Potential Treatment of Chinese and Western Medicine Targeting Nsp14 of SARS-CoV-2

Liu, Chao; Zhu, Xiaoxiao; Lu, Yiyao; Zhang, Xianqin; Jia, Xu; Yang, Tai

The outbreak of coronavirus disease 2019 (COVID-19) by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) is a serious global health threat. This raises an urgent need for the development of effective drugs against the deadly disease. SARS-CoV-2 nonstructural protein 14 (NSP14) carrying RNA cap guanine N7-methyltransferase and 3'-5' exoribonuclease activities could be a potential drug target for intervention. NSP14 of SARS-CoV-2 shared 98.7% similarity with the one (PDB 5NFY) of acute respiratory syndrome (SARS) by ClustalW. Then, the SARS-CoV-2 NSP14 structures were modelled by Modeller9.18 using SARS NSP14 (PDB 5NFY) as template for virtual screening. Based on the docking score from AutoDock Vina1.1.2, 18 small molecule drugs were selected for further evaluation. Based on the 5 ns MD simulation trajectory, binding free energy (ΔG) was calculated by MM/GBSA method. The calculated binding free energies of Saquinavir, Hypericin, Baicalein and Bromocriptine for the N-terminus of the homology model were -37.2711±3.2160, -30.1746±3.1914, -23.8953±4.4800, -34.1350±4.3683 kcal/mol, respectively, while the calculated binding free energies were -60.2757±4.7708, -30.9955±2.9975, -46.3099±3.5689, -59.8104±3.5389 respectively when binding to the C-terminus. Thus, the compounds including Saquinavir, Hypericin, Baicalein and Bromocriptine, could bind the N-terminus and C-terminus of the homology model of the SARS-CoV-2 Nsp14, providing as a candidate drug against SARS-CoV-2 for further study.