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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V132?S139、F154?D168、D79?D81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。
Faldaprevir analogue molecule (FAM), a potent anti-HCV lead compound, can effectively inhibit the catalytic activity of HCV NS3 / 4A protease. The reported crystal structure of HCV NS3 / 4A protease was analyzed by bioinformatics, and the crystal structure of FAM-HCV NS3 / 4A protease was obtained. A 20.4 ns molecular dynamics simulation of the FAM-HCV NS3 / 4A protease complex was performed. The key residues and binding driving forces in the molecular recognition of the FAM-HCV NS3 / 4A protease complex were analyzed from the perspective of hydrogen bonding and free energy binding. Hydrogen bonding and van der Waals forces are the main driving forces behind the specific binding of FAM to the active pocket of proteins V132? S139, F154? D168, D79? D81 and V55, in good agreement with the experimental data. Resistance mutations were analyzed experimentally R155K, D168E / V and V170T site-directed mutagenesis on the FAM molecular recognition, providing a molecular basis for the possible existence of FAM resistance. Finally, the conformational changes of the system were discussed by two methods, that is, free energy surface and conformation clustering. Four conformational conformations of the system were given, which would provide certain molecular conformations for the subsequent design of inhibitors of Faldaprevir analogues based on the HCV NS3 / 4A protease structure Theoretical help.