Homology modelling and molecular dynamics evaluation of kaempferol and quercetin binding to litchi polyphenol oxidase
Abstract
Abstract Postharvest pericarp browning, caused principally by the enzymatic oxidation of endogenous phenolics by polyphenol oxidase (PPO), is a major factor limiting the shelf life and commercial value of litchi ( Litchi chinensis Sonn.), yet no experimental three-dimensional structure of litchi PPO (LcPPO) is available and its candidate inhibitors have not previously been examined at the molecular level. This work establishes a structure-based, dynamics-tested framework for evaluating candidate anti-browning agents against LcPPO. A validated homology model of the mature enzyme, with its binuclear type-3 copper centre reconstituted and its auto-inhibitory C-terminal domain removed, was used to screen fourteen compounds. The two best-ranked litchi flavonols, kaempferol (− 6.89 kcal/mol) and quercetin (− 6.58 kcal/mol), obtained more favourable scores than the natural substrate (−)-epicatechin and were predicted to occupy the substrate-access channel, with quercetin forming more hydrogen bonds than kaempferol. Independent 20 ns molecular dynamics simulations showed that, although the enzyme remained structurally stable, neither flavonol persistently maintained its docked pose: quercetin reoriented abruptly at approximately 4–5 ns and kaempferol migrated more gradually, behaviour corroborated by RMSD, hydrogen-bond and centre-of-mass analyses, though both ligands remained protein-associated throughout. Classical metal-chelating inhibitors scored weakly, reflecting the inability…
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