Simulations reveal that the HIV-1 gp120-CD4 complex dissociates via complex pathways and is a potential target of the polyamidoamine (PAMAM) dendrimer

Journal of Chemical Physics

Volumn 139, Issue 2, 2013, Pages

  Nandy, Bidisha ^a   Bindu, D Hima ^a   Dixit, Narendra M ^a   Maiti, Prabal K ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ADHESION MOLECULES; COMPLEX DISSOCIATES; DISSOCIATION PATHWAYS; HYDROPHOBIC CAVITIES; MECHANISM OF ACTION; POLYAMIDOAMINE DENDRIMERS; SINGLE MOLECULE FORCE SPECTROSCOPY; STEERED MOLECULAR DYNAMICS SIMULATIONS;

DENDRIMERS; DISSOCIATION; HYDRATION; HYDROGEN BONDS; MOLECULAR DYNAMICS;

LOADING;

ANTI HUMAN IMMUNODEFICIENCY VIRUS AGENT; CD4 ANTIGEN; DENDRIMER; GLYCOPROTEIN GP 120; GP120 PROTEIN, HUMAN IMMUNODEFICIENCY VIRUS 1; POLYAMIDOAMINE; POLYAMINE; ANTIGEN ANTIBODY COMPLEX;

ANTIGEN ANTIBODY COMPLEX; ARTICLE; DRUG EFFECT; HOST PATHOGEN INTERACTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; IMMUNOLOGY; MOLECULAR DYNAMICS; MOLECULARLY TARGETED THERAPY; PHYSIOLOGY; VIRUS ENTRY; DRUG EFFECTS; HIV INFECTIONS;

ANTI-HIV AGENTS; ANTIGEN-ANTIBODY COMPLEX; ANTIGENS, CD4; DENDRIMERS; HIV ENVELOPE PROTEIN GP120; HIV INFECTIONS; HIV-1; HOST-PATHOGEN INTERACTIONS; HUMANS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR TARGETED THERAPY; POLYAMINES; VIRUS INTERNALIZATION;

EID: 84880420520     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4812801     Document Type: Article

References (47)

