In vitro and in silico antimicrobial activity of Aspergillus niger HG3 against carbapenem-resistant Escherichia coli and Klebsiella pneumoniae and their antioxidant potential

The emergence of carbapenem-resistant Enterobacteriaceae, particularly Escherichia coli and Klebsiella pneumoniae, represents a significant global health threat, underscoring the urgent need for novel antimicrobial and antioxidant agents. In this study, a fungal isolate identified as Aspergillus niger HG3 was characterized and investigated for its bioactive potential. Ethyl acetate extracts of the fungus demonstrated significant in vitro antimicrobial activity, with inhibition zones of 17.66 ± 1.52 mm for E. coli and 13.00 ± 1.00 mm for K. pneumoniae at 1 mg/mL. Antioxidant evaluation revealed dose-dependent radical scavenging activity with an IC50 of 152.05 µg/mL in the DPPH assay and dose-dependent increase in the total antioxidant activity (OD value 0.15 ± 0.004 at 200 µg/mL). The total phenolic and flavonoid content of Aspergillus niger HG3 extract was found to be 77.008 mg GAE/gm dry weight of the extract and 91.72 mg QE/gm dry weight of the extract, respectively. Polyphenolic profiling confirmed high levels of total phenolic and flavonoid content, both correlating strongly with antioxidant outcomes (R² >0.94). GC-MS analysis identified diverse secondary metabolites, including (2,3-diphenylcyclopropyl) methyl phenyl sulfone, 1,3,5-triphenyl-1,5-pentanedione, and others with known bioactivities. Molecular docking studies supported the experimental results, showing strong binding of these compounds to bacterial β-lactamase enzymes (NDM-1, KPC-2) and antioxidant targets (Catalase, SOD), with binding affinities up to − 8.6 kcal/mol. ADMET profiling further suggested favourable pharmacokinetic and safety attributes for the lead compounds. These findings collectively highlight the dual antimicrobial and antioxidant potential of A. niger HG3 metabolites and support their further development as natural therapeutic agents against drug-resistant pathogens and oxidative stress-related disorders.