Boronic acid inhibitors of penicillin-binding protein 1b: serine and lysine labelling agents

Abstract

Penicillin-binding proteins (PBPs) contribute to bacterial cell wall biosynthesis and are targets of antibacterial agents. Here, we investigated PBP1b inhibition by boronic acid derivatives. Chemical starting points were identified by structure-based virtual screening and aliphatic boronic acids were selected for further investigations. Structure–activity relationship studies focusing on the branching of the boron-connecting carbon and quantum mechanical/molecular mechanical simulations showed that reaction barrier free energies are compatible with fast reversible covalent binding and small or missing reaction free energies limit the inhibitory activity of the investigated boronic acid derivatives. Therefore, covalent labelling of the lysine residue of the catalytic dyad was also investigated. Compounds with a carbonyl warhead and an appropriately positioned boronic acid moiety were shown to inhibit and covalently label PBP1b. Reversible covalent labelling of the catalytic lysine by imine formation and the stabilisation of the imine by dative N–B bond is a new strategy for PBP1b inhibition.

Graphical abstract

Penicillin-binding protein (PBP) 1b is an antibacterial target with a serine-lysine catalytic dyad. Covalent boronic acid inhibitors targeting the serine residue and compounds containing both a boronic acid moiety and a carbonyl group targeting the lysine residue with a concomitant dative N–B bond formation were studied. Structure-activity studies were combined with QM/M free energy calculations to explore the mechanism of covalent inhibition.

Keywords:

• Penicillin-binding proteins
• covalent inhibitors
• boronic acids
• serine labelling
• lysine labelling

Acknowledgements

We thank Dr. Andrea Dessen (IBS, Grenoble) for donation of PBP1b plasmid and Dr. Pál Szabó for HRMS measurements. This study was supported by National Research, Development and Innovation Office Grants K135335, and by the National Drug Research and Development Laboratory (PharmaLab) project (RRF-2.3.1-21-2022-00015).

Author contributions

Conceptualisation: GGF, SG, GMK; Experiments and data acquisition: LK, KG, MHR, KB, TI, GGF; Data analysis: LK, MHR, GGF; Funding Acquisition: GGF, SG, GMK; writing-original draft preparation: LK, MHR, GGF writing-review and editing: SG, GMK. All authors have read and agreed to the published version of the manuscript.

Disclosure statement

The authors report there are no competing interests to declare.

Additional information

Funding

This research was funded by the National Research Development and Innovation Office (Grant Numbers: SNN 135335), Slovenian Research Agency (ARRS) Research Core Funding P1-0208, grant N1-0169 and a PhD grant to K.G. L.K. is supported by the Gedeon Richter Talentum Foundation and the József Varga Foundation and Javna Agencija za Raziskovalno Dejavnost RS.