Structure based virtual screening of Malaysian plants for pancreatic lipase inhibitors  

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Adibah Amirah Abdul Nasir*, and Ezatul Ezleen Kamarulzaman

Pharmaceutical Drug Simulation Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 USM, Pulau Pinang, Malaysia.

*Corresponding author: Email addresses:

Citation: Nasir AAA & Kamarulzaman EE (2015) Structure based virtual screening of Malaysian plants for pancreatic lipase inhibitorsGenomic Medicine 2015, eds Le L & Pham S (Ho Chi Minh City, Viet Nam). 
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VJS Editor: Thu V. Vuong, University of Toronto, Canada


Obesity is now become pandemic in the whole worldwide. Obesity usually caused among city people who are having sedentary lifestyles than those who live in countryside. In Southeast Asia, Malaysia has the highest population of people having obesity in ASEAN region (1). Obesity is one of metabolic disorder diseases, which occurred because of imbalance between energy intakes (4). A body mass index greater than 30 kg/m2 is classified as overweight or obese. Obesity problems usually associated with many chronic diseases such as cardiovascular disease, diabetes type II, arteriosclerosis, and stroke. Orlistat is a known anti-obesity drug, which has been proved to give lowering weight effect by 35 percent reduction in dietary fats absorption (9).

A study on the human pancreatic lipase (PDB ID: 1LPB) is the most well studied protein for therapeutics of obesity via inhibition of pancreatic lipase (5,6,7). The main role of pancreatic lipase is to hydrolyze the dietary fat into fatty acids and glycerides to be able absorbed into small intestine. Therefore, by reducing fat absorption via pancreatic lipase inhibition, obesity can be reduced and treated.

Studies on natural products especially plants give a huge contribution towards drug discovery today (2). Many plant extracts such as Prunella vulgaris, Achyrantes aspera, Plumbago zeylanica and Rheum palmatum have been tested through in vivo and in vitro studies and showed that chemical constituents of these plants exhibit anti-obesity activity by increasing thermogenesis, increasing fat metabolism, suppressing food intake, and retard fat absorption via pancreatic lipase inhibition. (3,4,8).

Experimental and results

In silico study was carried out on selected plants to find the lead compounds that can inhibit pancreatic lipase. Malaysian ethno botanical plants that have potential in reducing body weight were selected to be the candidates of pancreatic lipase inhibitors. The chemical structures of the plants were taken from NADI database ( The three dimensional structure of pancreatic lipase was obtained from Protein Data Bank (PDB ID: 1LPB) with its inhibitor, MUP. Hydrogen atoms were added to the protein. MUP ligand was re-docked into the active pocket of the macromolecule with 50 x 50 x 60 in grid points in x, y, and z coordinates. The RMSD value for control docking is 1.14 Å. Therefore, parameters used for control docking can be further utilized in virtual screening of pancreatic lipase inhibitor.

Figure 1. Three-dimensional structure of 1LPB with the catalytic triad

The docking results showed that five plants associated with its chemical compounds showing lower free energy binding such as 13-cis-beta-carotene from Anacardium occidentale (-13.52 kcal/mol), phyllocladene from Syzgium aromaticum (-9.22 kcal/mol), morinthone from Morinda citrofolia (-9.58 kcal/mol), stigmasterol from Punica granatum (-12.3 kcal/mol), and 3-beta-25-Dihydroxy-5-beta-19-epoxycucurbita-6,(23E)-diene from Momordica charantia (-11.78 kcal/mol). Docked ligands have formed molecular interactions with residues Ala178, Leu153, Phe77, Tyr114, Ser152 and Phe215 through hydrogen bond and hydrophobic interactions.

All docking simulation and visualization works were performed by Autodock Tools version 1.5.6, AutoDock4 software and Discovery Studio 4.0, Accelrys Software Inc. respectively.

Figure 2. Five chemical compounds from selected Malaysian plants with weight reducing potential


Bioactive compounds from Anacardium occidentale, Syzgium aromaticum, Morinda citrofolia, Punica granatum, and Momordica charantia could be a good potential as lead compounds for treating obesity via pancreatic lipase inhibition.


1. Thailand rank seconds in ASEAN for prevalence of obesity. Southeast Asian Consumer Council. 2014. Retreived from
2. Bhutani KK & Gohil VM (2010) Natural products drug discovery research in India: Status and appraisal. Indian Journal of Experimental Biology 48:199-207.
3. Zheng CD, Duan YQ, Gao JM, & Ruan ZG (2010) Screening for anti-lipase properties of 37 traditional Chinese medicinal herbs . Journal of Chinese Medicine Association 73(6):319-324 (View Article). 
4. Verma RK & Paraidathathu T (2014) Herbal medicines used in the traditional Indian medicinal system as a therapeutic treatment option for overweight and obesity management: A review. International Journal of Pharmacy and Pharmaceutical Sciences 6(2):40-47.
5. Nguyen HA, et al. (2013) Design, synthesis and biological evaluation of some chalcone derivatives as potential pancreatic lipase inhibitors. The 17th International Electronic Conference on Synthetic Organic Chemistry.
6. Mohammad M, Al-Masri IM, Issa A, Khdair A, & Bustanji Y (2012) Inhibition of pancreatic lipase by berberine and dihydroberberine: an investigation by docking simulation and experimental validation. Medicinal Chemistry Research 22 (5):2273-2278.
7. Al-Hiari YM, et al. (2014) Fluoroquinolones: novel class of gastrointestinal dietary lipid digestion and absorption inhibitors. Medicinal Chemistry Research 23 (7):3336-3346.
8. Bustanji Y, et al.  (2011) Screening of some medicinal plants for their pancreatic lipase inhibitory potential. Jordan Journal of Pharmaceutical Sciences 4(2):81-88.
9. Gholamhoseinian A, Shahouzehi B, & Sharifi-far F (2010) Inhibitory effect of some plant extracts on pancreatic lipase.  International Journal of Pharmacology, 6:18-24 (View Article)

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