SARS-CoV-2 main protease (M^pro) cleaves the viral polypeptide 1a and 1ab in a site-specific ((L-Q|(S, A, G)) manner and produce functional enzymes for mediating viral replication. Numerous studies have reported synthetic competitive inhibitors against this target enzyme but increase in substrate concentration often reduces the effectiveness of such inhibitors. Allosteric inhibition by natural compound can provide safe and effective treatment by alleviating this limitation. Present study deals with in silico allosteric inhibition analysis of quercetin, against SARS-CoV-2-M^pro. Molecular docking of quercetin with M^pro revealed consistent binding of quercetin at a site other than active site in multiple runs, with the highest binding energy of − 8.31 kcal/mol, forming 6 H-bonds with residues Gln127, Cys128, Lys137, Asp289 and Glu290. Molecular dynamic simulation of 50 ns revealed high stability of M^pro-quercetin complex with RMSD values ranging from 0.1 to 0.25 nm. Moreover, native-M^pro and M^pro-quercetin complex conformations extracted at different time points from simulation trajectories were subjected to active site-specific docking with modelled substrate peptide (AVLQSGFR) by ZDOCK server. Results displayed site-specific cleavage of peptide when docked with native-M^pro. While substrate peptide remained intact when docked with M^pro-quercetin complex, also the binding energy of peptide reduced from 785 to 86 from 1 to 50 ns as quercetin induced alterations in the active site cavity reducing its affinity for the substrate. Further, no interactions were noticed between peptide and active site residues of M^pro-quercetin complex conformations at 40 and 50 ns. Hence, quercetin displayed effective allosteric inhibition potential against SARS-CoV-2 M^pro, and can be developed into an efficient treatment for COVID-19.

SARS-CoV-2主要蛋白酶（M ^pro）以位点特异性（（LQ |（S，A，G））方式切割病毒多肽1a和1ab，并产生介导病毒复制的功能性酶。竞争性抑制剂对这种目标酶的抑制作用，但底物浓度的增加通常会降低这种抑制剂的效力。天然化合物的变构抑制作用可以减轻这一限制，从而提供安全有效的治疗方法。目前的研究涉及槲皮素的计算机化变构抑制分析，针对SARS- CoV-2-M ^pro槲皮素与M ^pro的分子对接揭示了槲皮素在多次运行中在活性位点以外的位点上具有一致的结合，最高结合能为-8.31 kcal / mol，与残基Gln127，Cys128，Lys137，Asp289和Glu290形成6个H键。50ns的分子动力学模拟揭示M的高稳定性^亲-quercetin复合物与RMSD值范围从0.1至0.25纳米。此外，由模拟轨迹在不同时间点提取的天然M ^pro和M ^pro槲皮素复合物构象通过ZDOCK服务器与建模的底物肽（AVLQSGFR）进行了活性位点特异性对接。当与native-M ^pro停靠时，结果显示了肽的位点特异性切割。与M停靠时，底物肽保持完整^亲-quercetin复杂，也结合肽的能量作为在活性位点空腔槲皮素诱导的改变减少其对底物亲和性从785从1至50纳秒减少到86。另外，也没有相互作用进行了肽和M的活性位点残基之间注意到^亲在40个50纳秒-quercetin复杂的构象。因此，槲皮素显示出针对SARS-CoV-2 M ^pro的有效变构抑制潜能，并且可以发展成为COVID-19的有效治疗方法。