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).