Modeling ligand-receptor interaction for some MHC class II HLA-DR4 peptide mimetic inhibitors using several molecular docking and 3D QSAR techniques

Journal of Chemical Information and Modeling

Volumn 45, Issue 5, 2005, Pages 1343-1351

  Wei, Hsin Yuan ^a   Tsai, Keng Chang ^a   Lin, Thy Hou ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; COMPUTER PROGRAMMING; CORRELATION METHODS; DOCKING; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; PROTEINS;

LIGAND-RECEPTOR; MHC PEPTIDE; MOLECULAR FIELDS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP (QSAR);

BIOMEDICAL ENGINEERING;

BIOMIMETIC MATERIAL; HLA DR4 ANTIGEN;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; COMPUTER SIMULATION; METABOLISM; MOLECULAR MIMICRY; PROTEIN BINDING; PROTEIN CONFORMATION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REPRODUCIBILITY;

BINDING SITES; BIOMIMETIC MATERIALS; COMPUTER SIMULATION; HLA-DR4 ANTIGEN; MODELS, MOLECULAR; MOLECULAR MIMICRY; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REPRODUCIBILITY OF RESULTS;

EID: 26944484425     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci050140y     Document Type: Article

References (37)

1. Watts, C. Capture and processing of exogenous antigens for presentation on MHC molecules. Annu. Rev. Immunol. 1997, 15, 821-850.
2. Rudensky, A.; Prestoa-Hurlburt, P.; Hong, S. C.; Barlow, A.; Janeway, C. A., Jr. Sequence analysis of peptides bound to MHC class II molecules. Nature 1991, 353, 622-627.
3. Chicz, R. M.; Urban, R. G.; Lone, W. S.; Gorga, J. C.; Stern, L. J.; Vignali, D. A.; Strominger, J. L. Predominant naturally processed peptides bound to HLA-DR1 are derived from MHC-related molecules and are heterogeneous in size. Nature 1992, 358, 764-768.
4. Tiwari, J.; Terasaki, P. HLA and disease association; Springer-Verlag: New York, 1985.
5. Rowley, M. J.; Stockman, A.; Bond, C. A.; Tait, B. D.; Rowley, G. L.; Sherritt, M. A.; Mackay, I. R.; Muirden, K. D.; Bernard, C. C. The effect of HLA-DRB1 disease susceptibility markers on the expression of RA. Scand. J. Rheumatol. 1997, 26, 448-455.
6. Weyand, C. M.; Goronzy, J. J. Inherited and noninherited risk factors in rheumatoid arthritis. Curr. Opin. Rheumatol. 1995, 7, 206-213.
7. Nepom, G. T.; Gersuk, V.; Nepom, B. S. Prognostic implications of HLA genotyping in the early assessment of patients with rheumatoid arthritis. J. Rheumatol. Suppl. 1996, 44, 5-9.
8. Wagner, U.; Kaltenhauser, S.; Sauer, H.; Arnold, S.; Seidel, W.; Hantzschel, H.; Kalden, J. R.; Wassmuth, R. HLA markers and prediction of clinical course and outcome in rheumatoid arthritis. Arthritis Rheum. 1997, 40, 341-351.
9. Perdriger, A.; Chales, G.; Semana, G.; Guggenbuhl, P.; Meyer, O.; Quillivic, F.; Pawlotsky, Y. Role of HLA-DR-DR and DR-DQ association in the expression of extraarticular manifestations and rheumatoid factor in rheumatoid arthritis. J. Rheumatol. 1997, 24, 1272-1276.
10. Stern, L. J.; Brown, J. H.; Jardetzky, T. S.; Gorga, J. C.; Urban, R. G.; Strominger, J. L.; Wiley, D. C. Crystal structure of the human class II MHC protein HLA-DR1 complexed with an influenza virus peptide. Nature 1994, 368, 215-221.
11. Jardetzky, T. S.; Brown, J. H.; Stern, L. J.; Urban, R. G.; Chi, Y. I.; Stauffacher C.; Strominger, J. L.; Wiley, D. C. Three-dimensional structure of a human class II histocompatability molecule complexed with superantigen. Nature 1994, 368, 711-718.
12. Ghosh, P.; Amaya, M.; Mellins, E.; Wiley, D. C. The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3. Nature 1995, 378, 457-462.
13. Brown, J. H.; Jardetzky, T. S.; Gorga, J. C.; Stern, L. J.; Urban, R. G.; Strominger, J. L.; Wiley, D. C. Three-dimensional structure of the human class II histocompatability antigen HLA-DR1. Nature 1993, 364, 33-39.
14. Dessen, A.; Lawrence, C. M.; Cupo, S.; Zaller, D. M.; Wiley, D. C. X-ray crystal structure of HLA-DR4 (DRA0101, DRB10401) complexed with a peptide from human collagen II. Immunity 1997, 7, 473-481.
15. Garboczi, D. N.; Ghosh, P.; Utz, F.; Oing, R.; Biddison, W. E.; Wiley, D. C. Structure of the complex between human T-cell receptor, viral peptide and HLA-A2. Nature 1996, 384, 134-141.
16. Garcia, K. C.; Degano, M.; Stanfield, R. L.; Brunmark, A.; Jackson, M. R.; Peterson, P. A.; Teyton, L.; Wilson, I. A. An αβ T cell receptor structure at 2.5 Å and its orientation in the TCR-MHC complex. Science 1996, 274, 209-219.
