Interaction of benzenesulfonamide derivatives with Smyd3 using a theoretical model
DOI:
https://doi.org/10.14295/bjs.v3i1.455Keywords:
cancer, smyd3, benzenesulfonamide, novobiocinAbstract
Cancer is a serious public health problem worldwide. This clinical pathology is associated with the activation/release of several biomolecules, including the Smyd proteins family. In this way, some studies indicate that Smyd3 is associated with cancer cells growth. It is important to mention that some drugs act as Smyd3 inhibitors in the treat some cancers. However, their interaction is very confusing; for this reason, the aim of this research was to evaluate the theoretical interaction of benzenesulfonamide and their derivatives (compounds 2 to 28) using 7o2c protein, novobiocin, BAY-6035, EPZ031686 and BCI-121 drugs as theoretical tools in DockingServer program. The results showed differences in the aminoacid residues involved in the interaction of benzenesulfonamide and their derivatives with 7o2c protein surface compared with novobiocin, BAY-6035, EPZ031686 and BCI-121 drugs. In additions, the inhibition constant (Ki) for benzenesulfonamide derivatives 2, 7, 8, 13, 14, 17, 20, 21, 24 and 28 was very lower compared to benzenesulfonamide, novobiocin, BAY-6035, EPZ031686 and BCI-121. In conclusion, the benzenesulfonamide derivatives 2, 7, 8, 13, 14, 17, 20, 21, 24 and 28 could be a good alternative as Smyd3 inhibitors to decrease cancer cells growth.
References
Abishad, P., Niveditha, P., Unni, V., Vergi, J., Kurkure, N., Chaudhari, S., Rawool, D. B., & Barduddhe, S. (2021). In silico molecular docking and in vitro antimicrobial efficacy of phytochemicals against multi-drug-resistant enteroaggregative Escherichia coli and non-typhoidal Salmonella spp. Gut Pathogens, 13(1), 1-11. https://doi.org/10.1186/s13099-021-00443-3 DOI: https://doi.org/10.1186/s13099-021-00443-3
Asuthkar, S., Venkataraman, S., Avilala, J., Shishido, K., Vibhakar, R., & Veo, B. (2022). SMYD3 promotes cell cycle progression by inducing cyclin D3 transcription and stabilizing the cyclin D1 protein in medulloblastoma. Cancers, 14(7), 1673. https://doi.org/10.3390/cancers14071673 DOI: https://doi.org/10.3390/cancers14071673
Banerjee, P., & Ulker, O. (2022). Combinative ex vivo studies and in silico models ProTox-II for investigating the toxicity of chemicals used mainly in cosmetic products. Toxicology Mechanism and Methods, 32(7), 542-548. https://doi.org/10.1080/15376516.2022.2053623 DOI: https://doi.org/10.1080/15376516.2022.2053623
Deng, X., Li, M., Deng, S., & Wang, L. (2022). Hybrid gene, selection approach using XGBoost and multi-objective genetic algorithm for cancer classification. Medical & Biological Engenineering & Computing, 60(3), 663-681. DOI: https://doi.org/10.1007/s11517-021-02476-x
Fenizia, C., Bottino, C., Corbetta, S., Fittipaldi, R., Floris, P., & Gaudenzi, G. (2019). SMYD3 promotes the epithelial–mesenchymal transition in breast cancer. Nucleic Acids Resesearch, 47(3), 1278-1293. https://doi.org/10.1093/nar/gky1221 DOI: https://doi.org/10.1093/nar/gky1221
Ferro, N., Tacoronte J, Reinard, T., Bultinck, P., Montero, L. (2006). Structure–activity analysis on ecdysteroids: A structural and quantum chemical approach based on two biological systems. Journal of Molecular Structure: THEOCHEM, 758(2-3), 263-274. https://doi.org/10.1016/j.theochem.2005.10.027 DOI: https://doi.org/10.1016/j.theochem.2005.10.027
Figueroa-Valverde, L., Alvarez-Ramirez, M., Rosas-Nexticapa, M., Cedillo, F., López-Ramos, M., & Mateu-Armad, M. (2021). Synthesis of two testosterone derivatives and their theoretical evaluation as serotonin reuptake transporter inhibitors. Biointerface Research in Applied Chemistry, 11, 12462-12470. https://doi.org/10.33263/ BRIAC115.1246212470 DOI: https://doi.org/10.33263/BRIAC115.1246212470
