160
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Computational-based drug design of novel small molecules targeting p53-MDMX interaction

, , , , , , , , , , , , , , & show all
Received 13 May 2023, Accepted 06 Jul 2023, Published online: 14 Aug 2023

References

  • Adelusi, T. I., Abdul-Hammed, M., Idris, M. O., Kehinde, O. Q., Boyenle, I. D., Divine, U. C., Adedotun, I. O., Folorunsho, A. A., & Kolawole, O. E. (2021). Exploring the inhibitory potentials of Momordica charantia bioactive compounds against Keap1-Kelch protein using computational approaches. In Silico Pharmacology, 9(1), 39. https://doi.org/10.1007/s40203-021-00100-2
  • Adelusi, T. I., Oyedele, A.-Q K., Boyenle, I. D., Ogunlana, A. T., Adeyemi, R. O., Ukachi, C. D., Idris, M. O., Olaoba, O. T., Adedotun, I. O., Kolawole, O. E., Xiaoxing, Y., & Abdul-Hammed, M. (2022). Molecular modeling in drug discovery. Informatics in Medicine Unlocked, 29, 100880. https://doi.org/10.1016/j.imu.2022.100880
  • Allen, J. G., Bourbeau, M. P., Wohlhieter, G. E., Bartberger, M. D., Michelsen, K., Hungate, R., Gadwood, R. C., Gaston, R. D., Evans, B., Mann, L. W., Matison, M. E., Schneider, S., Huang, X., Yu, D., Andrews, P. S., Reichelt, A., Long, A. M., Yakowec, P., Yang, E. Y., Lee, T. A., & Oliner, J. D. (2009). Discovery and optimization of chromenotriazolopyrimidines as potent inhibitors of the mouse double minute 2-tumor protein 53 protein-protein interaction. Journal of Medicinal Chemistry, 52(22), 7044–7053. https://doi.org/10.1021/jm900681h
  • Beckerman, R., & Prives, C. (2010). Transcriptional regulation by p53. Cold Spring Harbor Perspectives in Biology, 2(8), a000935. https://doi.org/10.1101/cshperspect.a000935
  • Bharatham, N., Bharatham, K., Shelat, A. A., & Bashford, D. (2014). Ligand binding mode prediction by docking: Mdm2/mdmx inhibitors as a case study. Journal of Chemical Information and Modeling, 54(2), 648–659. https://doi.org/10.1021/ci4004656
  • Boyenle, I. D., Ogunlana, A. T., Kehinde Oyedele, A. Q., Olokodana, B. K., Owolabi, N., Salahudeen, A., Aderenle, O. T., Oloyede, T. O., & Adelusi, T. I. (2023). Reinstating apoptosis using putative Bcl-xL natural product inhibitors: Molecular docking and ADMETox profiling investigations. Journal of Taibah University Medical Sciences, 18(3), 461–469. https://doi.org/10.1016/j.jtumed.2022.10.014
  • Brooks, C. L., & Gu, W. (2006). p53 ubiquitination: Mdm2 and beyond. Molecular Cell, 21(3), 307–315. https://doi.org/10.1016/j.molcel.2006.01.020
  • Carter, B. Z., Mak, D. H., Schober, W. D., Koller, E., Pinilla, C., Vassilev, L. T., Reed, J. C., & Andreeff, M. (2010). Simultaneous activation of p53 and inhibition of XIAP enhance the activation of apoptosis signaling pathways in AML. Blood, 115(2), 306–314. https://doi.org/10.1182/blood-2009-03-212563
  • Cheok, C. F., Verma, C. S., Baselga, J., & Lane, D. P. (2011). Translating p53 into the clinic. Nature Reviews. Clinical Oncology, 8(1), 25–37. https://doi.org/10.1038/nrclinonc.2010.174
  • Cummings, M. D., Schubert, C., Parks, D. J., Calvo, R. R., LaFrance, L. V., Lattanze, J., Milkiewicz, K. L., & Lu, T. (2006). Substituted 1,4-benzodiazepine-2,5-diones as alpha-helix mimetic antagonists of the HDM2-p53 protein-protein interaction. Chemical Biology & Drug Design, 67(3), 201–205. https://doi.org/10.1111/j.1747-0285.2006.00365.x
  • Dickens, M. P., Fitzgerald, R., & Fischer, P. M. (2010). Small-molecule inhibitors of MDM2 as new anticancer therapeutics. Seminars in Cancer Biology, 20(1), 10–18. https://doi.org/10.1016/j.semcancer.2009.10.003
  • Ding, K., Lu, Y., Nikolovska-Coleska, Z., Wang, G., Qiu, S., Shangary, S., Gao, W., Qin, D., Stuckey, J., Krajewski, K., Roller, P. P., & Wang, S. (2006). Structure-based design of spiro-oxindoles as potent, specific small-molecule inhibitors of the MDM2-p53 interaction. Journal of Medicinal Chemistry, 49(12), 3432–3435. https://doi.org/10.1021/jm051122a
