Integrated Computational Exploring of Benzoyl Thienopyrimidine Derivatives as Potential ERα Regulators in Breast Cancer Treatment

Authors

  • Hassan Badaoui Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Morocco.
  • Marwa Alaqarbeh Basic Science Department, Prince Al Hussein bin Abdullah II Academy for Civil Protection, Al-Balqa Applied University, Al-Salt, Jordan.
  • Youness Moukhliss Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Morocco.
  • Hanane Zaki Biotechnology, Bioresources, and Bioinformatics Laboratory, Higher School of Technology, University of Sultan Moulay Sliman, Khenifra Morocco.
  • Moulay Ahfid El alaouy Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Morocco.
  • M'barek Choukrad Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Morocco.
  • Abdelouahid Sbai Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Morocco.
  • Hamid Maghat Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Morocco.
  • Tahar Lakhlifi Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Morocco.
  • Mohammed Bouachrine Molecular Chemistry and Natural Substances Laboratory, Faculty of Science, Moulay Ismail University of Meknes, Morocco.

DOI:

https://doi.org/10.35516/jjps.v18i2.2805

Keywords:

ADME/Tox, Breast cancer, Computational Modeling, 3D-QSAR, Thienopyrimidine

Abstract

Estrogen receptor-positive (ER+) hormone-dependent breast cancer is the most common type in women, accounting for approximately 75% of all cases. This study aims to propose new potential therapeutic agents for breast cancer using computational methods. A 3D-QSAR study screened 22 compounds based on previous research, demonstrating strong predictive capabilities, as indicated by high Q² values of 0.516 and 0.787 for CoMFA and CoMSIA, respectively. Six new molecules (T1–T6) were proposed to enhance inhibitory activity, and the results of molecular docking analysis show that these drug candidates exhibit significant docking scores and form stable interactions within the receptor (PDB code: 1SJ0). The proposed compounds exhibited favorable pharmacokinetic and pharmacodynamic properties, except for T3, which showed mild toxicity. Molecular dynamics simulations also confirmed the stability of the T1–1SJ0 and 2D–1SJ0 complexes within the active site of ERα (estrogen receptor alpha). These findings highlight the potential of thienopyrimidine-based compounds as anti-breast cancer agents and open new avenues for experimental and clinical research.

References

Antebi A. Nuclear receptor signal transduction in C. elegans. In: WormBook: The Online Review of C. elegans Biology. WormBook. 2018.

Jeon S-Y., Hwang K-A., Choi K-C. Effect of steroid hormones, estrogen and progesterone, on epithelial mesenchymal transition in ovarian cancer development. J Steroid Biochem Mol Biol. 2016;158:1–8. https://doi.org/10.1016/j.jsbmb.2016.02.005 DOI: https://doi.org/10.1016/j.jsbmb.2016.02.005

Merrheim J., Villegas J., Van Wassenhove J., Khansa R., Berrih-Aknin S., le Panse R., Dragin N. Estrogen, estrogen-like molecules and autoimmune diseases. Autoimmun Rev. 2020;19:102468. https://doi.org/10.1016/j.autrev.2020.102468 DOI: https://doi.org/10.1016/j.autrev.2020.102468

Speltz T.E., Mayne C.G., Fanning S.W., Siddiqui Z., Tajkhorshid E., Greene G.L., Moore T.W. A “Cross-Stitched” Peptide with Improved Helicity and Proteolytic Stability. Org Biomol Chem. 2018;16:3702–6. https://doi.org/10.1039/c8ob00790j DOI: https://doi.org/10.1039/C8OB00790J

Hegde M., Girisa S., Naliyadhara N., Kumar A., Alqahtani M.S., Abbas M., Mohan C.D., Warrier S., Hui K.M., Rangappa K.S., Sethi G., Kunnumakkara A.B. Natural compounds targeting nuclear receptors for effective cancer therapy. Cancer Metastasis Rev. 2023;42:765–822. https://doi.org/10.1007/s10555-022-10068-w DOI: https://doi.org/10.1007/s10555-022-10068-w

