Title:Effect of Withaferin-A, Withanone, and Caffeic Acid Phenethyl Ester on
DNA Methyltransferases: Potential in Epigenetic Cancer Therapy
Volume: 24
Issue: 4
Author(s): Vipul Kumar, Jaspreet Kaur Dhanjal, Anissa Nofita Sari, Mallika Khurana, Sunil C. Kaul, Renu Wadhwa*Durai Sundar*
Affiliation:
- Department of Cellular and Molecular
Biotechnology, National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba, 3058565, Japan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas,
New Delhi, 110016, India
Keywords:
Withaferin-A, Withanone, Caffeic acid phenethyl ester, DNMT, Methyltransferase, Cancer, Therapy.
Abstract:
Background: DNA methyltransferases (DNMTs) have been reported to be potential
drug targets in various cancers. The major hurdle in inhibiting DNMTs is the lack of knowledge
about different DNMTs and their role in the hypermethylation of gene promoters in cancer cells.
Lack of information on specificity, stability, and higher toxicity of previously reported DNMT inhibitors
is the major reason for inadequate epigenetic cancer therapy. DNMT1 and DNMT3A are
the two DNMTs that are majorly overexpressed in cancers.
Objective: In this study, we have presented computational and experimental analyses of the potential
of some natural compounds, withaferin A (Wi-A), withanone (Wi-N), and caffeic acid
phenethyl ester (CAPE), as DNMT inhibitors, in comparison to sinefungin (SFG), a known dual inhibitor
of DNMT1 and DNMT3A.
Methods: We used classical simulation methods, such as molecular docking and molecular dynamics
simulations, to investigate the binding potential and properties of the test compounds with
DNMT1 and DNMT3A. Cell culture-based assays were used to investigate the inactivation of
DNMTs and the resulting hypomethylation of the p16INK4A promoter, a key tumour suppressor that
is inactivated by hypermethylation in cancer cells, resulting in upregulation of its expression.
Results: Among the three test compounds (Wi-A, Wi-N, and CAPE), Wi-A showed the highest
binding affinity to both DNMT1 and DNMT3A; CAPE showed the highest affinity to DNMT3A,
and Wi-N showed a moderate affinity interaction with both. The binding energies of Wi-A and
CAPE were further compared with SFG. Expression analysis of DNMTs showed no difference between
control and treated cells. Cell viability and p16INK4A expression analysis showed a dose-dependent
decrease in viability, an increase in p16INK4A, and a stronger effect of Wi-A compared to
Wi-N and CAPE.
Conclusion: The study demonstrated the differential binding ability of Wi-A, Wi-N, and CAPE to
DNMT1 and DNMT3A, which was associated with their inactivation, leading to hypomethylation
and desilencing of the p16INK4A tumour suppressor in cancer cells. The test compounds, particularly
Wi-A, have the potential for cancer therapy.
