Coronavirus disease 2019 (COVID-19) is an infectious disease brought on by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a global treat in early 2020. Despite worldwide research proving different medications used to treat COVID-19, the infection still affects the human race; we need to continue researching the virus to protect humanity and reduce the complications that some medications might cause. This study focuses on finding another promising therapeutic compound against SARS-CoV-2. Twenty-four (24) bioactive compounds were selected from the following African plants' Adansonia digitata L, Aframomum melegueta K. Schum, Ageratum conyzoides (L.) L, and Boswellia dalzielii, and Remdesivir was used as the control medication. The PubChem web server acquired the 3D structures of bioactive compounds in the plant and the control medication. The SARS-CoV-2 main protease (Mpro) crystal structure was obtained using the Protein Data Bank (PDB). Using the SwissADME web server, the bioactive compounds' drug-likeness was assessed, and AutoDock was employed for the molecular docking with the Mpro. The Proteins Plus and Protein–Ligand Interaction Profiler web servers were used to analyse the docked complexes. Furthermore, the admetSAR website was utilized to predict the ligands' absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. Based on the drug-likeness screening, Rutin violated more than one of the Lipinski rules of five, while Remdesivir violated two. Molecular docking analysis results indicated that Catechin, Epicatechin, Vitexin, Quercetin, Kaempferol, Gamma-Sitosterol, and Kaur-16-ene exhibited a stronger binding affinity with Mpro, with binding scores of − 7.1, − 7.1, − 8.0, − 7.3, − 7.2, − 6.8, and − 6.5 kcal/mol, respectively, compared to Remdesivir's binding score of − 6.3 kcal/mol. Consequently, binding scores of bioactive compounds suggest their potential biological activity against the SARS-CoV-2 main protease. Additionally, these bioactive compounds exhibited favourable ADMET properties. Vitexin also has a plasma protein binding below 90%, a promising medication distribution feature. This study shows that Catechin, Epicatechin, Vitexin, Quercetin, Kaempferol, Gamma-Sitosterol, and Kaur-16-ene have better binding affinities with Mpro than Remdesivir. Molecular dynamics simulation in vitro and in vivo investigation is required to support this study.

中文翻译：

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评估选定非洲植物中针对 SARS-CoV-2 主要蛋白酶 (Mpro) 的一些生物活性化合物的治疗潜力：分子对接研究

2019 冠状病毒病 (COVID-19) 是一种由严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 引起的传染病，该疾病于 2020 年初在全球范围内得到治疗。尽管全球研究证明用于治疗 COVID-19 的药物不同，感染仍然影响着人类；我们需要继续研究这种病毒，以保护人类并减少某些药物可能引起的并发症。本研究的重点是寻找另一种有前景的针对 SARS-CoV-2 的治疗化合物。从以下非洲植物：Adansonia digitalata L、Aframomum melegueta K. Schum、Ageratum conyzoides (L.) L 和 Boswellia dalzielii 中筛选出二十四 (24) 种生物活性化合物，并使用瑞德西韦作为对照药物。PubChem 网络服务器获取植物和对照药物中生物活性化合物的 3D 结构。使用蛋白质数据库（PDB）获得了 SARS-CoV-2 主蛋白酶（Mpro）晶体结构。使用SwissADME网络服务器评估生物活性化合物的药物相似性，并使用AutoDock与Mpro进行分子对接。Proteins Plus 和 Protein-Ligand Interaction Profiler 网络服务器用于分析对接的复合物。此外，admetSAR 网站用于预测配体的吸收、分布、代谢、排泄和毒性 (ADMET) 特性。根据药物相似性筛选，芦丁违反了利平斯基五项规则中的一项以上，而瑞德西韦则违反了两项。分子对接分析结果表明，儿茶素、表儿茶素、牡荆素、槲皮素、山奈酚、γ-谷甾醇和Kaur-16-ene与Mpro表现出更强的结合亲和力，结合分数分别为- 7.1、- 7.1、- 8.0、- 7.3、分别为 - 7.2、 - 6.8 和 - 6.5 kcal/mol，而瑞德西韦的结合分数为 - 6.3 kcal/mol。因此，生物活性化合物的结合分数表明它们对 SARS-CoV-2 主要蛋白酶具有潜在的生物活性。此外，这些生物活性化合物表现出良好的 ADMET 特性。牡荆素的血浆蛋白结合率也低于 90%，这是一个很有前景的药物分布特征。这项研究表明，儿茶素、表儿茶素、牡荆素、槲皮素、山奈酚、γ-谷甾醇和 Kaur-16-ene 与 Mpro 的结合亲和力比瑞德西韦更好。需要体外和体内研究的分子动力学模拟来支持这项研究。