Vishnoi K., Viswakarma N., Rana A., Rana B. Transcription Factors in Cancer Development and Therapy. Cancers (Basel). 2020;12:2296. https://doi.org/10.3390/cancers12082296 DOI: https://doi.org/10.3390/cancers12082296

Taheri M., Shoorei H., Dinger M.E., Ghafouri-Fard S. Perspectives on the Role of Non-Coding RNAs in the Regulation of Expression and Function of the Estrogen Receptor. Cancers (Basel). 2020;12:2162. https://doi.org/10.3390/cancers12082162 DOI: https://doi.org/10.3390/cancers12082162

Tetruashvili N., Domar A., Bashiri A. Prevention of Pregnancy Loss: Combining Progestogen Treatment and Psychological Support. JCM. 2023;12:1827. https://doi.org/10.3390/jcm12051827 DOI: https://doi.org/10.3390/jcm12051827

Ali I., Lone M.N., Aboul-Enein H.Y. Imidazoles as potential anticancer agents †The authors declare no competing interests. Medchemcomm. 2017;8:1742–1773. https://doi.org/10.1039/c7md00067g DOI: https://doi.org/10.1039/C7MD00067G

George S., Abrahamse H. Redox Potential of Antioxidants in Cancer Progression and Prevention. Antioxidants (Basel). 2020;9:1156.

https://doi.org/10.3390/antiox9111156 DOI: https://doi.org/10.3390/antiox9111156

Song S., Kim S., El-Sawy E.R., Cerella C., Orlikova-Boyer B., Kirsch G., Christov C., Dicato M., Diederich M. Anti-Leukemic Properties of Aplysinopsin Derivative EE-84 Alone and Combined to BH3 Mimetic A-1210477. Mar Drugs. 2021;19:285.

https://doi.org/10.3390/md19060285 DOI: https://doi.org/10.3390/md19060285

Ardevines S., Marqués-López E., Herrera R.P. Heterocycles in Breast Cancer Treatment: The Use of Pyrazole Derivatives. Curr Med Chem. 2023;30:1145–1174. https://doi.org/10.2174/0929867329666220829091830 DOI: https://doi.org/10.2174/0929867329666220829091830

Kolawole O.A., Banjo S. In Vitro Biological Estimation of 1,2,3-Triazolo[4,5-d]pyrimidine Derivatives as Anti-breast Cancer Agent: DFT, QSAR and Docking Studies. Curr Pharm Biotechnol. 2020;21:70–78.

https://doi.org/10.2174/1389201020666190904163003 DOI: https://doi.org/10.2174/1389201020666190904163003

Thapa R., Flores R., Cheng K.H., Mochona B., Sikazwe D. Design and Synthesis of New Acyl Urea Analogs as Potential σ1R Ligands. Molecules. 2023;28:2319. https://doi.org/10.3390/molecules28052319 DOI: https://doi.org/10.3390/molecules28052319

Aati H.Y., Attia H., Babtin R., Al-Qahtani N., Wanner J. Headspace solid phase micro-extraction of volatile constituents produced from Saudi Ruta chalepensis and molecular docking study of potential antioxidant activity. Molecules. 2023;28:1891.

https://doi.org/10.3390/molecules28041891 DOI: https://doi.org/10.3390/molecules28041891

Frant M.P., Trytek M., Deryło K., Kutyła M., Paduch R. Cellular localization of selected porphyrins and their effect on the in vitro motility of human colon tumors and normal cells. Molecules. 2023;28:2907. https://doi.org/10.3390/molecules28072907 DOI: https://doi.org/10.3390/molecules28072907

[Author(s) missing] Antimicrobial, antibiofilm, and anticancer activities of Syzygium aromaticum essential oil nanoemulsion. PMC. [n.d.]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10421252/

Maimaitiming M., Lv L., Zhang X., Xia S., Li X., Wang P., Liu Z., Wang C.-Y. Semi-synthesis and biological evaluation of 25(R)-26-acetoxy-3β,5α-dihydroxycholest-6-one. Mar Drugs. 2023;21:191.

