The molecular docking and molecular dynamics study of flavonol synthase and flavonoid 3’-monooxygenase enzymes involved for the enrichment of kaempferol

Abstract

Kaempferol is a natural flavonol that shows many pharmacological properties including anti-inflammatory, antioxidant, anticancer, antidiabetic activities etc. It has been reported in many vegetables, fruits, herbs and medicinal plants. The enzyme flavonol synthase (FLS, EC 1.14.20.6) catalyses the conversion of dihydroflavonols to flavonols. Whereas flavonoid 3’-monooxygenase (F3’H, EC 1.14.14.82) catalyses the hydroxylation of dihydroflavonol, and flavonol. FLS is involved in the synthesis of the kaempferol whereas F3’H causes degradation of kaempferol. The present study aimed to analyse the binding affinity, stability and activating activity of enzyme FLS as well as inhibitory activity of enzyme F3’H involved in the enrichment of the kaempferol using the in-silico approaches. Computational study for physico-chemical properties, conserved domain identification, 3-D structure prediction and its validation, conservation analysis, molecular docking followed by molecular dynamics analysis of FLS and F3’H, protein-activator (FLS-LIG Complex) and protein-inhibitor (F3’H-LIG Complex) complexes have been performed. Other structural analyses like root mean square fluctuation (RMSF), root mean square deviation (RMSD), surface area solvent accessibility (SASA), radius of gyration (Rg), hydrogen bond analysis, principal component analysis (PCA), Poisson-Boltzmann analysis (MM_PBSA) and the dynamic cross correlation map (DCCM) analysis to explore the structural, functional and thermodynamic stability of the proteins and the complexes were also studied. The molecular docking result showed that FLS binds strongly with the activator ascorbate (CID _54670067) while F3’H binds with the inhibitor ketoconazole (CID_456201). The most powerful inhibitor (ketoconazole for F3’H) and activator (ascorbate for FLS) is determined by computing the thermodynamic binding free energy through MM_PBSA analysis. The current work provides wide-ranging structural and functional information about FLS and F3’H enzymes showing detailed molecular mechanism of kaempferol biosynthesis and its degradation and hence kaempferol enrichment. Finding of the present work opens up new possibilities for future research towards enrichment of kaempferol by using activator (ascorbate) for FLS and inhibitor (ketoconazole) for F3’H as well as for its large-scale production using in vitro approaches.

Communicated by Ramaswamy H. Sarma

Keywords:

• Conformational flexibility
• Docking
• dynamic cross correlation matrix (DCCM)
• Flavonol synthase (FLS)
• Flavonoid 3’-monooxygenase (F3’H)
• FLS-LIG Complex
• F3’H-LIG Complex
• Molecular dynamics (MD)
• Poisson-Boltzmann analysis
• Principal Component Analysis (PCA)
• Root mean square deviation (RMSD)
• Root mean square fluctuation (RMSF)

Acknowledgement

Bioinformatics facility provided by DBT, GOI, through BTISnet SubDIC to Department of the Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, India for docking and molecular dynamics studies is acknowledged. Suggestions related to docking and molecular dynamics studies provided by Dr. Alok Jain, Assistant Professor, Department of the Bioengineering and Biotechnology, BIT Mesra Ranchi, India is also acknowledged.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by DST/INSPIRE Fellowship (as Junior Research Fellowship) awarded to GK by GOVERNMENT OF INDIA, MINISTRY OF SCIENCE and TECHNOLOGY, Department of Science and Technology Bhawan, New Mehrauli Road, New Delhi-110016, India having Grant No. [IF180386].