Binding Free Energy Calculations for Bromodomain Ligands: A Binding Affinity Tool-Based Approach

We have calculated the free absolute binding affinities for seven ligands that form a stable complex with the Plasmodium vivax binding domain 1 using a freely accessible binding affinity tool (BAT) (Heinzelmann and Gilson, Scientific reports, 11.1, 2021, 1116). The protein under review belongs to the class of bromodomains, which are crucial in the epigenetic regulation in the plasmodium malaria pathogen. The BAT approach involves the attachment of conformational restraints on protein and ligand, alchemically decoupling the ligand within the binding pocket, recoupling it in the bulk solvent, and subsequently releasing the restraints to the separated protein and ligand. We find a structural and a methodological aspect to be crucial to achieve an accuracy in the binding energies of 0.6 kcal/mol. Upon ligand binding, a loop region of the protein next to the ligand binding position undergoes a conformational change that amounts to a free energy difference of 1.75 kcal/mol. In addition, the procedure of determining the ligand atomic charges has a surprisingly large effect on the accuracy of the binding energies.