A comprehensive review on promising anti-viral therapeutic candidates identified against main protease from SARS-CoV-2 through various computational methods

Singh, Ekampreet; Khan, Rameez Jabeer; Jha, Rajat Kumar; Amera, Gizachew Muluneh; Jain, Monika; Singh, Rashmi Prabha; Muthukumaran, Jayaraman; Singh, Amit Kumar

doi:10.1186/s43141-020-00085-z

Journal of Genetic Engineering and Biotechnology

Table 1 Existing promising and potential molecules against 3CLpro from SARS CoV-2

From: A comprehensive review on promising anti-viral therapeutic candidates identified against main protease from SARS-CoV-2 through various computational methods

S/No	PubChem CID	Binding free energy (kcal/mol)	Tools used	Interacting residues	Refs
1	5,7,3′,4′-Tetrahydroxy-2′-(3,3-dimethylallyl) isoflavone(11610052)	− 29.57	Molecular operating environment (MOE)	Thr25, Thr26, Leu26, His41, Val42, Ser46, Met49, Tyr54, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, Leu167, Pro168, Asp187, Arg188, Gln189, Thr190, Ala191, Gln192	[42]
2	Cyanidin 3-glucoside(197081)	− 8.4	Autodock Vina	Glu166, Asn142, His163, Gln189, Asp187, Thr26, Met49, Gly143, His164, Gln189, Cys145	[43]
3	Baicalin(64982)	− 8.1	Autodock Vina	Gly143, Leu141, Gln189, Met165, Asn142, Glu166, Pro168	[43]
4	Glabridin(124052)	− 8.1	Autodock Vina	Leu141, Glu166, Met49, His41, Met165	[43]
5	Quercetin 3-vicianoside(44259139)	− 8.3	Autodock Vina	His163, Glu166, Ser144, Leu114, Gly143, Thr26, Arg188, Asp187, Met165, His164, Gln189, His41, Thr25, Asn142, Phe140, Cys145	[44]
6	Myricitrin(5281673)	− 8.9	Autodock Vina	Tyr54, Asp187, Arg188, Leu141, Phe140, His172, Glu166, Ser144, His164, His163, Leu37, Asn142, Gly143, Thr26, Cys145, Met165, Met49, His41	[45]
7	Oolonghomobisflavan-A(14520989)	− 75.5	CDOCKER	Thr25, Asn142, His163, Glu166, Arg188, His164, Gly143, Met165, His41, Phe140, Leu141, His172, Ser144, Thr24, Cys145, Leu27, Met49, Asp187, Gln189, Gln192, Val186, Thr190, Pro168, Leu167	[46]
8	Birinapant(49836020)	− 8.1	Glide Schrodinger Suite	Thr25, Thr26, Leu26, His41, Val42, Ser46, Met49, Tyr54, Leu141, Asn142, Gly143, Ser144, Cys145, His163, His164, Met165, Glu166, Leu167, Pro168, Asp187, Arg188, Gln189, Thr190, Ala191, Gln192	[47]
9	Carfilzomib(11556711)	− 8.6	Glide Schrodinger Suite	Cys145, His164, Glu166, Gln192, Asn142, Gln189, His41	[48]
10	6-Oxoisoiguesterin(21575473)	− 9.1	Autodock Vina	Arg189, Met49, Met165, Cys145	[49]
11	22-Hydroxyhopan-3-one(21582894)	− 8.6	Autodock Vina	Arg189, Met49, Met165, Cys145	[49]
12	Crocin(5281233)	− 8.2	Autodock 1.5.4 tools	Thr135, Asn133, Thr199, Lys137, Lys5, Phe3, Arg4, Arg131, Asp197	[50]
13	Carnosol(442009)	− 8.2	Autodock 1.5.6 tools	Cys145, His164, Glu166, Gln189, Met165, Arg188, Cys44, Met49, His41, Thr45, Thr25, Thr26, Leu27, Gly143, Ser46, Asn142	[51]
