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首页> 美国卫生研究院文献>Nature Public Health Emergency Collection >Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors
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Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors

机译：严重急性呼吸综合征冠状病毒解旋酶ATP酶催化域的三维模型和严重急性呼吸综合征冠状病毒解旋酶抑制剂的分子设计

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摘要

The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors—molecules possessing two phosphonic acid moieties at distal ends of the molecule.
机译：使用蛋白结构预测Meta Server和3D Jury方法进行重症急性呼吸综合征冠状病毒解旋酶ATPase催化域的建模，以进行模型选择，从而确定了1JPR，1UAA和1W36 PDB结构作为创建模板的合适模板。全原子3D模型。该模型被进一步用于设计有望阻止ATPase催化口袋从而抑制酶活性的小分子。在一系列分子动力学计算中，确定了各种官能团的结合位点。它们在催化口袋中的位置被用作剑桥结构数据库中的限制条件，以搜索具有在所需位置与酶相互作用最强的药效团的分子。随后的MD模拟以及随后计算的设计分子的结合能与ATP进行了比较，从而确定了最可能的抑制剂，即可能的抑制剂-在分子的末端具有两个膦酸部分的分子。

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