Figueroa-Valverde, L., Rosas-Nexticapa, M., Alvarez-Ramirez, M., Lopez-Ramos, M., & Mateu-Armand V. (2022). Theoretical evaluation of interaction of some dibenzo derivatives on both androgen receptor and 5a-reductase enzyme. Clinical Cancer Investigation Journal, 11(5), 11-16. https://doi.org/10.51847/fIVMfELA7I DOI: https://doi.org/10.51847/fIVMfELA7I
Figueroa-Valverde, L., Rosas-Nexticapa, M., Alvarez-Ramirez, M., López-Ramos, M., Díaz-Cedillo, F., & Mateu-Armad, M. (2023). Evaluation of Biological Activity Exerted by Dibenzo [b, e] Thiophene-11 (6H)-One on Left Ventricular Pressure Using an Isolated Rat Heart Model. Drug Research, 263-270. https://doi.org/10.1055/a-1995-6351 DOI: https://doi.org/10.1055/a-1995-6351
Figueroa-Valverde, L., Rosas-Nexticapa, M., Montserrat, M., Díaz-Cedillo, F., López-Ramos, M. & Alvarez-Ramirez, M. (2023). Synthesis and Theoretical Interaction of 3-(2-oxabicyclo [7.4. 0] trideca-1 (13), 9, 11-trien-7-yn-12-yloxy)-steroid Deriva-tive with 17β-hydroxysteroid Dehydrogenase Enzyme Surface. Biointerface Research in Applied Chemistry, 13, 266. https://doi.org/10.33263/BRIAC133.266 DOI: https://doi.org/10.33263/BRIAC133.266
Giakountis, A., Moulos, P., Sarris, M., Hatzis, P., & Talianidis, I. (2017). Smyd3-associated regulatory pathways in cancer. Seminars in Cancer Biology, 42, 70-80. https://doi.org/10.1016/j.semcancer.2016.08.008 DOI: https://doi.org/10.1016/j.semcancer.2016.08.008
Gradl, S., Steuber, H., Weiske, J., Szewczyk, M., Schmees, N., & Siegel, S. (2021). Discovery of the SMYD3 inhibitor BAY-6035 using thermal shift assay (TSA)-based high-throughput screening. SLAS DISCOVERY: Advancing the Science of Drug Discovery, 26(8), 947-960. https://doi.org/10.1177/24725552211019 DOI: https://doi.org/10.1177/24725552211019409
Hanahan, D. (2022). Hallmarks of cancer: new dimensions. Cancer Discovery, 12(1), 31-46. https://doi.org/10.1158/2159-8290.CD-21-1059 DOI: https://doi.org/10.1158/2159-8290.CD-21-1059
He, Y., Ca, Y., Fan, S., Meng, T., Zhang, Y., & Li, X. (2022) Hydroxyl radicals can significantly influence the toxicity of ofloxacin transformation products during ozonation. Journal of Hazardous Materials, 438, 129503. https://doi.org/10.1016/j.jhazmat.2022.129503 DOI: https://doi.org/10.1016/j.jhazmat.2022.129503
Hecht, S., & Hatsukami, D. (2022). Smokeless tobacco and cigarette smoking: chemical mechanisms and cancer prevention. Nature Review Cancer, 22(3), 143-155. DOI: https://doi.org/10.1038/s41568-021-00423-4
Hol, J., Kuiper, R., Van-Dijk, F., Waanders, E., Van-Peer S. E., Koudijs, M. J., Bladergroen, R., van Reijmersdal, S. V., Morgado, L. M., Bliek, J., Lombardi, M. P., Hopman, S., Drost, J., Krijger, R. R., van den Heuvel-Eibrink, M. M., &
Jongmans, M. C. J. (2022). Prevalence of (Epi) genetic predisposing factors in A 5-year unselected national Wilms tumor cohort: a comprehensive clinical and genomic characterization. Journal of Clinical Oncology, 40(17), 1892-1902. https://doi.org/10.1200%2FJCO.21.02510 DOI: https://doi.org/10.1200/JCO.21.02510
Jukarainen, S., Kiiskinen, T., Kuitunen, S., Havulinna, A., Karjalainen, J., & Cordioli M. (2022). Genetic risk factors have a substantial impact on healthy life years. Nature Medicine, 28(9), 1893-1901. DOI: https://doi.org/10.1038/s41591-022-01957-2
Karpenko, Y., Hunchak, Y., Gutyj, B., Hunchak, A., Parchenko, M., & Parchenko, V. (2022). Advanced research for physico-chemical properties and parameters of toxicity piperazinium 2-((5-(furan-2-YL)-4-phenyl-4H-1, 2, 4-triazol-3-YL) THIO) acetate. ScienceRise:Pharmaceutical Science, 2(36): 18-25. DOI: https://doi.org/10.15587/2519-4852.2022.255848
