Design and In Silico Optimization of Pyrazolopyridine-Based Pantothenate Synthetase (PanC) Inhibitors as Novel Anti-Tuberculosis Leads

Background Tuberculosis (TB), caused by Mycobacterium tuberculosis , remains a major global health challenge, particularly due to the rising prevalence of multidrug-resistant strains. Pantothenate synthetase (PanC), a key enzyme in coenzyme A biosynthesis, represents a promising and selective therapeutic target. Methods This study employed an integrated structure-based drug design workflow combining energy-optimized pharmacophore modeling, enrichment validation, molecular docking, MM-GBSA binding free energy calculations, ADMET prediction, and 200 ns molecular dynamics (MD) simulations to optimize pyrazolopyridine derivatives targeting PanC (PDB ID: 3COY). Results A validated six-feature pharmacophore model demonstrated strong screening performance (AUC = 0.86; EF1% = 12.4). Virtual screening of 1,000 ChEMBL compounds yielded 55 high-confidence candidates, followed by hierarchical docking and free energy analysis. Designed derivatives M45 and M10 showed superior binding (XP scores: –10.96 and –10.49 kcal/mol; ΔGBind: –76.40 and –74.59 kcal/mol), outperforming the reference ligand (–40.10 kcal/mol). Key stabilizing residues included Lys269, Asp139, Tyr175, and Ser301. MD simulations confirmed high stability (RMSD ≤ 2.3 Å; hydrogen bond occupancy > 65%), with M45 exhibiting a deeper free energy minimum. ADME analysis indicated favorable drug-likeness and high gastrointestinal absorption. Conclusion M45 emerges as a promising PanC inhibitor with strong thermodynamic stability and favorable pharmacokinetic properties. This study establishes a robust computational framework for accelerating early-stage anti-TB drug discovery. However, the study is limited by the absence of experimental IC₅₀ and MIC validation data, possible synthetic accessibility constraints that may affect high-throughput synthesis, and predicted CYP inhibition profiles that suggest potential drug-drug interaction risks requiring further preclinical evaluation.