What question did this study set out to answer?

The study aims to characterize chalcone synthase enzymes from various medicinal plants using structural and physicochemical analyses.

March 26, 2026Open Access

Integrative structural and physicochemical characterization of chalcone synthase enzymes from medicinal plants using AlphaFold, molecular docking, and molecular dynamics

Key Points

The study aims to characterize chalcone synthase enzymes from various medicinal plants using structural and physicochemical analyses.
Conducted in silico analysis of CHS from 13 medicinal plants and Arabidopsis thaliana as reference.
Aligned protein sequences using ClustalW to reveal conserved motifs.
Utilized AlphaFold for predicting enzyme structures and performed molecular docking with p-coumaroyl-CoA.
Executed molecular dynamics simulations to assess the stability of CHS-ligand complexes.
Identified strong conservation of catalytic motifs across species, indicating structural adaptation.
AlphaFold structures displayed a common thiolase-like fold with species-specific substrate-binding channels.
Molecular docking confirmed stable substrate placement in the catalytic pocket of different CHS variants.
Molecular dynamics showed conformational stability of enzyme-ligand complexes with favorable binding energetics.

Abstract

Chalcone synthase (CHS) is the entry-point enzyme of the flavonoid biosynthetic pathway, catalyzing the first committed step toward the production of diverse bioactive metabolites with antioxidant, anti-inflammatory, and anticancer properties. Here, we conducted a comparative in silico characterization of CHS from 13 medicinal plants, with Arabidopsis thaliana included as reference species. Protein sequences retrieved from UniProtKB were aligned using ClustalW, revealing strong conservation of key motifs, particularly the catalytic triad (Cys-His-Asn), GFGPG motif, and catalytic loop. Physicochemical profiling indicated interspecies variability in predicted protein stability, hydrophobicity, and thermostability, reflecting structural adaptation rather than direct functional divergence. AlphaFold-predicted structures consistently adopted the conserved thiolase-like αβαβα-fold characteristic of type III polyketide synthases, while exhibiting species-specific variations in the substrate-binding channel architecture. These variations are interpreted as structural features that may influence substrate accommodation and selectivity. To assess functional relevance, molecular docking with p-coumaroyl-CoA further confirmed stable substrate placement within the conserved catalytic pocket across species. Furthermore, 100-ns molecular dynamics simulations of representative crystal-derived and AlphaFold-predicted CHS-ligand complexes confirmed conformational stability, which was supported by MM-PBSA calculations revealing favorable binding energetics dominated by van der Waals interactions. Collectively, this study integrates sequence, structural, and dynamic analyses to establish a computational framework for comparative CHS characterization in medicinal plants. While the findings are derived exclusively from in silico approaches, they provide structurally grounded hypotheses that may guide future experimental validation, enzyme engineering, and pathway-oriented exploration of flavonoid biosynthesis.

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