Combined Structural Analysis and Molecular Dynamics Reveal Penicillin-Binding Protein Inhibition Mode with β-Lactones

Parker L. Flanders, Carlos Contreras-Martel, Nathaniel W. Brown, Joshua D Shirley, Alexandre Martins, Kelsie N. Nauta, Andréa Dessen, Erin E Carlson, Elizabeth A. Ambrose

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

β-Lactam antibiotics comprise one of the most widely used therapeutic classes to combat bacterial infections. This general scaffold has long been known to inhibit bacterial cell wall biosynthesis by inactivating penicillin-binding proteins (PBPs); however, bacterial resistance to β-lactams is now widespread, and new strategies are urgently needed to target PBPs and other proteins involved in bacterial cell wall formation. A key requirement in the identification of strategies to overcome resistance is a deeper understanding of the roles of the PBPs and their associated proteins during cell growth and division, such as can be obtained with the use of selective chemical probes. Probe development has typically depended upon known PBP inhibitors, which have historically been thought to require a negatively charged moiety that mimics the C-terminus of the PBP natural peptidoglycan substrate, d-Ala-d-Ala. However, we have identified a new class of β-lactone-containing molecules that interact with PBPs, often in an isoform-specific manner, and do not incorporate this C-terminal mimetic. Here, we report a series of structural biology experiments and molecular dynamics simulations that we utilized to evaluate specific binding modes of this novel PBP inhibitor class. In this work, we obtained <2 Å resolution X-ray structures of four β-lactone probes bound to PBP1b from Streptococcus pneumoniae. Despite their diverging recognition modes beyond the site of covalent modification, these four probes all efficiently labeled PBP1b, as well as other PBPs from S. pneumoniae. From these structures, we analyzed protein-ligand interactions and characterized the β-lactone-bound active sites using in silico mutagenesis and molecular dynamics. Our approach has clarified the dynamic interaction profile in this series of ligands, expanding the understanding of PBP inhibitor binding.

Original languageEnglish (US)
Pages (from-to)3110-3120
Number of pages11
JournalACS Chemical Biology
Volume17
Issue number11
DOIs
StatePublished - Nov 18 2022

Bibliographical note

Funding Information:
This work used the platforms of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was also supported by the National Institutes of Health (R01 GM128439 A1, E.E.C. and E.A.A.), the University of Minnesota Department of Chemistry, the University of Minnesota Department of Medicinal Chemistry, and the Minnesota Supercomputing Institute for Advanced Computational Research (MSI). P.L.F. was partly supported by NIH/NIGMS Chemistry-Biology Interface Training Grant 5T32-GM008700. N.W.B. was supported by NIH Institutional Research and Academic Career Development Award K12 GM119955. J.D.S. was supported by the National Institutes of Health’s National Center for Advancing Translational Sciences, grants TL1R002493 and UL1TR002494. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health’s National Center for Advancing Translation Sciences. The authors thank the M. Winkler Lab at Indiana University for providing S. pneumoniae strains. Graphical figures were created with GraphPad Prism and BioRender.

Publisher Copyright:
© 2022 American Chemical Society.

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