黑草化合物作为靶向SARS-CoV-2刺突蛋白潜在药物的计算预测

L. Ali, R. Saif, Muhammad Hassan Raza, Muhammad Osama Zafar, Saeeda Zia, M. Shafiq, Tuba Ahmad, I. Anjum
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引用次数: 1

摘要

2019年12月,SARS-CoV-2首次在中国武汉被发现,并在全球迅速蔓延。缺乏批准的治疗药物加剧了全球形势,因此研究人员正在寻找使用常规药物和传统草药的潜在治疗方法。目的:从黑Nigella sativa中寻找抗SARS-CoV-2刺突蛋白(PDB ID: 7BZ5)的新药物。方法:利用分子操作环境(MOE)软件将46个化合物与刺突蛋白对接,并与市售抗病毒药物阿比多尔、法匹拉韦、瑞德西韦、奈非那韦、氯喹、羟氯喹进行比较。分子动力学模拟(MDS)分析也用于确定配体-蛋白复合物的稳定性。此外,还利用AdmetSAR和SwissADME分析了化合物的药理特性。结果:从46个配体中筛选出硬脂酸甲酯、二十二烯酸、油酸、硬脂酸、亚油酸、肉豆蔻酸、棕榈酸和法尼醇8个化合物,根据它们的最小结合能范围在-7.45 ~ -7.07 kcal/mol之间,进行进一步分析。苜蓿植物化合物的对接分数与对照药物相似。此外,模拟后分析硬脂酸甲酯络合物预测最稳定的构象。结论:进一步,建议通过体内实验验证硬脂酸甲酯作为抑制SARS-CoV-2刺突蛋白的潜在抑制剂的药用价值。
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Computational Prediction of Nigella sativa Compounds as Potential Drug Agents for Targeting Spike Protein of SARS-CoV-2
SARS-CoV-2 was first identified in Wuhan, China in December 2019 and has rapidly devastated worldwide. The lack of approved therapeutic drugs has intensified the global situation, so researchers are seeking potential treatments using regular drug agents and traditional herbs as well. Objectives: To identify new therapeutic agents from Nigella sativa against spike protein (PDB ID: 7BZ5) of SARS-CoV-2. Methods: The 46 compounds from N. sativa were docked with spike protein using Molecular Operating Environment (MOE) software and compared with commercially available anti-viral drugs e.g., Arbidol, Favipiravir, Remdesivir, Nelfinavir, Chloroquine, Hydroxychloroquine. The Molecular Dynamic Simulation (MDS) analysis was also applied to determine ligand-protein complex stability. Furthermore, the pharmacological properties of compounds were also analyzed using AdmetSAR and SwissADME. Results: Out of its total 46 ligands, 8 compounds i.e., Methyl stearate, Eicosadienoic acid, Oleic acid, Stearic acid, Linoleic acid, Myristoleic acid, Palmitic acid, and Farnesol were selected for further analysis based on their minimum binding energy ranges from -7.45 to -7.07 kcal/mol. The docking scores of N. sativa phytocompounds were similar to drugs taken as control. Moreover, post simulation analysis of Methyl stearate complex predicted the most stable conformer. Conclusions: Further, in-vivo experiments are suggested to validate the medicinal use of Methyl stearate as potential inhibitors against spike protein of SARS-CoV-2.
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