1. Y. Mehellou and E. De Clercq, J. Med. Chem. 53, 521 (2010). 10.1021/jm900492g
2. B. Berkhout and R. W. Sanders, Antiviral Res. 92, 7 (2011). 10.1016/j.antiviral.2011.04.002
3. D. C. Chan and P. S. Kim, Cell 93, 681 (1998). 10.1016/S0092-8674(00) 81430-0
4. P. Dorr, M. Westby, S. Dobbs, P. Griffin, B. Irvine, M. Macartney, J. Mori, G. Rickett, C. Smith-Burchnell, C. Napier, R. Webster, D. Armour, D. Price, B. Stammen, A. Wood, and M. Perros, Antimicrob. Agents Chemother. 49, 4721 (2005). 10.1128/AAC.49.11.4721-4732.2005
5. M. Roche, M. Jakobsen, A. Ellett, H. Salimiseyedabad, B. Jubb, M. Westby, B. Lee, S. Lewin, M. Churchill, and P. Gorry, Retrovirology 8, 89 (2011). 10.1186/1742-4690-8-89
6. V. Gajbhiye, V. K. Palanirajan, R. K. Tekade, and N. K. Jain, J. Pharm. Pharmacol. 61, 989 (2009). 10.1211/jpp.61.08.0002
7. C. F. Price, D. Tyssen, S. Sonza, A. Davie, S. Evans, G. R. Lewis, S. Xia, T. Spelman, P. Hodsman, T. R. Moench, A. Humberstone, J. R. A. Paull, and G. Tachedjian, PLoS ONE 6, e24095 (2011). 10.1371/journal.pone.0024095
8. T. S. Barata, I. Teo, S. Brocchini, M. Zloh, and S. Shaunak, PLoS Comput. Biol. 7, e1002095 (2011). 10.1371/journal.pcbi.1002095
9. M. Witvrouw, V. Fikkert, W. Pluymers, B. Matthews, K. Mardel, D. Schols, J. Raff, Z. Debyser, E. De Clercq, G. Holan, and C. Pannecouque, Mol. Pharmacol. 58, 1100 (2000).
10. A. Hantson, V. Fikkert, B. Van Remoortel, C. Pannecouque, P. Cherepanov, B. Matthews, G. Holan, E. De Clercq, A. M. Vandamme, Z. Debyser, and M. Witvrouw, Antivir. Chem. Chemother. 16, 253 (2005).
11. D. Tyssen, S. A. Henderson, A. Johnson, J. Sterjovski, K. Moore, J. La, M. Zanin, S. Sonza, P. Karellas, M. P. Giannis, G. Krippner, S. Wesselingh, T. McCarthy, P. R. Gorry, P. A. Ramsland, R. Cone, J. R. A. Paull, G. R. Lewis, and G. Tachedjian, PLoS ONE 5, e12309 (2010). 10.1371/journal.pone.0012309
12. M. Sotomayor and K. Schulten, Science 316, 1144 (2007). 10.1126/science.1137591
13. M. I. Chang, P. Panorchan, T. M. Dobrowsky, Y. Tseng, and D. Wirtz, J. Virol. 79, 14748 (2005). 10.1128/JVI.79.23.14748-14755.2005
14. T. M. Dobrowsky, Y. Zhou, S. X. Sun, R. F. Siliciano, and D. Wirtz, J. Virol. 82, 7022 (2008). 10.1128/JVI.00053-08
15. E. Evans and K. Ritchie, Biophys. J. 72, 1541 (1997). 10.1016/S0006-3495(97)78802-7
16. W. E. Thomas, E. Trintchina, M. Forero, V. Vogel, and E. V. Sokurenko, Cell 109, 913 (2002). 10.1016/S0092-8674(02)00796-1
17. S. Q. Liu, S. X. Liu, and Y. X. Fu, J. Mol. Model. 13, 411 (2007). 10.1007/s00894-006-0158-3
18. A. Bairoch, U. Consortium, L. Bougueleret, S. Altairac, V. Amendolia, A. Auchincloss, G. Argoud-Puy, K. Axelsen, D. Baratin, M. C. Blatter, B. Boeckmann, J. Bolleman, L. Bollondi, E. Boutet, S. B. Quintaje, L. Breuza, A. Bridge, E. Decastro, L. Ciapina, D. Coral, E. Coudert, I. Cusin, G. Delbard, D. Dornevil, P. D. Roggli, S. Duvaud, A. Estreicher, L. Famiglietti, M. Feuermann, S. Gehant, N. Farriol-Mathis, S. Ferro, E. Gasteiger, A. Gateau, V. Gerritsen, A. Gos, N. Gruaz-Gumowski, U. Hinz, C. Hulo, N. Hulo, J. James, S. Jimenez, F. Jungo, V. Junker, T. Kappler, G. Keller, C. Lachaize, L. Lane-Guermonprez, P. Langendijk-Genevaux, V. Lara, P. Lemercier, V. Le Saux, D. Lieberherr, T. D. Lima, V. Mangold, X. Martin, P. Masson, K. Michoud, M. Moinat, A. Morgat, A. Mottaz, S. Paesano, I. Pedruzzi, I. Phan, S. Pilbout, V. Pillet, S. Poux, M. Pozzato, N. Redaschi, S. Reynaud, C. Rivoire, B. Roechert, M. Schneider, C. Sigrist, K. Sonesson, S. Staehli, A. Stutz, S. Sundaram, M. Tognolli, L. Verbregue, A. L. Veuthey, L. Yip, L. Zuletta, R. Apweiler, Y. Alam-Faruque, R. Antunes, D. Barrell, D. Binns, L. Bower, P. Browne, W. M. Chan, E. Dimmer, R. Eberhardt, A. Fedotov, R. Foulger, J. Garavelli, R. Golin, A. Horne, R. Huntley, and J. Jacobsen, Nucleic Acids Res. 37, D169 (2009). 10.1093/nar/gkn664
