Secondary Metabolite Profiling, Anti-Mycobacterium tuberculosis Activity, Molecular Docking and Dynamics Studies of Carpobrotus edulis Leaf and Twig Extracts

Herein, we evaluated the antimycobacterial activity and cytotoxicity of Carpobrotus edulis (C. edulis) leaf and twig extracts, profiled their phytochemicals using LC-MS/MS, and investigated the predicted interactions of the putatively annotated metabolites towards the Mycobacterium tuberculosis (Mtb) InhA protein (PDB: 2NV6) using molecular docking. LC-MS/MS profiling and MS-DIAL spectral-library matching enabled the putative annotation of metabolites belonging to several chemical classes, including flavonoids, terpenoids, and nitrogen-containing compounds. The antimycobacterial activity of the C. edulis extracts was evaluated against the Mtb H37Rv strain, with both the leaf and twig ethyl acetate extracts exhibiting minimum inhibitory concentration (MIC) values of 7.81 µg/mL. Molecular docking of seven selected putatively annotated metabolites (PAMs) against InhA yielded predicted docking scores ranging from −6.323 to −8.053 kcal/mol. Molecular dynamics (MD) simulations were subsequently performed for 100 ns to evaluate the conformational behaviour and interaction persistence of PAMs 3 and 7 within the InhA binding environment. PAM 7 maintained comparatively persistent protein contacts throughout the simulation, whereas PAM 3 exhibited substantial positional rearrangements and transient separation from the protein, indicating distinct protein–ligand association patterns under the simulated conditions. Cytotoxicity was assessed using HepG2, NHEM-Ad, and HEK293 cell lines, with both ethyl acetate extracts showing no appreciable reduction in cell viability at the single concentration evaluated (100 µg/mL). The findings demonstrate the in vitro antimycobacterial activity of C. edulis ethyl acetate extracts and support further investigation to confirm the identities and biological activities of their putatively annotated metabolites.