The application of COVID-19 docking server and Discovery Studio software elucidated the interactions between the 20 lead-likeness compounds (S1, W5, MX17, MX16, W11, M5, XO1, MXO1, SO1, WO1, X4, MX8, M3, S5, SX1, O1, X2, X1, O2, MS1) and the 10 nonstructural and 2 structural proteins (Mpro, PLpro, nsp12 [RdRp with RNA], nsp12 [RdRp without RNA], nsp13 [Helicase ADP site], nsp13 [Helicase NCB site], nsp14 [ExoN], nsp14 [N7-MTase], nsp15 [endoribonuclease], nsp16 [2′-O-MTase], N protein NCB site, E protein [ion channel]). The docking scores were depicted in Table 3, Table 4 . The smaller of docking score, the lower of energy would be required, which means the binding between the compounds and the targets are stronger. There are 9 compounds presenting better bonding ability than other compounds.
Table 3 Docking score between specific ingredients of QFPD and 2019-nCov proteins.
Molecule M3 M5 S1 S5 W11 W5 X1 X2 X4 O1 O2
Main Protease −7.7 −7.3 −6.8 −6.9 −7.2 −7.5 −7.1 −7.9 −7.3 −7.1 −7.4
Papain-like protease −8.7 −8.5 −9.9 −7.7 −8 −8 −8.4 −8.7 −8.2 −8.6 −8.2
RdRp with RNA −8.4 −8.5 −8.5 −8.3 −9.1 −9.1 −8.4 −8.2 −8.2 −8.3 −8.6
RdRp without RNA −6.8 −6.8 −6.9 −6.8 −6.7 −6.9 −7.1 −7.2 −6.5 −7.3 −7.1
Helicase ADP site −6.3 −6.3 −7.3 −6.5 −6 −6 −6.3 −6.5 −6.2 −6.1 −6.5
Helicase NCB site −7.9 −6.9 −7.2 −7.1 −7.2 −7.2 −7.4 −7.5 −7.3 −7.4 −7.4
Nsp14(ExoN) −6.8 −6.6 −6.3 −6.4 −6.9 −6.8 −6.7 −6.9 −6.4 −6.6 −6.9
Nsp14(N7-MTase) −8.8 −8.1 −8.5 −7.5 −8.4 −8.4 −8.3 −8.5 −8 −8.3 −8.5
Nsp15(endoribonuclease) −6.6 −6.3 −6.3 −5.9 −6.2 −6.2 −6.2 −6.3 −6.2 −6.4 −6.4
Nsp16(2′-O-MTase) −7.5 −7.4 −7.5 −7.2 −8.2 −8.2 −7.7 −7.9 −7.7 −7.9 −8.4
N protein NCB site −7.6 −7.5 −7.8 −7.6 −7.6 −7.6 −8 −8 −7.5 −7.6 −7.6
E protein(ion channel) −8.1 −7 −7.8 −6.7 −6.4 −6.4 −7.2 −7.3 −7.2 −7.1 −6.8
M: MXSG, S: SGMH, X: XCH, O: Others.
Table 4 Evaluation of the effect of QFPD on the robustness disturbance of COVID-19 network.
Topology MXSG SGMH XCH WLS Others BXTM YDBF
DTS 25.66 26.71 21.02 17.64 23.16 14.52 22.71
AC −4.63 −5.21 −3.02 −3.49 −5.38 −2.32 −3.78
APL 13.35 13.40 9.96 6.49 10.66 4.59 11.17
CoC −1.44 −1.64 −1.59 −1.30 −1.23 −1.15 −1.25
ClC −6.24 −6.46 −6.45 −6.36 −5.88 −6.46 −6.52
Average connectivity (AC), Connection centrality (CoC), Closeness centrality (ClC): the larger the quotient is, the more stable the network and, the less the influence made by the drug. Disturbance total score (DTS), Average length of shortest path (APL), : the larger the quotient is, the less stable the network and, the larger the influence made by the drug. Negative control formula: BXTM. Positive control formula: YDBF.