https://doi.org/10.3390/md21030191 DOI: https://doi.org/10.3390/md21030191

Thiriveedhi A., Nadh R.V., Srinivasu N., Bobde Y., Ghosh B., Sekhar K.V.G.C. Design, synthesis and anti-tumour activity of new pyrimidine-pyrrole appended triazoles. Toxicol In Vitro. 2019;60:87–96. https://doi.org/10.1016/j.tiv.2019.05.009 DOI: https://doi.org/10.1016/j.tiv.2019.05.009

Kis B., Moacă E.-A., Tudoran L.B., Muntean D., Magyari-Pavel I.Z., Minda D.I., Lombrea A., Diaconeasa Z., Dehelean C.A., Dinu Ș., Danciu C. Green synthesis of silver nanoparticles using Populi gemmae extract: Preparation, physicochemical characterization, antimicrobial potential and in vitro antiproliferative assessment. Materials (Basel). 2022;15:5006. https://doi.org/10.3390/ma15145006 DOI: https://doi.org/10.3390/ma15145006

El-Sharkawy K.A., Bratty M.A., Alhazmi H.A., Najmi A. Design, synthesis, and biological activities of novel thiophene, pyrimidine, pyrazole, pyridine, coumarin and isoxazole: Dydrogesterone derivatives as antitumor agents. Open Chemistry. 2021;19:322–337. https://doi.org/10.1515/chem-2021-0028 DOI: https://doi.org/10.1515/chem-2021-0028

Wilkes J.G., Stoyanova-Slavova I.B., Buzatu D.A. Alignment-independent technique for 3D QSAR analysis. J Comput Aided Mol Des. 2016;30:331–345. https://doi.org/10.1007/s10822-016-9909-0 DOI: https://doi.org/10.1007/s10822-016-9909-0

Pan M., Cheng L., Wang Y., Lyu C., Hou C., Zhang Q. Exploration of 2D and 3D-QSAR analysis and docking studies for novel dihydropteridone derivatives as promising therapeutic agents targeting glioblastoma. Front Pharmacol. 2023;14:1249041.

https://doi.org/10.3389/fphar.2023.1249041 DOI: https://doi.org/10.3389/fphar.2023.1249041

Er-Rajy M., El Fadili M., Imtara H., Saeed A., Ur Rehman A., Zarougui S., Abdullah S.A., Alahdab A., Parvez M.K., Elhallaoui M. 3D-QSAR Studies, Molecular Docking, Molecular Dynamic Simulation, and ADMET Proprieties of Novel Pteridinone Derivatives as PLK1 Inhibitors for the Treatment of Prostate Cancer. Life (Basel). 2023;13:127. https://doi.org/10.3390/life13010127 DOI: https://doi.org/10.3390/life13010127

Aouidate A., Ghaleb A., Ghamali M., Chtita S., Ousaa A., Choukrad M., Sbai A., Bouachrine M., Lakhlifi T. Computer aided drug design based on 3D-QSAR and molecular docking studies of 5-(1H-indol-5-yl)-1,3,4-thiadiazol-2-amine derivatives as PIM2 inhibitors: a proposal to chemists. In Silico Pharmacol. 2018;6:5. https://doi.org/10.1007/s40203-018-0043-7 DOI: https://doi.org/10.1007/s40203-018-0043-7

Daina A., Michielin O., Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:42717. https://doi.org/10.1038/srep42717 DOI: https://doi.org/10.1038/srep42717

Benet L.Z., Hosey C.M., Ursu O., Oprea T.I. BDDCS, the Rule of 5 and Drugability. Adv Drug Deliv Rev. 2016;101:89–98. https://doi.org/10.1016/j.addr.2016.05.007 DOI: https://doi.org/10.1016/j.addr.2016.05.007

O’Shea J.P., Augustijns P., Brandl M., Brayden D.J., Brouwers J., Griffin B.T., Holm R., Jacobsen A.-C., Lennernäs H., Vinarov Z., O’Driscoll C.M. Best practices in current models mimicking drug permeability in the gastrointestinal tract - An UNGAP review. European Journal of Pharmaceutical Sciences. 2022;170:106098. https://doi.org/10.1016/j.ejps.2021.106098 DOI: https://doi.org/10.1016/j.ejps.2021.106098

