Functional annotation of hypothetical proteins in Enterobacter cloacae 1382: investigating novel targets for antimicrobial resistance

Introduction Antimicrobial resistance (AMR) is a growing global health concern, with multidrug-resistant pathogens such as Enterobacter cloacae posing significant challenges in clinical settings. Enterobacter cloacae is increasingly associated with nosocomial infections, particularly among immunocompromised patients, necessitating the identification of novel therapeutic targets. Hypothetical proteins (HPs), whose functions remain uncharacterized, may play crucial roles in bacterial survival and resistance mechanisms and represent a promising yet underexplored target space for antimicrobial intervention. Methods The complete proteome of E. cloacae comprising 4,820 protein sequences, was analyzed, from which 233 hypothetical proteins (HPs) were identified. Comprehensive bioinformatics analyses, including gene ontology (GO) classification, functional annotation, physicochemical characterization, subcellular localization prediction, protein–protein interaction network analysis, protein structure prediction and validation, molecular docking, and molecular dynamics simulations, were performed to identify and characterize putative AMR-associated targets. Results Gene Ontology analysis predicted functions for 125 hypothetical proteins, of which 16 HPs were shortlisted through comprehensive functional annotation. Based on ARGOT-derived homologs, functional information from the corresponding UniProt entries, and supporting literature, three putative AMR-associated hypothetical proteins were selected for structural and molecular interaction studies. Structural validation demonstrated that the predicted protein models met established quality criteria for subsequent molecular interaction studies. Molecular docking identified several natural compounds with strong binding affinities toward selected targets, and molecular dynamics simulations demonstrated stable protein–ligand interactions, supporting the potential of these compounds as inhibitors. Conclusion This study provides a comprehensive in silico framework for the characterization and prioritization of hypothetical proteins as putative AMR-associated targets in E. cloacae , identifying three promising candidates for further investigation and establishing the foundation for future experimental validation of their roles and interactions with natural compounds in antimicrobial drug discovery.