抗新冠肺炎候选病毒Sars-Cov-2六蛋白靶点生物活性化合物的分子动力学模拟

Fikry Awaluddin, I. Batubara, S. T. Wahyudi
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摘要

严重急性呼吸综合征冠状病毒2(SARS-CoV-2)是导致2019冠状病毒(新冠肺炎)的病毒。迄今为止,还没有被证明有效的药物用于治疗或预防新冠肺炎。利用分子动力学模拟对开发这种病毒的抑制剂进行了研究。以3CL-Pro、PL-Pro、Helicase、N、E和M蛋白作为蛋白靶标。本研究旨在通过Amber20的分子动力学模拟来确定所选蛋白质-配体复合物的稳定性,以从天然产物中提出具有治疗新冠肺炎药物潜力的生物活性化合物。基于我们之前的研究,通过分子对接获得了每个靶蛋白的候选化合物的自由结合能和蛋白质-配体相互作用的最佳值。Corilagin(-14.42 kcal/mol)、黄芩苷7-芸香糖苷(-13.2 kcal/mol。在分子动力学模拟中,与其他配合物相比,3CL-Pro Corilagin配合物是最稳定的,因此它是最推荐的化合物。需要进一步的研究来测试所选择的配体活性,它具有六种靶蛋白中最低的自由能值。
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Molecular Dynamics Simulation of Bioactive Compounds Against Six Protein Target of Sars-Cov-2 As Covid-19 Antivirus Candidates
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the virus that causes Coronavirus 2019 (COVID-19). To date, there has been no proven effective drug for the treatment or prevention of COVID-19. A study on developing inhibitors for this virus was performed using molecular dynamics simulation. 3CL-Pro, PL-Pro, Helicase, N, E, and M protein were used as protein targets. This study aimed to determine the stability of the selected protein-ligand complex through molecular dynamics simulation by Amber20 to propose bioactive compounds from natural products that have potential as a drug for COVID-19. Based on our previous study, the best value of free binding energy and protein-ligand interactions of the candidate compounds are obtained for each target protein through molecular docking. Corilagin (-14.42 kcal/mol), Scutellarein 7-rutinoside (-13.2 kcal/mol), Genistein 7-O-glucuronide (-10.52 kcal/mol), Biflavonoid-flavone base + 3O (-11.88 and -9.61 kcal/mol), and Enoxolone (-6.96 kcal/mol) has the best free energy value at each protein target. In molecular dynamics simulation, the 3CL-Pro-Corilagin complex was the most stable compared to other complexes, so that it was the most recommended compound. Further research is needed to test the selected ligand activity, which has the lowest free energy value of the six target proteins.
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CiteScore
0.80
自引率
0.00%
发文量
15
审稿时长
24 weeks
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