Molecular dynamics study of HIV‐1 RT‐DNA‐nevirapine complexes explains NNRTI inhibition and resistance by connection mutations

Abstract

HIV-1 reverse transcriptase (RT) is a multifunctional enzyme that is targeted by nucleoside analogs (NRTIs) and nonnucleoside inhibitors (NNRTIs). NNRTIs are allosteric inhibitors of RT, and constitute an integral part of the highly active antiretroviral therapy (HAART) regimen. Under selective pressure, HIV-1 acquires resistance against NNRTIs primarily by selecting mutations around the NNRTI pocket. Complete RT sequencing of clinical isolates revealed that spatially distal mutations arising in connection and the RNase H domain also confer NNRTI resistance and contribute to NRTI resistance. However, the precise structural mechanism by which the connection domain mutations confer NNRTI resistance is poorly understood. We performed 50-ns MD simulations, followed by essential dynamics, free-energy landscape analyses and network analyses of RT-DNA, RT-DNA-nevirapine, and N348I/T369I mutant RT-DNA-nevirapine complexes. MD simulation studies revealed altered global motions and restricted conformational landscape of RT upon nevirapine binding. Analysis of protein structure network parameters demonstrated a dissortative hub pattern in the RT-DNA complex and an assortative hub pattern in the RT-DNA-nevirapine complex suggesting enhanced rigidity of RT upon nevirapine binding. The connection subdomain mutations N348I/T369I did not induce any significant structural change; rather, these mutations modulate the conformational dynamics and alter the long-range allosteric communication network between the connection subdomain and NNRTI pocket. Insights from the present study provide a structural basis for the biochemical and clinical findings on drug resistance caused by the connection and RNase H mutations.

Effects of HIV-1 reverse transcriptase connection subdomain mutations on polypurine tract removal and initiation of (+)-strand DNA synthesis

“…However, it is clear from our studies that when associated with RNA/DNA complexes, the combination of mutations N348I and T369I has a major impact in the RNase H activity of the RT. These results are also in agreement with the notion that a number of distal connection subdomain mutations contribute to drug resistance by altering the dynamic properties of the RT and contact networks involving amino acid residues in the viral enzyme, identified by using molecular dynamics ( 51 ).…”

“…Unlike mutations analyzed in our study whose prevalence in untreated patients is lower than 7.5%, A400T is a common polymorphism in HIV-1 group M isolates with a prevalence of nearly 56% in untreated patients. Modeling studies have shown little differences between ternary complexes containing the WT or the double-mutant N348I/T369I RT, associated with a DNA/DNA template-primer and nevirapine ( 51 ). However, it is clear from our studies that when associated with RNA/DNA complexes, the combination of mutations N348I and T369I has a major impact in the RNase H activity of the RT.…”

Drug Resistance in Non-B Subtype HIV-1: Impact of HIV-1 Reverse Transcriptase Inhibitors

“…We demonstrated that the N348I mutation increases the processivity of RT and enhances NVP dissociation from the NNIBP [ 38 ]. A molecular dynamics modeling study proposes that N348I contributes to NVP resistance through a long-range allosteric communication network between the connection and NNIBP [ 140 ]. More recently, Brehm et al [ 138 ] reported the presence of the N348I mutation in HIV-1C patients who failed d4T/3TC/NVP or d4T/3TC/EFV therapy.…”

Design, Synthesis, and Biological Evaluation of Novel Benzoyl Diarylamine/ether Derivatives as Potential Anti‐HIV‐1 Agents

“…Received 12 August 2014, revised 3 December 2014 and accepted for publication 6 December 2014 Acquired immune deficiency syndrome (AIDS) is mainly caused by HIV-1 infection and remains a global problem for human health (1). Almost half of the FDA-approved anti-HIV drugs target HIV-1 RT, which is a pivotal multifunctional enzyme in the replicative cycle of HIV-1 (2). The success of highly active antiretroviral therapy (HAART) regimens has significantly reduced the morbidity and mortality of HIV-infected individuals (1,(3)(4)(5)(6).…”

“…The success of highly active antiretroviral therapy (HAART) regimens has significantly reduced the morbidity and mortality of HIV‐infected individuals . Non‐nucleoside reverse transcriptase inhibitors (NNRTIs) are important and frequently clinical used components in HAART regimen for HIV‐1 infections .…”