Dihydropyrimidine derivatives as MDM2 inhibitors.

Dihydropyrimidine (DHPM) MDM2 inhibitor cytotoxicity in silico

Journal

Chemical biology & drug design
ISSN: 1747-0285
Titre abrégé: Chem Biol Drug Des
Pays: England
ID NLM: 101262549

Informations de publication

Date de publication:
27 Nov 2023
Historique:
revised: 22 08 2023
received: 14 06 2023
accepted: 07 11 2023
pubmed: 28 11 2023
medline: 28 11 2023
entrez: 27 11 2023
Statut: aheadofprint

Résumé

One of the chief pathways to regulate p53 levels is MDM2 protein, which negatively controls p53 by direct inhibition. Many cancers overproduce MDM2 protein to interrupt p53 functions. Therefore, impeding MDM2's binding to p53 can reactivate p53 in tumor cells may suggest an effective approach for tumor therapy. Here, some Monastrol derivatives were designed in silico as MDM2 inhibitors, and their initial cytotoxicity was evaluated in vitro on MFC-7 and MDA-MB-231 cells. A small library of Monastrol derivatives was created, and virtual screening (VS) was performed on them. The first-ranked compound, which was extracted from VS, and the other six compounds 5a-5f were selected to carry out the single-docking and docking with explicit waters. The compound with the best average results was then subjected to molecular dynamic (MD) simulation. Compounds 5a-5f were chemically synthesized and evaluated in vitro for their initial cytotoxicity on MFC-7 and MDA-MB-231 cells by MTT assay. The best compound was compound 5d with ΔG

Identifiants

pubmed: 38011915
doi: 10.1111/cbdd.14399
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

e14399

Informations de copyright

© 2023 John Wiley & Sons Ltd.

