Bulletin of the Korean Chemical Society

  • 제32권5호
  • /
  • Pages.1604-1612
  • /
  • 2011
  • /
  • 0253-2964(pISSN)
  • /
  • 1229-5949(eISSN)
대한화학회 (Korean Chemical Society)
권호 표지
DOI QR코드

DOI QR Code

Various Partial Charge Schemes on 3D-QSAR Models for P-gp Inhibiting Adamantyl Derivatives

  • Gadhe, Changdev G. (Department of Bio-New Drug Development, College of Medicine, Chosun University) ;
  • Madhavan, Thirumurthy (Department of Bio-New Drug Development, College of Medicine, Chosun University) ;
  • Kothandan, Gugan (Department of Bio-New Drug Development, College of Medicine, Chosun University) ;
  • Lee, Tae-Bum (Research Center for Resistant Cells, College of Medicine, Chosun University) ;
  • Lee, Kyeong (College of Pharmacy, Dongguk University-Seoul) ;
  • Cho, Seung-Joo (Department of Cellular.Molecular Medicine and Research Center for Resistant Cells, College of Medicine, Chosun University)
  • 투고 : 2011.01.13
  • 심사 : 2011.03.22
  • 발행 : 2011.05.20
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

We developed three-dimensional quantitative structure activity relationship (3D-QASR) models for 17 adamantyl derivatives as P-glycoprotein (P-gp) inhibitors. Eighteen different partial charge calculation methods were tested to check the feasibility of the 3D-QSAR models. Best predictive comparative molecular field analysis (CoMFA) model was obtained with the Austin Model 1-Bond Charge Correction (AM1-BCC) atomic charge. The 3D-QSAR models were derived with CoMFA and comparative molecular similarity indices analysis (CoMSIA). The final CoMFA model ($q^2$ = 0.764, $r^2$ = 0.988) was calculated with an AM1-BCC charge and electrostatic parameter, whereas the CoMSIA model ($q^2$ = 0.655, $r^2$ = 0.964) was derived with an AM1-BCC charge and combined steric, electrostatic, hydrophobic and HB-acceptor parameters. Leave-five-out (LFO) cross-validation was also performed, which yielded good correlation coefficient for both CoMFA (0.801) and CoMSIA (0.656) models. Robustness of the developed models was checked further with 1000 run bootstrapping analyses, which gave an acceptable correlation coefficient for CoMFA (BS-$r^2$ = 0.997, BS-SD = 0.003) and CoMSIA (BS-$r^2$ = 0.996, BS-SD = 0.018).

