LC–MS Profiling, In Silico Docking–MD and ADMET of Uncaria gambir Roxb. for p38 MAPK Inhibition

Introduction: p38 mitogen-activated protein kinase (MAPK) is a pivotal regulator of inflammatory and cancer pathways. This study investigates phytochemicals from Bajakah (Uncaria gambir Roxb.) bark as potential p38 MAPK inhibitors, integrating LC–MS profiling with computational drug discovery. Methods: Bajakah bark extract was profiled by liquid chromatography–high-resolution mass spectrometry (LC–HRMS) to identify major phytochemicals. Promising non-toxic candidates were selected via in silico toxicity prediction (ProTox-II) and ADME assessment (pkCSM). Molecular docking against p38 MAPK (PDB ID: 3QUE) was performed using AutoDock Vina, followed by 50 ns molecular dynamics simulations with GROMACS and MM/PBSA binding free energy calculations using gmx_MMPBSA. Results: LC–HRMS identified ten major phytochemicals; 8-methylnaphthalene-1,2-diol (Diol) and methyl cinnamate exhibited non-toxic profiles (LD_₅₀ > 2,600 mg/kg; no CYP450 liabilities) with favorable ADME properties. Molecular docking revealed binding energies of −8.04 kcal/mol (Diol), −11.4 kcal/mol (Skepinone-L reference), and −6.4 kcal/mol (methyl cinnamate). Both Diol and Skepinone-L engaged conserved hydrophobic residues (VAL38 and LYS53), with Diol showing additional engagement at LEU104, and docking RMSD validation within 2.5 Å. Molecular dynamics confirmed stable Diol–p38 complex binding (RMSD ~0.30 nm), with balanced solvent accessibility, stable dynamic binding dominated by electrostatic interactions, and adaptive conformational sampling. MM/PBSA analysis revealed binding free energies of −21.9 kcal/mol (Diol) and −32.9 kcal/mol (Skepinone-L), with Diol's affinity driven by electrostatic interactions (−29.62 kcal/mol). Conclusions: 8-Methylnaphthalene-1,2-diol emerges as a promising natural p38 MAPK inhibitor candidate with favorable safety profiles and dynamic binding properties, warranting biochemical validation and structure–activity relationship optimization.