Development of antibacterial compounds targeting validated enzymes in peptidoglycan biosynthesis




01. September 2020 - 31. August 2023


1,13 FTE


Stanislav Gobec


1-09 Natural sciences and Mathematics - Pharmacy

Research Organisation:




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Infections caused by antibiotic-resistant bacteria continue to challenge health-care systems worldwide. We face a growing resistance of Gram-positive and Gram-negative pathogens that cause infections in hospitals and in the community, with the so-called antibiotic-resistant ‘superbugs’ that now represent a major global health problem. The obstacles of having only a few new antimicrobials on the horizon and facing increasing frequency of multidrug resistance mean that we must redouble our efforts in the search for new antimicrobials. There is therefore an urgent need that medicinal chemists develop new antibacterial lead compounds and clinical candidates that bind to validated antibacterial drug targets, as this will enable development of novel antimicrobial drugs.
Peptidoglycan is a macromolecule that is essential for bacterial survival and unique to the bacterial cell wall. The enzymes involved in its biosynthetic pathway constitute potential targets for the discovery of new antimicrobials. Among the intracellular enzymes of peptidoglycan biosynthesis, only two enzymes are validated antibacterial targets by inhibitors that are in clinical use: MurA is validated by fosfomycin, which is used for the treatment of urinary infections, and DdlB is validated by cycloserine, which is a second line drug for the treatment of tuberculosis. Therefore, these two enzymes will be targeted in the present Project by fragment-based drug discovery (FBDD). 
FBDD identifies low-molecular-weight ligands (~150 Da) that bind to biologically important macromolecules. The three-dimensional experimental binding mode of these fragments is determined and is used to facilitate their optimization into potent lead compounds. In addition to classical FBDD approach, where fragments with non-covalent interactions with the target protein are sought, we will also use an innovative approach, where FBDD is used to develop covalent inhibitors. Covalent inhibitors are compounds designed to bind covalently to a specific molecular target and thereby supress its biological function. By careful design, a high degree of selectivity has recently been built into covalent inhibitors, resulting in many clinical candidates and approved drugs.
During this Project, we aim to achieve two major objectives: objective 1 is to perform screening of a library of covalent and non-covalent fragments on target enzymes MurA and DdlB, and objective 2 is to perform fragment-to-lead development of selected hit-fragments. First, libraries of fragments will be screened on target enzymes, and then the binding modes of fragments will be determined with X-ray crystallography or NMR. In the next step, structure-based design will be used to generate the ideas how to improve and grow the fragments, and these improved compounds will be synthesized. All target compounds will be pharmacologically evaluated. The work will be iterative and will proceed in a typical drug discovery iterative loop consisting of design, synthesis, biochemical evaluation and structural evaluation, where the latter will be used to start new development iteration.
We expect to identify at least five fragment hits on each enzyme (MurA and DdlB) with micromolar inhibitory potency (IC50 or Ki values below 100 μM) and to develop these hits into 1-2 lead compounds active against each target enzyme with sub-micromolar inhibitory potencies (IC50 or Ki values below 1 μM) and good in vitro antibacterial activities (MIC values on most important pathogenic strain below 16 mg/L). The lead compounds developed will have drug-like properties, low or no in vitro cytotoxicity, and good in vitro pharmacokinetics properties. These results will represent significant contribution to the development of new antibacterials that target early stages of peptidoglycan biosynthesis.



Phase 1: hit finding

Financed by: