Abstract A12: Brazilian propolis as a source of novel DNA methyltransferase inhibitors: A computer-aided discovery and in vitro approaches
Authors: João Henrique Maia Assumpção, Agnes Alessandra Sekijima Takeda, José Maurício Sforcin, Cláudia Aparecida Rainho
Journal: Clinical Cancer Research (2018)

Abstract Over the past decades, propolis has been attracting scientific attention due to its biologic and pharmacologic properties. Propolis is a natural resinous substance produced by honeybees from several parts of plants, which are related to its chemical composition. Around 300 substances have been identified in different samples of propolis, whose extract shows a plethora of biologic and therapeutic activities, including the antitumor effects reported in preclinical researches. Globally, it has been demonstrated that this complex mixture can disrupt oncogene signaling pathways, inhibit cell growth and proliferation, induce apoptosis, and show antiangiogenic effects. Indeed, in a preliminary assay, we observed that a Brazilian ethanolic extract of propolis (EEP) inhibits cell proliferation of triple-negative breast cancer cell lines (BT-20, BT-549, MDA-MB-231, and MDA-MB-436) in a dose- and time-dependent manner. The chemical composition of this propolis sample was determined by Gas Chromatography-Mass Spectrometry (GC-MS): flavonoids, phenolic acids, and esters were the major compounds. Previous studies reported that compounds of natural origin target epigenetic-modifying enzymes, such as DNA methyltransferases (DNMTs), and reactivates methylation-silenced genes in cancer. Thus, we hypothesized that the effects of propolis in cancer cell lines are, in part, mediated by epigenetic mechanisms. Thus, the present study aims at the identification of propolis-derived molecules able to interact with human DNMT1 using an in silico approach and experimental evaluation by in vitro DNA methylation assay. The potential ligands were selected based on the chemical composition of Brazilian propolis sample: benzyl benzoate, caffeic acid, CAPE (caffeic acid phenethyl ester), dihydrocinnamic acid, farnesol, ferulic acid, kampeferide, p-coumaric acid, hydrocinnamic acid, and spathulenol. For molecular docking predictions two software programs were selected: SwissDock webserver (www.swissdock.ch) and AutoDock 4.2 (autodock.scripps.edu/). The chemical structures of probable ligands were retrieved from PubChem database (pubchem.ncbi.nlm.nih.gov) and the crystallographic model of human DNMT1 in complex with S-adenosyl-homocisteine (SAH) (PDBID: 4WXX) was used as a receptor for docking. All structures were prepared for docking using Chimera 1.11.2 (cgl.ucsf.edu/chimera). The known interactions of methyl group donator S-adenosyl-methionine (SAM) and the intrinsic inhibitor (SAH) of the DNMT1 were used as references. The active site of the interaction located in the Methyltransferase (Mtase) domain (amino acids residues 1135-1605) between DNMT1 and SAH was defined as an area of interest on both programs. The highest accuracy configuration was chosen for molecular docking in the SwissDock. The Autodock 4.2 predictions used the Lamarckian Genetic Algorithm (LA-GA) and 150 runs were performed in both programs. The calculated conformations were clustered using Gromacs (www.gromacs.org) with the Gromos algorithm, using a RMSD (Root-Mean-Square Deviation) of atomic positions cutoff of 1Å. The representative structure of the 3 clusters with more conformations of each ligand was analyzed with LigPlot+ (www.ebi.ac.uk/thornton-srv/software/LigPlus/) to verify the contacts with the amino acids residues of DNMT1. Our docking results indicate that dihydrocinnamic acid, farnesol, and CAPE have the most contacts in common to SAH-DNMT1 complex obtained from the crystallographic model and negative free binding energy: -5.09, -6.05, and -7.99 kcal/mol, respectively. These finding are suggestive of ligand-receptor interactions and are being validated by in vitro assay by inhibition of M.SssI methylase activity in the presence of the selected compounds in the final concentrations varying from 10 to 500 μmol/L. Our data suggest that propolis-derived compounds can interact with DNMT1 and could be included in future studies of new drugs for epigenetic therapy. Citation Format: João Henrique Maia Assumpção, Agnes Alessandra Sekijima Takeda, José Maurício Sforcin, Cláudia Aparecida Rainho. Brazilian propolis as a source of novel DNA methyltransferase inhibitors: A computer-aided discovery and in vitro approaches [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A12.