Ghosh Rajesh, Chakraborty Ayon, Biswas Ashis, Chowdhuri Snehasis
School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India.
J Mol Struct. 2021 Apr 5;1229:129489. doi: 10.1016/j.molstruc.2020.129489. Epub 2020 Oct 19.
The COVID-19 pandemic, caused by SARS CoV-2, is responsible for millions of death worldwide. No approved/proper therapeutics is currently available which can effectively combat this outbreak. Several attempts have been undertaken in the search of effective drugs to control the spread of SARS CoV-2 infection. The main protease (Mpro), key component for the cleavage of the viral polyprotein, is considered to be one of the important drug targets for treating COVID-19. Various phytochemicals, including polyphenols and alkaloids, have been proposed as potent inhibitors of Mpro. The alkaloids from leaf extracts of have also been reported to possess anti-viral activity. But whether these alkaloids exhibit any inhibitory effect on SARS CoV-2 Mpro is far from clear. To explore this in detail, we have adopted computational approaches. alkaloids possessing proper drug-likeness properties and two anti-HIV drugs (lopinavir and darunavir; having binding affinity -7.3 to -7.4 kcal/mol) were docked against SARS CoV-2 Mpro to study their binding properties. Only one alkaloid (anisotine) had interaction with both the catalytic residues (His41 and Cys145) of Mpro and exhibited good binding affinity (-7.9 kcal/mol). Molecular dynamic simulations (100 ns) revealed that Mpro-anisotine complex is more stable, conformationally less fluctuated; slightly less compact and marginally expanded than Mpro-darunavir/lopinavir complex. Even the number of intermolecular H-bonds and MM-GBSA analysis suggested that anisotine is a more potent Mpro inhibitor than the two previously recommended antiviral drugs (lopinavir and darunavir) and may evolve as a promising anti-COVID-19 drug if proven in animal experiments and on patients.
由严重急性呼吸综合征冠状病毒2(SARS-CoV-2)引起的2019冠状病毒病大流行已导致全球数百万人死亡。目前尚无经批准的/合适的治疗方法能够有效对抗此次疫情。人们已经进行了多次尝试来寻找有效的药物以控制SARS-CoV-2感染的传播。主要蛋白酶(Mpro)是病毒多聚蛋白切割的关键成分,被认为是治疗2019冠状病毒病的重要药物靶点之一。各种植物化学物质,包括多酚和生物碱,已被提议作为Mpro的有效抑制剂。据报道,[具体植物名称]叶提取物中的生物碱也具有抗病毒活性。但这些生物碱是否对SARS-CoV-2 Mpro有任何抑制作用尚不清楚。为了详细探究这一点,我们采用了计算方法。将具有适当类药性质的生物碱和两种抗HIV药物(洛匹那韦和达芦那韦;结合亲和力为-7.3至-7.4千卡/摩尔)与SARS-CoV-2 Mpro进行对接,以研究它们的结合特性。只有一种生物碱(山油柑碱)与Mpro的两个催化残基(His41和Cys145)相互作用,并表现出良好的结合亲和力(-7.9千卡/摩尔)。分子动力学模拟(100纳秒)显示,Mpro-山油柑碱复合物更稳定,构象波动更小;与Mpro-达芦那韦/洛匹那韦复合物相比,稍微不那么紧凑且略有扩展。甚至分子间氢键的数量和MM-GBSA分析都表明,山油柑碱是一种比之前推荐的两种抗病毒药物(洛匹那韦和达芦那韦)更有效的Mpro抑制剂,如果在动物实验和患者身上得到证实,可能会成为一种有前景的抗2019冠状病毒病药物。