937-11942.
35. Seeger RC, Rayner SA, Banerjee A, Chung H, Laug WE, et al. (1977) Morphology, growth, chromosomal pattern and fibrinolytic activity of two new human neuroblastoma cell lines. Cancer Res 37: 1364-1371.
36. Chee DO, Boddie AW, Roth JA, Holmes EC, Morton DL, (1976) Production of melanoma-associated antigen(s) by a defined malignant melanoma cell strain grown in chemically defined medium. Cancer Res 36: 1503-1509.
37. Kan-Mitchell J, Mitchell MS, Rao N, Liggett PE, (1989) Characterization of uveal melanoma cell lines that grow as xenografts in rabbit eyes. Invest Ophthalmol Vis Sci 30: 829-834.