Durán-Iturbide N.A., Díaz-Eufracio B.I., Medina-Franco J.L. In Silico ADME/Tox Profiling of Natural Products: A Focus on BIOFACQUIM. ACS Omega. 2020;5:16076–16084. https://doi.org/10.1021/acsomega.0c01581 DOI: https://doi.org/10.1021/acsomega.0c01581

Sharma D., Kumar S., Narasimhan B. Estrogen alpha receptor antagonists for the treatment of breast cancer: a review. Chem Cent J. 2018;12:107.

https://doi.org/10.1186/s13065-018-0472-8 DOI: https://doi.org/10.1186/s13065-018-0472-8

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;31:455–461.

https://doi.org/10.1002/jcc.21334 DOI: https://doi.org/10.1002/jcc.21334

Bank R.P.D. RCSB PDB - 1SJ0: Human Estrogen Receptor Alpha Ligand-binding Domain in Complex with the Antagonist Ligand 4-D. RCSB Protein Data Bank. [Online] Available from:

https://www.rcsb.org/structure/1sj0

Kumar R., Zakharov M.N., Khan S.H., Miki R., Jang H., Toraldo G., Singh R., Bhasin S., Jasuja R. The Dynamic Structure of the Estrogen Receptor. J Amino Acids. 2011;2011:812540. https://doi.org/10.4061/2011/812540 DOI: https://doi.org/10.4061/2011/812540

Fu Y., Zhao J., Chen Z. Insights into the Molecular Mechanisms of Protein-Ligand Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of Oligopeptide Binding Protein. Comput Math Methods Med. 2018;2018:3502514.

https://doi.org/10.1155/2018/3502514 DOI: https://doi.org/10.1155/2018/3502514

Kognole A.A., Lee J., Park S.-J., Jo S., Chatterjee P., Lemkul J.A., Huang J., MacKerell A.D., Im W. CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. J Comput Chem. 2022;43:359–375. https://doi.org/10.1002/jcc.26795 DOI: https://doi.org/10.1002/jcc.26795

Kim S., Lee J., Jo S., Brooks C.L., Lee H.S., Im W. CHARMM-GUI Ligand Reader & Modeler for CHARMM Force Field Generation of Small Molecules. J Comput Chem. 2017;38:1879–1886.

https://doi.org/10.1002/jcc.24829 DOI: https://doi.org/10.1002/jcc.24829

Alencar W.L.M., da Silva Arouche T., Neto A.F.G., de Castro Ramalho T., de Carvalho Júnior R.N., de Jesus Chaves Neto A.M. Publisher Correction: Interactions of Co, Cu, and non-metal phthalocyanines with external structures of SARS-CoV-2 using docking and molecular dynamics. Sci Rep. 2022;12:4326.

https://doi.org/10.1038/s41598-022-08312-y DOI: https://doi.org/10.1038/s41598-022-08312-y

Lee J., Cheng X., Swails J.M., Yeom M.S., Eastman P.K., Lemkul J.A., Wei S., Buckner J., Jeong J.C., Qi Y., Jo S., Pande V.S., Case D.A., Brooks C.L., MacKerell A.D., Klauda J.B., Im W. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. J Chem Theory Comput. 2016;12:405–413.

https://doi.org/10.1021/acs.jctc.5b00935 DOI: https://doi.org/10.1021/acs.jctc.5b00935

Pereira G.R.C., Abrahim-Vieira B. de A., de Mesquita J.F. In Silico Analyses of a Promising Drug Candidate for the Treatment of Amyotrophic Lateral Sclerosis Targeting Superoxide Dismutase I Protein. Pharmaceutics. 2023;15:1095. https://doi.org/10.3390/pharmaceutics15041095 DOI: https://doi.org/10.3390/pharmaceutics15041095

Kumari R., Kumar R., Open Source Drug Discovery Consortium, Lynn A. g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations. J Chem Inf Model. 2014;54:1951–1962.

