Lead generation of UPPS inhibitors targeting MRSA: Using 3D-QSAR pharmacophore modeling, virtual screening, molecular docking, and molecular dynamic simulations

Table 8 The average binding free energy (kcal/mol) of protein–ligand complexes during the 100 ns MD run using MM-GBSA and MM-PBSA methods

Complex	ΔE_vdW	ΔE_elec	ΔE_EGB	ΔE_ESURF	ΔG_gas	ΔG_solv	ΔG_bind
MM-GBSA
5KH5-6TC	− 67.364 ± 0.000	− 5.128 ± 0.000	33.456 ± 0.000	− 8.0885 ± 0.000	− 72.493 ± 0.000	25.367 ± 0.000	− 47.125 ± 0.000
5KH5-Top hit 1	− 58.883 ± 0.000	− 3.782 ± 0.000	26.950 ± 0.000	− 6.940 ± 0.000	− 62.666 ± 0.000	20.010 ± 0.000	− 42.656 ± 0.000
5KH5-Top hit 2	− 65.679 ± 0.937	− 17.530 ± 3.473	41.416 ± 2.894	− 7.724 ± 0.081	− 83.210 ± 3.420	33.692 ± 2.888	− 49.518 ± 1.013
5KH5-Top hit 3	− 57.009 ± 1.301	− 33.640 ± 2.566	53.189 ± 1.918	− 7.373 ± 0.098	− 90.649 ± 2.521	45.815 ± 1.925	− 44.833 ± 0.932
5KH5-Top hit 4	− 63.784 ± 2.687	− 19.368 ± 2.557	38.279 ± 2.054	− 7.368 ± 0.206	− 83.152 ± 4.578	30.911 ± 1.898	− 52.240 ± 2.928
5KH5-Top hit 5	− 61.684 ± 0.933	− 2.815 ± 0.382	23.045 ± 0.574	− 6.949 ± 0.567	− 64.500 ± 1.064	16.095 ± 0.573	− 48.404 ± 1.195

Complex	ΔE_vdW	ΔE_elec	ΔE_EPB	ΔE_ENPOLAR	ΔG_gas	ΔG_solv	ΔG_bind
MM-PBSA
5KH5-6TC	− 67.364 ± 0.000	− 5.128 ± 0.000	35.881 ± 0.000	− 46.028 ± 0.000	− 72.493 ± 0.000	71.519 ± 0.000	− 0.973 ± 0.000
5KH5-Top hit 1	− 58.883 ± 0.000	− 3.782 ± 0.000	32.393 ± 0.000	− 40.349 ± 0.000	− 62.666 ± 0.000	64.686 ± 0.000	2.020 ± 0.000
5KH5-Top hit 2	− 65.679 ± 0.937	− 17.530 ± 3.473	50.633 ± 2.421	− 43.790 ± 0.260	− 83.210 ± 3.420	83.267 ± 2.535	0.057 ± 2.058
5KH5-Top hit 3	− 57.009 ± 1.301	− 33.640 ± 2.566	61.030 ± 2.665	− 39.322 ± 0.477	− 90.649 ± 2.521	88.946 ± 2.806	− 1.702 ± 1.379
5KH5-Top hit 4	− 63.784 ± 2.687	− 19.368 ± 2.557	53.131 ± 3.455	− 41.448 ± 0.972	− 83.152 ± 4.578	85.068 ± 4.289	1.915 ± 1.265
5KH5-Top hit 5	− 61.684 ± 0.933	− 2.815 ± 0.382	30.604 ± 1.113	− 39.894 ± 0.262	− 64.500 ± 1.064	61.418 ± 1.288	− 3.081 ± 1.789

ISSN: 2661-801X