What is the problem?

Enzyme-catalysed antibiotic degradation, or modification or degradation of antibiotics or their targets, is one of the major mechanisms of antibiotic resistance. Plasmid borne genes encoding modifying enzymes such as beta-lactamases, that confer resistance to penicillins and related antibiotics, or, more recently, phosphoethanolamine transferases, that confer resistance to the last resort agent colistin, are spreading in Gram-negative bacteria and threaten continued effectiveness of key antibiotic classes. 

A potential solution

Enzyme-mediated resistance can be overcome in two ways: by modifying antibiotics to render them less susceptible to resistance enzymes, or by developing small molecule inhibitors of resistance enzymes that can be co-administered with antibiotics in combination therapies. Both approaches require understanding of the structure and mechanism of resistance enzymes to guide development of new antibiotics and inhibitor combinations.

An international team led by Professor Jim Spencer (School of Cellular and Molecular Medicine) have applied a combination of microbiological, biochemical, structural biological and computational chemistry approaches to study beta-lactamases that are active upon carbapenems, the most potent beta-lactam antibiotics, and the mobile colistin resistance determinant MCR-1. The team is investigating interactions of these enzymes with their physiological substrates, or analogues thereof, to understand how they recognise and modify antibiotics or antibiotic targets and identify key intermediates that might form the basis for mechanism-based inhibitors. 

Outcome and next steps

The team have identified the structural basis for the differences in activity of class A enzymes, the most widely distributed beta lactamases, against carbapenem antibiotics, and used this information to develop simulation protocols that can differentiate enzymes active against carbapenems from those unable to do so. A consensus mechanism has been proposed for activity of zinc-dependent (metallo) beta-lactamases that accommodates the heterogeneity of this enzyme group and can account for their broad spectrum of activity. A combination of crystal structures and quantum calculations has enabled us to propose a mechanism for phosphoethanolamine transfer by MCR-1. 

The next steps are to extend our beta-lactamase simulation protocols to examine additional substrate classes and to differentiate enzymes and variants showing more subtle variations in activity against different beta-lactams; to provide experimental validation of mechanistic predictions arising from simulations; and to identify how new mechanistic information can be exploited to design new inhibitors of these resistance mechanisms.

Published papers