Leinhart, K., & Brown, M. (2011). SET/MYND lysine methyltransferases regulate gene transcription and protein activity. Genes, 2(1), 210-218. https://doi.org/10.3390/ genes2010210 DOI: https://doi.org/10.3390/genes2010210
Li, X., Wang, L., Wang, L., Yu, J., Lu, G., & Zhao W. (2020). Overcoming therapeutic failure in osteosarcoma via Apatinib-encapulated hydrophobic poly (ester amide) nanoparticles. Biomaterials Science, 2020; 8(21), 5888-5899. DOI: https://doi.org/10.1039/D0BM01296C
Liu, D., Liu, M., Wang, W., Li, X., Shi, E., & Zhang, C. (2023). SMYD Family Members Serve as Potential Prognostic Markers and Correlate with Immune Infiltrates in Gastric Cancer. Journal of Oncology, 1-16. https://doi.org/10.1155/2023/6032864 DOI: https://doi.org/10.1155/2023/6032864
Luo, X., Zou, J., Wang, S,, Zhang, T., & Xi, T. (2010). Novobiocin decreases SMYD3 expression and inhibits the migration of MDA‐MB‐231 human breast cancer cells. IUBMB Life, 62(3), 194-199. https://doi.org/10.1002/iub.288 DOI: https://doi.org/10.1002/iub.288
Manoj, K., Elangovan, N., & Chandrasekar, S. (2022). Synthesis, XRD, hirshfeld surface analysis, ESP, HOMO-LUMO, quantum chemical modeling and anticancer activity of di (p-methyl benzyl)(dibromo)(1, 10-phenanthroline) tin (IV) complex. Inorganic Chemistry Communications, 139, 109324. https://doi.org/10.1016/j.inoche.2022.109324 DOI: https://doi.org/10.1016/j.inoche.2022.109324
Matunová, V., & Rezek, B. (2019). DFT calculations reveal pronounced HOMO–LUMO spatial separation in polypyrrole–nanodiamond systems. Physical Chemistry Chemical Physics, 21(21), 11033-11042. https://doi.org/10.1039/C8CP07622G DOI: https://doi.org/10.1039/C8CP07622G
Mekky, A., Sanad, S., & Abdelfattah, A. (2022) Tandem synthesis, antibacterial evaluation and SwissADME prediction study of new bis (1, 3, 4-oxadiazoles) linked to arene units. Mendeleev Communications, 32(5), 612-614. DOI: https://doi.org/10.1016/j.mencom.2022.09.014
Miller, K., Nogueira, L., Devasia, T., Mariotto, A., Yabroff, K., & Jemal A. (2022) Cancer treatment and survivorship statistics, 2022. CA: A Cancer journal for Clinicians, 72(5), 409-436. https://doi.org/10.3322/caac.21731 DOI: https://doi.org/10.3322/caac.21731
Mitchell, L., Boriack-Sjodin, P., Smith, S., Thomenius, M., Rioux, N., & Munchhof. (2016). Novel oxindole sulfonamides and sulfamides: EPZ031686, the first orally bioavailable small molecule SMYD3 inhibitor. Medicinal Chemistry Letters, 7(2), 134-138. https://doi.org/10.1021/acsmedchemlett.5b00272 DOI: https://doi.org/10.1021/acsmedchemlett.5b00272
Mosquera-Yuqui, F., Lopez-Guerra, N., & Moncayo-Palacio, E. A. (2022). Targeting the 3CLpro and RdRp of SARS-CoV-2 with phytochemicals from medicinal plants of the Andean Region: molecular docking and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 40(5), 2010-2023. https://doi.org/10.1080/07391102.2020.1835716 DOI: https://doi.org/10.1080/07391102.2020.1835716
Pasha, F., Srivastava, H., & Singh, P. (2005). Comparative QSAR study of phenol derivatives with the help of density functional theory. Bioorganic Medicinal Chemistry, 13(24), 6823-6829. https://doi.org/10.1016/j.bmc. 2005.07.064 DOI: https://doi.org/10.1016/j.bmc.2005.07.064
Pérez, S., La-Farré, M., Garcı́a, M., & Barceló, D. (2001). Occurrence of polycyclic aromatic hydrocarbons in sewage sludge and their contribution to its toxicity in the ToxAlert® 100 bioassay. Chemosphere, 45(6-7), 705-712. https://doi.org/10.1016/S0045-6535(01)00152-7 DOI: https://doi.org/10.1016/S0045-6535(01)00152-7
