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. 2021 Mar 30;133:104359. doi: 10.1016/j.compbiomed.2021.104359

Table 4.

Virtual screening (obtained by AutoDock VINA), molecular docking (obtained by AutoDock 4.2.6) results and ROC probability of compounds binding to nucleocapsid protein. Details see Table 3.

Dataset ROC probability VINA defined LBE AutoDock defined LBE Interacting amino acid residues
FDA-approved drugs:
paritaprevir 0.999 −11.30 ± 0.06 −13.50 ± 0.40 Gly170, Ala173, Leu161, Gln163, Thr165, Pro168, Lys169, Phe171, Tyr172
trypan blue 0.999 −10.80 ± 0.05 −12.17 ± 0.07 Gln70, Val72, Ile74, Leu161, Pro162, Gln163, Thr165, Leu167
simeprevir 0.999 −10.60 ± 0.1 −11.58 ± 0.50 Glu62, Leu161, Gln163, Thr165, Leu167, Pro168, Lys169, Phe171, Ala173
dihydroergotamine 0.999 −10.50 ± 0.1 −11.46 ± 0.20 Ala173, Leu161, Pro162, Gln163, Leu167, Phe171
conivaptan 0.995 −10.90 ± 0.06 −10.795 ± 0.3 Pro73, Ile74, Asn75, Thr76, Ser78, Pro80, Gln83
ergotamine 0.993 −10.50 ± 0.2 −10.61 ± 0.50 Leu161, Pro162, Thr165, Leu167, Phe171
venetoclax 0.995 −10.60 ± 0.1 −10.50 ± 0.60 Leu167, Pro162, Gln163, Thr165, Thr166, Tyr17, Ala173
idarubicin 0.990 −10.10 ± 0.1 −8.35 ± 0.30 Gly69, Ala134, Phe66, Arg68, Tyr123, Trp132, Val133, Glu136
ivermectin 0.999 −10.60 ± 0.1 −8.33 ± 0.40 Arg89, Gln58, Lys61, Arg88, Thr91, Asp128, Gly129, Ile130
nystatin
 0.999
 −10.30 ± 0.1
 −7.45 ± 0.60
 Thr76, Ile74, Gln160, Pro162, Gln163, Tyr172, Ala173
Natural compounds from literature:
ilexsaponinB1 0.999 −9.40 ± 0.20 −9.55 ± 0.30 Asn75, Thr135, Pro73, Pro163, Gln163, Leu167
ilexsaponinB2 1.000 −9.20 ± 0.10 −9.50 ± 0.50 Asn75, Pro162, Gln163, Gly164, Leu167, Tyr172, Ala173
procyanidin 0.999 −8.90 ± 0.10 −8.47 ± 0.60 Gln163, Leu161, Gly164, Leu167, Phe171, Tyr172, Ala173
crinine 0.999 −8.80 ± 0.10 −7.74 ± 0.30 His59, Thr54, Asn77, Val158, Ser78
strictinin 0.999 −9.40 ± 0.10 −7.31 ± 0.30 Asn75, Thr165, Gln163, Gly164, Leu167, Tyr172, Ala173
ilexsaponinB3 1.000 −8.60 ± 0.10 −6.54 ± 0.60 Gly164, Asn75, Ile74, Pro73, Thr76, Ser78, Pro80, Gln83
rutin 0.999 −9.10 ± 0.10 −6.34 ± 0.10 Gly170, Pro162, Gln163, Gly164, Leu167, Tyr172, Ala173
forsythiaside 0.999 −9.20 ± 0.10 −4.56 ± 0.20 Tyr123, Leu113, Gly114, Ala119, Gly120, Pro122
punicalagin 1.000 −9.50 ± 0.10 −4.54 ± 0.30 Leu167, Gln163, Gly164, Thr165, Thr166, Tyr172, Ala173
tirucallinA
 1.000
 −9.60 ± 0.10
 −4.44 ± 0.60
 Leu167, Gln163, Gly164, Thr165, Thr166, Tyr172, Ala173
Natural compounds from ZINC database:
ZINC000027215482; (1R,4S,7S)-4-benzyl-9-[(1R,4S,7S)-4-benzyl-3,6-dioxo-2,5,16-triazatetracyclo [7.7.0.02,⁷.01⁰,1⁵]hexadeca-10,12,14-trien-9-yl]-2,5,16-triazatetracyclo [7.7.0.02,⁷.01⁰,1⁵]hexadeca-10 (15),11,13-triene-3,6-dione 1.000 −10.47 ± 0.12 −10.89 ± 0.03 Thr76, Ser78, Ser79, Pro80, Leu161, Pro162, Gln163, Gly164, Thr165, Leu167, Phe171, Tyr172, Ala173
