Scientific breakthrough will help design the antibiotics of the future

A carbapenem molecule, a last resort antibiotic, enters the carbapenemase enzyme (blue arrow), where the crucial beta-lactam structure gets broken down. The ineffective molecule then leaves (orange arrow)

Press release issued: 17 October 2014

Scientists have used computer simulations to show how bacteria are able to destroy antibiotics – a breakthrough which will help develop drugs which can effectively tackle infections in the future.

Researchers at the University of Bristol focused on the role of enzymes in the bacteria, which split the structure of the antibiotic and stop it working, making the bacteria resistant.

The new findings, published in Chemical Communications, show that it’s possible to test how enzymes react to certain antibiotics.

It’s hoped this insight will help scientists to develop new antibiotics with a much lower risk of resistance, and to choose the best medicines for specific outbreaks.

Using a Nobel Prize-winning technique called QM/MM - quantum mechanics/molecular mechanics simulations – the Bristol research team were able to gain a molecular-level insight into how enzymes called ‘beta-lactamases’ react to antibiotics.

Researchers specifically want to understand the growing resistance to carbapenems, which are known as the ‘last resort’ antibiotics for many bacterial infections and super bugs such as E. coli.

Resistance to carbapenems makes some bacterial infections untreatable, resulting in minor infections becoming very dangerous and potentially deadly.

The QM/MM simulations revealed that the most important step in the whole process is when the enzyme 'spits out' the broken down antibiotic. If this happens quickly, then the enzyme is able to go on chewing up antibiotics and the bacterium is resistant. If it happens slowly, then the enzyme gets 'clogged up' and can't break down any more antibiotics, so the bacterium is more likely to die.

The rate of this 'spitting out' depends on the height of the energy barrier for the reaction - if the barrier is high, it happens slowly; if it's low, it happens much more quickly.

Professor Adrian Mulholland, from Bristol University’s School of Chemistry, said: “We've shown that we can use computer simulations to identify which enzymes break down and spit out carbapenems quickly and those that do it only slowly.

“This means that these simulations can be used in future to test enzymes and predict and understand resistance. We hope that this will identify how they act against different drugs – a useful tool in developing new antibiotics and helping to choose which drugs might be best for treating a particular outbreak.”

The research, carried out by academics and postgraduate and undergraduate students in the School of Chemistry and the School of Cellular and Molecular Medicine, was funded by the Engineering and Physical Sciences Research Council (EPSRC).

Paper

‘QM/MM Simulations as an Assay for Carbapenemase Activity in Class A β-Lactamases’ by Ewa I. Chudyk, Michael A. L. Limb, Charlotte Jones, James Spencer, Marc W. van der Kamp and Adrian J. Mulholland in Chemical Communications.

Further information

Using computers to understand biological catalysts (the QM/MM technique)

Computer simulations provide a way to 'see' a chemical reaction taking place in the heart of the complex protein structure of an enzyme, showing the subtle atomic details of biochemical reactions, using the molecular simulation methods developed by the winners of the 2013 Nobel Prize in Chemistry, Martin Karplus, Michael Levitt and Arieh Warshel. For further information, please see the Chemistry website.

About EPSRC

The Engineering and Physical Sciences Research Council (EPSRC) is the UK's main agency for funding research in engineering and physical sciences. EPSRC invests around £800m a year in research and postgraduate training to help the nation handle the next generation of technological change. The areas covered range from information technology to structural engineering, and mathematics to materials science. This research forms the basis for future economic development in the UK and improvements for everyone's health, lifestyle and culture. EPSRC works alongside other Research Councils with responsibility for other areas of research. The Research Councils work collectively on issues of common concern via Research Councils UK.