Department of Bioinformatics, SRM University, Delhi-NCR, Sonepat, Sonepat, Haryana, India.
Department of Computer Science, Jamia Millia Islamia, New Delhi, India.
J Biomol Struct Dyn. 2023 Jun;41(9):4013-4023. doi: 10.1080/07391102.2022.2060308. Epub 2022 Apr 22.
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is one of the rapid spreading coronaviruses that belongs to the Coronaviridae family. The rapidly evolving nature of SARS-CoV-2 results in a variety of variants with a capability of evasion to existing therapeutics and vaccines. So, there is an imperative need to discover potent drugs that can able to disrupt the function of multiple drug targets to tackle the SARS-CoV-2 menace. Here in this study, we took the different targets of SARS-CoV-2 prepared in the Schrodinger maestro. The library of the DrugBank database is screened against the selected crucial targets. Our molecular docking, Molecular Mechanics/Generalized Born Surface Area (MMGBSA), and molecular dynamics simulation studies led to identifying dinaciclib and theodrenaline as potential drugs against multiple drug targets: main protease, NSP15-endoribonuclease and papain-like-protease, of SARS-CoV-2. Dinaciclib with papain-like protease and NSP15-endoribonuclease show the docking score of -7.015 and -8.737, respectively, while the theodrenaline with NSP15-endoribonuclease and main protease produced the docking score of -8.507 and -7.289, respectively. Furthermore, the binding free energy calculations with MM/GBSA and molecular dynamics simulation studies of the complexes confirm the reliability of the drugs. The selected drugs are capable of binding to multiple targets simultaneously, thus withstanding their activity of target disruption in different variants of SARS-CoV-2. Although, the repurposed drugs are showing potent activity, but may need further in-vitro and in-vivo validations.Communicated by Ramaswamy H. Sarma.
严重急性呼吸系统综合症冠状病毒 2 型(SARS-CoV-2)是一种快速传播的冠状病毒,属于冠状病毒科。SARS-CoV-2 的快速进化特性导致其产生了多种能够逃避现有治疗方法和疫苗的变异体。因此,迫切需要发现能够破坏多种药物靶点功能的有效药物,以应对 SARS-CoV-2 的威胁。在这项研究中,我们针对 SARS-CoV-2 的不同靶点,使用 Schrödinger maestro 进行了处理。我们筛选了 DrugBank 数据库的库,以针对选定的关键靶点进行筛选。我们的分子对接、分子力学/广义 Born 表面积(MMGBSA)和分子动力学模拟研究导致确定了二氮嗪和去甲肾上腺素是针对 SARS-CoV-2 的多种药物靶点(主蛋白酶、NSP15-内切核糖核酸酶和木瓜蛋白酶样蛋白酶)的潜在药物。二氮嗪与木瓜蛋白酶样蛋白酶和 NSP15-内切核糖核酸酶的对接评分分别为-7.015 和-8.737,而去甲肾上腺素与 NSP15-内切核糖核酸酶和主蛋白酶的对接评分分别为-8.507 和-7.289。此外,结合 MM/GBSA 的结合自由能计算和复合物的分子动力学模拟研究证实了这些药物的可靠性。所选药物能够同时结合多个靶点,因此能够抵抗不同 SARS-CoV-2 变异体中靶点破坏的活性。虽然这些重新利用的药物显示出强大的活性,但可能需要进一步的体外和体内验证。由 Ramaswamy H. Sarma 传达。