Peserico, A., Germani, A., Sanese, P., Barbosa, A., Di-Virgilio, V., & Fittipaldi, R. (2015). A SMYD3 Small-Molecule Inhibitor Impairing Cancer Cell Growth. Journal of Cellular Physiology, 230, 2447–2460. https://doi.org/10.1002/jcp.24975. DOI: https://doi.org/10.1002/jcp.24975
Phan, D., Rasmussen, T., Nakagawa, O., McAnally, J., Gottlieb, P., & Tucker, P. (2005). BOP, a regulator of right ventricular heart development, is a direct transcriptional target of MEF2C in the developing heart. Development and Dissease, 132(11), 2669-2678. https://doi.org/10.1242/dev.01849 DOI: https://doi.org/10.1242/dev.01849
Prasad, Y., Kumar, P., Smiles, D., & Babu, P. (2008). QSAR studies on chalcone derivatives as antibacterial agents against Bacillus pumilis. Arkivoc, 11: 266-276. DOI: https://doi.org/10.3998/ark.5550190.0009.b26
Rijal, R., Lamichhane, H., & Pudasainee, K. (2022). Molecular structure, homo-lumo analysis and vibrational spectroscopy of the cancer healing pro-drug temozolomide based on dft calculations. AIMS Biophysics, 9, 208-220. DOI: https://doi.org/10.3934/biophy.2022018
Qu, X., Dong, L., Zhang, J., Si, Y., & Wang, B. (2022). Systematic Improvement of the Performance of Machine Learning Scoring Functions by Incorporating Features of Protein-Bound Water Molecules. Journal of Chemical Information and Modeling, 62(18), 4369-4379. https://doi.org/10.1021/acs.jcim.2c00916 DOI: https://doi.org/10.1021/acs.jcim.2c00916
Shah, A. (2022). Pharmacokinetic Modeling Program (PKMP): A Software for PK/PD Data Analysis. In Pharmacokinetics and Pharmacodynamics of Nanoparticulate Drug Delivery Systems, pp. 101-139. Cham: Springer International Publishing. DOI: https://doi.org/10.1007/978-3-030-83395-4_7
Shah, D., & Bentrem, D. (2022). Environmental and genetic risk factors for gastric cancer. Journal of Surgical Oncology, 125(7), 1096-1103. https://doi.org/10.1002/jso.26869 DOI: https://doi.org/10.1002/jso.26869
Shen, C., Ding, J., Wang, Z., Cao, D., Ding, X, & Hou, T. (2020). From machine learning to deep learning: Advances in scoring functions for protein–ligand docking. Wires Computational Molecular Science, 10(1), 1-23. https://doi.org/10.1002/wcms.1429 DOI: https://doi.org/10.1002/wcms.1429
Song, J., Liu, Y., Chen, Q., Yang, J., Jiang, Z, Zhang, H., Liu, Z., & Jin, B. (2019). Expression patterns and the prognostic value of the SMYD family members in human breast carcinoma using integrative bioinformatics analysis. Oncology Letters, 17(4), 3851-3861. https://doi.org/10.3892/ol.2019.10054 DOI: https://doi.org/10.3892/ol.2019.10054
Spillane, W., Kelly, L., Feeney, B., Drew, M., & Hattotuwagama, C. (2003). Synthesis of heterosulfamates. Search for structure-taste relationships. Arkivoc, 7, 297-309. https://www.arkat-usa.org/get-file.php?fileid=19751 DOI: https://doi.org/10.3998/ark.5550190.0004.725
Stopsack, K., Nandakumar, S., Arora, K., Nguyen, B., Vasselman, S., Nweji, B., mCbride, S. M., Morris, M. J., Rathkof, D. E., Slovin, S. F., Danila, D. C., Autio, K. A., Scher, H. I., Mucci, L. A., Solit, D. B., Gönen, M., Chen, Y., Berger, M. F., Schultz, N., Abida, W., & Kantoff, P. W. (2022). Differences in prostate cancer genomes by self-reported race: contributions of genetic ancestry, modifiable cancer risk factors, and clinical factors. Clinical Cancer Research, 28(2), 318-326. https://doi.org/10.1158/1078-0432.CCR-21-2577 DOI: https://doi.org/10.1158/1078-0432.CCR-21-2577
Tian, T., Li, J., Shi, D., Zen, Y., Yu, B., & Li, X. (2022). SMYD3 promotes aerobic glycolysis in diffuse large B-cell lymphoma via H3K4me3-mediated PKM2 transcription. Cell Death & Disease, 13(9), 763. https://doi.org/10.1038/s41419-022-05208-7 DOI: https://doi.org/10.1038/s41419-022-05208-7
