# Small molecule inhibitors of lytic transglycosylase to potentiate beta-lactam antibiotics

> **NIH NIH R21** · CASE WESTERN RESERVE UNIVERSITY · 2020 · $240,750

## Abstract

The rapid emergence of antibiotic-resistant bacteria is a major global health threat. This spurs the need to revisit
key antibacterial drug targets such as the peptidoglycan (PG) layer. The PG synthesis machinery is targeted by
β-lactam antibiotics that inhibit penicillin-binding proteins (PBP) which crosslink PG strands. A main resistance
mechanism is the expression of β-lactamases that can degrade β-lactams. There is thus a critical need for new
antibiotics or for avenues to re-sensitize bacteria to β-lactam antibiotics. For the latter, one approach is
developing β-lactamase inhibitors; unfortunately, the 5 current inhibitors do not inhibit certain key β-lactamases,
and there are resistance mechanisms via inhibitor-resistant β-lactamases. A second approach is to inhibit PG
degrading lytic transglycosylases (LT), the focus of this application.
 Inhibition of LTs or knocking out LTs genetically has been shown to restore the efficacy of β-lactam
antibiotics in many serious pathogens including Escherichia coli, Neisseria meningitides, Pseudomonas
aeruginosa, Enterobacter aerogenes, Acinetobacter baumannii, Helicobacter pylori, and Campylobacter jejuni.
This β-lactam potentiation involves two possible mechanisms of which, depending on the pathogen, either or
both contribute. In the first mechanism, the inhibition of both PBP and LT leads to long non-cross-linked PG
strands that cause cell wall bulges, weakening the cell wall. In the second mechanism, LT activity generates
disaccharide PG product that, when recycled to the cytoplasm, increases β-lactamase expression in certain
pathogens. Despite these compelling observations, there is only one promising LT inhibitor known, bulgecin A;
however, this natural product carbohydrate-based inhibitor is very challenging for medicinal chemistry efforts. As
a result, bulgecin A has not been very amenable to advancing inhibition studies towards animal studies and
beyond. This application proposes to overcome this key roadblock by developing new LT inhibitors with
scaffold(s) different from bulgecin A via biased (Aim 1) and non-biased fragment-based approaches (Aim 2).
 Aim 1: To identify new inhibitor fragments that retain bulgecin A's key N-acetyl group. N-acetyl containing
compounds will be selected or designed aided by docking; their LT binding and inhibition will be probed by
biophysical techniques, protein crystallography, and enzymatic assays. Compounds will be tested against
multiple LTs known to bind bulgecin A, and which are amenable to crystallography (E. coli, P. aeruginosa, and
C. jejuni) in order to identify at least one fragment binding to one LT as a novel starting point for optimization.
 Aim 2: To identify non-acetyl containing fragments that bind to the active site of LT, we will screen non-
biased fragments against LTs for binding and inhibition as in Aim 1. Such fragments could bind to the N-acetyl
binding pocket or to the adjacent pockets. Compounds will be obtained from an sp3 fragment lib...

## Key facts

- **NIH application ID:** 9874302
- **Project number:** 1R21AI148875-01
- **Recipient organization:** CASE WESTERN RESERVE UNIVERSITY
- **Principal Investigator:** FOCCO VAN DEN AKKER
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $240,750
- **Award type:** 1
- **Project period:** 2020-01-01 → 2021-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9874302

## Citation

> US National Institutes of Health, RePORTER application 9874302, Small molecule inhibitors of lytic transglycosylase to potentiate beta-lactam antibiotics (1R21AI148875-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9874302. Licensed CC0.

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