Identification of zebrafish fumarate hydratase active site by molecular docking and simulation studies

Abstract

Fumarate hydratase (FH), one of the members of TCA cycle, acts as a catalyte for the synthesis of malate from fumarate. FH has been proposed to play as a tumour suppressor leading to the pathogenicity of leiomyomas, renal cell carcinoma and paraganglioma. Mutations in the active site of FH lead to alteration in the protein structure. Similarly, binding of several chemical inhibitors to the active site also leads to the disruption of protein structural integrity thereby leading to protein dysfunction. Therefore, in order to address this mechanism leading to cancer, the binding efficiency of potential human FH inhibitor citrate to zebrafish fh has been extensively analysed in this study by molecular docking and simulation experiments followed by quantification of fumarate hydratase enzyme activity to validate and confirm the findings. Molecular docking revealed stronger interaction of zebrafish fh protein with inhibitor citrate when compared to natural substrate fumarate. Study on the dynamics of docked structures further confirmed that citrate was found to possess more binding affinity than fumarate. In vitro biochemical analysis also revealed concentration dependent potential inhibitory effect of citrate on zebrafish fh, thus confirming the findings of the in-silico experiments.

Communicated by Ramaswamy H. Sarma

Keywords:

• Fumarate hydratase
• zebrafish
• citrate
• molecular dynamics
• TCA cycle
• in silico

Acknowledgements

The authors would also like to thank SRMIST for the facilities for carrying out the experiments. The authors of the article would like to thank DST-SERB, Government of India for the funding (grant no. YSS/2014/000017).

Disclosure statement

No potential conflict of interest was reported by the author(s).