In silico discovery and cellular validation of PBM-342: a novel PPAR-β/δ modulator for skeletal muscle differentiation

Modulation of the peroxisome proliferator-activated receptor beta/delta (PPAR-β/δ) holds therapeutic potential for skeletal muscle regeneration and metabolism. However, the clinical development of classical agonists has been hampered by severe issues of non-specificity and metabolic toxicity. In this study, we implemented an in-silico strategy coupled with in-vitro functional validation to discover selective and safe modulators. Through a ligand-based virtual screening of the ZINC database, using the crystallographic agonist 'Compound 9' (PBM-0) as a structural template to favor isotype selectivity, and molecular docking analysis, PBM-342 was identified as the top-ranked candidate, exhibiting a favorable docking score (ΔG = −12.86 kcal/mol by flexible docking). Subsequent molecular dynamics simulations revealed that PBM-342 constrains the conformational dynamics of Tyrosine-437 in Helix-12, the structural determinant of the receptor transcriptional activation. Pharmacokinetic (ADME) profiling confirmed its optimal lipophilicity (Log P = 3.86) and the absence of inhibition of the critical hepatic isoenzyme CYP2D6. Consequently, in murine C2C12 cultures, the working concentration of PBM-342 (100 nM) promoted morphologically and transcriptionally, myotube fusion index (p < 0.0001) and fiber-type reprogramming, as evidenced by selective upregulation of the specific oxidative muscle fibers, myosin isoform MHCIIa (p < 0.01).