  • Evan, G. I., & Vousden, K. H. (2001). Proliferation, cell cycle and apoptosis in cancer. Nature, 411(6835), 342–348. https://doi.org/10.1038/35077213
  • Golestanian, S., Sharifi, A., Popowicz, G. M., Azizian, H., Foroumadi, A., Szwagierczak, A., Holak, T. A., & Amanlou, M. (2016). Discovery of novel dual inhibitors against Mdm2 and Mdmx proteins by in silico approaches and binding assay. Life Sciences, 145, 240–246. https://doi.org/10.1016/j.lfs.2015.12.047
  • Grasberger, B. L., Lu, T., Schubert, C., Parks, D. J., Carver, T. E., Koblish, H. K., Cummings, M. D., LaFrance, L. V., Milkiewicz, K. L., Calvo, R. R., Maguire, D., Lattanze, J., Franks, C. F., Zhao, S., Ramachandren, K., Bylebyl, G. R., Zhang, M., Manthey, C. L., Petrella, E. C., … Bone, R. F. (2005). Discovery and cocrystal structure of benzodiazepinedione HDM2 antagonists that activate p53 in cells. Journal of Medicinal Chemistry, 48(4), 909–912. https://doi.org/10.1021/jm049137g
  • Haupt, S., Berger, M., Goldberg, Z., & Haupt, Y. (2003). Apoptosis - the p53 network. Journal of Cell Science, 116(Pt 20), 4077–4085. https://doi.org/10.1242/jcs.00739
  • Hsu, K. C., Chen, Y. F., Lin, S. R., & Yang, J. M. (2011). iGEMDOCK: A graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis. BMC Bioinformatics, 12(Suppl 1), S33. https://doi.org/10.1186/1471-2105-12-S1-S33
  • Khoutoul, M., Lamsayah, M., Al-Blewi, F. F., Rezki, N., Aouad, M. R., Mouslim, M., & Touzani, R. (2016). Liquid–liquid extraction of metal ions, DFT and TD-DFT analysis of some 1, 2, 4-triazole Schiff Bases with high selectivity for Pb (II) and Fe (II). Journal of Molecular Structure, 1113, 99–107. https://doi.org/10.1016/j.molstruc.2016.02.046
  • Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., & Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–13. https://doi.org/10.1093/nar/gkv951
  • Lee, G. R., Shin, W. H., Park, H. B., Shin, S. M., & Seok, C. O. (2012). Conformational sampling of flexible ligand-binding protein loops. Bulletin of the Korean Chemical Society, 33(3), 770–774. https://doi.org/10.5012/bkcs.2012.33.3.770
  • Liu, K., Watanabe, E., & Kokubo, H. (2017). Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations. Journal of Computer-Aided Molecular Design, 31(2), 201–211. https://doi.org/10.1007/s10822-016-0005-2
  • Menéndez, C. A., Accordino, S. R., Gerbino, D. C., & Appignanesi, G. A. (2016). Hydrogen bond dynamic propensity studies for protein binding and drug design. PloS One, 11(10), e0165767. https://doi.org/10.1371/journal.pone.0165767
  • Millard, M., Pathania, D., Grande, F., Xu, S., & Neamati, N. (2011). Small-molecule inhibitors of p53-MDM2 interaction: The 2006-2010 update. Current Pharmaceutical Design, 17(6), 536–559. https://doi.org/10.2174/138161211795222649
  • O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3, 33. https://doi.org/10.1186/1758-2946-3-33
  • Ogunlana, A. T., Oyedele, A. K., Boyenle, I. D., Ayoola, S. O., Ajibare, A. C., Adeyemi, A. O., Jinadu, L. A., Adenrele, O. T., Alausa, A. O., & Adelusi, T. I. (2022). Computer-aided drug design of some KRAS G12C inhibitors: Targeting the covalent and allosteric binding site for cancer therapy. Informatics in Medicine Unlocked, 32, 101032. https://doi.org/10.1016/j.imu.2022.101032
  • Oyedele, A. K., Adelusi, T. I., Ogunlana, A. T., Adeyemi, R. O., Atanda, O. E., Babalola, M. O., Ashiru, M. A., Ayoola, I. J., & Boyenle, I. D. (2022). Integrated virtual screening and molecular dynamics simulation revealed promising drug candidates of p53-MDM2 interaction. Journal of Molecular Modeling, 28(6), 142. https://doi.org/10.1007/s00894-022-05131-w
