Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
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Characterization of Binding Mode of the Heterobiaryl gp120 Inhibitor in HIV-1 Entry: A Molecular Docking and Dynamics Simulation Study

  • Gadhe, Changdev G. (Department of Bio-New Drug Development, College of Medicine, Chosun University) ;
  • Kothandan, Gugan (Department of Bio-New Drug Development, College of Medicine, Chosun University) ;
  • Cho, Seung Joo (Department of Bio-New Drug Development, College of Medicine, Chosun University)
  • Received : 2013.05.05
  • Accepted : 2013.05.30
  • Published : 2013.08.20
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Abstract

Human immunodeficiency virus type-1 (HIV-1) is a causative agent of Acquired immunodeficiency syndrome (AIDS), which has affected a large population of the world. Viral envelope glycoprotein (gp120) is an intrinsic protein for HIV-1 to enter into human host cells. Molecular docking guided molecular dynamics (MD) simulation was performed to explore the interaction mechanism of heterobiaryl derivative with gp120. MD simulation result of inhibitor-gp120 complex demonstrated stability. Our MD simulation results are consistent with most of the previous mutational and modeling studies. Inhibitor has an interaction with the CD4 binding region. Van der Waals interaction between inhibitor and Val255, Thr257, Asn425, Met426 and Trp427 were important. This preliminary MD model could be useful in exploiting heterobiaryl-gp120 interaction in greater detail, and will likely to shed lights for further utilization in the development of more potent inhibitors.

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References

  1. De Clercq, E. J. Med. Chem. 1995, 38, 2491. https://doi.org/10.1021/jm00014a001
  2. Gallo, R. C.; Salahuddin, S. Z.; Popovic, M.; Shearer, G. M.; Kaplan, M.; Haynes, B. F.; Palker, T. J.; Redfield, R.; Oleske, J.; Safai, B. Science 1984, 224, 500. https://doi.org/10.1126/science.6200936
  3. Barre-Sinoussi, F.; Chermann, J. C.; Rey, F.; Nugeyre, M. T.; Chamaret, S.; Gruest, J.; Dauguet, C.; Axler-Blin, C.; Vezinet-Brun, F.; Rouzioux, C. Science 1983, 220, 868. https://doi.org/10.1126/science.6189183
  4. Starcich, B. R.; Hahn, B. H.; Shaw, G. M.; McNeely, P. D.; Modrow, S.; Wolf, H.; Parks, E. S.; Parks, W. P.; Josephs, S. F.; Gallo, R. C. Cell 1986, 45, 637. https://doi.org/10.1016/0092-8674(86)90778-6
  5. Leonard, C. K.; Spellman, M. W.; Riddle, L.; Harris, R. J.; Thomas, J. N.; Gregory, T. J. Biol. Chem. 1990, 265, 10373.
  6. Moore, J. P. Science 1997, 276, 51. https://doi.org/10.1126/science.276.5309.51
  7. Moore, J. P.; Doms, R. W. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 10598. https://doi.org/10.1073/pnas.1932511100
  8. Blair, W. S.; Lin, P. F.; Meanwell, N. A.; Wallace, O. B. Drug Discov. Today 2000, 5, 183. https://doi.org/10.1016/S1359-6446(00)01484-7
  9. Guo, Q.; Ho, H. T.; Dicker, I.; Fan, L.; Zhou, N.; Friborg, J.; Wang, T.; McAuliffe, B. V.; Wang, H. H.; Rose, R. E. J. Virol. 2003, 77, 10528. https://doi.org/10.1128/JVI.77.19.10528-10536.2003
  10. Dalgleish, A. G.; Beverley, P. C. L.; Clapham, P. R.; Crawford, D. H.; Greaves, M. F.; Weiss, R. A. Nature 1984, 312, 763. https://doi.org/10.1038/312763a0
  11. Lasky, L. A.; Nakamura, G.; Smith, D. H.; Fennie, C.; Shimasaki, C.; Patzer, E.; Berman, P.; Gregory, T.; Capon, D. J. Cell 1987, 50, 975. https://doi.org/10.1016/0092-8674(87)90524-1
