New starting points for antibiotics targeting P. aeruginosa FabF discovered by crystallographic fragment screening followed by hit expansion

21 December 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

There is an urgent need for new antibiotics. FabF (3-oxoacyl-[acyl-carrier-protein] synthase 2), which catalyses the rate limiting condensation reaction in the fatty acid synthesis II pathway, is an attractive target. Very few inhibitors of FabF are known and most are derived from natural products. In an effort to further explore the chemical space of FabF ligands, we have carried out fragment screening by X-ray crystallography against an intermediated state-mimicking variant of P. aeruginosa FabF (PaFabF C164Q). This screen has screen resulted in 16 hits binding in or close to the malonyl-CoA or fatty acid binding site or an adjacent dimer interface. More than 80 analogues of the hit compounds have been explored making use of either commercially available or synthesised compounds. For 8 of those co-crystal structures could be determined and the most potent ligand has a binding affinity of 65 µM. This data package forms a strong foundation for the development of more potent and diverse FabF inhibitors.

Keywords

anibiotics
structure-based drug design
fragment screening
FabF

Supplementary materials

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Supplementary Information
Description
The Supporting Information includes Figures showing the binding modes of all hit compounds and analogues, Tables listing the PDB codes not listed in the main text and the chemical structures of all hits and purchased or synthesised analogues. Further, the synthetic routes are described in the supporting information.
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