In Silico Identification of Natural Compounds Targeting the Essential ClpP1P2 Protease in Mycobacterium tuberculosis

Drug-resistant strains of tuberculosis (TB) is caused by Mycobacterium tuberculosis and are making the disease a global health emergency. This calls for new treatments that target unidentified bacterial pathways. In order to find natural inhibitors of the ClpP1P2 protease that is a crucial virulence factor for mycobacterial survival, our study used computational techniques. We used molecular docking to screen 100 compounds against the ClpP1P2 structure (PDB: 4U0G) while giving preference to ligands with higher binding affinities than reference medications (ethambutol, isoniazid). To evaluate therapeutic potential, we subjected top hits to target fishing, toxicity prediction and pharmacokinetic profiling. Our top two hit compounds were neodiospyrin and arbutin respectively. According to physiologically-based pharmacokinetic modelling, neodiospyrin was the best candidate due to its remarkable binding energy (−13.28 kcal/mol), ligand efficiency (0.474), and intracellular lung accumulation. Also, Arbutin showed good safety but restricted tissue penetration. Through Prediction of Activity Spectra of substances (PASS) analysis, both compounds demonstrated complementary biological activities like modulation of apoptosis and anti-inflammatory effects. Target fishing indicated possible human off-target interactions (GPCRs for arbutin, kinases for neodiospyrin) but this requires further experimental validation. Our findings presented and demonstrated the potential of ClpP1P2 inhibition for tuberculosis treatment, with neodiospyrin identified as a key candidate for further improvement against drug-resistant strains.