키워드

참고문헌

  1. Gottesman, M. M.; Fojo, T.; Bates, S. E. Nat. Rev. Cancer 2002, 2, 48. https://doi.org/10.1038/nrc706
  2. Ambudkar, S. V.; Dey, S.; Hrycyna, C. A.; Ramachandra, M.; Pastan, I.; Gottesman, M. M. Annu. Rev. Pharmacol. Toxicol. 1999, 39, 361. https://doi.org/10.1146/annurev.pharmtox.39.1.361
  3. Avendano, C.; Carlos, M. J. Curr. Med. Chem. 2002, 9, 159. https://doi.org/10.2174/0929867023371175
  4. Thomas, H.; Coley, H. M. Cancer Control 2003, 10, 159. https://doi.org/10.1177/107327480301000207
  5. Stavrovskaya, A. A. Biochemistry 2000, 65, 95.
  6. Advani, S. H. Ranbaxy Science Foundation Fourth Annual Symposium; November, 1997; p 47.
  7. Choi, C. H. Cancer Cell Int. 2005, 5, 30. https://doi.org/10.1186/1475-2867-5-30
  8. Gottesman, M. M.; Pastan, I. Annu. Rev. Biochem. 1993, 62, 385. https://doi.org/10.1146/annurev.bi.62.070193.002125
  9. Sarkadi, B.; Homolya, L.; Szakacs, G.; Varadi, A. Physiol. Rev. 2006, 86, 1179. https://doi.org/10.1152/physrev.00037.2005
  10. Tsuruo, T.; Iida, H.; Yamashiro, M.; Tsukagoshi, S.; Sakurai, Y. Biochem. Pharmacol. 1982, 31, 3138. https://doi.org/10.1016/0006-2952(82)90097-1
  11. Krishna, R.; Mayer, L. D. Eur. J. Pharm. Sci. 2000, 11, 265. https://doi.org/10.1016/S0928-0987(00)00114-7
  12. Min, K. H.; Xia, Y.; Kim, E. K.; Jin, Y.; Kaur, N.; Kim, E. S.; Kim, D. K.; Jung, H. Y.; Choi, Y.; Park, M. K. Bioorg. Med. Chem. Lett. 2009, 19, 5376. https://doi.org/10.1016/j.bmcl.2009.07.127
  13. Aller, S. G.; Yu, J.; Ward, A.; Weng, Y.; Chittaboina, S.; Zhuo, R.; Harrell, P. M.; Trinh, Y. T.; Zhang, Q.; Urbatsch, I. L. Science 2009, 323, 1718. https://doi.org/10.1126/science.1168750
  14. Cramer, R. D.; Patterson, D. E.; Bunce, J. D. J. Am. Chem. Soc. 1988, 110, 5959. https://doi.org/10.1021/ja00226a005
  15. Klebe, G.; Abraham, U.; Mietzner, T. J. Med. Chem. 1994, 37, 4130. https://doi.org/10.1021/jm00050a010
  16. Kubinyi, H. Drug Discovery Today 1997, 2, 457. https://doi.org/10.1016/S1359-6446(97)01079-9
  17. Kubinyi, H. Drug Discovery Today 1997, 2, 538. https://doi.org/10.1016/S1359-6446(97)01084-2
  18. Tervo, A. J.; Nyroenen, T. H.; Roenkkoe, T.; Poso, A. J. Chem. Inf. Comput. Sci. 2004, 44, 807. https://doi.org/10.1021/ci0342268
  19. Peterson, S. D.; Schaal, W.; Karlén, A. J. Chem. Inf. Model. 2006, 46, 355. https://doi.org/10.1021/ci049612j
  20. Mittal, R. R.; McKinnon, R. A.; Sorich, M. J. J. Mol. Model. 2008, 14, 59. https://doi.org/10.1007/s00894-007-0252-1
  21. Mittal, R. R.; Harris, L.; McKinnon, R. A.; Sorich, M. J. J. Chem. Inf. Model. 2009, 49, 704. https://doi.org/10.1021/ci800390m
  22. Tsai, K. C.; Chen, Y. C.; Hsiao, N. W.; Wang, C. L.; Lin, C. L.; Lee, Y. C.; Li, M.; Wang, B. Eur. J. Med. Chem. 2010, 45, 1544. https://doi.org/10.1016/j.ejmech.2009.12.063
  23. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902. https://doi.org/10.1021/ja00299a024
  24. Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. J. Comput. Chem. 2000, 21, 132. https://doi.org/10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P
  25. Del Re, G.; Pullman, B.; Yonezawa, T. Biochim. Biophys. Acta 1963, 75, 153. https://doi.org/10.1016/0006-3002(63)90595-X
  26. Del Re, G. J. Chem. Soc. 1958, 4031. https://doi.org/10.1039/jr9580004031
  27. Gasteiger, J.; Marsili, M. Tetrahedron 1980, 36, 3219. https://doi.org/10.1016/0040-4020(80)80168-2
  28. Gasteiger, J.; Marsili, M. Tetrahedron Lett. 1980, 19, 3181.
  29. Halgren, T. A. J. Comput. Chem. 1996, 17, 520. https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6<520::AID-JCC2>3.0.CO;2-W
  30. Berthod, H.; Giessner-Prettre, C.; Pullman, A. Theor. Chim. Acta 1967, 8, 212. https://doi.org/10.1007/BF00527306
  31. S. H. R. SYBYL 8.1; Tripos Inc., St. Louis, MO 63144 USA.
  32. Gaussian 03, Revision C.02, Frisch, M. J.; Trucks, G. W.; Schlegel,H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian, Inc., Wallingford CT, 2004.
  33. Besler, B. H.; Merz, K. M., Jr.; Kollman, P. A. J. Comp. Chem. 1990, 11, 431. https://doi.org/10.1002/jcc.540110404
  34. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollmann, P. A. J. Am. Chem. Soc. 1993, 115, 9620. https://doi.org/10.1021/ja00074a030
  35. Jakalian, A.; Jack, D. B.; Bayly, C. I. J. Comp. Chem. 2002, 23, 1623. https://doi.org/10.1002/jcc.10128
  36. Cramer, R. D. Perspect. Drug Discovery Des. 1993, 1, 269. https://doi.org/10.1007/BF02174528
  37. Wold, S.; Sjostrom, M.; Eriksson, L. Chemom. Intell. Lab. Syst. 2001, 58, 109. https://doi.org/10.1016/S0169-7439(01)00155-1
  38. Dunn, W. J.; Wold, S.; Edlund, V.; Hellherg, S.; Gasteiger, J. Quant. Struct.-Act. Relat. 1984, 3, 131. https://doi.org/10.1002/qsar.19840030402
  39. Cecil, N.; Antti, P.; Kari, T.; Jukka, G. Quant. Struct-Act. Relat. 1996, 15, 189. https://doi.org/10.1002/qsar.19960150302
  40. Park Choo, H. Y.; Choi, S.; Jung, S. H.; Koh, H. Y.; Pae, A. N. Bioorg. Med. Chem. 2003, 11, 4585. https://doi.org/10.1016/S0968-0896(03)00530-3
  41. Tsai, K. C.; Wang, S. H.; Hsiao, N. W.; Li, M.; Wang, B. Bioorg. Med. Chem. Lett. 2008, 18, 3509. https://doi.org/10.1016/j.bmcl.2008.05.026

피인용 문헌

  1. Large variation in electrostatic contours upon addition of steric parameters and the effect of charge calculation schemes in CoMFA on mutagenicity of MX analogues vol.38, pp.11, 2012, https://doi.org/10.1080/08927022.2012.659182
  2. The effect of various atomic partial charge schemes to elucidate consensus activity-correlating molecular regions: a test case of diverse QSAR models vol.34, pp.3, 2016, https://doi.org/10.1080/07391102.2015.1044474
  3. Generation of Non-Nucleotide CD73 Inhibitors Using a Molecular Docking and 3D-QSAR Approach vol.22, pp.23, 2011, https://doi.org/10.3390/ijms222312745