  • Oyedele, A. K., Owolabi, N. A., Odunitan, T. T., Ajibare, A. C., Jimoh, R. O., Abdul Azeez, W. O., Bello-Hassan, M. T., Soares, A. S., Adekola, A. T., Abdulkareem, T. O., Oyelekan, S. O., Ashiru, M. A., Gbadebo, I. O., Olajumoke, H. E., Boyenle, I. D., & Ogunlana, A. T. (2023). The discovery of some promising putative binders of KRAS G12D receptor using computer-aided drug discovery approach. Informatics in Medicine Unlocked, 37, 101170. https://doi.org/10.1016/j.imu.2023.101170
  • Popowicz, G. M., Czarna, A., Wolf, S., Wang, K., Wang, W., Dömling, A., & Holak, T. A. (2010). Structures of low molecular weight inhibitors bound to MDMX and MDM2 reveal new approaches for p53-MDMX/MDM2 antagonist drug discovery. Cell Cycle (Georgetown, Tex.), 9(6), 1104–1111. https://doi.org/10.4161/cc.9.6.10956
  • Ray-Coquard, I., Blay, J. Y., Italiano, A., Le Cesne, A., Penel, N., Zhi, J., Heil, F., Rueger, R., Graves, B., Ding, M., Geho, D., Middleton, S. A., Vassilev, L. T., Nichols, G. L., & Bui, B. N. (2012). Effect of the MDM2 antagonist RG7112 on the P53 pathway in patients with MDM2-amplified, well-differentiated or dedifferentiated liposarcoma: An exploratory proof-of-mechanism study. The Lancet. Oncology, 13(11), 1133–1140. https://doi.org/10.1016/S1470-2045(12)70474-6
  • Ryan, K. M., Phillips, A. C., & Vousden, K. H. (2001). Regulation and function of the p53 tumor suppressor protein. Current Opinion in Cell Biology, 13(3), 332–337. https://doi.org/10.1016/s0955-0674(00)00216-7
  • Shangary, S., Qin, D., McEachern, D., Liu, M., Miller, R. S., Qiu, S., Nikolovska-Coleska, Z., Ding, K., Wang, G., Chen, J., Bernard, D., Zhang, J., Lu, Y., Gu, Q., Shah, R. B., Pienta, K. J., Ling, X., Kang, S., Guo, M., … Wang, S. (2008). Temporal activation of p53 by a specific MDM2 inhibitor is selectively toxic to tumors and leads to complete tumor growth inhibition. Proceedings of the National Academy of Sciences of the United States of America, 105(10), 3933–3938. https://doi.org/10.1073/pnas.0708917105
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–171. https://doi.org/10.1002/jcc.20291
  • Vassilev, L. T. (2007). MDM2 inhibitors for cancer therapy. Trends in Molecular Medicine, 13(1), 23–31. https://doi.org/10.1016/j.molmed.2006.11.002
  • Wade, M., Li, Y. C., & Wahl, G. M. (2013). MDM2, MDMX and p53 in oncogenesis and cancer therapy. Nature Reviews. Cancer, 13(2), 83–96. https://doi.org/10.1038/nrc3430
  • Wang, Y. T., & Cheng, T. L. (2021). Computational modeling of cyclic peptide inhibitor-MDM2/MDMX binding through global docking and Gaussian accelerated molecular dynamics simulations. Journal of Biomolecular Structure & Dynamics, 39(11), 4005–4014. https://doi.org/10.1080/07391102.2020.1773317
  • Wang, X., & Jiang, X. (2012). Mdm2 and MdmX partner to regulate p53. FEBS Letters, 586(10), 1390–1396. https://doi.org/10.1016/j.febslet.2012.02.049
  • Yamasaki, S., Yagishita, N., Sasaki, T., Nakazawa, M., Kato, Y., Yamadera, T., Bae, E., Toriyama, S., Ikeda, R., Zhang, L., Fujitani, K., Yoo, E., Tsuchimochi, K., Ohta, T., Araya, N., Fujita, H., Aratani, S., Eguchi, K., Komiya, S., … Nakajima, T. (2007). Cytoplasmic destruction of p53 by the endoplasmic reticulum-resident ubiquitin ligase 'Synoviolin’. The EMBO Journal, 26(1), 113–122. https://doi.org/10.1038/sj.emboj.7601490
  • Yu, S., Qin, D., Shangary, S., Chen, J., Wang, G., Ding, K., McEachern, D., Qiu, S., Nikolovska-Coleska, Z., Miller, R., Kang, S., Yang, D., & Wang, S. (2009). Potent and orally active small-molecule inhibitors of the MDM2-p53 interaction. Journal of Medicinal Chemistry, 52(24), 7970–7973. https://doi.org/10.1021/jm901400z

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.