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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]