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. 2020 Jun 1:1–13. doi: 10.1080/07391102.2020.1768149

Table 2.

Energetic components of the binding free energy for SARS-CoV-2-inhibitors complexes calculated using MM-PBSA (kcal/mol). Standard errors of the mean (SEM) are provided in parentheses.

Components α-ketoamide Z31792168 Lopinavir (Wang, 2020) Darunavir (Sang et al., 2020)
ΔEvdW −61.63 (0.10) −31.61 (0.06) −20.09 (0.63) −41.32
ΔEelec −35.23 (0.13) −13.64 (0.09) −52.46 (0.33) −5.80
ΔGpol 62.94 (0.13) 27.08 (0.09) 46.58 (0.56) 29.01
ΔGnp −5.31 (0.00) −2.99 (0.00) −4.59 (0.02) −4.75
ΔGsolva 57.63 (0.13) 24.09 (0.09) 41.99 (0.56) 24.26
ΔGpol + elecb 27.71 (0.18) 13.44 (0.13) −5.88 (0.65) 23.21
ΔEMMc −96.86 (0.16) −45.25 (0.11) −30.56 (0.71) −47.12
-TΔSd 30.18 (0.81) 17.92 (0.88) −23.93 (0.01) NA
ΔGTotale −39.23 (0.11) −21.16 (0.01) −30.56 −22.86
ΔGBindsim −9.05 (0.82) −3.25 (0.88) −6.63 (0.28) NA
IC50Exp 0.67 ± 0.18 μM NA NA NA
a

ΔGsolv = ΔGnp + ΔGpol;

b

ΔGpol + elec = ΔEelec + ΔGpol;

c

ΔEMM = ΔEvdW + ΔEelec;

d

ΔS = configuration entropy;

e

ΔG = EvdW + ΔEelec + ΔGnp + ΔGpol, ΔGBind sim = EvdW + ΔEelec + ΔGnp + ΔGpol - (TΔS).