AMBER force field implementation of the boronate function to simulate the inhibition of β-lactamases by alkyl and aryl boronic acids

Abstract

Boronic acids are a very appealing class of serine proteases inhibitors whose rational design suffers, in spite of their therapeutic potential, from the lack of boron-related parameters in force fields commonly used for proteins. We introduced bonded, non-bonded and point charges in the MacroModel/Amber force field, as well as GB/SA solvation parameters, to model boronic acids as tetrahedral adducts formed after protease’s serine Oγ coordination. With the aim to check the implemented force field, flexible docking studies were performed on three crystallographic complexes of β-lactamases with boronic acids that output the crystallographic conformation of the complexes as the global minimum energy structure. Although the used approach was basic, nevertheless the resultant force field seems to be efficient and suitable for the structure-based design of new boronic inhibitors of β-lactamases.