分子动力学
虚拟筛选
蛋白酶
回转半径
化学
组合化学
严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)
2019年冠状病毒病(COVID-19)
计算生物学
均方根
计算化学
生物化学
酶
生物
医学
有机化学
物理
传染病(医学专业)
病理
聚合物
疾病
量子力学
作者
Shafi Mahmud,Mohammad Abu Raihan Uddin,Gobindo Kumar Paul,Mst. Sharmin Sultana Shimu,Saiful Islam,Md. Ekhtiar Rahman,Ariful Islam,Md. Samiul Islam,Maria Meha Promi,Talha Bin Emran,Md. Abu Saleh
摘要
The new coronavirus (SARS-CoV-2) halts the world economy and caused unbearable medical emergency due to high transmission rate and also no effective vaccine and drugs has been developed which brought the world pandemic situations. The main protease (Mpro) of SARS-CoV-2 may act as an effective target for drug development due to the conservation level. Herein, we have employed a rigorous literature review pipeline to enlist 3063 compounds from more than 200 plants from the Asian region. Therefore, the virtual screening procedure helps us to shortlist the total compounds into 19 based on their better binding energy. Moreover, the Prime MM-GBSA procedure screened the compound dataset further where curcumin, gartanin and robinetin had a score of (-59.439, -52.421 and - 47.544) kcal/mol, respectively. The top three ligands based on binding energy and MM-GBSA scores have most of the binding in the catalytic groove Cys145, His41, Met165, required for the target protein inhibition. The molecular dynamics simulation study confirms the docked complex rigidity and stability by exploring root mean square deviations, root mean square fluctuations, solvent accessible surface area, radius of gyration and hydrogen bond analysis from simulation trajectories. The post-molecular dynamics analysis also confirms the interactions of the curcumin, gartanin and robinetin in the similar binding pockets. Our computational drug designing approach may contribute to the development of drugs against SARS-CoV-2.
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