利用 HCV NS5A GT-4a 的新同源模型研究达卡他韦及其类似物的对称结合模式。
Studies of the symmetric binding mode of daclatasvir and analogs using a new homology model of HCV NS5A GT-4a.
机构信息
Department of Pharmaceutical Chemistry, Tanta University, Tanta, 31527, Egypt.
Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA.
出版信息
J Mol Model. 2022 Dec 29;29(1):25. doi: 10.1007/s00894-022-05420-4.
CONTEXT
Egypt has a high prevalence of the hepatitis C virus (HCV) genotype 4a (GT-4a). Unfortunately, the high resistance it exhibited still was not given the deserved attention in the scientific community. There is currently no consensus on the NS5A binding site because the crystal structure of HCV NS5A has not been resolved. The prediction of the binding modes of direct-acting antivirals (DAA) with the NS5A is a point of controversy due to the fact that several research groups presented different interaction models to elucidate the NS5A binding site. Consequently, a 3D model of HCV NS5A GT-4a was constructed and evaluated using molecular dynamics (MD) simulations. The generated model implies an intriguing new orientation of the AH relative to domain I. Additionally, the probable binding modes of marketed NS5A inhibitors were explored. MD simulations validated the stability of the predicted protein-ligand complexes. The suggested model predicts that daclatasvir and similar drugs bind symmetrically to HCV NS5A GT-4a. This will allow for the development of new NS5A-directed drugs, which may result in reduced resistance and/or a wider range of effectiveness against HCV.
METHODS
The 3D model of HCV NS5A GT-4a was constructed using the comparative modeling approach of the web-based application Robetta. Its stability was tested with 200-ns MD simulations using the Desmond package of Schrodinger. The OPLS2005 force field was assigned for minimization, and the RMSD, RMSF, and rGyr were tracked throughout the MD simulations. Fpocket was used to identify druggable protein pockets (cavities) over the simulation trajectories. The binding modes of marketed NS5A inhibitors were then generated and refined with the aid of docking predictions made by FRED and AutoDock Vina. The stability of these drugs in complex with GT-4a was investigated by using energetic and structural analyses over MD simulations. The Prime MM-GBSA (molecular mechanics/generalized Born surface area) method was used as a validation tool after the docking stage and for the averaged clusters after the MD simulation stage. We utilized PyMOL and VMD to visualize the data.
背景
埃及丙型肝炎病毒（HCV）基因型 4a（GT-4a）的流行率很高。不幸的是，它表现出的高耐药性在科学界仍未得到应有的关注。目前，由于 HCV NS5A 的晶体结构尚未解析，因此对于 NS5A 结合位点尚无共识。由于几个研究小组提出了不同的相互作用模型来阐明 NS5A 结合位点，因此直接作用抗病毒药物（DAA）与 NS5A 的结合模式预测成为一个争议点。因此，构建并使用分子动力学（MD）模拟评估了 HCV NS5A GT-4a 的 3D 模型。生成的模型暗示了 AH 相对于结构域 I 的一种新颖的取向。此外，还探讨了市售 NS5A 抑制剂的可能结合模式。MD 模拟验证了预测蛋白-配体复合物的稳定性。提出的模型预测，达拉他韦和类似药物以对称方式结合 HCV NS5A GT-4a。这将允许开发新的 NS5A 定向药物，这可能会降低耐药性和/或扩大对 HCV 的有效性范围。
方法
使用基于网络的 Robetta 应用程序的比较建模方法构建了 HCV NS5A GT-4a 的 3D 模型。使用 Schrödinger 软件包中的 Desmond 对其进行了 200-ns MD 模拟测试。分配 OPLS2005 力场进行最小化，并在整个 MD 模拟过程中跟踪 RMSD、RMSF 和 rGyr。使用 Fpocket 来识别模拟轨迹上可药用的蛋白口袋（腔）。然后，借助 FRED 和 AutoDock Vina 的对接预测，生成并优化市售 NS5A 抑制剂的结合模式。使用 MD 模拟进行的能量和结构分析来研究这些药物与 GT-4a 结合的稳定性。对接阶段后和 MD 模拟阶段后，使用 Prime MM-GBSA（分子力学/广义 Born 表面积）方法作为验证工具。我们使用 PyMOL 和 VMD 来可视化数据。
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