Poster Presentation 11th Annual Conference of the International Chemical Biology Society 2022

Bacterial dephospho-coenzyme A kinase: The fragment hit-to-lead story thus far (#133)

Vrinda Gupta 1 , Barbara Schroeder 2 3 , Junwen Zheng 1 , Christoph Nitsche 2 , Christina Spry 1
  1. Research School of Biology, The Australian National University, Acton, ACT, Australia
  2. Research School of Chemistry, The Australian National University, Acton, ACT, Australia
  3. Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany

Coenzyme A (CoA) is a ubiquitous enzyme cofactor and its biosynthesis has been highlighted as a promising target for antibacterial drug discovery. Of particular interest, is the final step of CoA biosynthesis, in which dephospho-CoA kinase (DPCK) phosphorylates dephospho-CoA; this is an essential step of bacterial CoA biosynthesis, with bacteria possessing no known bypass mechanisms for DPCK phosphorylation. Fundamental differences between the bacterial DPCK and its eukaryotic counterpart should also allow for selective bacterial targeting. As such, DPCK is considered an attractive antibacterial drug target.

A fragment-based drug design approach is being employed to identify inhibitors targeting the Escherichia coli DPCK. Attempts to co-crystallise apo E. coli DPCK with prioritised fragment hits from a biophysical screen proved unsuccessful. However, binding of a lead fragment could be confirmed by protein-based-NMR. Through structure-activity relationship (SAR) exploration, fragment analogues which bound with up to 10-fold higher affinity to E. coli DPCK were identified.

Structural information provided by NMR and X-ray studies has now informed continued elaboration of the lead fragment. To explore the binding site, a series of elaborated compounds were synthesised to explore the effect of different substituents at different positions. The best of these elaborated compounds was found to inhibit DPCK activity with an IC50 of 2-4 µM. Additionally, testing of the elaborated compounds against the human DPCK counterpart was promisingly consistent with bacterial specificity. Unfortunately, antimicrobial activity of the compounds was not observed in whole cell bacterial screening carried out by the Community for Open Antimicrobial Drug Discovery (CO-ADD); at a concentration of 32 µg/L the compounds were without effect on key tested ESKAPE pathogens and two fungi. We are currently exploring the reasoning behind the absence of whole cell activity and using rational structure-based design principles to guide further compound elaboration.

  1. Spry, C., Kirk, K. and Saliba, K. (2008). Coenzyme A biosynthesis: an antimicrobial drug target. FEMS Microbiology Reviews, 32(1), pp.56-106.