Table 1.

Binding affinity of inhibitors with COVID-19 main protease using molecular docking approach and the structures obtained from X-ray crystallography and 100 ns MD simulation.

PubChem ID	IUPAC name	Binding affinity using PDB structure (kcal/mol)	Binding affinity using MD structure (kcal/mol)
118098670	(2R,15R)-2-[(1-Aminoisoquinolin-6-yl)amino]-4,15,17-trimethyl- 7-[1-(2H-tetrazol-5-yl)cyclopropyl]-13-oxa-4,11-diazatricyclo [14.2.2.16,10]henicosa-1(18),6,8,10(21),16,19-hexaene-3,12-dione	−10.6	−10.0
104161460	(R)-6-(2″-((3-hydroxypyrrolidin-1-yl)methyl)biphenyl-4-yl)-1-(3- (5-oxo-4,5-dihydro-1h-1,2,4-triazol-3-yl)phenyl)-3-(trifluoromethyl)- 5,6-dihydro-1H-pyrazolo[3,4-c]pyridin-7(4H)-one	−10.2	−9.4
5289412	N-[(5S,9S,10S,13S)-9-Hydroxy-5,10-bis(2-methylpropyl)-4,7,12,16- tetraoxo-3,6,11,17-tetrazabicyclo[17.3.1]tricosa-1(22),19(23), 20-trien-13-yl]-3-naphthalen-1-yl-2-(naphthalen-1-ylmethyl)propanamide	−9.4	−9.7
137349331	[(2′S,5R,8S,10R,14S)-2′-ethenyl-26-fluoro-14-[[(3S)-1-methyl- 2-oxopiperidine-3-carbonyl]amino]-2,2,4,7,13-pentaoxospiro[2lambda6 -thia-3,6,12,22-tetrazatricyclo[21.4.0.08,12]heptacosa-1(23),24,26-triene-5, 1′-cyclopropane]-10-yl] 4-fluoro-1,3-dihydroisoindole-2-carboxylate	−10.0	−9.3
44228999	2-[6-[3-[3-(aminomethyl)phenyl]phenoxy]-4-[(3R)-3-(dimethylamino) pyrrolidin-1-yl]-3,5-difluoropyridin-2-yl]oxy-4-(dimethylamino)benzoic acid	−9.8	–
163632044	6-[3-([1,3]oxazolo[4,5-B]pyridin-2-Yl)-2-(Trifluoromethyl)phenoxy]-1- (2,4,6-Trifluorobenzyl)quinazolin-4(1H)-One	−9.6	−8.8
656932	[(1R)-2-[3-[methyl-[1-(naphthalene-2-carbonyl)piperidin-4-yl]carbamoyl] naphthalen-2-yl]-1-naphthalen-1-yl-2-oxoethyl]phosphonic acid	−9.6	–
N3*	N-[(5-methylisoxazol-3-yl)carbonyl]alanyl-l-valyl-n∼1∼-(1R,2Z)-4-(benzyloxy)- 4-oxo-1-{[(3R)-2-oxopyrrolidin-3-yl]methyl}but-2-enyl)-l-leucinamide	−7.3	–
90176081	(11S)-4,9-Dioxo-N-[(2S)-1-oxo-3-phenylpropan-2-yl]-17,22-dioxa-10, 30-diazatetracyclo[21.2.2.213,16.15,8]triaconta-1(26),5,7,13,15,23(27), 24,28-octaene-11-carboxamide	−9.3	−9.2
10Q*	2-{(2E,4aR,7aR)-7a-[4-(3-cyanophenyl)thiophen-2-yl]-2-imino-3-methyl- 4-oxooctahydro-6H-pyrrolo[3,4-d]pyrimidin-6-yl}pyridine-3-carbonitrile	−9.5	–
25141820	(1R,18R,22R,26S,29S)-26-cyclopentyl-N-[(1R,2S)-1-(cyclopropylsulfonylcarbamoyl)-2- ethenylcyclopropyl]-24,27-dioxo-2,23-dioxa-11,25,28-triazapentacyclo[26.2.1.03, 12.05,10.018,22]hentriaconta-3,5,7,9,11-pentaene-29-carboxamide	−9.6	–

*Represents chemical ID from PDB.