Generic placeholder image

Anti-Cancer Agents in Medicinal Chemistry


ISSN (Print): 1871-5206
ISSN (Online): 1875-5992

Research Article

Novel Dihydropyrimidinone-Derived Selenoesters as Potential Cytotoxic Agents to Human Hepatocellular Carcinoma: Molecular Docking and DNA Fragmentation

Author(s): Jean C. Benassi, Flavio A.R. Barbosa, Valdelúcia M.A.S. Grinevicius, Fabiana Ourique, Daniela Coelho, Karina B. Felipe, Antônio L. Braga, Danilo W. Filho and Rozangela C. Pedrosa*

Volume 21 , Issue 6 , 2021

Published on: 28 July, 2020

Page: [703 - 715] Pages: 13

DOI: 10.2174/1871520620666200728124640

Price: $65


Background and Objective: Evidence point out promising anticancer activities of Dihydropyrimidinones (DHPM) and organoselenium compounds. This study aimed to evaluate the cytotoxic and antiproliferative potential of DHPM-derived selenoesters (Se-DHPM), as well as their molecular mechanisms of action.

Methods: Se-DHPM cytotoxicity was evaluated against cancer lines (HeLa, HepG2, and MCF-7) and normal cells (McCoy). HepG2 clonogenic assay allowed verifying antiproliferative effects. The propidium iodide/ orange acridine fluorescence readings showed the type of cell death induced after treatments (72h). Molecular simulations with B-DNA and 49H showed docked positions (AutoDock Vina) and trajectories/energies (GROMACS). In vitro molecular interactions used CT-DNA and 49H applying UV-Vis absorbance and fluorescence. Comet assay evaluated DNA fragmentation of HepG2 cells. Flow cytometry analysis verified HepG2 cell cycle effects. Levels of proteins (β-actin, p53, BAX, HIF-1α, γH2AX, PARP-1, cyclin A, CDK-2, and pRB) were quantified by immunoblotting.

Results: Among Se-DHPM, 49H was selectively cytotoxic to HepG2 cells, reduced cell proliferation, and increased BAX (80%), and p53 (66%) causing apoptosis. Molecular assays revealed 49H inserted in the CT-DNA molecule causing the hypochromic effect. Docking simulations showed H-bonds and hydrophobic interactions, which kept the ligand partially inserted into the DNA minor groove. 49H increased the DNA damage (1.5 fold) and γH2AX level (153%). Besides, treatments reduced PARP-1 (60%) and reduced pRB phosphorylation (21%) as well as decreased cyclin A (46%) arresting cell cycle at the G1 phase.

Conclusion: Together all data obtained confirmed the hypothesis of disruptive interactions between Se-DHPM and DNA, thereby highlighting its potential as a new anticancer drug.

Keywords: HepG2, dihydropyrimidinones, organoselenium, molecular docking, DNA damage, cell, apoptosis.

