Integrated production and protein-protein docking analysis of L-methionase from Klebsiella oxytoca for enzyme-based anticancer therapy via methionine starvation and epigenetic modulation.

Intracellular L-methionine γ-lyase (MGL) from Klebsiella oxytoca BLM-1 was produced and optimized using a combination of One-Factor-at-a-Time and Response Surface Methodology. Optimal culture conditions, such as pH 9.0, 3% (w/v) lactose, and 1.02% (w/v) malt extract, resulted in the highest intracellular MGL activity (0.235 U/mL), representing a 1.13-fold improvement over initial conditions, with a total yield of 40.80 U from a 2 L optimized broth. Purification using Octyl-Sepharose chromatography produced a highly active multimeric enzyme (~ 250 kDa) with 0.384 U/mL activity, which was confirmed as a heteromeric complex (~ 63 kDa and ~ 117 kDa subunits) by SDS-PAGE. The enzyme displayed strong cytotoxic activity toward methionine-dependent cancer cell lines, with IC₅₀ values of 0.023 U for HepG2 and 0.0045 U for A549, while exerting minimal effects on HEK-293 cells. Molecular docking revealed that L-methionine binds to the MGL active site with a binding energy of - 6.5 kcal/mol, and protein-protein docking identified favorable interactions with key methionine pathway enzymes, including METAP2 (- 902.3), MAT2A (- 895.1), and SAHH (- 890.9). These findings highlight the successful optimization of MGL production, its effective purification, and its significant anticancer potential, providing a strong foundation for its development as a therapeutic enzyme for methionine-dependent tumors. The online version contains supplementary material available at 10.1007/s13205-025-04501-4.