• Igustingurah Raka Bhaskarawilaputraka Department of Pharmacy, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia.
  • Azminah Azminah Department of Pharmacy, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia.
  • Linda Erlina Department of Pharmacy, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia.
  • Rezi Riadhi Syahdi Department of Pharmacy, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia.
  • Arry Yanuar Department of Pharmacy, Faculty of Pharmacy, Universitas Indonesia, Depok, Indonesia.


Objective: DNA hypermethylation is an abnormal epigenetic process catalyzed by DNA methyltransferase 1 (DNMT1). It is also one of the factors that cause non-communicable diseases such as cancer, diabetes, and other metabolic diseases. DNA hypermethylation can be reversed by suppressing DNMT1 activity using a DNMT inhibitor. This study was conducted to seek out inhibitor candidates among natural products.

Methods: The search for potential inhibitors was conducted through a virtual screening of the Indonesian Herbal Database using AutoDockVina as docking software. Twenty-five compounds known for their inhibitory activity against DNMT1 were used as actives and as a reference for generating decoys, which was done using the Directory of Useful Decoys, Enhanced.

Results: The 12 compounds with binding energies below the cutoff value were cassiamin C (A1), procyanidin B2 (B2), ent-epicatechin- (4alpha->8)-ent-epicatechin (C3), epicatechin-(4beta->8)-epicatechin-3-O-gallate (D4), neorhusflavanone (E5), 3-O-galloylepicatechin- (4beta->6)-epicatechin-3-O-gallate (F6), withanolide (G7), 3-O-galloylepigallocatechin-(4beta->6)-epigallocatechin-3-O-gallate (H8), cyanidin 3-(6’’-caffeylsophoroside)-5-glucoside (I9), epifriedelanol (J10), gallocatechin-(4alpha->8)-epicatechin (K11), and scutellarein 7-glucosyl-(1->4)- rhamnoside (L12). A1 had the lowest binding energy of −12.7 kcal/mol, whereas K11 had the highest of −11.5 kcal/mol.

Conclusions: The virtual screening yielded five potential DNMT1 inhibitors: Procyanidin B2, ent-epicatechin-(4alpha->8)-ent-epicatechin, epicatechin-(4beta->8)-epicatechin-3-O-gallate, neorhusflavanone, and cyanidin 3-(6’’-caffeylsophoroside)-5-glucoside.  

Keywords: Epigenetic, DNA methyltransferase inhibitor, Indonesian Herbal Database, Virtual screening, AutoDockVina.


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How to Cite
Bhaskarawilaputraka, I. R., A. Azminah, L. Erlina, R. R. Syahdi, and A. Yanuar. “VIRTUAL SCREENING OF INDONESIAN HERBAL DATABASE FOR DNA METHYLTRANSFERASE INHIBITORS”. Asian Journal of Pharmaceutical and Clinical Research, Vol. 10, no. 17, Oct. 2017, pp. 153-7, doi:10.22159/ajpcr.2017.v10s5.23120.
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