Structure-Based Virtual Screening, Docking, ADMET, Molecular Dynamics, and MM-PBSA Calculations for the Discovery of Potential Natural SARS-CoV-2 Helicase Inhibitors from the Traditional Chinese Medicine

Table 3

∆G (in kcal/mole) of the most similar 40 compounds to VXG.

Compound	Name	∆G (kcal/mole)
48	(+)-Methylpseudoephedrine	−15.92
57	(1R,2S)-Ephedrine	−15.64
58	(1R,2S)-N-methylephedrine	−15.24
59	(1R,2S)-Norephedrine	−14.29
64	(1S,2S)-Norpseudoephedrine	−13.65
65	(1S,2S)-Pseudoephedrine	−11.66
80	(3S)-2,2-Dimethyl-3,5-dihydroxy-8-hydroxymethyl-3,4-dihydro-2H,6H-benzo[1,2-b5,4-b′]dipyran-6-one	−14.27
84	2-(4-(Pyrrolidin-1-yl) phenyl) acetic acid	−15.46
85	(4S,5R)-Ephedroxane	−14.01
91	(E)-3-Butylidene phthalide	−13.31
100	(S)-Cathinone	−12.6
102	(Z)-3-Butylidene phthalide	−13.9
114	1-(2,4-Dimethoxyphenyl)-1-propanone	−13.53
118	1,3,6,6-Tetramethyl-6,7-dihydroisoquinolin-8(5H)-one	−12.41
150	(4S,5R)-Ephedroxane	−13.02
195	1-Phenylpropane-1,2-dione	−11.07
208	2,3,4-Trimethyl-5-phenyloxazolidine	−13.76
245	2-Methoxycinnamaldehyde	−14.92
246	2-Methoxycinnamic acid	−14.22
260	2-Phenylethyl acetate	−13.29
280	3,4-Dimethyl-5-phenyloxazolidine	−13.21
342	3-Butylidene-4-hydro-phthalide	−13.24
364	2-Methoxybenzoic acid	−12.16
374	3′-o-Acetylhamaudol	−18.21
388	3′-o-Propionylhamaudol	−18.13
398	4-(4-Hydroxyphenyl)-2-butanone	−12.88
405	(R)-2-((R)-5-Oxopyrrolidin-3-yl)-2-phenylacetic acid	−15.74
433	4-Hydroxy-3-methoxycinnamaldehyde	−13.11
533	(Z)-6-(3-Hydroxy-4-methoxystyryl)-4-methoxy-2H-pyran-2-one	−17.1
539	6,7-Dihydroxy-2-(2-phenylethyl)-5,6,7,8-tetrahydrochromone	−18.36
610	7-Demethylsuberosin	−15.48
637	8-Chloro-2-(2-phenylethyl)-5,6,7-trihydroxy-5,6,7,8-tetrahydrochromone	−18.85
816	3-((R)-Hydroxy ((S)-1-methylpiperidin-2-yl)methyl)phenol	−17.09
817	(R)-((S)-1-Methylpiperidin-2-yl) (phenyl)methanol	−15.95
818	3-((1R,2S)-2-(Dimethylamino)-1-hydroxypropyl)phenol	−15.79
5153	(R)-4-(1-Hydroxy-2-(methylamino)ethyl)-7,7-dimethyl-5,6,7,8-tetrahydronaphthalen-1-ol	−17.84
5155	(R)-4-(1-Hydroxy-2-(methylamino)ethyl)-8,8-dimethyl-6,7,8,9-tetrahydro-5H-benzo[7]annulen-1-ol	−16.59
5159	(R)-2-Ethyl-4-(1-hydroxy-2-(methylamino)ethyl)phenol	−17.89
5168	(R)-2-((1S,2S,5S)-2-Benzyl-5-hydroxy-4-methylcyclohex-3-en-1-yl)propane-1,2-diol	−18.4
5169	(1S,4R,5S)-4-Benzyl-5-(2-hydroxypropan-2-yl)-2-methylcyclohex-2-en-1-ol	−17.42
VXG	(3S,4R)-1-Acetyl-4-phenylpyrrolidine-3-carboxylic acid	−19.37