State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University , Lanzhou 730000, China.
J Chem Inf Model. 2014 Feb 24;54(2):621-33. doi: 10.1021/ci400060j. Epub 2013 Jun 28.
Hepatitis C virus (HCV) NS3/4A protease is an important and attractive target for anti-HCV drug development and discovery. Vaniprevir (phase III clinical trials) and MK-5172 (phase II clinical trials) are two potent antiviral compounds that target NS3/4A protease. However, the emergence of resistance to these two inhibitors reduced the effectiveness of vaniprevir and MK-5172 against viral replication. Among the drug resistance mutations, three single-site mutations at residues Arg155, Ala156, and Asp168 in NS3/4A protease are especially important due to their resistance to nearly all inhibitors in clinical development. A detailed understanding of drug resistance mechanism to vaniprevir and MK-5172 is therefore very crucial for the design of novel potent agents targeting viral variants. In this work, molecular dynamics (MD) simulation, binding free energy calculation, free energy decomposition, residue interaction network (RIN), and substrate envelope analysis were used to study the detailed drug resistance mechanism of the three mutants R155K, A156T, and D168A to vaniprevir and MK-5172. MD simulation was used to investigate the binding mode for these two inhibitors to wild-type and resistant mutants of HCV NS3/4A protease. Binding free energy calculation and free energy decomposition analysis reveal that drug resistance mutations reduced the interactions between the active site residues and substituent in the P2 to P4 linker of vaniprevir and MK-5172. Furthermore, RIN and substrate envelope analysis indicate that the studied mutations of the residues are located outside the substrate (4B5A) binding site and selectively decrease the affinity of inhibitors but not the activity of the enzyme and consequently help NS3/4A protease escape from the effect of the inhibitors without influencing the affinity of substrate binding. These findings can provide useful information for understanding the drug resistance mechanism against vaniprevir and MK-5172. The results can also provide some potential clues for further design of novel inhibitors that are less susceptible to drug resistance.
丙型肝炎病毒 (HCV) NS3/4A 蛋白酶是抗 HCV 药物开发和发现的重要且有吸引力的靶标。凡尼帕韦（III 期临床试验）和 MK-5172（II 期临床试验）是两种针对 NS3/4A 蛋白酶的强效抗病毒化合物。然而，对这两种抑制剂的耐药性的出现降低了凡尼帕韦和 MK-5172 抑制病毒复制的有效性。在耐药性突变中，NS3/4A 蛋白酶中三个残基 Arg155、Ala156 和 Asp168 的单点突变尤其重要，因为它们对几乎所有临床开发中的抑制剂都有耐药性。因此，详细了解凡尼帕韦和 MK-5172 的耐药机制对于设计针对病毒变异体的新型强效药物非常重要。在这项工作中，使用分子动力学（MD）模拟、结合自由能计算、自由能分解、残基相互作用网络（RIN）和底物包络分析来研究三种突变体 R155K、A156T 和 D168A 对凡尼帕韦和 MK-5172 的耐药机制。使用 MD 模拟研究了这两种抑制剂与 HCV NS3/4A 蛋白酶野生型和耐药突变体的结合模式。结合自由能计算和自由能分解分析表明，耐药突变降低了活性位点残基与凡尼帕韦和 MK-5172 的 P2 到 P4 连接子中的取代基之间的相互作用。此外，RIN 和底物包络分析表明，研究的残基突变位于底物（4B5A）结合位点之外，选择性地降低了抑制剂的亲和力，但不影响酶的活性，从而帮助 NS3/4A 蛋白酶逃避抑制剂的作用，而不影响底物结合的亲和力。这些发现可以为理解对凡尼帕韦和 MK-5172 的耐药机制提供有用的信息。这些结果还可以为进一步设计不易产生耐药性的新型抑制剂提供一些潜在线索。
