In-silico structural and functional annotation of hypothetical proteins from Nocardia asteroides NCTC11293: A computational approach for novel drug target identification and therapeutic development

Nocardiosis, an infectious disease caused by the opportunistic pathogen Nocardia asteroides, primarily affects immunocompromised individuals, often presenting as a pulmonary infection initiated by inhalation. Despite extensive research, there is still a need for novel therapeutic targets and effective lead molecules. Whole genome sequencing of N. asteroides strain NCTC11293 revealed a high completeness level (98.19 % based on CheckM analysis), encoding 6476 proteins, including 1130 (17.45 %) hypothetical proteins (HPs). Functional annotation studies identified 59 HPs, categorized into Binding Proteins (17 %), Enzymes (68 %), Cell Regulatory Proteins (3 %), Transporters (5 %), and Other Proteins (7 %). Metabolic pathway analysis suggested the Aldolase 1-epimerase (A1-E) protein (WP_019046482.1) as a potential therapeutic target due to its versatile roles in pathophysiology. Structure-based virtual screening (SBVS) of A1-E against bioactive molecules from the IMPPAT database identified five hit compounds (IMPHY003535.1, IMPHY011540.1, IMPHY010165.1, IMPHY003784.1, IMPHY007341.1) with molecular docking scores ranging from -8.2 to -8.5 kcal/mol, MMGBSA binding energy scores between -46.82 and -59.93 kcal/mol, and key residue interactions (Gly41, Phe45, Met47, Ala51, Met77, His78, His143, Trp145, Asn169, Asp188, Trp221, Pro237, Asp238). These hit molecules passed Lipinski's Rule of Five and exhibited satisfactory pharmacokinetics properties along with favourable highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) features. Molecular dynamics simulations (MDS) and essential dynamics (ED), including principal component (PC) based free energy landscape (FEL) analyses, demonstrated stable binding of the selected compounds within the active site of the A1-E protein. These computational findings suggested that the identified bioactive molecules are promising therapeutic agents for nocardiosis, although further experimental validation is needed to assess their therapeutic potential.