Targeting the essential transcriptional regulator hp1043 for novel antimicrobial approaches in helicobacter pylori infection

Helicobacter pylori is a highly prevalent and pathogenic bacterium that colonises the gastric mucosa and is responsible for various gastrointestinal disorders. Remarkably, the bacterium exhibits rapid development of resistance to standard antibiotics, reducing the effectiveness of therapies and eradication efforts. The growing challenge of antimicrobial resistance calls for new strategies. Innovative approaches are exploring the potential of targeting bacterial transcriptional regulators (TRs) modulating the expression of essential genes. Among the TRs in H. pylori, HP1043 was discovered as a crucial factor that has control key cellular processes. Playing a central role, hp1043 gene cannot be deleted, and the protein's level cannot be modulated. This intrinsic property renders it a challenging research subject yet places it as a potential focus for innovative antimicrobial strategies. In this study, we employed a gene reporter system to investigate HP1043's regulatory function in vivo and in vitro on a cluster of validated targets. This approach allows us also to study the effect of a variable distance between the HP1043 consensus sequence and the -10 Pribnow box element on its transcription regulation. In parallel, in silico screening and drug repositioning methods involving high-throughput-virtual-screening and molecular dynamics simulations were employed to identify candidate compounds that could inhibit HP1043's DNA-binding activity. Secondly, a crystal engineering approach aiming to reduce antibiotic dosage was employed to generate co-crystals capable of exploiting multiple mechanisms of action including the reported inhibitory activity on HP1043 binding. Finally, we explored the potential and versatility of peptide nucleic acids (PNAs) in modulating HP1043 expression. As short antisense oligomers, PNAs demonstrated to selectively block the translation of target genes, leveraging their precise gene knockdown capacity for antimicrobial purposes. This work represents the first examples of multi-targeting antimicrobial strategies against H. pylori, with a focus on the crucial regulator HP1043 and its regulatory mechanisms.