Faldaprevir analogue molecule (FAM) has been reported to effectively inhibit the catalytic activity of HCV NS3/4A protease, making it a potential lead compound against HCV. A series of HCV NS3/4A protease crystal structures were analyzed by bioinformatics methods, and the FAM-HCV NS3/4A protease crystal structure was chosen for this study. A 20.4 ns molecular dynamics simulation of the complex consists of HCV NS3/4A protease and FAM was conducted. The key amino acid residues for interaction and the binding driving force for the molecular recognition between the protease and FAM were identified from the hydrogen bonds and binding free energy analyses. With the driving force of hydrogen bonds and van der Waals, FAM specifically bind to the active pocket of HCV NS3/4A protease, including V130-S137, F152-D166, D77-D79 and V55, which agreed with the experimental data. The effect of R155K, D168E/V and V170T site-directed mutagenesis on FAM molecular recognition was analyzed for their effect on drug resistance, which provided the possible molecular explanation of FAM resistance. Finally, the system conformational change was explored by using free energy landscape and conformational cluster. The result showed four kinds of dominant conformation, which provides theoretical basis for subsequent design of Faldaprevir analogue inhibitors based on the structure of HCV NS3/4A protease.
Faldaprevir 类似物 (Faldaprevir analogue molecule, FAM) 能有效抑制HCV NS3/4A 蛋白酶的催化活性，是一种潜在抗HCV 先导化合物。通过生物信息学统计分析了已报道的HCV NS3/4A 蛋白酶晶体结构，得到了FAM-HCV NS3/4A 蛋白酶晶体结构。对FAM-HCV NS3/4A 蛋白酶复合物进行了20.4 ns 的分子动力学模拟，重点从氢键和结合自由能两个角度分析了二者分子识别中的关键残基及结合驱动力。氢键和范德华力是促使FAM 特异性结合到蛋白V132S139、F154D168、D79D81 和V55 的活性口袋中的主要驱动力，这与实验数据较为吻合。耐药性突变实验分析了R155K、D168E/V 和V170T 定点突变对FAM 分子识别的影响，为可能存在的FAM 耐药性提供了分子依据。最后，用自由能曲面和构象聚类两个方法探讨了体系的构象变化，给出体系的4 种优势构象，为后续的基于HCV NS3/4A 蛋白酶结构的Faldaprevir 类似物抑制剂分子设计提供一定的理论帮助。.
Keywords: Faldaprevir analogue molecule; HCV NS3/4A protease; binding free energy; conformational change; molecular dynamics simulation.