In silico prediction of β-lactamase hydrolysis efficiency: Finding the right balance between kinetic and thermodynamic terms

Abstract

International audienceDuring recent decades, an alarming worldwide spread and diversification of β-lactamases has been obsd. in Gram-neg. species, conferring resistance to β-lactam antibiotics. In this context, the prediction of future β-lactamase mutants becomes an essential issue and we have developed a protocol that allows the evaluation of the energetic cost (thermodn.) assocd. with a mutation in the active site of a β-lactamase, in the presence of the β-lactam substrate. The catalytic efficiency for the β-lactamase-mediated hydrolysis of β-lactam antibiotics is represented by the ratio of a kinetic term (kcat) and a thermodn. term (Km). Here we present an approach based on quantum calcns. and mol. dynamics simulations allowing to est. the kcat term by evaluating β-lactamases from different classes, in the presence of several β-lactam substrates. Therefore, we are now able to predict in silico the overall catalytic efficiency for a large panel of β-lactamases. The precision of this prediction, which depends in turn on the precision for predicting the individual terms kcat and Km, will be discussed and compared with the precision of exptl. values. These results will ultimately provide essential information for the fight against resistance to β-lactam antibiotics