Elucidating mechanisms of beta-lactam antibiotic resistance through serial crystallography and molecular simulations

Bacterial antibiotic resistance is a global public health emergency, already responsible for >1.2 m deaths per annum
worldwide with up to 10 m predicted by 2050. Beta-lactams (penicillins and related drugs) are the most widely used
antibiotics. In Gram-negative bacteria such as Escherichia coli (the leading cause of bloodstream infections in the U.K.)
beta-lactam resistance is usually due to beta-lactamase enzymes that cleave the amide bond in the beta-lactam ring and
abolish antibiotic activity.
This proposal applies state-of-the-art approaches in X-ray crystallography and computational simulations of chemical
reactions to study the mechanism(s) by which beta-lactamases degrade beta-lactams, information that will guide
development of small molecule inhibitors that block their activity and restore beta-lactam effectiveness against beta-
lactamase producing bacteria. X-ray crystallography provides near-atomic resolution structural information on proteins,
and their interactions with small molecules, but is traditionally a static technique unable to describe transiently
present species or capture dynamic information on e.g. interconversion of states in chemical reactions. Recently
developed serial methods, where reactions in micron-scale crystals are initiated by rapid mixing or light-
dependent chemistry and a single image per crystal subsequently collected after a defined time interval, can however now
yield structural information on the millisecond time scale. This offers potential to create "molecular movies" composed of
a series of structural snapshots at different time points along a reaction pathway, for the first time enabling structural
descriptions of transient, mechanistically important states in enzyme-catalysed reactions. In this project we will apply
serial techniques, working together with scientists at Diamond Light Source, to investigate reactions of beta-
lactamases with their antibiotic substrates and with inhibitor candidates. Structures that we obtain will be used in
molecular simulations to understand the dynamic properties of enzyme bound species and to investigate the
energetics of their interconversion. Simulations based on classical (Newtonian) mechanics will investigate the
conformational flexibility of individual states along a reaction pathway, while quantum mechanical methods will enable
us to calculate the energy barriers controlling their interconversion and so assess the reactivity of individual complexes.
In combination, these two approaches will reveal how different beta-lactamases employ different mechanisms to degrade
common substrates, and how and why different enzymes vary in their reactivity varies towards different antibiotics
and susceptibility towards different inhibitors. This information will be valuable in identifying how beta-lactams may
be modified to evade beta-lactamase activity, and how beta-lactamase inhibitors may be optimised for activity against
the widest range of beta-lactamase targets.