Table 2.
MM/GBSA derived binding free energies of CsrA-inhibitor complexes calculated from the MD simulations using different GB Models.
| Compounds | ΔG MM-GBSA a (igb = 1) | ΔG MM-GBSA a (igb = 2) | ΔG MM-GBSA a (igb = 5) | ΔG MM-GBSA a (igb = 7) | ΔG MM-GBSA a (igb = 8) | IC50 (uM) | ΔGcalc a,b |
|---|---|---|---|---|---|---|---|
| 1 | −19.81 ± 0.24 | −15.74 ± 0.20 | −15.83 ± 0.20 | −14.73 ± 0.18 | −13.66 ± 0.17 | 39 | −6.05 |
| 2 | −13.39 ± 0.26 | −9.87 ± 0.23 | −9.96 ± 0.24 | −7.03 ± 0.20 | −9.52 ± 0.20 | 71 | −5.70 |
| 3 | −21.12 ± 0.12 | −17.51 ± 0.12 | −18.40 ± 0.13 | −12.48 ± 0.12 | −13.80 ± 0.11 | 27 | −6.27 |
| 4 | −30.39 ± 0.18 | −25.20 ± 0.17 | −25.95 ± 0.18 | −21.27 ± 0.17 | −21.23 ± 0.16 | 11 | −6.80 |
| 5 | −16.20 ± 0.12 | −18.07 ± 0.16 | −19. 00 ± 0.17 | −21.27 ± 0.19 | −20.94 ± 0.18 | 24 | −6.34 |
aAll values are given in kcal/mol, and ΔGMM-GBSA values are given as average ± SEM (standard error of the mean). bBinding free energies ΔGcalc were calculated from experimental IC50 using the equation: ΔG calc ≈ RTln IC50, where R is ideal gas constant, T is the temperature in K (300 K is used in this paper)53,54.