Torchala, M., Gerguri, T., Chaleil, R. A., Gordon, P., Russell, F., Keshani, M., & Bates, P. A. (2020). Enhanced sampling of protein conformational states for dynamic cross‐docking within the protein‐protein docking server SwarmDock. Proteins: Structure, Function, and Bioinformatics, 88(8), 962-972. https://publons.com/ publon/10.1002/prot.25851. DOI: https://doi.org/10.1002/prot.25851
Wang, L., Du, M., Wang, K., Khandpur, N., Rossato, S. L., Drouin-Chartier., j-p., Steele, E. M., Giovannucci, E., Song, M., Zhang, F. F. (2022). Association of ultra-processed food consumption with colorectal cancer risk among men and women: results from three prospective US cohort studies. The BMJ, 378. https://doi.org/10.1136/bmj-2021-068921 DOI: https://doi.org/10.1136/bmj-2021-068921
Xia, C, Dong, X., Li, H., Cao, M., Sun, D., He, S., Yang, F., Yan, X., Zhang, S., Li, N., & Chen, W. (2022). Cancer statistics in China and United States, 2022: profiles, trends, and determinants. Chinese Medical Journal, 135(05), 584-590. https://mednexus.org/doi/full/10.1097/CM9.0000000000002108 DOI: https://doi.org/10.1097/CM9.0000000000002108
Yang, Y., Qiu, R., Zhao, S., Shen, L., Tang, B., Weng, Q., Xu, Z., Zheng, L., Chen, W., Shu, G., Wang, Y., Zhao, Z., Chen, M., & Ji, J. (2022). SMYD3 associates with the NuRD (MTA1/2) complex to regulate transcription and promote proliferation and invasiveness in hepatocellular carcinoma cells. BMC Biology, 20(1), 20-22294. https://doi.org/10.1186/s12915-022-01499-6 DOI: https://doi.org/10.1186/s12915-022-01499-6
Yang, Z., Liu, F., Li, Z., Liu, N., Yao, X., Zhou, Y., Zhang, L., Jiang, P., Liu, H., Kong, L., Lang, C., Xu, X., Jia, J., Nakajima, T., Gu, W., Zheng, L., & Zhang, Z. (2023). Histone lysine methyltransferase SMYD3 promotes oral squamous cell carcinoma tumorigenesis via H3K4me3-mediated HMGA2 transcription. Clinical Epigigenetics, 15(1), 1-21. https://doi.org/10.1186/s13148-023-01506-9 DOI: https://doi.org/10.1186/s13148-023-01506-9
Ye, W., Shen, C., Xiong, G. L., Ding, J., Lu, A., Hou, T., & Cao, D. (2020). Improving docking-based virtual screening ability by integrating multiple energy auxiliary terms from molecular docking scoring. Journal of Chemical Information and Modeling, 60(9), 4216-4230. https://doi.org/10.1021/acs.jcim.9b00977 DOI: https://doi.org/10.1021/acs.jcim.9b00977
Yoo, J. E., Han, K., Shin, D. W., Kim, D. W., Kim, D., Kim, B-S., Chun, S., Jeon, K. H., Jung, W., Park, J., Park, J. H., Choi, K. S., & Kim, J. S. (2022). Association between changes in alcohol consumption and cancer risk. Journal American Medical Association, 5(8), 1-14. doi:10.1001/jamanetworkopen.2022.28544 DOI: https://doi.org/10.1001/jamanetworkopen.2022.28544
Zhao, Y., Chen, P., Dou, L., Li, F., L., M., Xu, L., Chen, J., Jia, M., Huang, S., Wang, N., Luan, S., Yang, J., Bai, N., & Liu, D. (2022). Co-administration with voriconazole doubles the exposure of ruxolitinib in patients with hematological malignancies. Drug Design, Development and Therapy, 16, 817-825. https://www.tandfonline.com/doi/full/10.2147/DDDT.S354270 DOI: https://doi.org/10.2147/DDDT.S354270
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2024 Maria Lopez-Ramos, Lauro Figueroa-Valverde, Marcela Rosas-Nexicapa, Catalina Cervantes-Ortega, Magdalena Alvarez-Ramirez, Francisco Diaz-Cedillo, Maria Virginia Mateu-Armand, Tomas Lopez-Gutierrez
This work is licensed under a Creative Commons Attribution 4.0 International License.
Authors who publish with this journal agree to the following terms:
1) Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
2) Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
3) Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work.