Journal of Molecular Graphics and Modelling 29 (2010) 137–147 Contents lists available at ScienceDirect Journal of Molecular Graphics and Modelling journal homepage: www.elsevier.com/locate/JMGM Understanding the HIV-1 protease nelfinavir resistance mutation D30N in subtypes B and C through molecular dynamics simulations Rosemberg O. Soares a,b , Paulo R. Batista b , Mauricio G.S. Costa b , Laurent E. Dardenne a , Pedro G. Pascutti b , Marcelo A. Soares c,d,∗ a Laboratório Nacional de Computac ¸ ão Científica, Petrópolis, Brazil b Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil c Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil d Programa de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil article info Article history: Received 25 August 2009 Received in revised form 12 May 2010 Accepted 14 May 2010 Available online 11 June 2010 Keywords: HIV-1 Protease Nelfinavir Drug resistance Subtype C Molecular dynamics abstract A major concern in the antiretroviral (ARV) treatment of HIV infections with protease inhibitors (PI) is the emergence of resistance, which results from the selection of distinct mutations within the viral protease (PR) gene. Among patients who do not respond to treatment with the PI nelfinavir (NFV), the D30N mutation is often observed. However, several reports have shown that D30N emerges with different frequencies in distinct HIV-1 genetic forms or subtypes. In the present work, we analyzed the binding of NFV and the Gag substrate CA/p2 to PR from HIV-1 subtypes B and C through molecular dynamics (MD) simulations. The wild-type and drug-resistant D30N mutants were investigated in both subtypes. The compensatory mutations N83T and N88D, observed in vitro and in vivo when subtype C acquires D30N, were also studied. D30N appears to facilitate conformational changes in subtype B PR, but not in that from subtype C, and this could be associated with disestablishment of an -helical region of the PR. Furthermore, the total contact areas of NFV or the CA/p2 substrate with the mutant PR correlated with changes in the resistance patterns and replicative capacity. Finally, we observed in our MD simulations that mutant PR proteins show different patterns for hydrophobic/van der Waals contact. These findings suggest that different molecular mechanisms contribute to resistance, and we propose that a single mutation has distinct impacts on different HIV-1 subtypes. © 2010 Elsevier Inc. All rights reserved. 1. Introduction Human immunodeficiency virus type 1 protease (HIV-1 PR) is a symmetric homodimeric aspartyl protease that cleaves the Gag and Gag-Pol viral polyproteins, allowing the virus to become infec- tious [1]. Drugs designed to inhibit HIV-1 PR have been developed in the past decades and their introduction into clinics to counter HIV infection has improved the treatment of HIV/AIDS patients [2]. The clinical success of these drugs is, however, frequently threatened by the occurrence of drug resistance mutations in the target enzyme. Currently, over 50 different drug resistance mutations at almost 30 different codon positions of HIV-1 PR have already been charac- terized [3], mainly due to the gene’s highly polymorphic nature. Different HIV-1 subtypes possess distinct amino acid signatures and polymorphisms in the PR coding region [4–6], and the bio- ∗ Corresponding author at: Laboratório de Virologia Humana, CCS – Bloco A – sala A2-120, Cidade Universitária – Ilha do Fundão, 21949-570 Rio de Janeiro, RJ, Brazil. Tel.: +55 21 2562 6383; fax: +55 21 2562 6396. E-mail address: masoares@biologia.ufrj.br (M.A. Soares). logical and phenotypic impact of these differences is yet to be fully appreciated [7]. The mutation D30N in HIV-1 PR is an amino acid change uniquely selected by virus exposure to the protease inhibitor (PI) nelfinavir (NFV) [8]. It confers reduced susceptibility of viruses to that drug per se, constituting a well established primary resis- tance mutation. Previous studies conducted in patients infected with distinct HIV-1 non-B subtypes have shown that these patients rarely develop the mutation compared with patients infected with subtype B [9–12]. The low frequency of D30N in subtype C has been associated with a more dramatic reduction in viral replicative capacity (RC) compared with subtype B counterparts carrying the same mutation [13]. Moreover, the occurrence of D30N in subtype C has been strongly associated with the compensatory mutations N88D and N83T in vivo and in vitro, respectively [12,13]. However, the structural hindrances governing the differences in replicative fitness and the requirement for those compensatory mutations are yet to be determined. In the present work, the binding of NFV and of the Gag substrate cleavage site CA/p2 to both subtype B and C wild-type and D30N mutant PR was investigated by molecular dynamics (MD) and sub- 1093-3263/$ – see front matter © 2010 Elsevier Inc. All rights reserved. doi:10.1016/j.jmgm.2010.05.007