DD-Ligases as a Potential Target for Antibiotics: Past, Present and Future

Abstract

DD-ligases catalyze the synthesis of the D-Ala-D-Ala and D-Ala-D-Ser dipeptides or the D Ala-D-Lac depsipeptide in an early step of peptidoglycan synthesis. Their function is essential for bacterial growth and specific to bacteria, making them attractive targets for the development of novel antibiotics. This review examines the biochemical and structural features of these enzymes and presents the main families of inhibitors described so far. Over the last 20 years, 7 structures of DD-ligases have been solved by X-ray crystallography, giving a detailed view of the general topology of the active site and of the residues in the catalytic pocket that play a central role in substrate recognition. This has paved the way to the rational design of inhibitors, which can be classified as (i) analogues of substrates, (ii) analogues of the product of the reaction, (iii) analogues of the transition state, and (iv) original scaffolds discovered by screening or by rational computer-aided design. The three first strategies have led to molecules that are polar by nature and have therefore poor access to their cytosolic target. The fourth one is potentially most promising as it yields more diverse structures. The most active molecules show affinity constants in the microM range, but microbiological evaluation remains scarce (typical MIC 1-8 mg/L for the tested compounds). These data strongly suggest targeting DD-ligases is a promising approach for discovery of new antibiotics. Future research should, however, aim at finding more potent inhibitors endowed with the appropriate pharmacokinetic properties that ensure access to their intracellular target.

Function of the d-Alanine:d-Alanine Ligase Lid Loop: A Molecular Modeling and Bioactivity Study

“…Residues 206−220 constitute the head of the lid loop and include a two-turn α-helix (residues 212−217). 15 The proximity of hinge residues 200 and 226 qualifies the Ddl lid loop as an ω-loop protein motif. 16 During its catalytic cycle, DdlB undergoes two major conformational changes.…”

Structure‐Based Design of Benzoxazoles as new Inhibitors for D‐Alanyl – D‐Alanine Ligase

“…Correlation is not perfect, however as IT8, which is only 3 times less potent on ligase than IT16, is unable to prevent bacterial growth. Among the families of inhibitors described so far, only a few were tested for their antimicrobial activity [12]. In these studies also, there was no clear correlation between enzymatic inhibition and antimicrobial potency, as illustrated for (i) diazenecarboxamides [14], which show IC 50 towards Ddl 20 times lower than d-cycloserine but higher MICs, (ii) the natural compound quercetin [49], which shows lower IC 50 and K i values than apigenin towards the H. pylori enzyme, but 8 times higher MIC towards the bacterium, or (iii) two molecules from the NCI database [16] which display similar MIC towards S. aureus but K i differing by one order of magnitude.…”

“…The development of synthetic inhibitors has recently regained interest, and new ligands have been identified [12]. Most of them were discovered by screening of chemical banks [13 -16] with one active compound (3-chloro-2,2-dimethyl-N-[4(trifluoromethyl) phenyl]propanamide) subsequently shown by X-ray crystallography to bind in a pocket adjacent to the substrate binding site [13].…”

“…However the potency of all ligands discovered thus far remains low, and only a few of them were evaluated for their antibacterial potency against living bacteria, making difficult to apprehend their potential interest as leads for the search of new antibacterial agents [12]. Identification of new scaffolds that could form the base of a new series of inhibitors is desirable.…”

6-Arylpyrido[2,3-d]pyrimidines as Novel ATP-Competitive Inhibitors of Bacterial D-Alanine:D-Alanine Ligase

“…Ddl catalyzes the ATP-dependent formation of a dipeptide D-Ala-D-Ala that subsequently occupies the terminal position of the cell wall UDP-Mur N Ac-pentapeptide precursor units. This terminal dipeptide plays a pivotal role in the extracellular steps of peptidoglycan assembly, where cross-linking of adjacent peptidoglycan chains occurs via breaking a dipeptide bond and forming a new one [10].…”