Direct acting antivirals have dramatically increased the efficacy and tolerability of hepatitis C treatment, but drug resistance has emerged with some of these inhibitors, including nonstructural protein 3/4 A protease inhibitors (PIs). Although many co-crystal structures of PIs with the NS3/4A protease have been reported, a systematic review of these crystal structures in the context of the rapidly emerging drug resistance especially for early PIs has not been performed. To provide a framework for designing better inhibitors with higher barriers to resistance, we performed a quantitative structural analysis using co-crystal structures and models of HCV NS3/4A protease in complex with natural substrates and inhibitors. By comparing substrate structural motifs and active site interactions with inhibitor recognition, we observed that the selection of drug resistance mutations correlates with how inhibitors deviate from viral substrates in molecular recognition. Based on this observation, we conclude that guiding the design process with native substrate recognition features is likely to lead to more robust small molecule inhibitors with decreased susceptibility to resistance.

直接作用抗病毒药极大地提高了丙型肝炎治疗的疗效和耐受性，但是其中一些抑制剂（包括非结构蛋白3/4 A蛋白酶抑制剂（PIs））已经出现了耐药性。尽管已经报道了PI与NS3 / 4A蛋白酶的许多共晶体结构，但是在快速出现的耐药性的背景下，特别是对于早期PI，尚未对这些晶体结构进行系统的综述。为了提供一个设计框架，以设计具有更高抗性屏障的抑制剂，我们使用了与天然底物和抑制剂复合的HCV NS3 / 4A蛋白酶的共晶体结构和模型，进行了定量结构分析。通过比较底物的结构基序和活性位点与抑制剂的识别作用，我们观察到耐药性突变的选择与抑制剂在分子识别中偏离病毒底物的方式有关。基于此观察结果，我们得出结论，用天然底物识别功能指导设计过程可能会导致更强大的小分子抑制剂，且对耐药性的敏感性降低。