In silico characterization of the bromelain–NLRP3 inflammasome interaction: Insights from homology modeling, molecular docking, and MD simulation

Abstract

• A docking-grade bromelain homology model was built (ERRAT: 100; QMEANDisCo: 0.91). • HADDOCK 2.4 docking revealed electrostatic-driven binding to the NLRP3 pyrin domain. • Sub-nanomolar affinity was predicted (Kd = 0.74 nM; ΔG = −12.5 kcal/mol). • Dual salt bridges (Lys64–Asp60; Lys179–Glu110) anchor the interfacial recognition. • 100 ns MD simulation confirmed complex stability, compactness, and interfacial tightening. Aberrant activation of the NLRP3 inflammasome underpins a broad range of chronic inflammatory conditions, yet pharmacologically safe agents capable of directly intercepting its assembly remain scarce. Bromelain, a multi-enzyme cysteine protease cocktail sourced from Ananas comosus stems, possesses well-characterized immunomodulatory properties; however, whether it can physically occupy the NLRP3 pyrin domain has not been investigated at the atomic level. A stereochemically validated comparative model of stem bromelain (ERRAT quality factor: 100; QMEANDisCo: 0.91) was subjected to semi-flexible protein–protein docking against the human NLRP3 pyrin domain (PDB: 3QF2 ) via HADDOCK 2.4, guided by consensus-derived interfacial residues. Thermodynamic favorability was quantified using PRODIGY and independently cross-checked by MM/GBSA decomposition. Temporal persistence of the predicted pose was evaluated over a 100 ns unrestrained molecular dynamics trajectory (GROMACS/CHARMM36; physiological ionic strength, 0.15 M NaCl). The preferred docking solution was governed by charge–charge complementarity (ΔG_elec = −390.1 kcal/mol; buried interface > 2000 Ų), yielding a predicted dissociation constant in the sub-nanomolar regime (K_d = 0.74 nM; ΔG = −12.5 kcal/mol). Nine intermolecular hydrogen bonds and two salt bridges were mapped, with the Lys 64–Asp 60 contact serving as the principal dual-function anchor. The hundred-nanosecond trajectory confirmed conformational equilibrium (RMSD plateau ∼0.45 nm); preserved globular compactness (R_g = 2.64–2.71 nm); and showed spontaneous interfacial tightening marked by concurrent hydrogen bond accumulation and solvent-accessible surface contraction across the 70–100 ns window. These findings provide a detailed residue-resolution computational demonstration that bromelain occupies the NLRP3 pyrin domain with sub-nanomolar predicted affinity, maintained by a dual electrostatic anchor topology. The results establish bromelain as a structurally rationalized natural candidate for inflammasome-directed anti-inflammatory drug development.