A simple, automated quasi-4D-QSAR, quasi-multi way PLS approach to develop highly predictive QSAR models for highly flexible CXCR4 inhibitor cyclic pentapeptide ligands using scripted common molecular modeling tools

QSAR and Combinatorial Science

Volumn 24, Issue 5, 2005, Pages 620-630

  Bhonsle, Jayendra B ^a   Wang, Zi Xuan ^b   Tamamura, Hirokazu ^c   Fujii, Nobutaka ^c   Peiper, Stephen C ^b   Trent, John O ^a  

^a University of Louisville School of Medicine   (United States)

^b MEDICAL COLLEGE OF GEORGIA   (United States)

^c KYOTO UNIVERSITY   (Japan)

Author keywords

Alignment; Automated quasi multi way PLS; Conformers; CXCR4 inhibitors; Sybyl Programming Language (SPL)

Indexed keywords

ALIGNMENT; AUTOMATION; COMPUTATIONAL CHEMISTRY; MOLECULAR GRAPHICS;

3D-QSAR; AUTOMATED QUASI-MULTI-WAY PARTIAL LEAST SQUARE; CONFORMER; CXCR4 INHIBITOR; CYCLIC PENTAPEPTIDES; LEAST-SQUARES APPROACH; PARTIAL LEAST-SQUARES; QSAR MODEL; SIMPLE++; SYBYL PROGRAMMING LANGUAGE;

MOLECULAR MODELING;

CHEMOKINE RECEPTOR CXCR4; CHEMOKINE RECEPTOR CXCR4 INHIBITOR; LIGAND; PENTAPEPTIDE; UNCLASSIFIED DRUG;

ARTICLE; AUTOMATION; CONFORMATION; DRUG ACTIVITY; FOUR DIMENSIONAL QUANTITATIVE STRUCTURE ACTIVITY RELATION; INHIBITION KINETICS; METHODOLOGY; MOLECULAR MODEL; MONTE CARLO METHOD; NONHUMAN; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REGRESSION ANALYSIS; SEQUENCE DATABASE; STRUCTURE ANALYSIS;

EID: 23044486029     PISSN: 1611020X     EISSN: None     Source Type: Journal    
DOI: 10.1002/qsar.200430912     Document Type: Article

References (47)

