EKSAKTA: Berkala Ilmiah Bidang MIPA
Open Access

Potential Hydrophobic Pocket of Squalene Synthase: An In Silico Analysis

1 Department of Chemistry, Faculty of Mathematics and Natural Sciences (FMIPA), Universitas Negeri Padang, Indonesia
Download PDF

Abstract

Cardiovascular disease cases increase due to consumption cholesterol dietary habit. It is well-known that squalence synthase (SQS) is the first committed enzyme for cholesterol synthesis. Therefore, SQS become target of anti-cholesterol. This paper aims to determine the potential binding pocket of SQS (PDB ID: 1EZF). Dogsitescorer, siteFinder, and DEPTH were used for binding pocket prediction and MOE 2009.10 was performed for molecular docking. We found that there are five out of 37 pockets which have druggability score above 0.8. Pocket_5 is the highest drugability and favorable for hydrophobic interaction, yet lower number of hydrogen bond with the ligand. However, Pocket_2, and Pocket_3 are suitable for hydrogen bond formation of ligand-protein. Molecular docking study showed that TAK-475, D99, and Cynarin inhibitors were embedded on the P_2 and P_3 of SQS, showing that P2_and P3 are promising binding pocket for ligand interactions. These results show a promising alternative to design anti-cholesterol using these potential pocket in silico.

References

1
Dietschy J M and Siperstein M D 1967 Effect of cholesterol feeding and fasting on sterol synthesis in seventeen tissues of the rat. J. Lipid Res. 8 97–104
2
WHO Raised cholesterol: Situation and trends
3
Sando K R and Knight M 2015 Nonstatin therapies for management of dyslipidemia: a review. Clin. Ther. 37 2153–79
4
Souich P du, Roederer G and Dufour R 2017 Myotoxicity of statins: Mechanism of action Pharmacol. Ther. 175 1–16
5
Mil A H M van, Westendorp R G J, Bollen E L E M, Lagaay M A and Blauw G J 2000 HMG-CoA Reductase Inhibitors in the Prevention of Stroke Drugs 59 1–6
Downloads
Download data is not yet available.

How to Cite

1.
Potential Hydrophobic Pocket of Squalene Synthase: An In Silico Analysis. EKSAKTA [Internet]. 2021 Mar. 27 [cited 2026 Sep. 4];22(1):18-26. Available from: https://eksakta.ppj.unp.ac.id/index.php/eksakta/article/view/263

Most read articles by the same author(s)