Molecular Dynamics and First Principles Modelling of Novel Antimicrobial Molecules

A major health crisis is looming – the resistance of bacterial species to antibiotics. As bacteria evolve rapidly, many species are now able to evade standard treatments and are becoming increasingly difficult to eliminate. As such, common diseases that we routinely treat with antibiotics, may once again become deadly. In addition to rapid evolution, bacteria are also able to protect themselves from human interventions, such as pharmaceuticals, by forming biofilms.

These are sticky matrices composed of sugars and proteins in which the bacteria can remain successfully hidden for long periods. Biofilms are notoriously difficult to deal with and can be found in many locations including in the body (e.g. in the lungs of cystic fibrosis patients), on medical equipment (e.g. catheters), on plants and crops (e.g. tuber soft rot) and on machinery (e.g. in food processing). To combat these problems there is now a drive to find new antimicrobial molecules that can be used against these pathogenic bacterial species.

In this project, you will explore the structures and chemistry of some novel plant-derived antimicrobial molecules and will model their interactions with biological structures and surfaces.

The project, which is entirely computational, will use large-scale quantum mechanical and molecular dynamics simulations, which will be run on the University of Leeds supercomputer, ARC3.