https://doi.org/10.1021/ci500020m DOI: https://doi.org/10.1021/ci500020m

Gundelach L., Fox T., Tautermann S.T., Skylaris C.-K. Protein–ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange–correlation functional. Physical Chemistry Chemical Physics. 2021; 23:9381–9393. DOI: https://doi.org/10.1039/D1CP00206F

In silico studies of a novel scaffold of benzoxazole derivatives as anticancer agents by 3D-QSAR, molecular docking and molecular dynamics simulations. RSC Advances. 2023; DOI:10.1039/D3RA01316B. DOI: https://doi.org/10.1039/D3RA01316B

Pandey P.K., Sharma A.K., Gupta U. Blood brain barrier: An overview on strategies in drug delivery, realistic in vitro modeling and in vivo live tracking. Tissue Barriers. 2016; 4:e1129476. DOI: https://doi.org/10.1080/21688370.2015.1129476

Wu Q., Yan R., Sun J. Probing the drug delivery strategies in ischemic stroke therapy. Drug Delivery. 2020; 27:1644–1655. DOI: https://doi.org/10.1080/10717544.2020.1850918

Iacopetta D., Ceramella J., Catalano A., Scali E., Scumaci D., Pellegrino M., Aquaro S., Saturnino C., Sinicropi M.S. Impact of Cytochrome P450 Enzymes on the Phase I Metabolism of Drugs. Applied Sciences. 2023; 13:6045. DOI: https://doi.org/10.3390/app13106045

Miners J.O., Birkett D.J. Cytochrome P4502C9: an enzyme of major importance in human drug metabolism. British Journal of Clinical Pharmacology. 1998; 45:525–538Jarvis, J.P., Peter, A.P., Shaman, J.A.: Consequences of CYP2D6 Copy-Number Variation for Pharmacogenomics in Psychiatry. Frontiers in Psychiatry. 10, (2019) DOI: https://doi.org/10.1046/j.1365-2125.1998.00721.x

Sarkar P., Alheety M.A., Srivastava V. Molecular docking and ADMET study of spice-derived potential phytochemicals against human DNA topoisomerase III alpha. Macromolecular Symposia. 2023; 407:2200108. DOI: https://doi.org/10.1002/masy.202200108

Samiei M., Asgary S., Farajzadeh M., Bargahi N., Abdolrahimi M., Kananizadeh U., Dastmalchi S. Investigating the mutagenic effects of three commonly used pulpotomy agents using the Ames test. Advanced Pharmaceutical Bulletin. 2015; 5:121–125.

Al-Shaar M., Mando H., Alkhatib R. In silico antioxidant activity of six volatile constituents in Capsella bursa-pastoris. Jordan Journal of Pharmaceutical Sciences. 2025; 18(1):230–244. DOI: https://doi.org/10.35516/jjps.v18i1.2537

Maslov O., Komisarenko M., Kolisnyk S., Derymedvid L. Evaluation of anti-inflammatory, antioxidant activities and molecular docking analysis of Rubus idaeus leaf extract. Jordan Journal of Pharmaceutical Sciences. 2024; 17(1):105–122. DOI: https://doi.org/10.35516/jjps.v17i1.1808

Msafer B.A.A., Abbas M.A., Shaer W.A., Arafat S. Enhanced platelet activation induced by palbociclib treatment in MCF-7 breast cancer cells. Jordan Journal of Pharmaceutical Sciences. 2025; 18(1):10–20. DOI: https://doi.org/10.35516/jjps.v18i1.2459

Downloads

Published

2025-06-25

How to Cite

Badaoui , H. ., Alaqarbeh, M., Moukhliss, Y., Zaki, H., Ahfid El alaouy, M. ., Choukrad, M., Sbai, A., Maghat, H., Lakhlifi, T., & Bouachrine, M. (2025). Integrated Computational Exploring of Benzoyl Thienopyrimidine Derivatives as Potential ERα Regulators in Breast Cancer Treatment. Jordan Journal of Pharmaceutical Sciences, 18(2), 596–616. https://doi.org/10.35516/jjps.v18i2.2805

Issue

Section

Articles