Inactivation of TEM-1 by Avibactam (NXL-104): Insights from Quantum Mechanics/Molecular Mechanics Metadynamics Simulations

The fast and constant development of drug-resistant bacteria represents
a serious medical emergence. To overcome this problem, the development
of drugs with new structures and modes of action is urgently needed. In
this context, avibactam represents a promising, innovative inhibitor of
beta-lactamases with a novel molecular structure compared to previously
developed inhibitors, showing a promising inhibitory activity toward a
significant number of beta-lactamase enzymes. In this work, we studied,
at the atomistic level, the mechanisms of formation of the covalent
complex between avibactam and TEM-1, an experimentally
well-characterized class A beta-lactamase, using classical and quantum
mechanics/molecular mechanics (QM/MM) simulations combined with
metadynamics. Our simulations provide a detailed structural and
energetic picture of the molecular steps leading to the formation of the
avibactam/TEM-1 covalent adduct. In particular, they support a mechanism
in which the rate-determining step is the water-assisted Glu166
deprotonation by Ser70. In this mechanistic framework, the predicted
activation energy is in good agreement with experimental kinetic
measurements. Additionally, our simulations highlight the important role
of Lys73 in assisting the Ser70 and Ser130 deprotonations. While based
on the specific case of the avibactam/TEM-1, the simple protocol we
present here can be immediately extended and applied to the study of
covalent complex formation in different enzyme-inhibitor pairs.