id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-217961-2rczhxp2	Chitsaz, Mohsen	A small molecule drug candidate targeting SARS-CoV-2 main protease	2020-06-16		.txt	text/plain	2298	133	56	We aligned the inhibitor on the protein and on the initial conformation of the ligand and computed structural deviations RMSDs. To observe the interaction of the inhibitor with the active site and confirming that the inhibitor stays in the active site of SARS-CoV-2 protease, we ran a simulation of 250ns that was 10 times longer than two previous MD simulations. For each of the two complexes, we analyzed the active-site by investigating all hydrophobic, H-bond, ionic and water bridge interactions of the inhibitor with SARS-Cov-2 protease and SARS-CoV protease (see Fig. 5 and Fig. 6 respectively) . We observed that the inhibitor remains in the active site for the entire duration of the simulation and maintains H-bond and water bridge contacts with GLU166 and hydrophobic Pi-Pi stacking contact with HIS41 (see Fig. 13 ). Our primary observation was that the molecule remained in the active site of SARS-CoV-2 protease for the entire duration of the simulation.	./cache/cord-217961-2rczhxp2.txt	./txt/cord-217961-2rczhxp2.txt