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. 2021 Nov 29;11(61):38495–38504. doi: 10.1039/d1ra06534c

The calculated results of 41 compounds to SARS-CoV-2 Mpro using molecular docking and FPL simulations.

No. Code PubChem ID Name ΔGDock F Max W ΔGPreFPLa ICPre50 rangeb ΔGEXPc
1 T82 28523 Tomatine −8.9 721.5 ± 38.2 108.6 ± 5.7 −11.59 Nanomolar
2 T17 159331 Thevetine −7.7 635.7 ± 34.6 86.3 ± 2.3 −10.35 High-nanomolar
3 T56 10175330 Tribuloside −7.9 701.2 ± 45.1 80.5 ± 4.2 −10.02 High-nanomolar
4 T117 5282160 Quercimeritrin −7.7 634.7 ± 35.0 75.4 ± 4.1 −9.73 Sub-micromolar
5 T25 31310 Scillaren −8.3 599.2 ± 44.4 72.1 ± 3.9 −9.55 Sub-micromolar
6 T61 73568 Corilagin −8.1 700.2 ± 40.5 72.2 ± 3.8 −9.55 Sub-micromolar
7 T44 6325292 Gomphrenin III −7.6 597.7 ± 27.5 65.6 ± 1.7 −9.19 Sub-micromolar
8 T26 222154 Proscillaridin −8.2 578.7 ± 28.1 63.0 ± 4.3 −9.04 Sub-micromolar
9 T33 185586 Melianotriol −7.7 686.1 ± 36.9 61.8 ± 4.1 −8.98 Sub-micromolar
10 T52 441840 Adynerin −8.1 542.3 ± 24.9 61.1 ± 2.3 −8.93 Sub-micromolar
11 T24 5317157 Equisetrin −7.9 557.0 ± 29.2 59.1 ± 4.7 −8.82 Sub-micromolar
12 T3 5281627 Hinokiflavone −8.6 574.4 ± 41.0 57.7 ± 3.8 −8.74 Sub-micromolar
13 T202 441295 Ginkgolide C −7.9 639.4 ± 23.8 55.3 ± 2.4 −8.61 Sub-micromolar
14 T55 5316647 Cynarine −7.7 488.7 ± 33.5 55.3 ± 6.1 −8.61 Sub-micromolar
15 T126 5280805 Rutin −7.6 539.7 ± 39.7 55.2 ± 4.4 −8.60 Sub-micromolar
16 T34 185617 Scutellarin −7.7 543.9 ± 34.8 55.0 ± 4.7 −8.59 Sub-micromolar
17 T19 10028469 Melianodiol −7.8 563.8 ± 23.4 54.8 ± 2.9 −8.58 Sub-micromolar
18 T13 5281600 Amentoflavone −8.6 508.0 ± 35.7 53.4 ± 3.0 −8.50 Micromolar
19 T121 32024 Alpha-antiarin −7.9 558.6 ± 28.0 53.2 ± 3.4 −8.49 Micromolar
20 T27 11013 Rhodexin A −7.8 509.3 ± 37.7 51.6 ± 3.3 −8.40 Micromolar
21 T115 15515703 Jujubogenin −7.7 603.8 ± 24.0 51.3 ± 2.5 −8.39 Micromolar
22 T182 3032482 Ecdysterone −7.7 544.1 ± 37.3 50.3 ± 4.0 −8.33 Micromolar
23 T14 65071 Limonin −8.9 540.0 ± 13.0 49.9 ± 1.5 −8.31 Micromolar
24 W22 3000706 Valinomycin −7.6 493.2 ± 35.4 47.0 ± 3.1 −8.14 Micromolar
25 T179 73432 Brusatol −7.7 483.7 ± 34.3 43.6 ± 3.4 −7.95 Micromolar
26 T58 10494 Oleanolic acid −7.6 495.0 ± 39.1 42.2 ± 1.7 −7.87 Micromolar
27 T65 131900 Peimine −8.1 460.9 ± 29.4 42.0 ± 2.1 −7.86 Micromolar
28 T35 3083631 Chlorogenin −7.8 486.4 ± 42.1 42.0 ± 3.5 −7.86 Micromolar
29 T119 65064 (−)-Epigallocatechin 3-gallate (EGCG) −7.5 517.5 ± 24.1 41.9 ± 3.4 −7.86 Micromolar −8.30
30 T23 72307 Sesamin −7.7 514.2 ± 34.5 39.8 ± 3.0 −7.74 Micromolar
31 T107 4970 Protopine −8.1 546.0 ± 35.2 37.5 ± 2.4 −7.61 Micromolar
32 T20 167691 Peiminine −8.1 441.9 ± 34.8 36.9 ± 4.2 −7.58 Micromolar
33 T7 5270604 Taraxasterol −7.7 461.9 ± 32.3 36.9 ± 2.3 −7.58 Micromolar
34 T50 119041 Obacunone −7.8 440.2 ± 19.1 35.9 ± 1.9 −7.52 Micromolar
35 T180 98570 Allocryptopine −8.4 432.8 ± 22.7 34.6 ± 1.8 −7.45 Micromolar
36 T30 470259 Arnidiol −7.6 407.9 ± 31.5 34.4 ± 1.4 −7.44 Micromolar
37 T4 15560423 Kulactone −7.6 434.8 ± 16.9 34.3 ± 2.6 −7.43 Micromolar
38 T8 91453 Hecogenin −7.7 422.4 ± 26.1 33.9 ± 2.8 −7.41 Micromolar
39 T102 442814 Pachyrrhizone −7.7 449.3 ± 28.9 32.9 ± 2.8 −7.35 Micromolar
40 T1 31342 Salasodine −7.7 376.8 ± 29.2 31.5 ± 2.7 −7.28 Micromolar
41 T11 5154 Sanguinarine −8.2 424.6 ± 30.5 29.1 ± 2.6 −7.14 Micromolar
a

The predicted binding free energy ΔGPreFPL = −0.056 × W − 5.512 kcal mol−1.58

b

The predicted ICPre50 was calculated via formula Inline graphic using hypothesis that IC50 equals inhibition constant ki.

c

The experimental affinity ΔGEXP was approximately calculated via the IC50 value (ref. 70) with an assumption that the IC50 equal to ki (inhibition constant). The calculated error is the standard error of the average (SE). The unit of force and energy in pN and kcal mol−1, respectively.