Screening Virtual and Binding Mode Elucidation of Compounds in Garlic (Allium Sativum L.) as an Inhibitor Advanced Glycation end Products Receptor

  • Esti Mulatsari Universitas Pancasila
  • Esti Mumpuni Fakultas Farmasi Universitas Pancasila
  • Ikhsan Ramadhan Fakultas Farmasi Universitas Pancasila


Diabetic has long-term effects such as atherosclerosis, nephropathy, and retinopathy caused by the formation of Advanced Glycation End Products (AGEs). In vitro studies on garlic extract (Allium sativum L.) have been carried out on the inhibition activity of AGEs formation, but inhibitory mechanisms and which active compounds are involved in these activities are unknown. This study aims to do a virtual screening of garlic compounds (Allium sativum L.) on Advanced Glycation Endproduct receptors so that active compounds can be considered as candidates for drug compounds. The method used is molecular docking with PLANTS, YASARA, MarvinSketch software, and visualization of test compound bonds on receptor amino acids using PyMOL. Pyridoxamine and Aminoguanidine as a positive control of AGEs inhibitors. The docking results of 24 test compounds obtained seven compounds that active in inhibiting 3B75 receptor and five compounds in 3O3U receptor. Candidates for drug compounds consist of organosulfur, phenols and flavonoids. Ɣ-glutamyl-cysteine, E-ajoene, Nα- (1-Deoxy-Dfructose-1-YL) -L-Arginine, Kaempferol-3-o-β-D-glucopyranose, and Iso-rhamnetin-3-o-β -D-glucopyranose are compounds in garlic which have an ability to inhibit 3B75 and 3O3U receptors and predicted have better activity than pyridoxamine and aminoguanidine.


1. Rashid G, Korzets Z, Bernheim J. Advanced glycation end products stimulate tumor necrosis factor-alpha and interleukin-1 beta secretion by peritoneal macrophages in patients on continuous ambulatory peritoneal dialysis. Isr Med Assoc J. 2006; 8(1):36–9.

2. Sovia E, Jenderal U, Yani A. Aktivitas inhibisi ekstrak bawang putih dan S-metil sistein terhadap reaksi glikasi albumin secara in vitro. Maranatha Journal of Medicine and Health 2014 ; 98 – 109.

3. Singh R. Morinda citrifolia L. (Noni): A review of the scientific validation for its nutritional and therapeutic properties. J Diabetes Endocrinol. 2012 ; 3(6):77–91.

4. Neeper M, Marie A, Brett J, Yanq S Du, Pan YE, Elliston K, et al. Cloning and expression of a cell surface receptor for advanced glycosylation end products of proteins. J Biol Chem. 1992 ; 30 : 14998–5004.

5. Penumutchu SR, Chou R-H, and Yu C. Structural Insights into Calcium-Bound S100P and the V Domain of the RAGE Complex. PLoS ONE 2014 ; 9(8): e103947.

6. Adrover M, Vilanova B, Frau J, Muñoz F, and Donoso J. The pyridoxamine action on Amadori compounds : A reexamination of its scavenging capacity and chelating effect. Bioorg Med Chem. 2008 ; 16:5557–69.

7. Saputri KE, Fakhmi N, Kusumaningtyas E, Priyatama D, Santoso B. Docking molekular potensi anti diabetes melitus tipe 2 turunan zerumbon sebagai inhibitor aldosa reduktase dengan autodock-vina. Chim Nat Acta. 2016;4(1):16.

8. Purwanggana A, Mumpuni E, Mulatsari E. In vitro and In silico antibacterial activity of 1,5-bis(3’-ethoxy-4’-hydroxyphenyl)-1,4-pentadiene-3-one. Int J. Pham Pham Sci 2018 ;(10) 5 : 71 – 76.

9. Mumpuni E and Mulatsari E., Molecular Docking and Toxicity Test of Apigenin Derivative Compounds as an Anti-Aging Agent. J Applied Chem. Sci. 2018 ; 5(1): 409-413.

10. Anita Y, Radifar, M., Kardono, L.B., & Hanafi, M. & Istyantono, E.P,. Structure-based design of eugenol analogs as potential estrogen receptor antagonists. Bioinformation. 2012 ; 8 (19) : 901 – 6.

11. Triana V. Macam-macam vitamin dan fungsinya dalam tubuh manusia. J Kesehat Masy. 2006 ; 40–7.

12. Korb O, Stützle T, Exner TE. PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design. Lect notes Comput Sci vol 4150 Ant colony Optim swarm Intell - ANTS2006 Proc. 2006 ; 4150 : 247–58.

13. Purnomo H. Molecular docking PLANTS (Penambatan molekul PLANTS) (Protein-Ligand-Ant-System). Yogyakarta: Pustaka Pelajar; 2011.

14. Balavignesh V, Srinivasan E, Ramesh Babu NG, Saravanan N. Molecular docking study on NS5B polymerase
of hepatitis c virus by a screening of volatile compounds from acacia concinna and ADMET prediction. Int J Pharm Life Sci 2013 ; 4 : 2548 - 58.

15. Kumar KM, Anitha P, Sivasakthi V, Bag S, Lavanya P, Anbarasu A, et al. In silico study on penicillin derivatives and cephalosporins for upper respiratory tract bacterial pathogens. Biotech. 2014 ; 4 : 241-51.

16. diakses 3 Juni 2018

17. diakses 3 Juni 2018
How to Cite
MULATSARI, Esti; MUMPUNI, Esti; RAMADHAN, Ikhsan. Screening Virtual and Binding Mode Elucidation of Compounds in Garlic (Allium Sativum L.) as an Inhibitor Advanced Glycation end Products Receptor. JURNAL ILMU KEFARMASIAN INDONESIA, [S.l.], v. 17, n. 2, p. 210-217, oct. 2019. ISSN 2614-6495. Available at: <>. Date accessed: 18 nov. 2019. doi: