Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CLpro targeting repurposed drug candidates

Chitranshi, Nitin; Gupta, Vivek K.; Rajput, Rashi; Godinez, Angela; Pushpitha, Kanishka; Shen, Ting; Mirzaei, Mehdi; You, Yuyi; Basavarajappa, Devaraj; Gupta, Veer; Graham, Stuart L.

doi:10.1186/s12967-020-02448-z

Table 1 Dataset of 20 repurposed drugs and reference ligand (O6K) corresponding energies obtained from the docking test performed using AutoDock 4.2 program

From: Evolving geographic diversity in SARS-CoV2 and in silico analysis of replicating enzyme 3CL^pro targeting repurposed drug candidates

S. no	C. name	BE^e (kcal/mol)	Ki (µM)	IME^e (kcal/mol)	V_dw-H_b-D_s (kcal/mol)	E^e (kcal/mol)	IE^e (kcal/mol)	TFE^e (kcal/mol)	USE	RMSD (Å)
1	O6K	− 6.45	18.72	− 10.33	− 10.36	+ 0.03	− 2.10	+ 3.88	− 2.10	5.59
1	7, DHF	− 6.24	26.49	− 7.14	− 6.83	− 0.31	− 1.45	+ 0.89	− 1.45	32.85
2	Apigenin	− 7.52	3.05	− 8.75	− 8.52	− 0.20	+ 9.72	+ 1.19	+ 9.72	33.64
3	Luteolin	− 5.59	80.53	− 7.08	− 6.78	− 0.29	− 1.84	+ 1.49	− 184	33.26
4	Quercetin	− 6.16	30.49	− 7.95	− 7.56	− 0.39	− 1.96	+ 1.79	− 1.96	32.79
5	Amentoflavone	− 8.49	0.59	− 11.18	− 10.97	− 0.21	− 3.34	+ 2.68	− 3.34	35.22
6	Bilobetin	− 8.29	0.83	− 10.98	− 10.68	− 0.30	− 4.30	+ 2.68	− 4.30	35.32
7	Ginkgetin	− 8.14	1.09	− 10.82	− 10.52	− 0.30	− 3.51	+ 2.68	− 3.51	34.77
8	Chloroquine	− 4.95	233.3	− 7.34	− 6.96	− 0.38	− 1.34	+ 2.39	− 1.34	30.78
9	Hy-chloroquine	− 5.77	58.47	− 8.76	− 8.53	− 0.23	− 0.68	+ 2.98	− 0.68	30.56
10	Artemisinin	− 6.40	20.22	− 6.70	− 6.50	− 0.20	+ 0.06	+ 0.30	+ 0.06	31.94
11	Remdesivir	− 6.40	28.28	− 11.47	− 11.55	+ 0.07	− 4.52	+ 5.07	− 4.52	31.05
12	Darunavir	− 7.16	5.64	− 11.34	− 11.26	− 0.08	− 3.75	+ 4.18	− 375	33.98
13	Lopinavir	− 6.98	7.68	− 11.75	− 11.57	− 0.18	− 4.92	+ 4.77	− 4.92	29.98
14	Galidesivir	− 4.69	362.43	− 6.48	− 5.79	− 0.70	− 2.02	+ 1.79	− 2.02	32.04
15	Favipiravir	− 4.15	905.42	− 4.45	− 4.31	− 0.14	− 0.09	+ 0.30	− 0.09	32.27
16	Ritonavir	− 7.45	3.49	− 13.11	− 13.15	+ 0.03	− 3.46	+ 5.67	− 5.67	28.61
17	Umifenovir	− 5.71	65.42	− 8.39	− 8.13	− 0.26	− 1.81	+ 2.68	− 1.81	31.86
18	Vitamin C	− 4.22	805.2	− 6.01	− 5.72	− 0.29	− 2.03	+ 17.79	− 2.03	29.14
19	Vitamin D	− 7.75	2.08	− 9.84	− 9.78	− 0.06	− 1.75	+ 2.09	− 1.75	33.21
20	Vitamin E	− 7.59	2.75	− 11.46	− 11.40	− 0.06	− 1.57	+ 3.88	− 1.57	25.17

BE^e estimated binding free energy in kcal mol⁻¹; Ki inhibitory constant in micro-molar; IME^e final Intermolecular energy in kcal mol⁻¹; V_dw–H_b–D_s Van der waals-hydrogen bond-desolvation energy component of binding free energy in kcal mol⁻¹; E^e electrostatic energy in kcal mol⁻¹; IE^e final total internal energy in kcal mol⁻¹; TFE^e torsional free energy in kcal mol⁻¹; USE unbound system’s energy; RMSD root mean square deviation (Å)

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