Virtual screening and docking analysis of novel ligands for selective enhancement of tea (Camellia sinensis) flavonoids

Food Chem X. 2022 Jan 18:13:100212. doi: 10.1016/j.fochx.2022.100212. eCollection 2022 Mar 30.

Abstract

Flavour of tea is mainly contributed by a group of polyphenols - flavonoids. However, the content of flavonoid fluctuates seasonally and is found to be higher in the first flush of tea, when compared to the second flush. This disparity in the flavonoid content, and hence taste, incurs heavy economic losses to the tea plantation industry each harvest season. For our present study, four key product-specific enzymes (PAL, FNS, FLS and ANS) of the tea-specific flavonoid pathway were selected to perform molecular docking studies with specific virtually screened allosteric modulators. Results of docking analyses showed Naringenin, 2-Morpholin-4-ium-4-ylethanesulfonate, 6-C-Glucosylquercetin, 2-Oxoglutaric acid, 3,5,7,3',4'-pentahydroxyflavone to be capable of improving the spontaneity of the enzyme-substrate reactions in terms of docking score, RMSD values, and non-covalent interactions (H-bond,hydrophobic interaction, Π-stacking, salt bridge, etc.). Further, the evolutionary relationship of tea flavonoid pathway enzymes was constructed and compared with related taxa. The codon usage-based of tea flavonoid biosynthetic genes indicated the non-biasness of their nucleotide composition. Overall this study will provide a direction towards putative ligand-dependent enhancement of flavonoid content, irrespective of seasonal variation.

Keywords: 4CL, Tyrosine ammonia lyase; AMF, Arbuscular Mycorrhizal Fungi; ANR, anthocyanidin reductase; ANS, anthocyanidinsynthase; C4H, trans-cinnamate-4-; CAI, Codon Adaptation Index; CHI, chalcone isomerase; CHS, 4-coumarat; CoA, ligase chalcone synthase; Codon usage indices; DFR, dihydroflavonol 4-reductase; ENc, Effective number of codons; F3H, flavanone 3-hydroxylase; F3′5′H, flavonoid 3′5′-hydroxylase; F3′H, flavonoid 3′-hydroxylase; FLS, Flavonol synthase; FNS, flavone synthase; Flavonoids; GC1, GC2, and GC3-GC, content at the first, second, and third codon positions; GC3s, frequency of either G or C at the third codon position of synonymous codons; H 0, null hypothesisno selection; IAA, Indole acetic acid; LAR, leucoanthocyanidin reductase; Ligands; Molecular docking; PAL, phenylalanine ammonia-lyase; RMSD, root-mean-square deviation; RSCU, Relative Synonymous Codon Usage; TAL, monooxygenase; Tea flush; UGT72, UDP-3 glycosyltransferases; Virtual screening.