Graphical Abstract
World Health Organization. Cancer: Key Facts. (Accessed July 15, 2019).
Rawla, P.; Sunkara, T.; Muralidharan, P.; Raj, J.P. Update in global trends and aetiology of hepatocellular carcinoma. Contemp. Oncol. (Pozn.), 2018, 22(3), 141-150.
[] [PMID: 30455585]
Alfarouk, K.O.; Stock, C.M.; Taylor, S.; Walsh, M.; Muddathir, A.K.; Verduzco, D.; Bashir, A.H.; Mohammed, O.Y.; Elhassan, G.O.; Harguindey, S.; Reshkin, S.J.; Ibrahim, M.E.; Rauch, C. Resistance to cancer chemotherapy: Failure in drug response from ADME to P-gp. Cancer Cell Int., 2015, 15, 71.
[] [PMID: 26180516]
Domínguez-Álvarez, E.; Plano, D.; Font, M.; Calvo, A.; Prior, C.; Jacob, C.; Palop, J.A.; Sanmartín, C. Synthesis and antiproliferative activity of novel selenoester derivatives. Eur. J. Med. Chem., 2014, 73, 153-166.
[] [PMID: 24389510]
Kaur, R.; Chaudhary, S.; Kumar, K.; Gupta, M.K.; Rawal, R.K.; Rawal, R.K. Recent synthetic and medicinal perspectives of dihydropyrimidinones: A review. Eur. J. Med. Chem., 2017, 132, 108-134.
[] [PMID: 28342939]
de Fátima, Â.; Braga, T.C.; Neto, L.S.; Terra, B.S.; Oliveira, B.G.; da Silva, D.L.; Modolo, L.V. A mini-review on Biginelli adducts with notable pharmacological properties. J. Adv. Res., 2015, 6(3), 363-373.
[] [PMID: 26257934]
Mayer, T.U.; Kapoor, T.M.; Haggarty, S.J.; King, R.W.; Schreiber, S.L.; Mitchison, T.J. Small molecule inhibitor of mitotic spindle bipolarity identified in a phenotype-based screen. Science, 1999, 286(5441), 971-974.
[] [PMID: 10542155]
Wang, G.; Li, X.; Gou, Y.; Chen, Y.; Yan, C.; Lu, Y. DNA binding properties and biological evaluation of dihydropyrimidinones derivatives as potential antitumor agents. Spectrochim. Acta A Mol. Biomol. Spectrosc., 2013, 114, 214-219.
[] [PMID: 23778166]
Martins, I.L.; Charneira, C.; Gandin, V.; Ferreira da Silva, J.L.; Justino, G.C.; Telo, J.P.; Vieira, A.J.S.C.; Marzano, C.; Antunes, A.M.M. Selenium-containing chrysin and quercetin derivatives: attractive scaffolds for cancer therapy. J. Med. Chem., 2015, 58(10), 4250-4265.
[] [PMID: 25906385]
Brown, K.M.; Arthur, J.R. Selenium, selenoproteins and human health: a review. Public Health Nutr., 2001, 4(2B), 593-599.
[] [PMID: 11683552]
Barbosa, F.A.R.; Canto, R.F.S.; Saba, S.; Rafique, J.; Braga, A.L. Synthesis and evaluation of Alzheimer’s disease. Bioorg. Med. Chem., 2016, 24, 5762-5770.
[] [PMID: 27681239]
Barbosa, F.A.R.; Siminski, T.; Canto, R.F.S.; Almeida, G.M.; Mota, N.S.R.S.; Ourique, F.; Pedrosa, R.C.; Braga, A.L. Novel pyrimidinic selenourea induces DNA damage, cell cycle arrest, and apoptosis in human breast carcinoma. Eur. J. Med. Chem., 2018, 155, 503-515.
[] [PMID: 29908443]
Sashidhara, K.V.; Singh, L.R.; Shameem, M.; Shakya, S.; Kumar, A.; Laxman, T.S.; Krishna, S.; Siddiqi, M.I.; Bhattac, R.S.; Dibyendu Banerjee, D. Design, synthesis and anticancer activity of dihydropyrimidinone–semicarbazone hybrids as potential human DNA ligase 1 inhibitors. MedChemComm, 2016, 7, 2349-2363.
Pagadala, N.S.; Syed, K.; Tuszynski, J. Software for molecular docking: A review. Biophys. Rev., 2017, 9(2), 91-102.
[] [PMID: 28510083]
Mosmann, T. Rapid colorimetric assay for cellular growth and survival: Application to proliferation and cytotoxicity assays. J. Immunol. Methods, 1983, 65(1-2), 55-63.
[] [PMID: 6606682]
Badisa, R.B.; Darling-Reed, S.F.; Joseph, P.; Cooperwood, J.S.; Latinwo, L.M.; Goodman, C.B. Selective cytotoxic activities of two novel synthetic drugs on human breast carcinoma MCF-7 cells. Anticancer Res., 2009, 29(8), 2993-2996.
[PMID: 19661306]
Franken, N.A.P.; Rodermond, H.M.; Stap, J.; Haveman, J.; van Bree, C. Clonogenic assay of cells in vitro. Nat. Protoc., 2006, 1(5), 2315-2319.
[] [PMID: 17406473]
McGahon, A.J.; Martin, S.J.; Bissonnette, R.P.; Mahboubi, A.; Shi, Y.; Mogil, R.J.; Nishioka, W.K.; Green, D.R. The end of the (cell) line: methods for the study of apoptosis in vitro. Methods Cell Biol., 1995, 46, 153-185.
