Computational Simulation Of Small Molecule Inhibitors About Traditional Chinese Medicine Targeting M^pro For COVID-19

BackgroundCurrently,there are 480 million confirmed cases of COVID-19 caused by SARS-Co V-2 infection worldwide,with 6 million deaths and 57 million confirmed cases,and there is still a lack of effective clinical therapeutics.The main protease(M^pro)of SARS-Co V-2 is an important target for the development of inhibitors against COVID-19 and its active site residues are highly conserved.Given the important role of traditional Chinese medicine in the prevention and clinical treatment of COVID-19,it is important to explore potential neo-coronavirus therapeutic agents targeting M^pro in traditional Chinese medicine for the treatment of pneumonia caused by SARS-Co V-2 as well as for the research and development of traditional Chinese medicine.Objective1.The traditional Chinese medicine M^pro inhibitors with high affinity to M^pro and potential for drug discovery were screened and further identified from the traditional Chinese medicine small molecule database（TCM database）.2.By analyzing the binding mode of potential inhibitors to M^pro,we explore the residues in M^pro that are necessary for the inhibitory effect of the inhibitor and provide information to guide the design of M^pro inhibitors.Method1.The M^pro crystal structure was obtained from the NCBI database and its structure was optimized.The TCM database was obtained and pre-screening,structure optimization,protonation and 3D structure reconstruction were performed basing on the drug-like principle.2.The processed TCM database was subjected to a molecular docking-based virtual screen with the optimized M^pro protein.3.Molecular dynamics simulations（MD）were performed on the screened small molecule-M^pro complex systems and binding patterns were analyzed.4.Pharmacokinetic prediction of absorption,metabolism,distribution,excretion and toxicological properties of small molecule inhibitors of traditional Chinese medicine.Results1.The percentage of residues of M^pro falling in the most favorable region after optimization reached 91.7%,and the small molecules of the TCM small molecule database were screened for drug-like properties to obtain a database containing 21604 drug-like herbal small molecules.Six small molecule inhibitors of TCM were identified by two screens based on semi-flexible molecular docking and induced fit mode molecular docking,respectively.2.The results of molecular dynamics simulations showed that four of the small molecules,Hc1,Hc2,Hc3 and Hc4,have higher binding energies to M^pro（-34.62 kcal/mol,-25.20 kcal/mol,-26.72 kcal/mol,-32.02 kcal/mol,respectively）than Cg1（-16.04 kcal/mol）and Cg2（-23.38 kcal/mol）,in addition,they are able to form hydrogen bonds with M^pro and bind stably.The binding mode analysis showed that residues such as Met49,Met165,Gln189and Thr190 made prominent energetic contributions during the binding of these 4 small molecules to M^pro.Analysis of the conformations of four small molecules during the kinetics revealed key amino acids such as Met49,Met165,Gln189 and Thr190 that contribute important roles to the binding of small molecules and M^pro.3.Pharmacokinetic predictions showed that the four herbal small molecules had high oral utilization and good intra-tissue distribution,and were not neurologically or genos-toxically toxic.ConclusionIn this study,four small molecules of traditional Chinese medicine,Hc1,Hc2,Hc3 and Hc4,were identified as M^pro inhibitors using computer-aided drug design methods based on molecular docking virtual screening,molecular dynamics,and pharmacokinetic prediction.All of them were able to bind stably to M^pro and form hydrogen bonds,and in addition,exhibited good pharmacokinetic properties.These four traditional Chinese medicine small molecules,especially Hc1 and Hc4,are expected to be novel anti-COVID-19 inhibitors targeting M^pro.This research can provide guidance for the research and development of M^pro inhibitors.