  12. Berger, E. A.; Fuerst, T. R.; Moss, B. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 2357. https://doi.org/10.1073/pnas.85.7.2357
  13. Borkow, G.; Lapidot, A. Curr. Drug Targets-Infect. Disord. 2005, 5, 3. https://doi.org/10.2174/1568005053174645
  14. Harrison, S. C. Adv. Virus Res. 2005, 64, 231. https://doi.org/10.1016/S0065-3527(05)64007-9
  15. Cerutti, N.; Mendelow, B. V.; Napier, G. B.; Papathanasopoulos, M. A.; Killick, M.; Khati, M.; Stevens, W.; Capovilla, A. J. Biol. Chem. 2010, 285, 25743. https://doi.org/10.1074/jbc.M110.144121
  16. Kwong, P. D.; Wyatt, R.; Robinson, J.; Sweet, R. W.; Sodroski, J.; Hendrickson, W. A. Nature 1998, 393, 648. https://doi.org/10.1038/31405
  17. Huang, C.; Tang, M.; Zhang, M. Y.; Majeed, S.; Montabana, E.; Stanfield, R. L.; Dimitrov, D. S.; Korber, B.; Sodroski, J.; Wilson, I. A. Science 2005, 310, 1025. https://doi.org/10.1126/science.1118398
  18. Diskin, R.; Marcovecchio, P. M.; Bjorkman, P. J. Nat. Struct. Mol. Biol. 2010, 17, 608. https://doi.org/10.1038/nsmb.1796
  19. Huang, C.; Lam, S. N.; Acharya, P.; Tang, M.; Xiang, S. H.; Hussan, S. S.; Stanfield, R. L.; Robinson, J.; Sodroski, J.; Wilson, I. A. Science 2007, 317, 1930. https://doi.org/10.1126/science.1145373
  20. Huang, C.; Venturi, M.; Majeed, S.; Moore, M. J.; Phogat, S.; Zhang, M. Y.; Dimitrov, D. S.; Hendrickson, W. A.; Robinson, J.; Sodroski, J. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 2706. https://doi.org/10.1073/pnas.0308527100
  21. Zhou, T.; Xu, L.; Dey, B.; Hessell, A. J.; Van Ryk, D.; Xiang, S. H.; Yang, X.; Zhang, M. Y.; Zwick, M. B.; Arthos, J. Nature 2007, 445, 732. https://doi.org/10.1038/nature05580
  22. LaLonde, J. M.; Kwon, Y. D.; Jones, D. M.; Sun, A. W.; Courter, J. R.; Soeta, T.; Kobayashi, T.; Princiotto, A. M.; Wu, X.; Schon, A. J. Med. Chem. 2012, 55, 4382. https://doi.org/10.1021/jm300265j
  23. Wyatt, R.; Kwong, P. D.; Desjardins, E.; Sweet, R. W.; Robinson, J.; Hendrickson, W. A.; Sodroski, J. G. Nature 1998, 393, 705. https://doi.org/10.1038/31514
  24. Wang, T.; Zhang, Z.; Wallace, O. B.; Deshpande, M.; Fang, H.; Yang, Z.; Zadjura, L. M.; Tweedie, D. L.; Huang, S.; Zhao, F. J. Med. Chem. 2003, 46, 4236. https://doi.org/10.1021/jm034082o
  25. Yang, Z.; Zadjura, L.; D'Arienzo, C.; Marino, A.; Santone, K.; Klunk, L.; Greene, D.; Lin, P. F.; Colonno, R.; Wang, T. Biopharm. Drug Dispos. 2005, 26, 387. https://doi.org/10.1002/bdd.471
  26. Madani, N.; Perdigoto, A. L.; Srinivasan, K.; Cox, J. M.; Chruma, J. J.; LaLonde, J.; Head, M.; Smith Iii, A. B.; Sodroski, J. G. J. Virol. 2004, 78, 3742. https://doi.org/10.1128/JVI.78.7.3742-3752.2004
  27. Lin, P. F.; Blair, W.; Wang, T.; Spicer, T.; Guo, Q.; Zhou, N.; Gong, Y. F.; Wang, H. G. H.; Rose, R.; Yamanaka, G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 11013. https://doi.org/10.1073/pnas.1832214100
  28. Teixeira, C.; Serradji, N.; Maurel, F.; Barbault, F. Eur. J. Med. Chem. 2009, 44, 3524. https://doi.org/10.1016/j.ejmech.2009.03.028
  29. Gadhe, C. G.; Kothandan, G.; Madhavan, T.; Cho, S. J. Med. Chem. Res. 2012, 21, 1892. https://doi.org/10.1007/s00044-011-9711-4
  30. Kong, R.; Tan, J. J.; Ma, X. H.; Chen, W. Z.; Wang, C. X. BBA-Proteins & Proteomics 2006, 1764, 766. https://doi.org/10.1016/j.bbapap.2005.12.017
  31. Yang, Q.; Stephen, A. G.; Adelsberger, J. W.; Roberts, P. E.; Zhu, W.; Currens, M. J.; Feng, Y.; Crise, B. J.; Gorelick, R. J.; Rein, A. R. J. Virol. 2005, 79, 6122. https://doi.org/10.1128/JVI.79.10.6122-6133.2005