[] [PMID: 7541883]
Gfeller, D. SwissSidechain ‐ Documentation. 2012. Swiss Institute of Bioinformatics. Lausane, Swiss. , 2012; p. 13.
Sbirkova-Dimitrova, H.I.; Shivachev, B. Crystal structure of the DNA sequence d(CGTGAATTCACG)2 with DAPI. Acta Crystallogr. F Struct. Biol. Commun., 2017, 73(Pt 9), 500-504.
[] [PMID: 28876227]
Forli, S.; Huey, R.; Pique, M.E.; Sanner, M.F.; Goodsell, D.S.; Olson, A.J. Computational protein-ligand docking and virtual drug screening with the AutoDock suite. Nat. Protoc., 2016, 11(5), 905-919.
[] [PMID: 27077332]
Trott, O.; Olson, A.J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem., 2010, 31(2), 455-461.
[PMID: 19499576]
Laskowski, R.A.; Swindells, M.B. LigPlot+: Multiple ligand-protein interaction diagrams for drug discovery. J. Chem. Inf. Model., 2011, 51(10), 2778-2786.
[] [PMID: 21919503]
Sousa da Silva, A.W.; Vranken, W.F. ACPYPE - antechamber python parser interface. BMC Res. Notes, 2012, 5, 367.
[] [PMID: 22824207]
Salomon-Ferrer, R.; Case, D.A.; Walker, R.C. An overview of the Amber biomolecular simulation package. WIREs Comput. Mol. Sci., 2012, 3(2), 198-210.
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins, 2006, 65(3), 712-725.
[] [PMID: 16981200]
Abraham, M.J.; Murtola, T.; Schulz, R.; Páll, S.; Smith, J.C.; Hess, B.; Lindahl, E. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 2015, 1(2), 19-25.
Van Der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A.E.; Berendsen, H.J. GROMACS: fast, flexible, and free. J. Comput. Chem., 2005, 26(16), 1701-1718.
[] [PMID: 16211538]
Jorgensen, W.L.; Chandrasekhar, J.; Madura, J.D.; Impey, R.W. Klein. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 1983, 79(2), 926-935.
Lemkul, J.A.; Allen, W.J.; Bevan, D.R. Practical considerations for building GROMOS-compatible small-molecule topologies. J. Chem. Inf. Model., 2010, 50(12), 2221-2235.
[] [PMID: 21117688]
Humphrey, W.; Dalke, A.; Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph., 1996, 14(1), 33-38. , 27-28
[] [PMID: 8744570]
Hsin, J.; Arkhipov, A.; Yin, Y.; Stone, J.E.; Schulten, K. Using VMD: An introductory tutorial. In: Curr. Protoc. Bioinformatics; , 2008; Chapter 5, p. (1)7.
[PMID: 19085979]
Pettersen, E.F.; Goddard, T.D.; Huang, C.C.; Couch, G.S.; Greenblatt, D.M.; Meng, E.C.; Ferrin, T.E. UCSF Chimera--a visualization system for exploratory research and analysis. J. Comput. Chem., 2004, 25(13), 1605-1612.
[] [PMID: 15264254]
Verlet, L. Computer “Experiments” on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules. Phys. Rev., 1967, 159(1), 98-103.
Kumari, R.; Kumar, R.; Lynn, A. Open Source Drug Discovery Consortium. g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations. J. Chem. Inf. Model., 2014, 54(7), 1951-1962.
[] [PMID: 24850022]
Sirajuddin, M.; Ali, S.; Badshah, A. Drug-DNA interactions and their study by UV-Visible, fluorescence spectroscopies and cyclic voltametry. J. Photochem. Photobiol. B, 2013, 124, 1-19.
[] [PMID: 23648795]
da Silveira, V.C.; Luz, J.S.; Oliveira, C.C.; Graziani, I.; Ciriolo, M.R.; da Costa Ferreira, A.M. Double-strand DNA cleavage induced by oxindole-Schiff base copper(II) complexes with potential antitumor activity. J. Inorg. Biochem., 2008, 102(5-6), 1090-1103.
[] [PMID: 18295339]
Singh, N.P.; McCoy, M.T.; Tice, R.R.; Schneider, E.L. A simple technique for quantitation of low levels of DNA damage in individual cells. Exp. Cell Res., 1988, 175(1), 184-191.
[] [PMID: 3345800]
Ross, G.M.; McMillan, T.J.; Wilcox, P.; Collins, A.R. The single cell microgel electrophoresis assay (comet assay): Technical aspects and applications. Report on the 5th LH Gray Trust Workshop, Institute of Cancer Research, 1994. Mutat. Res., 1995, 337(1), 57-60.
[] [PMID: 7596358]
Soumyanarayananl, U. Varadaraj; Bhat1, V.G.; Kar1, S.S.; Mathew, J.A. Monastrol mimic Biginelli dihydropyrimidinone derivatives: synthesis, cytotoxicity screening against HepG2 and HeLa cell lines and molecular modeling study. Org. Med. Chem. Lett., 2012, 2, 1-11.
