Impact of Resistance Mutations on Inhibitor Binding to HIV‑1 Integrase Qi Chen, † John K. Buolamwini, ‡ Jeremy C. Smith, §,∥ Aixiu Li, ⊥ Qin Xu, † Xiaolin Cheng,* ,§,∥ and Dongqing Wei* ,† † State Key Laboratory of Microbial Metabolism and College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China ‡ Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States § UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States ∥ Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States ⊥ Drug Design Laboratory of the Basic Science Department, Logistics College of Chinese People’s Armed Police Force, Tianjin 300162, China * S Supporting Information ABSTRACT: HIV-1 integrase (IN) is essential for HIV-1 replication, catalyzing two key reaction steps termed 3′ processing and strand transfer. Therefore, IN has become an important target for antiviral drug discovery. However, mutants have emerged, such as E92Q/N155H and G140S/Q148H, which confer resistance to raltegravir (RAL), the first IN strand transfer inhibitor (INSTI) approved by the FDA, and to the recently approved elvitegravir (EVG). To gain insights into the molecular mechanisms of ligand binding and drug resistance, we performed molecular dynamics (MD) simulations of homology models of the HIV-1 IN and four relevant mutants complexed with viral DNA and RAL. The results show that the structure and dynamics of the 140s’ loop, comprising residues 140 to 149, are strongly influenced by the IN mutations. In the simulation of the G140S/Q148H double mutant, we observe spontaneous dissociation of RAL from the active site, followed by an intrahelical swing-back of the 3′-OH group of nucleotide A17, consistent with the experimental observation that the G140S/Q148H mutant exhibits the highest resistance to RAL compared to other IN mutants. An important hydrogen bond between residues 145 and 148 is present in the wild-type IN but not in the G140S/Q148H mutant, accounting for the structural and dynamical differences of the 140s’ loop and ultimately impairing RAL binding in the double mutant. End-point free energy calculations that broadly capture the experimentally known RAL binding profiles elucidate the contributions of the 140s’ loop to RAL binding free energies and suggest possible approaches to overcoming drug resistance. ■ INTRODUCTION Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is essential for HIV-1 replication, which facilitates the insertion of viral DNA into the genome of the host cell. HIV-1 IN is a 32 kDa protein, consisting of three structurally and functionally distinct domains, the N-terminal domain (NTD, residues 1− 49), the catalytic core domain (CCD, residues 50−212), and the C-terminal domain (CTD, residues 213−288). The CCD domain contains a highly conserved catalytic triad motif, D64D116E152, which is required for the enzymatic activity. 1 IN catalyzes two key chemical reactions, termed 3′ processing and strand transfer. During 3′ processing, IN removes two terminal nucleotides from the 3′ ends of both viral DNA strands to expose the invariant CA 3′-OH DNA ends. In the subsequent strand transfer step, IN catalyzes the integration of the viral DNA into the host cell chromatin using its exposed 3′-OHs to attack the phosphodiester backbones of the host DNA. 2 Given its importance in HIV replication together with the fact that no human counterpart exists for the enzyme, IN has become a promising target for antiviral drug discovery. From the time IN was first considered as a potential drug target, more than a decade elapsed before raltegravir (RAL) was approved by the FDA (in 2007). 3,4 Later, in 2012, elvitegravir (EVG) was also approved by the FDA for HIV treatment. 5 Both RAL and EVG bind to the CCD of IN and specifically block the strand transfer step, and they thus belong to IN strand transfer inhibitors (INSTIs), the latest class of antiretroviral drugs for HIV treatment. Other INSTIs in clinical trials include Received: September 15, 2013 Published: November 8, 2013 Article pubs.acs.org/jcim © 2013 American Chemical Society 3297 dx.doi.org/10.1021/ci400537n | J. Chem. Inf. Model. 2013, 53, 3297−3307