ZINC000252515584; (1R,3S,6S,7E,13S,16R,17R,21S,22S)-28-hydroxy-17-[(2R,4R,5S,6R)-4-hydroxy-5-[(2S,4R,5R,6R)-5-hydroxy-4-(2-methoxy-6-methylbenzoyl)oxy-6-methyloxan-2-yl]oxy-6-methyloxan-2-yl]oxy-3,22-dimethyl-23,26-dioxo-24,27-dioxapentacyclo [23.2.1.01,6.013,22.016,21]octacosa-4,7,14,25 (28)-tetraene-4-carboxylic acid 1.000 −11.00 ± 0.10 −10.87 ± 0.05 Asn75, Thr76, Gln163, Gly164, Thr166, Leu167, Tyr172
ZINC000004149988; 2-(2,2,2-trifluoroacetyl)-N-[(1S,2S,5S,6S,9S,16S)-5,9,16-trimethyl-4-oxo-3-oxa-12-thia-14-azatetracyclo [7.7.0.02,⁶.011,1⁵]hexadeca-11 (15),13-dien-13-yl]-1,2,3,4-tetrahydroisoquinoline-7-sulfonamide 0.999 −10.20 ± 0.10 −10.30 ± 0.05 Gly69, Gln70, Gly71, Val72, Pro73, Ile74, Asn75, Thr76, Pro80, Gln83, Thr135, Pro162, Gln163, Gly164
ZINC000004097766; Albanol A 0.999 −10.33 ± 0.06 −10.16 ± 0.05 Ile74, Asn75, Ser78, Gln83, Leu161, Pro162, Thr165, Leu167, Phe171, Tyr172, Ala173
ZINC000004098521; Hinokiflavone 0.995 −10.57 ± 0.06 −9.84 ± 0.05 Gly69, Gln70, Val72, Asn75, Thr76, Ser78, Pro80, Gln83, Thr135, Pro162, Leu167, Phe171, Tyr172, Ala173
ZINC000005433649; (3R,3aS,6S,6aR)-6-[(4-{[1,1′-biphenyl]-4-yl}pyrimidin-2-yl)amino]-hexahydrofuro [3,2-b]furan-3-yl N-(naphthalen-1-yl)carbamate 0.999 −10.88 ± 0.08 −9.39 ± 0.07 Val72, Pro73, Ile74, Asn75, Thr76, Gln83, Thr135, Leu161, Gln163, Thr165, Leu167, Ala173
ZINC000253504770; 4-(7-)[5-()5-[(4,5-dihydroxy-6-methyloxan-2-yl)oxy]-4-hydroxy-6-methyloxan-2-yl)oxy)-4-hydroxy-6-methyloxan-2-yl]oxy)-3a,11-dihydroxy-9a,11a-dimethyl-hexadecahydro-1H-cyclopenta [a]phenanthren-1-yl)-2,5-dihydrofuran-2-one 0.999 −10.37 ± 0.12 −9.17 ± 0.06 Gly69, Val72, Ile74, Asn75, Thr76, Gln83, Thr135, Leu159, Leu161, Pro162, Leu167
ZINC000015675926; 5-[(6S)-5-(4-fluorobenzoyl)-1H,4H,5H,6H,7H-imidazo [4,5-c]pyridin-6-yl]-3-(naphthalen-2-yl)-1,2,4-oxadiazole 0.994 −10.95 ± 0.05 −9.06 ± 0.06 Asn75, Thr76, Ser78, Gln83, Leu161, Gln163, Thr165, Leu167, Tyr172, Ala173
ZINC000253504766; 4-(7-)[5-()5-[(4,5-dihydroxy-6-methyloxan-2-yl)oxy]-4-hydroxy-6-methyloxan-2-yl)oxy)-4-hydroxy-6-methyloxan-2-yl]oxy)-3a,11-dihydroxy-9a,11a-dimethyl-hexadecahydro-1H-cyclopenta [a]phenanthren-1-yl)-2,5-dihydrofuran-2-one 0.999 −10.80 ± 0.10 −8.62 ± 0.04 Gln70, Val72, Ile74, Asn75, Thr76, Pro80, Gln83, Thr135, Pro162, Gln163, Gly164, Thr165, Leu167, Tyr172, Ala173
ZINC000005434062; (3R,3aS,6S,6aR)-6-{[4-(3-fluorophenyl)pyrimidin-2-yl]amino}-hexahydrofuro [3,2-b]furan-3-yl N-(naphthalen-1-yl)carbamate 0.998 −10.67 ± 0.12 −8.39 ± 0.05 Ile74, Thr76, Asn77, Ile157, Gln160, Pro162, Gln163, Thr165, Ala173