Hanahan, D.; Weinberg, R.A. Hallmarks of cancer: The next generation. Cell, 2011, 144(5), 646-674.
[] [PMID: 21376230]
Haanen, C.; Vermes, I. Apoptosis and inflammation. Mediators Inflamm., 1995, 4(1), 5-15.
[] [PMID: 18475609]
Sinha, R.; El-Bayoumy, K. Apoptosis is a critical cellular event in cancer chemoprevention and chemotherapy by selenium compounds. Curr. Cancer Drug Targets, 2004, 4(1), 13-28.
[] [PMID: 14965264]
Suzuki, M.; Endo, M.; Shinohara, F.; Echigo, S.; Rikiishi, H. Differential apoptotic response of human cancer cells to organoselenium compounds. Cancer Chemother. Pharmacol., 2010, 66(3), 475-484.
[] [PMID: 19940991]
Benchimol, S. p53-dependent pathways of apoptosis. Cell Death Differ., 2001, 8(11), 1049-1051.
[] [PMID: 11687883]
Wan, J.P.; Pan, Y. Recent advance in the pharmacology of dihydropyrimidinone. Mini Rev. Med. Chem., 2012, 12(4), 337-349.
[] [PMID: 22303940]
Guido, B.C.; Ramos, L.M.; Nolasco, D.O.; Nobrega, C.C.; Andrade, B.Y.; Pic-Taylor, A.; Neto, B.A.; Corrêa, J.R. Impact of kinesin Eg5 inhibition by 3,4-dihydropyrimidin-2(1H)-one derivatives on various breast cancer cell features. BMC Cancer, 2015, 15(283), 283.
[] [PMID: 25885813]
Nardinocchi, L.; Puca, R.; D’Orazi, G. HIF-1α antagonizes p53-mediated apoptosis by triggering HIPK2 degradation. Aging (Albany NY), 2011, 3(1), 33-43.
[] [PMID: 21248371]
Dreher, M.; Piuzzi, M.; Turki, A.; Chavent, M.; Baaden, M.; Féreyd, N.; Limet, S.; Raffin, B.; Robert, S. Interactive molecular dynamics: Scaling up to large systems. Procedia Comput. Sci., 2013, 18, 20-29.
Wong, C.F.; McCammon, J.A. Protein flexibility and computer-aided drug design. Annu. Rev. Pharmacol. Toxicol., 2003, 43, 31-45.
[] [PMID: 12142469]
Adcock, S.A.; McCammon, J.A. Molecular dynamics: Survey of methods for simulating the activity of proteins. Chem. Rev., 2006, 106(5), 1589-1615.
[] [PMID: 16683746]
Szyc, Ł.; Yang, M.; Elsaesser, T. Ultrafast energy exchange via water-phosphate interactions in hydrated DNA. J. Phys. Chem. B, 2010, 114(23), 7951-7957.
[] [PMID: 20481569]
O’Connor, M.J. Targeting the DNA damage response in cancer. Mol. Cell, 2015, 60(4), 547-560.
[] [PMID: 26590714]
Wang, G.; Yan, C.; Wang, D.; Lu, D.L.Y. Specific binding of a dihydropyrimidinone derivative with DNA: Spectroscopic, calorimetric and modeling investigations. J. Lumin., 2012, 132, 1656-1662.
Marques, L.A.; Semprebon, S.C.; Sartori, D.; D.E., Fátima Â.; Ribeiro, L.R.; Mantovani, M.S. Comparison of the effects of monastrol and oxomonastrol on human hepatoma cell line HepG2/C3A. Anticancer Res., 2017, 37(3), 1197-1204.
[] [PMID: 28314282]
Rogakou, E.P.; Nieves-Neira, W.; Boon, C.; Pommier, Y.; Bonner, W.M. Initiation of DNA fragmentation during apoptosis induces phosphorylation of H2AX histone at serine 139. J. Biol. Chem., 2000, 275(13), 9390-9395.
[] [PMID: 10734083]
Chaitanya, G.V.; Steven, A.J.; Babu, P.P. PARP-1 cleavage fragments: Signatures of cell-death proteases in neurodegeneration. Cell Commun. Signal., 2010, 8(31), 31.
[] [PMID: 21176168]
Helleday, T.; Petermann, E.; Lundin, C.; Hodgson, B.; Sharma, R.A. DNA repair pathways as targets for cancer therapy. Nat. Rev. Cancer, 2008, 8(3), 193-204.
[] [PMID: 18256616]
Macaluso, M.; Montanari, M.; Cinti, C.; Giordano, A. Modulation of cell cycle components by epigenetic and genetic events. Semin. Oncol., 2005, 32(5), 452-457.
[] [PMID: 16210085]
Müller, H.; Helin, K. The E2F transcription factors: Key regulators of cell proliferation. Biochim. Biophys. Acta, 2000, 1470(1), M1-M12.
[PMID: 10656985]
Vermeulen, K.; Berneman, Z.N.; Van Bockstaele, D.R. Cell cycle and apoptosis. Cell Prolif., 2003, 36(3), 165-175.
[] [PMID: 12814432]
Hartwell, L.H.; Kastan, M.B. Cell cycle control and cancer. Science, 1994, 266(5192), 1821-1828.
[] [PMID: 7997877]

Rights & Permissions Print Export Cite as
© 2022 Bentham Science Publishers | Privacy Policy