  32. Gadhe, C. G.; Madhavan, T.; Kothandan, G.; Lee, T. B.; Lee, K.; Cho, S. J. Bull. Korean Chem. Soc. 2011, 32, 1605.
  33. Gadhe, C. G.; Kothandan, G.; Cho, S. J. Mol. Simulat. 2012, 38, 861. https://doi.org/10.1080/08927022.2012.659182
  34. Gadhe, C. G.; Lee, S. H.; Madhavan, T.; Kothandan, G.; Choi, D. B.; Cho, S. J. Bull. Korean Chem. Soc. 2010, 31, 2761. https://doi.org/10.5012/bkcs.2010.31.10.2761
  35. Kothandan, G.; Gadhe, C. G.; Madhavan, T.; Cho, S. J. Chem. Biol. Drug Des. 2011, 78, 161. https://doi.org/10.1111/j.1747-0285.2011.01095.x
  36. Kothandan, G.; Gadhe, C. G.; Cho, S. J. PLoS One 2012, 7, e32864. https://doi.org/10.1371/journal.pone.0032864
  37. Gadhe, C. G.; Kothandan, G.; Cho, S. J. J. Biomol. Struct. Dyn. 2012, DOI: 10.1080/07391102.2012.732342.
  38. Gadhe, C. G.; Madhavan, T.; Kothandan, G.; Cho, S. J. BMC Struct. Biol. 2011, 11, 5. https://doi.org/10.1186/1472-6807-11-5
  39. Kothandan, G.; Gadhe, C. G.; Madhavan, T.; Choi, C. H.; Cho, S. J. Eur. J. Med. Chem. 2011, 46, 4078. https://doi.org/10.1016/j.ejmech.2011.06.008
  40. Madhavan, T.; Chung, J. Y.; Kothandan, G.; Gadhe, C. G.; Cho, S. J. Chem. Biol. Drug Des. 2012, 79, 53. https://doi.org/10.1111/j.1747-0285.2011.01168.x
  41. Lu, R. J.; Tucker, J. A.; Pickens, J.; Ma, Y. A.; Zinevitch, T.; Kirichenko, O.; Konoplev, V.; Kuznetsova, S.; Sviridov, S.; Brahmachary, E. J. Med. Chem. 2009, 52, 4481. https://doi.org/10.1021/jm900330x
  42. SYBYL U.S.A., 2008.
  43. Word, J. M.; Lovell, S. C.; Richardson, J. S.; Richardson, D. C. J. Mol. Biol. 1999, 285, 1735. https://doi.org/10.1006/jmbi.1998.2401
  44. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. J. Comput. Chem. 1998, 19, 1639. https://doi.org/10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
  45. Cordonnier, A.; Montagnier, L.; Emerman, M. Nature 1989, 340,571. https://doi.org/10.1038/340571a0
  46. Olshevsky, U.; Helseth, E.; Furman, C.; Li, J.; Haseltine, W.; Sodroski, J. J. Virol. 1990, 64, 5701.
  47. Hess, B.; Kutzner, C.; Van Der Spoel, D.; Lindahl, E. J. Chem. Theory Comput. 2008, 4, 435. https://doi.org/10.1021/ct700301q
  48. Oostenbrink, C.; Villa, A.; Mark, A. E.; Van Gunsteren, W. F. J. Comput. Chem. 2004, 25, 1656. https://doi.org/10.1002/jcc.20090
  49. Aalten, D. M. F.; Bywater, R.; Findlay, J. B. C.; Hendlich, M.; Hooft, R. W. W.; Vriend, G. J. Comput.-Aided Mol. Des. 1996, 10, 255. https://doi.org/10.1007/BF00355047
  50. Hermans, J.; Berendsen, H. J. C.; Van Gunsteren, W. F.; Postma, J. P. M. Biopolymers 1984, 23, 1513. https://doi.org/10.1002/bip.360230807
  51. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089. https://doi.org/10.1063/1.464397
  52. Miyamoto, S.; Kollman, P. A. J. Comput. Chem. 1992, 13, 952. https://doi.org/10.1002/jcc.540130805
  53. Hess, B. J. Chem. Theory Comput. 2008, 4, 116. https://doi.org/10.1021/ct700200b
  54. Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; DiNola, A.; Haak, J. R. J. Chem. Phys. 1984, 81, 3684. https://doi.org/10.1063/1.448118
  55. Shrivastava, I.; LaLonde, J. M. Biochemistry 2011, 50, 4173. https://doi.org/10.1021/bi2002218
  56. Moebius, U.; Clayton, L. K.; Abraham, S.; Harrison, S. C.; Reinherz, E. L. J. Exp. Med. 1992, 176, 507. https://doi.org/10.1084/jem.176.2.507
  57. Sweet, R. W.; Truneh, A.; Hendrickson, W. A. Curr. Opin. Biotech. 1991, 2, 622. https://doi.org/10.1016/0958-1669(91)90089-N
  58. Stricher, F.; Martin, L.; Barthe, P.; Pogenberg, V.; Mechulam, A.; Menez, A.; Roumestand, C.; Veas, F.; Royer, C.; Vita, C.; Biochem. J. 2005, 390, 29. https://doi.org/10.1042/BJ20041953