Selective binding of small molecules to Vibrio cholerae DsbA offers a starting point for the design of novel antibacterials

Identification of small covalent inhibitors targeting DsbA using virtual screening, covalent docking, and molecular dynamics simulations

Antimicrobial resistance (AMR) is a growing global health threat, highlighting the urgent need for new therapeutic strategies. The development of bacterial antivirulence agents and antibiotic adjuvants offers two promising strategies for combating bacterial infections. The DsbA protein is crucial for bacterial virulence and resistance, catalyzing the formation of disulfide bonds in bacterial proteins, making it an attractive target for novel antibiotics. In this study, we employed virtual screening, covalent docking, and molecular dynamics simulations to screen a library of 69,579 compounds for inhibitors targeting Cys30, a key nucleophilic residue in the CXXC catalytic motif of DsbA. We identified four small molecule covalent inhibitors that form covalent bonds with DsbA. The MM/PBSA results indicate that three covalent compounds (Cov28322, Cov16876, and Cov64052) have lower binding energies than the positive control. However, covalent binding typically offers superior target specificity and durability. These inhibitors primarily interact with key regions of DsbA, including the CXXC motif and L2 loop, suggesting their potential to disrupt DsbA's catalytic activity. This study provides a theoretical basis for designing DsbA covalent inhibitors as antibiotic adjuvants, presenting a promising strategy to combat bacterial infections and AMR.

Exploring the inhibitory potential of in silico-designed small peptides on Helicobacter pylori Hp0231 (DsbK), a periplasmic oxidoreductase involved in disulfide bond formation

Introduction: Helicobacter pylori is a bacterium that colonizes the gastric epithelium, which affects millions of people worldwide. H. pylori infection can lead to various gastrointestinal diseases, including gastric adenocarcinoma and mucosa-associated lymphoid tissue lymphoma. Conventional antibiotic therapies face challenges due to increasing antibiotic resistance and patient non-compliance, necessitating the exploration of alternative treatment approaches. In this study, we focused on Hp0231 (DsbK), an essential component of the H. pylori Dsb (disulfide bond) oxidative pathway, and investigated peptide-based inhibition as a potential therapeutic strategy. Methods: Three inhibitory peptides designed by computational modeling were evaluated for their effectiveness using a time-resolved fluorescence assay. We also examined the binding affinity between Hp0231 and the peptides using microscale thermophoresis. Results and discussion: Our findings demonstrate that in silico-designed synthetic peptides can effectively inhibit Hp0231-mediated peptide oxidation. Targeting Hp0231 oxidase activity could attenuate H. pylori virulence without compromising bacterial viability. Therefore, peptide-based inhibitors of Hp0231 could be candidates for the development of new targeted strategy, which does not influence the composition of the natural human microbiome, but deprive the bacterium of its pathogenic properties.

Fragment-Based Lead Discovery Strategies in Antimicrobial Drug Discovery

Fragment-based lead discovery (FBLD) is a powerful application for developing ligands as modulators of disease targets. This approach strategy involves identification of interactions between low-molecular weight compounds (100-300 Da) and their putative targets, often with low affinity (K_D ~0.1-1 mM) interactions. The focus of this screening methodology is to optimize and streamline identification of fragments with higher ligand efficiency (LE) than typical high-throughput screening. The focus of this review is on the last half decade of fragment-based drug discovery strategies that have been used for antimicrobial drug discovery.