Tolufashe Gideon, Viswanathan Usha, Kulp John, Guo Ju-Tao
Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, PA 18902, USA.
Viruses. 2025 Feb 27;17(3):332. doi: 10.3390/v17030332.
Capsid assembly modulators (CAMs) are a novel class of antiviral agents in clinical development for the treatment of chronic hepatitis B. CAMs inhibit hepatitis B virus (HBV) replication by binding to a hydrophobic pocket, i.e., HAP pocket, between HBV capsid protein (Cp) dimer-dimer interfaces to misdirect its assembly into empty capsids or aberrant structures and designated as CAM-E and CAM-A, respectively. Because the emergence of CAM-resistant variants results in the failure of antiviral therapy, it is important to rationally design CAMs with a high barrier of resistance for development. To establish computational approaches for the prediction of Cp mutations that confer resistance to CAMs, we investigated the interaction of representative CAM-A and CAM-E compounds, BAY 41-4109 and JNJ-56136379, with wild-type and 35 naturally occurring mutations of Cp residues at the HAP pocket using molecular docking, prime molecular mechanics with generalized Born and surface area solvation (MM/GBSA) and molecular dynamics (MD) simulation methods. Out of nine publicly available HBV capsid or CpY132A hexamer structures in the protein database, molecular docking correctly predicted the resistance and sensitivity of more than 50% Cp mutations to JNJ-56136379 with structures 5D7Y and 5T2P-FA. MM/GBSA correctly predicted the resistance and sensitivity of more than 50% Cp mutations to BAY41-4109 with the structures 5E0I-BC and 5WRE-FA, and to JNJ-56136379 with the 5E0I-FA structure. Our work indicates that only the capsid or CpY132A hexamer structure bound with a CAM with similar chemical scaffold can be used for more accurately predicting the resistance and sensitivity of Cp mutations to a CAM molecule under investigation by molecular docking and/or MM/GBSA methods.
衣壳组装调节剂（CAMs）是一类新型抗病毒药物，正处于治疗慢性乙型肝炎的临床开发阶段。CAMs通过与乙肝病毒（HBV）衣壳蛋白（Cp）二聚体 - 二聚体界面之间的疏水口袋（即HAP口袋）结合来抑制HBV复制，从而将其组装误导为空衣壳或异常结构，分别命名为CAM - E和CAM - A。由于CAM耐药变异体的出现会导致抗病毒治疗失败，因此合理设计具有高耐药屏障的CAMs对于开发至关重要。为了建立预测赋予对CAMs耐药性的Cp突变的计算方法，我们使用分子对接、广义Born表面面积溶剂化的主分子力学（MM/GBSA）和分子动力学（MD）模拟方法，研究了代表性的CAM - A和CAM - E化合物BAY 41 - 4109和JNJ - 56136379与野生型以及HAP口袋处Cp残基的35种天然存在突变的相互作用。在蛋白质数据库中九个公开可用的HBV衣壳或CpY132A六聚体结构中，分子对接利用5D7Y和5T2P - FA结构正确预测了超过50%的Cp突变对JNJ - 56136379的耐药性和敏感性。MM/GBSA利用5E0I - BC和5WRE - FA结构正确预测了超过50%的Cp突变对BAY41 - 4109的耐药性和敏感性，利用5E0I - FA结构正确预测了对JNJ - 56136379的耐药性和敏感性。我们的工作表明，只有与具有相似化学支架的CAM结合的衣壳或CpY132A六聚体结构，才能用于通过分子对接和/或MM/GBSA方法更准确地预测Cp突变对所研究的CAM分子的耐药性和敏感性。