1. H. K. Deng, R. Liu, W. Ellmeier, S. Choe, D. Unutmaz, M. Burkhart, P. DiMarzio, S. Marmon, R. E. Sutton, C. M. Hill, C. B. Davis, S. C. Peiper, T. J. Schall, D. R. Littman, N. R. Landau, Nature 1996, 381, 661-666.
2. Y. Feng, C. C. Broder, P. E. Kennedy, E. A. Berger, Science 1996, 272, 872-877.
3. A. Muller, B. Homey, H. Soto, N. Ge, D. Catron, M. E. Buchanan, T. McClanahan, E. Murphy, W. Yuan, S. N. Wagner, J. L. Barrera, A. Mohar, E. Verastegui, A. Zlotnik, Nature 2001, 410, 50-56.
4. P. Matthys, S. Hatse, K. Vermeire, A. Wuyts, G. Bridger, G. W. Henson, E. De Clercq, A. Billiau, D. Schols, J. Immunol. 2001, 167, 4686-4692.
5. M. Masuda, H. Nakashima, T. Ueda, H. Naba, R. Ikoma, A. Otaka, Y. Terakawa, H. Tamamura, T. Ibuka, T. Murakami, Y. Koyanagi, M. Waki, A. Matsumoto, N. Yamamoto, S. Funakoshi, N. Fujii, Biochem. Biophys. Res. Commun. 1992, 189, 845-850.
6. H. Tamamura, Y. Xu, T. Hattori, X. Zhang, R. Arakaki, K. Kanbara, A. Omagari, A. Otaka, T. Ibuka, N. Yamamoto, H. Nakashima, N. Fujii, Biochem. Biophys. Res. Commun. 1998, 253, 877-882.
7. N. Fujii, S. Oishi, K. Hiramatsu, T. Araki, S. Ueda, H. Tamamura, A. Otaka, S. Kusano, S. Terakubo, H. Nakashima, J. A. Broach, J. O. Trent, Z. Wang, S. C. Peiper, Angew. Chem. Int. Ed. 2003, 42, 3251-3253.
8. C. A. Hansch, Accts. Chem. Res. 1969, 2, 232-239.
9. R. D. Cramer III, D. E. Patterson, J. D. Bunce, J. Am. Chem. Soc. 1988, 110, 5959-5967.
10. A. J. Hopfinger, B. J. Burke, Molecular Shape Analysis: a formalism to quantitatively establish spatial molecular similarity in: Concepts and Applications of Molecular Similarity, G. M. Maggiora (Ed.), Wiley and Sons, New York, 1990, p. 173-209.
11. S. Srivastava, Richardson, W. W., Bradley, M. P., Crippen, G. M., Three-dimensional receptor modeling using distance geometry and Voronoi polyhedra, ESCOM, Leiden, The Netherlands, 1993.
12. A. C. Good, S. J. Peterson, W. G. Richards, J. Med. Chem. 1993, 36, 2929-2937.
13. G. Klebe, Prospect. Drug Disc. Design 1998, 12, 87-104.
14. A. N. Jain, T. G. Dietterich, R. H. Lathrop, D. Chapman, R. E. Critchlow, B. E. Bauer, T. A. Webster, T. Lozanoperez, J. Comput.-Aided Mol. Des. 1194, 8, 635-652.
15. A. M. Doweyko, J. Math. Chem. 1991, 7, 273-285.
16. G. Folkers, A. Merz, D. Rognan, CoMFA: scope and limitation in: 3D QSAR in Drug Design, H. Kubinyi (Ed.), ESCOM, Leiden, The Netherlands, 1993, pp. 583-618.
17. K. H. Kim, Comparative molecular field analysis (CoMFA) in: Molecular Similarity in Drug Design, P. M. Dean (Ed.), Blackie Academic, Glasgow, UK, 1995, pp. 291-331.
18. G. Folkers, A. Merz, D. Rognan, CoMFA as a tool for active site modeling in: Trends in QSAR Molecular Modeling 92, ESCOM, Leiden, The Netherlands, 1993, pp. 233-244.
19. S. J. Cho, A. Tropsha, J. Med. Chem 1995, 38, 1060-1066.
20. A. J. Hopfinger, S. Wang, J. S. Tokarski, B. Jin, M. Albuquerque, P. J. Madhav, C. Duraiswami, J. Am. Chem. Soc. 1997, 119, 10509-10524.
21. K. Hasegawa, M. Arakawa, K. Funatsu, Comp. Bio. Chem. 2003, 27, 211-216.
22. A. Vedani, D. R. McMasters, M. Dobler, Quant. Struct.-Act. Relat. 2000, 19, 149-161.
23. M. Appell, W. J. Dunn III, M. E. A. Reith, L. Miller, J. L. Flippen-Anderson, Bioorg. Med. Chem. 2002, 10, 1197-1206.
24. K. Hasegawa, M. Arakawa, K. Funatsu, K. Chemom. Intell. Lab. Syst. 2000, 50, 253-261.
25. N. E. Jewell, D. B. Turner, P. Willett, G. J. Sexton, J. Mol. Graph. Mod. 2001, 20, 111-121.
26. A. J. Tervo, T. H. Nyronen, T. Ronkko, A. Poso, J. Chem. Inf. Comput. Sci. 2004, 44, 807-816.
27. W. Sippl, H.-D. Höltje, J. Mol. Struct. 2000, 503, 31-50.
28. P. M. Kroonenberg, W. J. Dunn III, J. J. F. Commandeur, J. Chem. Inf. Comput. Sci. 2003, 43, 2025-2032.
29. D. D. Robinson, P. D. Lyne, W. G. Richards, J. Chem. Inf. Comput. Sci. 2000, 40, 503-512.
30. K. Hasegawa, M. Arakawa, K. Funatsu, Chemom. Intell. Lab. Syst. 1999, 47, 33-40.
31. 1500 S. W. First Avenue, Suite 1180 Portland, OR 97201.
32. 1699 Hanley Road St. Louis, MO USA.
33. J. O. Trent, K. Napier, A. N. Lane (private communication; unpublished 3D coordinates of FC131 were determined by NMR).
34. S. Guccione, A. M. Doweyko, H. Chen, G. U. Barretta, F. Balzano, J. Comput.-Aided Mol. Des. 2000, 14, 647-657.
35. R. E. Taylor, J. Zajicek, J. Org. Chem. 1999, 64, 7224-7228.
36. D. M. Ferguson, P. A. Kollman, J. Comput. Chem. 1991, 12, 620-626.
37. E. Polak, G. Ribiere, Rev. Fr. Inform. Rech. O. 1969, 16, 35-45.
38. G. Chang, W. C. Guida, W. C. Still, J. Am. Chem. Soc. 1989, 111, 4379-4386.
39. W. C. Still, A. Tempczyk, R. C. Hawley, T. Hendrickson, J. Am. Chem. Soc. 1990, 112, 6127-6129.
40. J. B. Bhonsle, J. O. Trent, Available upon request.
41. P. Walters, M. Stahl, Dolata Research Group, Department of Chemistry, University of Arizona, Tucson, AZ 85721, 1994.
42. J. B. Bhonsle, J. O. Trent, Available upon request.
43. J. B. Bhonsle, J. O. Trent, Available upon request.
44. J. B. Bhonsle, J. O. Trent, Available upon request.
45. J. B. Bhonsle, J. O. Trent, Available upon request.
46. R. Bro, J. Chemom. 1996, 10, 47-61.
47. H. Tamamura, A. Omagari, S. Oishi, T. Kanamoto, N. Yamamoto, S. C. Peiper, H. Nakashima, A. Otaka, N. Fujii, Bioorg. Med. Chem. Lett. 2000, 10, 2633-2637.