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 1

Fingerprint similarity between 187 natural compounds and VXG.

Comp.	Similarity	SA	SB	SC	Comp.	Similarity	SA	SB	SC
VXG	1	166	0	0	5412	0.582205	602	580	−148
138	1	160	100	6	1585	0.581927	586	553	−132
167	1	169	118	−3	1566	0.581457	439	301	15
215	1	180	166	−14	810	0.581121	197	173	−31
258	1	153	128	13	5449	0.580863	431	288	23
347	1	143	101	23	2379	0.580247	329	113	125
364	1	90	−7	76	5154	0.579775	258	−9	196
379	1	143	101	23	3239	0.579154	589	563	−135
380	1	143	101	23	2356	0.57854	523	450	−69
411	1	112	42	54	3258	0.578205	451	326	3
445	1	186	146	−20	3589	0.578089	496	404	−42
496	1	196	201	−30	362	0.577495	272	17	182
501	1	163	145	3	5439	0.577398	608	599	−154
507	1	158	136	8	3255	0.577267	452	329	2
526	1	143	101	23	1584	0.576874	454	333	0
533	1	133	70	33	71	0.576792	169	127	−3
552	1	173	123	−7	623	0.576792	169	127	−3
554	1	173	121	−7	38	0.576087	265	6	189
555	1	173	121	−7	5441	0.576077	602	591	−148
577	1	154	90	12	1982	0.575087	494	405	−40
610	1	116	39	50	398	0.57485	96	1	70
619	1	156	131	10	114	0.561111	101	14	65
637	1	162	108	4	816	0.56	112	34	54
733	1	169	157	−3	92	0.556886	93	1	73
756	1	206	193	−40	169	0.556886	93	1	73
782	1	220	219	−54	5157	0.556701	108	28	58
792	1	207	178	−41	451	0.554878	182	162	−16
794	1	196	177	−30	5154	0.554307	148	101	18
803	1	169	147	−3	768	0.55418	179	157	−13
806	1	210	206	−44	190	0.553299	109	31	57
807	1	183	144	−17	557	0.55298	167	136	−1
818	1	99	9	67	629	0.55	176	154	−10
2379	1	213	229	−47	495	0.543333	163	134	3
405	0.777	136	9	30	433	0.538462	91	3	75
442	0.738	127	6	39	754	0.537764	178	165	−12
85	0.731	125	5	41	566	0.534743	177	165	−11
260	0.722	117	−4	49	354	0.534535	178	167	−12
208	0.697	124	12	42	597	0.53271	171	155	−5
91	0.689	122	11	44	596	0.531148	162	139	4
102	0.689	122	11	44	601	0.528302	168	152	−2
195	0.681	109	−6	57	752	0.527473	192	198	−26
280	0.674	116	6	50	568	0.526946	176	168	−10
344	0.658	121	18	45	790	0.526012	182	180	−16
370	0.658	121	18	45	2368	0.523041	227	268	−61
672	0.652	167	90	−1	439	0.522222	188	194	−22
48	0.649	113	8	53	158	0.521978	95	16	71
58	0.649	113	8	53	5152	0.521898	143	108	23
100	0.646	104	−5	62	250	0.520408	153	128	13
246	0.644	105	−3	61	591	0.519737	158	138	8
84	0.638	118	19	48	5153	0.517699	117	60	49
5169	0.636	159	84	7	150	0.517241	90	8	76
817	0.633	126	33	40	297	0.515789	147	119	19
396	0.624	106	4	60	2370	0.515738	213	247	−47
245	0.622	102	−2	64	5167	0.51567	181	185	−15
57	0.62	106	5	60	413	0.513986	147	120	19
65	0.62	106	5	60	491	0.513699	150	126	16
1942	0.614339	497	355	−43	5177	0.512195	189	203	−23
5415	0.614108	592	510	−138	415	0.511945	150	127	16
5434	0.614017	587	502	−133	5151	0.511696	175	176	−9
3941	0.613833	426	240	28	2367	0.511364	225	274	−59
4050	0.613551	489	343	−35	544	0.511299	181	188	−15
5441	0.613124	626	567	−172	5159	0.511111	92	14	74
5039	0.613119	458	293	−4	266	0.510903	164	155	2
4055	0.612984	491	347	−37	374	0.510563	145	118	21
3591	0.612751	519	393	−65	418	0.510417	147	122	19
2348	0.612622	563	465	−109	5155	0.510288	124	77	42
3912	0.612319	507	374	−53	207	0.510274	149	126	17
3579	0.612128	535	420	−81	5149	0.51005	203	232	−37
3919	0.611429	428	246	26	5180	0.508197	186	200	−20
5055	0.611111	440	266	14	299	0.507042	144	118	22
5168	0.61	158	93	8	5158	0.506329	120	71	46
539	0.609	162	100	4	5176	0.505208	194	218	−28
342	0.608	110	15	56	397	0.505051	150	131	16
511	0.608	178	127	−12	614	0.505017	151	133	15
784	0.607	193	152	−27	622	0.504983	152	135	14
564	0.605	182	135	−16	512	0.504615	164	159	2
201	0.604	186	142	−20	5173	0.50358	211	253	−45
542	0.589905	187	151	−21	639	0.503356	150	132	16
492	0.58885	169	121	−3	50	0.503165	159	150	7
228	0.586319	180	141	−14	116	0.502982	253	337	−87
2365	0.584081	521	438	−67	80	0.502092	120	73	46
3254	0.58408	587	551	−133	3288	0.502092	240	312	−74
206	0.583178	624	616	−170	454	0.502075	121	75	45
1571	0.582915	464	342	−10	419	0.501742	144	121	22
3591	0.582851	503	409	−49	621	0.50165	152	137	14
1593	0.582512	473	358	−19	203	0.501449	173	179	−7
59	0.582353	99	4	67	3291	0.501006	249	331	−83
64	0.582353	99	4	67	86	0.5	154	142	12
86	0.582278	276	20	178	118	0.5	100	34	66

SA, bits number in both similar natural compounds and VXG; SB, bits number in the similar natural compounds but not in VXG; SC, bits number in VXG but not in the similar natural compounds.