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Structural and Mechanistic Characterisation of Bacterial Natural Product Targets

Principal Supervisor: Dr Lona Alkhalaf

Secondary Supervisor(s): Professor Greg Challis

University of Registration: University of Warwick

BBSRC Research Themes:

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Deadline: 23 May, 2024

Project Outline

Natural products are a vital source of medicines and agrichemicals. For example, over 70% of the antibiotics on the World Health Organisation’s list of essential medicines are derived from natural sources (plants, bacteria or fungus). In order to develop natural products as pharmaceutical or agrichemical leads a detailed understanding of their mechanism of action is required. Our lab uses X-ray crystallography alongside other techniques such as chemical synthesis, analytical chemistry, bioinformatics and enzymology to understand how bacterial natural products interact with their targets at a molecular level.

A project in the lab will typically involve natural product isolation and structural characterisation by mass spectrometry and NMR spectroscopy, enzyme overproduction and purification, assay development, X-ray crystallography molecular modelling and bioinformatics to identify key residues involved in binding, mutagenesis of residues to test hypotheses, and/or synthesis of small molecule substrate mimics or mechanistic probes.

We are particularly interested in cases for which several different isoforms of a natural product are made by different bacteria and the evolutionary driving force for incorporation of these modifications. For example, plant associated bacteria produce diverse bicyclic depispeptide histone deacetylase (HDAC) inhibitors, including romidepsin, an approved anticancer drug. They contain both a conserved sulphur pharmacophore, that binds to the zinc in the active site of HDACs, and a variable peptide region. We hypothesise that bacteria have evolved to make structural variants of the same scaffold to target different isoforms of HDACs depending on their environment. We are currently working on determining the activity of several HDAC inhibitors against representative plant and fungal HDACs and using structural biology techniques to understand any differences at a molecular level.


  • X-ray crystallography
  • Protein overproduction and purification
  • Enzymology
  • Small molecule NMR spectroscopy and mass spectrometry
  • Bacterial growth
  • LC-MS and HPLC
  • Bioinformatics
  • Chemical synthesis
  • Genetic manipulation