14	Rosmanol(13966122)	− 7.9	Autodock 1.5.6 tools	Cys145, Gly143, Thr25, His41, Met49, Asn142, His143, Glu166, Leu141, Ser144, Met165, Phe140	[51]
15	Withanone(21679027)	− 4.4	Glide Schrodinger Suite	Thr24, Thr25, Thr26, Leu27, His41, Met49, Tyr54, Asn142, Gly143, His164, Met165, Glu166, Arg188, Asp188, Gln189, Cys145	[52]
16	Nelfinavir(64143)	− 7	Autodock Vina	His163, Gln189	[53]
17	CMPD23B	− 118.6	Igemdock	Arg40, Tyr54, Cys85, Phe181, Arg188, Arg40, Tyr54, Glu55, Met82, Asn84	[54]
18	Amodiaquine(2165)	− 7.4	Glide Schrodinger Suite	Leu141, ARG187, Glu166, His41	[55]
19	Remdesivir(121304016)	− 7.9	Glide Schrodinger Suite	Gln191, Ala192, Thr190, Gln189, Arg188, Asp187, Leu141, Asn142, Gly143, Ser144, Cys145, His164, Met165, Glu166, Leu167, Pro168, Thr26, Leu27, Met49, Tyr54, His41	[56]
20	Ribavirin(37542)	2	Glide Schrodinger Suite	Leu4, Gln189, Met49, Val3, Ser46, Cys145, Thr25, Thr24, Thr45	[57]
21	Telbivudine(159269)	2	Glide Schrodinger Suite	Thr190, Leu50, Glu47, Ser46, Met49, Val3, Gln189	[57]
22	Lopinavir(92727)	− 10.8	MMPBSA.py module of AMBER16	Met49, Met165, Pro168, Gln189, His41, Ala46, Met49, Glu166, Leu167, Leu187, Gln189, Ala191, Ala193	[58]
23	Ritonavir(392622)	− 14.9	MMPBSA.py module of AMBER16	Leu27, His41, Met49, Phe140, Asn142, Gly143, His164, Met165, Glu166, Asn142, Gly143, Ser144, Cys145, Met165, Glu166, Asp187, Gln189	[58]
24	Saquinavir(441243)	− 9.8	Glide Schrodinger Suite	His41, Cys44, Tyr54, Met49, His172, Glu166, Met165, His164, His163, Phe140, Leu141, Asn142, Gly143, Ser144, Cys145, Thr25, Thr26, Leu27, Asp187, Arg188, Gln189, Thr190, Ala191	[56]
25	Simeprevir(24873435)	− 10	Autodock Vina	Glu166, Met165, Gln189, Phe140, Cys145, Asn142, Leu27, His41, Ser46	[59]
26	Paritaprevir(45110509)	− 9.8	PyRx v0.8(Autodock Vina)	Ser46, Met49, Leu50, Cys145, Pro168, Thr24, Thr25, Leu27, His41, Cys44, Thr45, Glu47, Phe140, Gly143, Glu166, Gln189	[60]
27	Hypericin(3663)	− 10.7	CDOCKER	Gly143, Glu166, Asn142, Glu166, His41, Cys145, Asn142, Glu166, Gln189, Met165	[43]
28	Eravacycline(54726192)	− 8.8	Glide Schrodinger Suite	Met49, Gln189, Tyr190, Gln192, Glu166, Met165, Asn142	[48]
29	Valrubicin(454216)	− 9.2	Glide Schrodinger Suite	His41, His164, Asn142, Met165, Glu166, Gln189	[48]
30	Viomycin(135398671)	− 77.2	CDOCKER	Glu166, Phe140, Asn142, His164, Ser144, Gly143, His41, Met49, Met145, Gln189, Arg188, Asp187, His163, Cys145	[61]
31	Elbasvir(71661251)	− 9.9	Glide Schrodinger Suite	Thr25, Thr26, His41, Met49, Met165, Gln189, Thr190.	[48]
32	Fluvastatin(446155)	− 7.7	Autodock Vina	Glu166, His163.	[62]
33	Methisazone(667492)	− 6.8	Glide Schrodinger Suite	His41, His49, Tyr54, Cys145, Met165, Gln166, Leu167, Pro168, Asp187, Arg188, Gln189, Thr190, Gln192.	[63]

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