Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase.
Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase.
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DOI：
10.1371/journal.pone.0246181
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发表时间：
2021
期刊：
影响因子：
3.7
通讯作者：
Armen RS
中科院分区：
文献类型：
--
作者：
Freidel MR;Armen RS
2019年，SARS-CoV-2的出现悲剧性地给人类生活造成了巨大的损失，并对社会产生了深远的影响。为了加速临床前的发展，有必要确定具有不同作用机制的有效抗病毒药物。本研究重点研究了5种最成熟的直接作用小分子抗病毒药物的靶蛋白：Nsp5主蛋白酶、Nsp12 RNA依赖的RNA聚合酶、Nsp13解旋酶、Nsp16 2‘-O甲基转移酶和Spike蛋白的S2亚基。使用溶剂作图和自由能计算的工作流程来识别和表征芳香族药效团(苯)的有利小分子结合部位。在确定最有利的位点后，利用计算片段筛选来比较计算的配基效率。最有利的位点位于Nsp12和Nsp16上，而Nsp13和S2的最有利位点的配基效率比Nsp12和Nsp16低。通过对Nsp13解旋酶上许多可能的位点进行片段筛选，我们在N端锌结合结构域(ZBD)上确定了一个有利的变构位点，该位点可能适合于虚拟或生物物理片段的筛选工作。最近对NSP12：NSP13复制-转录复合体的结构研究实验证实了该位点的配体结合，揭示了该复合体中一个功能性的NSP8：NSP13蛋白质-蛋白质相互作用位点。对Nsp13 ZBD构象的详细结构分析表明了该配体结合部位的诱导适配灵活性的作用，并确定了哪些构象状态与有效的配体结合有关。我们希望这些药物靶标的200多个可能的小分子结合位点的图谱可以用于正在进行的发现、设计和药物再利用的努力。这些信息可以用来确定筛选工作的优先顺序，或帮助破译筛选结果如何与特定靶蛋白结合的过程。
The 2019 emergence of, SARS-CoV-2 has tragically taken an immense toll on human life and far reaching impacts on society. There is a need to identify effective antivirals with diverse mechanisms of action in order to accelerate preclinical development. This study focused on five of the most established drug target proteins for direct acting small molecule antivirals: Nsp5 Main Protease, Nsp12 RNA-dependent RNA polymerase, Nsp13 Helicase, Nsp16 2’-O methyltransferase and the S2 subunit of the Spike protein. A workflow of solvent mapping and free energy calculations was used to identify and characterize favorable small-molecule binding sites for an aromatic pharmacophore (benzene). After identifying the most favorable sites, calculated ligand efficiencies were compared utilizing computational fragment screening. The most favorable sites overall were located on Nsp12 and Nsp16, whereas the most favorable sites for Nsp13 and S2 Spike had comparatively lower ligand efficiencies relative to Nsp12 and Nsp16. Utilizing fragment screening on numerous possible sites on Nsp13 helicase, we identified a favorable allosteric site on the N-terminal zinc binding domain (ZBD) that may be amenable to virtual or biophysical fragment screening efforts. Recent structural studies of the Nsp12:Nsp13 replication-transcription complex experimentally corroborates ligand binding at this site, which is revealed to be a functional Nsp8:Nsp13 protein-protein interaction site in the complex. Detailed structural analysis of Nsp13 ZBD conformations show the role of induced-fit flexibility in this ligand binding site and identify which conformational states are associated with efficient ligand binding. We hope that this map of over 200 possible small-molecule binding sites for these drug targets may be of use for ongoing discovery, design, and drug repurposing efforts. This information may be used to prioritize screening efforts or aid in the process of deciphering how a screening hit may bind to a specific target protein.
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