Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI)

Abstract

To validate a method for predicting the binding affinities of FabI inhibitors, three implicit solvent methods, MM-PBSA, MM-GBSA, and QM/MM-GBSA were carefully compared using 16 benzimidazole inhibitors in complex with Francisella tularensis FabI. The data suggests that the prediction results are sensitive to radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length, if only one simulation trajectory is used for each ligand. In this case, QM/MM-GBSA using 6 ns MD simulation trajectories together with GB(neck2) , PM3, and the mbondi2 radii set, generate the closest agreement with experimental values (r(2) = 0.88). However, if the three implicit solvent methods are averaged from six 1 ns MD simulations for each ligand (called "multiple independent sampling"), the prediction results are relatively insensitive to all the tested parameters. Moreover, MM/GBSA together with GB(HCT) and mbondi, using 600 frames extracted evenly from six 0.25 ns MD simulations, can also provide accurate prediction to experimental values (r(2) = 0.84). Therefore, the multiple independent sampling method can be more efficient than a single, long simulation method. Since future scaffold expansions may significantly change the benzimidazole's physiochemical properties (charges, etc.) and possibly binding modes, which may affect the sensitivities of various parameters, the relatively insensitive "multiple independent sampling method" may avoid the need of an entirely new validation study. Moreover, due to large fluctuating entropy values, (QM/)MM-P(G)BSA were limited to inhibitors' relative affinity prediction, but not the absolute affinity. The developed protocol will support an ongoing benzimidazole lead optimization program.

Keywords: enoyl acyl reductase (FabI), implicit solvent models; molecular dynamics; quantum mechanics/molecular mechanics; radii sets.

Figure 1

Representative Benzimidazole FabI Inhibitors and Triclosan. ^-

Figure 2

FtFabI: GRL-0056 energy components using MM-PBSA and the bondi radii setting. Black, red, blue, green, cyan and yellow lines indicate the ΔG_vdw, ΔG_GB, ΔG_solvation, ΔG_{electrostatic}, ΔG_nonpolar and ΔG_bind terms respectively. The x axis is the frame number. Each frame is 2.5 ps. The total frame number is 2,400 frames, equal to 6 ns MD simulations.

Figure 3

A. FtFabI: FabI 91 energy components using MM-GBSA, bondi radii and GB^HCT. Black, red, blue, green, cyan and yellow lines indicate the ΔG_vdw, ΔG_GB, ΔG_solvation, ΔG_{electrostatic}, ΔG_nonpolar and ΔG_bind terms respectively. The x axis is the frame number. Each frame is 2.5 ps. The total frame number is 2,400 frames, equal to 6 ns MD simulations. B. FtFabI: FabI 91 energy components using MM-GBSA, bondi radii and GB^Neck2. C. The quantile-quantile plot (Q-Q plot) of the ΔG_GB term in GB^HCT. D. The Q-Q plot of the ΔG_GB term in GB^Neck2. E. The Q-Q plot of the ΔG_bind term in GB^HCT. F. The Q-Q plot of the ΔG_bind term in GB^Neck2.

Figure 3

A. FtFabI: FabI 91 energy components using MM-GBSA, bondi radii and GB^HCT. Black, red, blue, green, cyan and yellow lines indicate the ΔG_vdw, ΔG_GB, ΔG_solvation, ΔG_{electrostatic}, ΔG_nonpolar and ΔG_bind terms respectively. The x axis is the frame number. Each frame is 2.5 ps. The total frame number is 2,400 frames, equal to 6 ns MD simulations. B. FtFabI: FabI 91 energy components using MM-GBSA, bondi radii and GB^Neck2. C. The quantile-quantile plot (Q-Q plot) of the ΔG_GB term in GB^HCT. D. The Q-Q plot of the ΔG_GB term in GB^Neck2. E. The Q-Q plot of the ΔG_bind term in GB^HCT. F. The Q-Q plot of the ΔG_bind term in GB^Neck2.

Figure 4

The FabI 138 inhibitor (pdb code: 3UIC) and other benzimidazole inhibitors (pdb codes: 4J1N, 4J3F, 4J4T) form key intermolecular hydrogen bonds with the FtFabI Tyr156 and the ribose on the nicotinamide ring of the cofactor NADH

Figure 5

A. FtFabI: FabI 91 energy components using QM/MM-GBSA, bondi radii and GB^HCT. Black, red, blue, green, cyan and yellow lines indicate the ΔG_vdw, ΔG_GB, ΔG_solvation, ΔG_SCF (Self Consistent Energy), ΔG_nonpolar and ΔG_bind terms respectively. The x axis is the frame number. Each frame is 2.5 ps. The total frame number is 2,400 frames, equal to 6 ns MD simulations. B. FtFabI: FabI 91 energy components using QM/MM-GBSA, bondi radii and GB^Neck2. One can see from the ΔG_GB term (the red line) and the ΔG_bind term (the yellow line) in GB^Neck2 fluctuates wilder than the one in GB^HCT (Figure 5a). C. The quantile-quantile plot (Q-Q plot) of the ΔG_GB term in GB^HCT. D. The Q-Q plot of the ΔG_GB term in GB^Neck2. E. The Q-Q plot of the ΔG_bind term in GB^HCT. F. The Q-Q plot of the ΔG_bind term in GB^Neck2.

Figure 5

A. FtFabI: FabI 91 energy components using QM/MM-GBSA, bondi radii and GB^HCT. Black, red, blue, green, cyan and yellow lines indicate the ΔG_vdw, ΔG_GB, ΔG_solvation, ΔG_SCF (Self Consistent Energy), ΔG_nonpolar and ΔG_bind terms respectively. The x axis is the frame number. Each frame is 2.5 ps. The total frame number is 2,400 frames, equal to 6 ns MD simulations. B. FtFabI: FabI 91 energy components using QM/MM-GBSA, bondi radii and GB^Neck2. One can see from the ΔG_GB term (the red line) and the ΔG_bind term (the yellow line) in GB^Neck2 fluctuates wilder than the one in GB^HCT (Figure 5a). C. The quantile-quantile plot (Q-Q plot) of the ΔG_GB term in GB^HCT. D. The Q-Q plot of the ΔG_GB term in GB^Neck2. E. The Q-Q plot of the ΔG_bind term in GB^HCT. F. The Q-Q plot of the ΔG_bind term in GB^Neck2.

Figure 6

A. The enthalpy, entropy and binding free energy components (48 frames) in the 6 ns MD simulation of FtFabI: FabI-135 using MM/GBSA, the bondi radii setting and GB^HCT. The upper solid black and dash red line represents instanenous and cumulative average entropy respectively and the lower solid black and dash red line represents instanenous and cumulative average enthalpy. The blue line represents binding free energy. B. The histogram view of the enthalpy, entropy and binding free energy (48 frames) in the 6 ns MD simulation of FtFabI: FabI-135 using MM/GBSA, the bondi radii setting and GB^HCT. C. The histogram view of the enthalpy (2,400 frames) in the 6 ns MD simulation of FtFabI: FabI-135 using MM/GBSA, the bondi radii setting and GB^HCT.

Figure 7

A. The correlation plot between experimental and predicited binding free energy using QM-MM/GBSA, GB^Neck2, mbondi2 & 2,400 frames evenly extracted from 6 ns long MD simulation trajectories (R² = 0.88). B. The correlation plot between experimental and predicited binding free energy using MM/GBSA, GB^HCT, mbondi & 600 frames evenly extracted from six 0.25 ns long MD simulation trajectories (R² = 0.84).