Supramolecular Chemistry Research Unit and Department of Chemistry, Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand.
Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH‒CIC), Faculty of Science, Mahasarakham University, Maha Sarakham, Thailand.
J Biomol Struct Dyn. 2022 Aug;40(12):5283-5294. doi: 10.1080/07391102.2020.1869587. Epub 2021 Jan 11.
Hepatitis C virus (HCV) NS3/4A serine protease is a promising drug target for the discovery of anti-HCV drugs. However, its amino acid mutations, particularly A156T, commonly lead to rapid emergence of drug resistance. Paritaprevir and glecaprevir, the newly FDA-approved HCV drugs, exhibit distinct resistance profiles against the A156T mutation of HCV NS3/4A serine protease. To illustrate their different molecular resistance mechanisms, molecular dynamics simulations and binding free energy calculations were carried out on the two compounds complexed with both wild-type (WT) and A156T variants of HCV NS3/4A protease. QM/MM-GBSA-based binding free energy calculations revealed that the binding affinities of paritaprevir and glecaprevir towards A156T NS3/4A were significantly reduced by ∼4 kcal/mol with respect to their WT complexes, which were in line with the experimental resistance folds. Moreover, the relatively weak intermolecular interactions with amino acids such as H57, R155, and T156 of NS3 protein, the steric effect and the destabilized protein binding surface, which is caused by the loss of salt bridge between R123 and D168, are the main contributions for the higher fold-loss in potency of glecaprevir due to A156T mutation. An insight into the difference of molecular mechanism of drug resistance against the A156T substitution among the two classes of serine protease inhibitors could be useful for further optimization of new generation HCV NS3/4A inhibitors with enhanced inhibitory potency.Communicated by Ramaswamy H. Sarma.
丙型肝炎病毒（HCV）NS3/4A 丝氨酸蛋白酶是发现抗 HCV 药物的有前途的药物靶点。然而，其氨基酸突变，特别是 A156T，通常导致快速出现耐药性。帕利昔洛韦和格卡瑞韦是最近获得 FDA 批准的 HCV 药物，它们对 HCV NS3/4A 丝氨酸蛋白酶的 A156T 突变表现出不同的耐药谱。为了说明它们不同的分子耐药机制，对两种化合物与 HCV NS3/4A 蛋白酶的野生型（WT）和 A156T 变体复合物进行了分子动力学模拟和结合自由能计算。基于 QM/MM-GBSA 的结合自由能计算表明，与 WT 复合物相比，帕利昔洛韦和格卡瑞韦对 A156T NS3/4A 的结合亲和力分别显著降低了约 4 kcal/mol，这与实验耐药折叠一致。此外，与 NS3 蛋白的氨基酸（如 H57、R155 和 T156）的分子间相互作用较弱，空间位阻以及 R123 和 D168 之间盐桥的丢失导致的蛋白结合表面的不稳定，是由于 A156T 突变导致格卡瑞韦效力降低的主要原因。深入了解两种类别的丝氨酸蛋白酶抑制剂对 A156T 取代的耐药分子机制的差异，对于进一步优化具有增强抑制效力的新一代 HCV NS3/4A 抑制剂可能是有用的。由 Ramaswamy H. Sarma 交流。
