Integrated subtractive genomics and inhibitor identification of novel FAD-dependent monooxygenase in Nocardia farcinica JJSBBCNF_01.

Nocardia farcinica is among the most common Nocardia species responsible for human nocardiosis. This study aims to identify potential drug targets involved in unique metabolic pathways of N. farcinica using a subtractive genomics approach and to prioritize potential inhibitors through structural bioinformatics. Compared to previous studies, this work integrates a subtractive genomics pipeline with diverse compound libraries and comprehensive molecular simulations, offering a more targeted and robust approach to drug discovery. The subtractive approach was applied to the pathogen's whole genome based on several criteria, including non-homology to human proteins, essentiality, druggability, subcellular localization, and virulence. The selected druggable targets were further analyzed using high-throughput virtual screening and molecular dynamics simulations. Among the four potent druggable targets identified, the FAD-dependent monooxygenase emerged as a promising novel therapeutic target. Virtual screening of CMNPD, MNPD, Seaweed, and Specs compound libraries revealed five promising therapeutic candidates based on their ADME profiles and binding affinities. Notably, the SeaweedBS009 compound demonstrated the highest therapeutic potential due to its stability throughout the molecular dynamics simulation and its lowest binding free energy. These findings provide a foundation for developing novel drugs targeting pathogen-specific metabolic pathways in N. farcinica. The identified drug targets and lead compounds could facilitate the design of effective therapeutics to combat drug-resistant N. farcinica infections.