19. H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, and P. Bourne, Nucleic Acids Res. 28, 235 (2000). 10.1093/nar/28.1.235
20. P. D. Kwong, R. Wyatt, J. Robinson, R. W. Sweet, J. Sodroski, and W. A. Hendrickson, Nature (London) 393, 648 (1998). 10.1038/31405
21. W. Vranken, M. Budesinsky, F. Fant, K. Boulez, and F. Borremans, FEBS Lett. 374, 117 (1995). 10.1016/0014-5793(95)01086-T
22. A. Sali and T. L. Blundell, J. Mol. Biol. 234, 779 (1993). 10.1006/jmbi.1993.1626
23. D. Eisenberg, R. Luthy, and J. U. Bowie, Methods Enzymol. 277, 396 (1997). 10.1016/S0076-6879(97)77022-8
24. R. Chen, L. Li, and Z. P. Weng, Proteins: Struct., Funct., Genet. 52, 80 (2003). 10.1002/prot.10389
25. P. K. Maiti and B. Bagchi, Nano Lett. 6, 2478 (2006). 10.1021/nl061609m
26. P. K. Maiti and R. Messina, Macromolecules 41, 5002 (2008). 10.1021/ma7025435
27. P. K. Maiti and B. Bagchi, J. Chem. Phys. 131, 214901 (2009). 10.1063/1.3266512
28. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983). 10.1063/1.445869
29. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977). 10.1016/0021-9991(77)90098-5
30. H. J. C. Berendsen, J. P. M. Postma, W. F. Vangunsteren, A. Dinola, and J. R. Haak, J. Chem. Phys. 81, 3684 (1984). 10.1063/1.448118
31. B. Nandy and P. K. Maiti, J. Phys. Chem. B. 115, 217 (2011). 10.1021/jp106776v
32. S. L. Mayo, B. D. Olafson, and W. A. Goddard, J. Phys. Chem. 94, 8897 (1990). 10.1021/j100389a010
33. D. Kosztin, S. Izrailev, and K. Schulten, Biophys. J. 76, 188 (1999). 10.1016/S0006-3495(99)77188-2
34. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kalé, and K. Schulten, J. Comput. Chem. 26, 1781 (2005). 10.1002/jcc.20289
35. I. Massova and P. A. Kollman, Perspect. Drug Discovery Des. 18, 113 (2000). 10.1023/A:1008763014207
36. D. Sitkoff, K. A. Sharp, and B. Honig, J. Phys. Chem. 98, 1978 (1994). 10.1021/j100058a043
37. W. Humphrey, A. Dalke, and K. Schulten, J. Mol. Graphics 14, 33 (1996). 10.1016/0263-7855(96)00018-5
38. D. G. Myszka, R. W. Sweet, P. Hensley, M. Brigham-Burke, P. D. Kwong, W. A. Hendrickson, R. Wyatt, J. Sodroski, and M. L. Doyle, Proc. Natl. Acad. Sci. U.S.A. 97, 9026 (2000). 10.1073/pnas.97.16.9026
39. B. Guo and W. H. Guilford, Proc. Natl. Acad. Sci. U.S.A. 103, 9844 (2006). 10.1073/pnas.0601255103
40. B. T. Marshall, M. Long, J. W. Piper, T. Yago, R. P. McEver, and C. Zhu, Nature (London) 423, 190 (2003). 10.1038/nature01605
41. E. Evans, A. Leung, V. Heinrich, and C. Zhu, Proc. Natl. Acad. Sci. U.S.A. 101, 11281 (2004). 10.1073/pnas.0401870101
42. Y. Suzuki and O. K. Dudko, Phys. Rev. Lett. 104, 048101 (2010). 10.1103/PhysRevLett.104.048101
43. W. L. Jorgensen, Nature (London) 466, 42 (2010). 10.1038/466042a
44. F. Colizzi, R. Perozzo, L. Scapozza, M. Recanatini, and A. Cavalli, J. Am. Chem. Soc. 132, 7361 (2010). 10.1021/ja100259r
45. S. P. Layne, M. J. Merges, M. Dembo, J. L. Spouge, and P. L. Nara, Nature (London) 346, 277 (1990). 10.1038/346277a0
46. S. E. Kuhmann, E. J. Platt, S. L. Kozak, and D. Kabat, J. Virol. 74, 7005 (2000). 10.1128/JVI.74.15.7005-7015.2000
47. See supplementary material at http://dx.doi.org/10.1063/1.4812801 E-JCPSA6-139-023327 for additional figures and analysis.