Computational identification of DprE1 and InhA inhibitors from Azadirachta indica using docking, MD simulation and DFT analysis

Tuberculosis remains a major global health burden, primarily driven by prolonged treatment regimens and the rapid emergence of drug-resistant Mycobacterium tuberculosis strains. In this study, a comprehensive silico study has been done to identify potential natural inhibitors of two essential mycobacterial enzymes, InhA and DprE1, from phytochemicals of Azadirachta indica. A total of 418 compounds derived from neem were screened, followed by drug likeness filtering and molecular docking against InhA and DprE1. The ADMET, Lipinski’s rule of five, and toxicity analysis were done of deacytylgedunin and melianone. To identify the stability and flexibility of the melianone-InhA and descytylgedunin-DprE1 complexes, MD simulation for 500 ns was performed by GROMACS. Finally, the electronic stability and charge distribution of the two ligands were analyzed by Gaussian tool. The highest binding affinities toward InhA and DprE1 were exerted by melianone (-10.1 kcal/mol) and deacytylgedunin (-9.1 kcal/mol) respectively, even higher than that of various standard anti-tuberculosis drugs. The most relevant protein-ligand interactions were realized with conserved active site residues that are crucial for enzymatic activity. For both complexes, molecular dynamics simulations over 500 ns indeed confirmed structural stability and favorable binding behavior under dynamic conditions. ADMET and toxicity prediction showed deacetylgedunin and melianone were both acceptable in terms of their physicochemical properties and risk of acute toxicity. The TPSA values (89.27 Å of deacetylgedunin and 59.06 Å of melianone) indicate good permeability of the membrane and justifies their possible oral bioavailability. Their electronic stability was further supported by analysis with density functional theory as indicated by a consistent charge distribution during the docking and molecular dynamics simulation process. Altogether, these results indicate that deacetylgedunin and melianone have potential to lead drug development of new anti-tuberculosis agents and should be subjected to further experimental validation but in silico drug design methodology is only predictive and may not be able to fully reflect the complex in vivo pharmacokinetics and toxicity profiles.