Références

Al-Masoudi, W. A., Al-Masoudi, N. A., Weibert, B., & Winter, R. (2017). Synthesis, X-ray structure, in vitro HIV and kinesin Eg5 inhibition activities of new arene ruthenium complexes of pyrimidine analogs. Journal of Coordination Chemistry, 70(12), 2061-2073.
Attaby, F. A., Ramla, M. M., & Harukuni, T. (2008). Synthesis and inhibitory activity against epstein-barr virus of some new 1, 2, 3, 4-tetrahydropyrimidine-2-thiones. Phosphorus, Sulfur, and Silicon, 183(12), 2956-2967.
Bahekar, S. S., & Shinde, D. B. (2004). Synthesis and anti-inflammatory activity of some [4, 6-(4-substituted aryl)-2-thioxo-1, 2, 3, 4-tetrahydro-pyrimidin-5-yl]-acetic acid derivatives. Bioorganic & Medicinal Chemistry Letters, 14(7), 1733-1736.
Berendsen, H. J., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1-3), 43-56.
Bertamino, A., Soprano, M., Musella, S., Rusciano, M. R., Sala, M., Vernieri, E., di Sarno, V., Limatola, A., Carotenuto, A., Cosconati, S., Grieco, P., Novellino, E., Illario, M., Campiglia, P., & Gomez-Monterrey, I. (2013). Synthesis, in vitro, and in cell studies of a new series of [indoline-3, 2′-thiazolidine]-based p53 modulators. Journal of Medicinal Chemistry, 56(13), 5407-5421.
Bidram, Z., Sirous, H., Khodarahmi, G. A., Hassanzadeh, F., Dana, N., Hariri, A. A., & Rostami, M. (2020). Monastrol derivatives: In silico and in vitro cytotoxicity assessments. Research in Pharmaceutical Sciences, 15(3), 249.
Blackie, J. A., Bloomer, J. C., Brown, M. J., Cheng, H.-Y., Hammond, B., Hickey, D. M., Ife, R. J., Leach, C. A., Lewis, V. A., Macphee, C. H., Milliner, K. J., Moores, K. E., Pinto, I. L., Smith, S. A., Stansfield, I. G., Stanway, S. J., Taylor, M. A., & Theobald, C. J. (2003). The identification of clinical candidate SB-480848: A potent inhibitor of lipoprotein-associated phospholipase A2. Bioorganic & Medicinal Chemistry Letters, 13(6), 1067-1070.
Bond, G. L., Hu, W., & Levine, A. J. (2005). MDM2 is a central node in the p53 pathway: 12 years and counting. Current Cancer Drug Targets, 5(1), 3-8.
Brown, C. J., Lain, S., Verma, C. S., Fersht, A. R., & Lane, D. P. (2009). Awakening guardian angels: Drugging the p53 pathway. Nature Reviews Cancer, 9(12), 862-873.
da Silva, D. L., Reis, F. S., Muniz, D. R., Ruiz, A. L. T., de Carvalho, J. E., Sabino, A. A., Modolo, L. V., & de Fátima, A. (2012). Free radical scavenging and antiproliferative properties of Biginelli adducts. Bioorganic & Medicinal Chemistry, 20(8), 2645-2650.
Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717.
Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. Methods in Molecular Biology, 1263, 243-250.
de Vasconcelos, A., Oliveira, P. S., Ritter, M., Freitag, R. A., Romano, R. L., Quina, F. H., Pizzuti, L., Pereira, C. M. P., Stefanello, F. M., & Barschak, A. G. (2012). Antioxidant capacity and environmentally friendly synthesis of dihydropyrimidin-(2H)-ones promoted by naturally occurring organic acids. Journal of Biochemical and Molecular Toxicology, 26(4), 155-161.
Desai, N. C., & Bhatt, M. J. (2016). Catalytic synthesis and antimicrobial activity of N-(3-chloro-2-oxo-4-phenylazetidin-1-yl)-4-(1H-indol-3-yl)-6-methyl-2-thioxo-1, 2, 3, 4-tetrahydropyrimidine-5-carboxamides. Heterocyclic Communications, 22(3), 131-136.
Durrant, J. D., & McCammon, J. A. (2011). Molecular dynamics simulations and drug discovery. BMC Biology, 9(1), 1-9.
Eberhardt, J., Santos-Martins, D., Tillack, A. F., & Forli, S. (2021). AutoDock Vina 1.2. 0: New docking methods, expanded force field, and python bindings. Journal of Chemical Information and Modeling, 61(8), 3891-3898.
Elmaghraby, A., Mousa, I., Harb, A., & Mahgoub, M. (2013). Three component reaction: An efficient synthesis and reactions of 3, 4-dihydropyrimidin-2 (1H)-ones and thiones using new natural catalyst. International Scholarly Research Notices, 2013, 1-13.
Fakharzadeh, S. S., Trusko, S. P., & George, D. L. (1991). Tumorigenic potential associated with enhanced expression of a gene that is amplified in a mouse tumor cell line. The EMBO Journal, 10(6), 1565-1569.
Fischer, P. M. (2006). Peptide, peptidomimetic, and small-molecule antagonists of the p53-HDM2 protein-protein interaction. International Journal of Peptide Research and Therapeutics, 12, 3-19.
Freedman, D., Wu, L., & Levine, A. (1999). Functions of the MDM2 oncoprotein. Cellular and Molecular Life Sciences CMLS, 55, 96-107.
Gelpi, J., Hospital, A., Goñi, R., & Orozco, M. (2015). Molecular Dynamics Simulations: Advances and Applications. Advances and Applications in Bioinformatics and Chemistry, 8, 37-47.
Geyer, R. K., Yu, Z. K., & Maki, C. G. (2000). The MDM2 RING-finger domain is required to promote p53 nuclear export. Nature Cell Biology, 2(9), 569-573.
Greenblatt, M., Bennett, W. P., Hollstein, M., & Harris, C. (1994). Mutations in the p53 tumor suppressor gene: Clues to cancer etiology and molecular pathogenesis. Cancer Research, 54(18), 4855-4878.
Gupta, A., Shah, K., Oza, M. J., & Behl, T. (2019). Reactivation of p53 gene by MDM2 inhibitors: A novel therapy for cancer treatment. Biomedicine & Pharmacotherapy, 109, 484-492.
Hansson, T., Oostenbrink, C., & van Gunsteren, W. (2002). Molecular dynamics simulations. Current Opinion in Structural Biology, 12(2), 190-196.
Hardcastle, I. R. (2014). Targeting the MDM2-p53 protein-protein interaction: Design, discovery, and development of novel anticancer agents. Cancer Drug Design and Discovery, 391-426.
Hardcastle, I. R. (2007). Inhibitors of the MDM2-p53 interaction as anticancer drugs. Drugs of the Future, 32, 883-896.
Harris, S. L., & Levine, A. J. (2005). The p53 pathway: Positive and negative feedback loops. Oncogene, 24(17), 2899-2908.