17. Reinherz, E. L.; Tan, K.; Tang, L.; Kern, P.; Liu, J.; Xiong, Y.; Hussey, E.; Smolyar, A.; Hare, B.; Zhong, R.; Joachimiak, A.; Chang, H.; Wagner, G.; Wang, J. The crystal structure of a T-cell receptor in complex with peptide and MHC class II. Science 1999, 286, 1913-1921.
18. Hammer, J.; Takacs, B.; Sinigaglia, F.; Identification of a motif for HLA-DR1 binding peptides using M13 display libraries. J. Exp. Med. 1993, 176, 1007-1013.
19. Hammer, J.; Valsasnini, P.; Tolba, K.; Bolin, D.; Higelin, J.; Takacs, B.; Sinigaglia, F. Promicsuous and allele-specific anchors in HLA-DR binding peptides. Cell 1994, 74, 197-203.
20. Hammer, J.; Bono, E.; Gallazzi, F.; Belunis, C.; Nagy, Z. A.; Sinigaglia, F. Precise prediction of major histocompatability complex class II-peptide interaction based on peptide side chain scanning. J. Exp. Med. 1995, 180, 2353-2358.
21. Hammer, J.; Callazzi, F.; Bono, E.; Karr, R. W.; Guenot, J.; Valsasin, P.; Nagy, Z. A.; Sinigaglia, F. Peptide binding specificity of HLA-DR4 molecules: correlation with rheumatoid arthritis association. J. Exp. Med. 1995, 181, 1847-1855.
22. Bolin, D. R.; Swain, A. L.; Ramakanth, S.; Berthel, S. J.; Gillespie, P.; Huby, N. J. S.; Makofske, R.; Orzechowski, L.; Perrotta, A.; Toth, K.; Cooper, J. P.; Jiang, N.; Falcion, F.; Campbell, R.; Cox, D.; Gaizband, D.; Belunis, C. J.; Vidovic, D.; Ito, K.; Crowther, R.; Kammlott, U.; Zhang, X.; Palermo, R.; Weber, D.; Guenot, J.; Nagy, Z.; Olson, G. L. Peptide and peptide mimetic inhibitors of antigen presentation by HLA-DR class II MHC molecules. Design, structure-activity relationship, and X-ray crystal structure. J. Med. Chem. 2000, 43, 2135-2148.
23. Hennecke, J.; Wiley, D. C. Structure of a complex of the human α/β T cell receptor (TCR) HA 1.7, influenza hemmagglutinin peptide and major histocompatability complex class II molecule, HLA-DR4 (DRA*0101 and DRB1*0401): insight into TCR cross-restriction and alloreactivity. J. Exp. Med. 2002, 195, 571-581.
24. Adorini, L.; Muller, S.; Cardinaux, F.; Lehmann, P. V.; Falcioni, F.; Nagy, Z. A. In vivo competition between self-peptides and foreign antigens in T-cell activation. Nature 1988, 334, 623-625.
25. Falcioni, F.; Ito, K.; Vidovic, D.; Belunis, C.; Campbell, R.; Berthel, S. J.; Bolin, D. R.; Gillespie, P. B.; Nuby, N.; Olson, G. L.; Sarabu, R.; Guenot, J.; Madison, V.; Hammer, J.; Sinigaglia, F.; Steinmetz, M.; Nagy, Z. A. Peptidomimetic compounds that inhibit antigen presentation by autoimmune disease-associated class II major histo-compatability molecules. Nature Biotechnol. 1999, 17, 562-567.
26. Zavala-Ruize, Z.; Sundberg, E. J.; Stone, J. D.; DeOliveira, D. B.; Chan, I. C.; Svendsent, J.; Mariuzza, R. A.; Stern, L. J. Exploration of the p6/p7 region of the peptide-binding site of the human class II major histocompatability complex protein HLA-DR1. J. Biol. Chem. 2003, 278, 44904-44912.
27. Cramer, R. D., III; Patterson, D. E.; Bunce, J. D. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc. 1988, 110, 5959-5967.
28. Klebe, G.; Abraham, U.; Mietzner, T. Molecular Similarity Indices in a Comparative Analysis (CoMSIA) of Drug Molecules to Correlate and Predict Their Biological Activity. J. Med. Chem. 1994, 37, 4130-4146.
29. Catalyst, version 4.9 (software package); Accelrys, Inc. (previously known as Molecular Simulations, Inc.): San Diego, CA, 2003. http:// www.accelrys.com.
30. SYBYL 6.9.1; The Tripos Associates, 1699 S. Hanley Rd., St. Louis, MO.
31. GOLD is distributed by the Cambridge Crystallographic Data Center, Cambridge, U.K. www.ccdc.ac.uk/prods/gold.html.
32. GLIDE, Schrödinger LLC: Portland, 2003. http://www.scnrodinger-.com/ Products/glide.html.
33. Halgren, T. A. Merck molecular force field I. Bassis, form, scope, parametrization, and performance of MMFF94. J. Comput. Chem. 1996, 17, 490-519.
34. Wang, R.; Lai, L.; Wang, S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput.-Aided. Mol. Des. 2002, 16, 11-26.
35. Viswanadhan, V. N.; Ghose, A. K.; Revankar, G. R.; Robins, R. K. Atomic physicochemical parameters for three-dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics. J. Chem. Inf. Comput. Sci. 1989, 29, 163-172.
36. Klebe, G. The use of composite crystal-field environments in molecular recognition and the de novo design of protein ligands. J. Mol. Biol. 1994, 237, 212-235.
37. Wallace, A. C.; Laskowski, R. A.; Thornton, J. M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 1995, 8, 127-134.