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- W4327680938 abstract "Abstract Carbonic anhydrase is an attractive drug target for the treatment of many diseases. This paper examines the ability of end-state MM/GBSA methods to rank inhibitors of carbonic anhydrase in terms of their binding affinities. The MM/GBSA binding energies were evaluated using different atomic charge schemes (Mulliken, ESP and NPA) at different levels of theories, including Hartree–Fock, B3LYP-D3(BJ), and M06-2X with the 6–31G(d,p) basis set. For a large test set of 32 diverse inhibitors, the use of B3LYP-D3(BJ) ESP atomic charges yielded the strongest correlation with experiment (R 2 = 0.77). The use of the recently enhanced Autodock Vina and zinc optimised AD4 Zn force field also predicted ligand binding affinities with moderately strong correlation (R 2 = 0.64) at significantly lower computational cost. However, the docked poses deviate significantly from crystal structures. Overall, this study demonstrates the applicability of docking to estimate ligand binding affinities for a diverse range of CA inhibitors, and indicates that more theoretically robust MM/GBSA simulations show promise for improving the accuracy of predicted binding affinities, as long as a validated set of parameters is used. Graphical abstract" @default.
- W4327680938 created "2023-03-18" @default.
- W4327680938 creator A5026120277 @default.
- W4327680938 creator A5069059768 @default.
- W4327680938 date "2023-03-17" @default.
- W4327680938 modified "2023-10-13" @default.
- W4327680938 title "MM/GBSA prediction of relative binding affinities of carbonic anhydrase inhibitors: effect of atomic charges and comparison with Autodock4Zn" @default.
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