Haupt, Y., Maya, R., Kazaz, A., & Oren, M. (1997). Mdm2 promotes the rapid degradation of p53. Nature, 387(6630), 296-299.
Jiang, P., Liu, J., Zeng, X., Li, W., & Tang, J. (2010). MDM2 gene promoter polymorphism and risk of cervical cancer in Chinese population. In 2010 4th International Conference on Bioinformatics and Biomedical Engineering pp. 1-4 IEEE.
Jones, S. N., Hancock, A. R., Vogel, H., Donehower, L. A., & Bradley, A. (1998). Overexpression of Mdm2 in mice reveals a p53-independent role for Mdm2 in tumorigenesis. National Academy of Sciences of the United States of America, 95(26), 15608-15612.
Kamal, A., Malik, M. S., Bajee, S., Azeeza, S., Faazil, S., Ramakrishna, S., Naidu, V. G., & Vishnuwardhan, M. V. (2011). Synthesis and biological evaluation of conformationally flexible as well as restricted dimers of monastrol and related dihydropyrimidones. European Journal of Medicinal Chemistry, 46(8), 3274-3281.
Kaur, R., Bansal, M., Kaur, B., Mishra, T., & Bhatia, A. (2011). Synthesis of 4-aryl-4, 5-dihydro-1 H-indeno [1, 2-d] pyrimidines by Biginelli condensation and their antibacterial activities. Journal of Chemical Sciences, 123, 443-451.
Klein, E., DeBonis, S., Thiede, B., Skoufias, D. A., Kozielski, F., & Lebeau, L. (2007). New chemical tools for investigating human mitotic kinesin Eg5. Bioorganic & Medicinal Chemistry, 15(19), 6474-6488.
Kumar, B. P., Sankar, G., Baig, R. N., & Chandrashekaran, S. (2009). Novel Biginelli dihydropyrimidines with potential anticancer activity: A parallel synthesis and CoMSIA study. European Journal of Medicinal Chemistry, 44(10), 4192-4198.
Leizerman, I., Avunie-Masala, R., Elkabets, M., Fich, A., & Gheber, L. (2004). Differential effects of monastrol in two human cell lines. Cellular and Molecular Life Sciences CMLS, 61, 2060-2070.
Levine, A. J. (1997). p53, the cellular gatekeeper for growth and division. Cell, 88(3), 323-331.
Levine, A. J., & Oren, M. (2009). The first 30 years of p53: Growing ever more complex. Nature Reviews Cancer, 9(10), 749-758.
Liu, Y., Wang, X., Wang, G., Yang, Y., Yuan, Y., & Ouyang, L. (2019). The past, present and future of potential small-molecule drugs targeting p53-MDM2/MDMX for cancer therapy. European Journal of Medicinal Chemistry, 176, 92-104.
Mayer, T. U., Kapoor, T. M., Haggarty, S. J., King, R. W., Schreiber, S. L., & Mitchison, T. J. (1999). Small molecule inhibitor of mitotic spindle bipolarity identified in a phenotype-based screen. Science, 286(5441), 971-974.
Momand, J., Zambetti, G. P., Olson, D. C., George, D., & Levine, A. J. (1992). The mdm-2 oncogene product forms a complex with the p53 protein and inhibits p53-mediated transactivation. Cell, 69(7), 1237-1245.
Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19(14), 1639-1662.
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785-2791.
Nagarajaiah, H., Mukhopadhyay, A., & Moorthy, J. N. (2016). Biginelli reaction: An overview. Tetrahedron Letters, 57(47), 5135-5149.
O'Boyle, N. M., Vandermeersch, T., Flynn, C. J., Maguire, A. R., & Hutchison, G. R. (2011). Confab-systematic generation of diverse low-energy conformers. Journal of Cheminformatics, 3(1), 1-9.
Oliner, J., Kinzler, K. W., Meltzer, P. S., George, D. L., & Vogelstein, B. (1992). Amplification of a gene encoding a p53-associated protein in human sarcomas. Nature, 358(6381), 80-83.
Ragab, F. A., Abou-Seri, S. M., Abdel-Aziz, S. A., Alfayomy, A. M., & Aboelmagd, M. (2017). Design, synthesis and anticancer activity of new monastrol analogues bearing 1, 3, 4-oxadiazole moiety. European Journal of Medicinal Chemistry, 138, 140-151.
Schüttelkopf, A. W., & van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355-1363.
Shaabani, A., Bazgir, A., & Teimouri, F. (2003). Ammonium chloride-catalyzed one-pot synthesis of 3, 4-dihydropyrimidin-2-(1H)-ones under solvent-free conditions. Tetrahedron Letters, 44(4), 857-859.
Shangary, S., & Wang, S. (2009). Small-molecule inhibitors of the MDM2-p53 protein-protein interaction to reactivate p53 function: A novel approach for cancer therapy. Annual Review of Pharmacology and Toxicology, 49, 223-241.
Singh, K., Arora, D., Singh, K., & Singh, S. (2009). Genesis of dihydropyrimidinonep calcium channel blockers: Recent progress in structure-activity relationships and other effects. Mini Reviews in Medicinal Chemistry, 9(1), 95-106.
Tanay, P., Pathan, A. H., Richa, G., Joginder, S., & Simranjeet, S. (2015). Dihydropyrimidinone derivatives: Green synthesis and effect of electronic factor on their antimicrobial properties. Research Journal of Pharmaceutical, Biological and Chemical Sciences, 6(1), 1152-1157.
Treptow, T. G., Figueiró, F., Jandrey, E. H., Battastini, A. M., Salbego, C. G., Hoppe, J. B., Taborda, P. S., Rosa, S. B., Piovesan, L. A., Montes D'Oca, M. G., Montes D'Oca, C.d R., Russowsky, D., & Montes D'Oca, M. G. (2015). Novel hybrid DHPM-fatty acids: Synthesis and activity against glioma cell growth in vitro. European Journal of Medicinal Chemistry, 95, 552-562.
Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455-461.
Vogelstein, B., Lane, D., & Levine, A. J. (2000). Surfing the p53 network. Nature, 408(6810), 307-310.

Auteurs

Ali Mehri (A)

Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Isfahan, Iran.

Karim Mahnam (K)

Biology Department, Faculty of Sciences, Shahrekord University, Shahrekord, Iran.

Hajar Sirous (H)

Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Science, Isfahan, Iran.

Mahmoud Aghaei (M)

Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Science, Isfahan, Iran.

Leila Rafiei (L)

Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Isfahan, Iran.

Mahboubeh Rostami (M)

Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Science, Isfahan, Iran.

Classifications MeSH