A comprehensive computer-based assessment of Deacetylnomilin as an inhibitor for antibiotic-resistant genes identified from the whole genome sequence of the multidrug-resistant Enterobacter cloacae isolate 1382.

Abstract

The twenty-first century presents a serious threat to public health due to the growth in antibiotic resistance among opportunistic bacteria, particularly within the ESKAPE group, which includes Enterobacter species with high morbidity, mortality, virulence, and nosocomial dissemination rates. Enterobacter species, especially Enterobacter cloacae, bacteria have developed resistance to multiple antibiotics through mechanisms, such as continuous production of AmpC beta-lactamase. In this study, a comprehensive bioinformatics approach was employed to analyze the genome of Enterobacter cloacae, utilizing sequence data from GenBank (ID: OW968328.1). The AbritAMR and ResFinder tools were utilized to identify antibiotic-resistant genes, which included the presence of blaOXA-48, blaCMH, FosA, OqxA, and OqxB each conferring resistance to specific antibiotics such as β-lactams and fluoroquinolones. These proteins were analyzed using bioinformatics tools such as ProtParam, SOPMA, Robetta, I-TASSER, AlphaFold, and PROCHECK to investigate different structural models and their properties. The models from AlphaFold had the best quality in terms of structural accuracy, providing valuable insights into the 3D conformations of these resistant proteins. Based on the Molecular docking studies, these constructed targets were docked with 20 natural compounds known for their activity against Gram-negative bacteria. Among them, Deacetylnomilin showed the highest docking score and passed their ADMET properties. Molecular dynamic (MD) simulation was conducted for 100 ns for Deacetylnomilin with different resistant proteins. Deacetylnomilin exhibited more favorable binding free energies compared to the reference compounds across all five proteins, indicating higher stability and affinity. These results suggest that Deacetylnomilin could be an effective inhibitor against the resistant proteins of Enterobacter cloacae, making it a promising candidate for further drug development.