Department of Biochemistry and Biophysics, and the UNC Center for AIDS Research, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States.
J Chem Theory Comput. 2017 Nov 14;13(11):5671-5682. doi: 10.1021/acs.jctc.7b00601. Epub 2017 Oct 9.
HIV-1 protease is responsible for the cleavage of 12 nonhomologous sites within the Gag and Gag-Pro-Pol polyproteins in the viral genome. Under the selective pressure of protease inhibition, the virus evolves mutations within (primary) and outside of (secondary) the active site, allowing the protease to process substrates while simultaneously countering inhibition. The primary protease mutations impede inhibitor binding directly, while the secondary mutations are considered accessory mutations that compensate for a loss in fitness. However, the role of secondary mutations in conferring drug resistance remains a largely unresolved topic. We have shown previously that mutations distal to the active site are able to perturb binding of darunavir (DRV) via the protein's internal hydrogen-bonding network. In this study, we show that mutations distal to the active site, regardless of context, can play an interdependent role in drug resistance. Applying eigenvalue decomposition to collections of hydrogen bonding and van der Waals interactions from a series of molecular dynamics simulations of 15 diverse HIV-1 protease variants, we identify sites in the protease where amino acid substitutions lead to perturbations in nonbonded interactions with DRV and/or the hydrogen-bonding network of the protease itself. While primary mutations are known to drive resistance in HIV-1 protease, these findings delineate the significant contributions of accessory mutations to resistance. Identifying the variable positions in the protease that have the greatest impact on drug resistance may aid in future structure-based design of inhibitors.
HIV-1 蛋白酶负责切割病毒基因组中 Gag 和 Gag-Pro-Pol 多蛋白内的 12 个非同源位点。在蛋白酶抑制的选择性压力下，病毒在活性位点内（主要突变）和外（次要突变）进化出突变，使蛋白酶能够在同时抵抗抑制的情况下处理底物。主要蛋白酶突变直接阻碍抑制剂结合，而次要突变被认为是补偿适应性丧失的辅助突变。然而，次要突变在赋予耐药性方面的作用仍然是一个尚未解决的主要问题。我们之前已经表明，远离活性位点的突变能够通过蛋白内部氢键网络干扰达芦那韦（DRV）的结合。在这项研究中，我们表明，无论上下文如何，远离活性位点的突变都可以在耐药性中发挥相互依赖的作用。通过对一系列 15 种不同 HIV-1 蛋白酶变体的分子动力学模拟的氢键和范德华相互作用集合进行特征值分解，我们确定了蛋白酶中的一些位点，在这些位点上，氨基酸取代会导致与 DRV 和/或蛋白酶自身氢键网络的非键相互作用发生扰动。虽然已知主要突变会导致 HIV-1 蛋白酶的耐药性，但这些发现阐明了辅助突变对耐药性的重要贡献。确定对耐药性影响最大的蛋白酶中的可变位置可能有助于未来基于结构的抑制剂设计。
