67
Views
0
CrossRef citations to date
0
Altmetric
Research Article

Insights into the selective mechanism of PDE2/9a inhibitors from silico aspects

, , , , , , , , & show all
Received 17 Jan 2024, Accepted 10 Mar 2024, Published online: 25 Mar 2024

References

  • Alaghaz, A.-N. M. A., & Aldulmani, S. A. A. (2019). Preparation, structural characterization and DNA binding/cleavage affinity of new bioactive nano-sized metal (II/IV) complexes with oxazon-Schiff’s base ligand. Applied Organometallic Chemistry, 33(10), e5135. https://doi.org/10.1002/aoc.5135
  • Alaghaz, A.-N. M. A., Ammar, Y. A., Bayoumi, H. A., & Aldhlmani, S. A. (2014). Synthesis, spectral characterization, thermal analysis, molecular modeling and antimicrobial activity of new potentially N2O2 azo-dye Schiff base complexes. Journal of Molecular Structure, 1074, 359–375. https://doi.org/10.1016/j.molstruc.2014.05.078
  • Alaghaz, A.-N M. A., Bayoumi, H. A., Ammar, Y. A., & Aldhlmani, S. A. (2013). Synthesis, characterization, and antipathogenic studies of some transition metal complexes with N,O-chelating Schiff’s base ligand incorporating azo and sulfonamide Moieties. Journal of Molecular Structure, 1035, 383–399. https://doi.org/10.1016/j.molstruc.2012.11.030
  • Alamier, W. M., & Alaghaz, A. M. A. (2023). Design, spectral characterization, quantum chemical investigation, biological activity of nano-sized transition metal complexes of tridentate 3-mercapto-4H-1,2,4-triazol-4-yl-aminomethylphenol Schiff base ligand. Journal of Biomolecular Structure & Dynamics, 2023, 1–21. https://doi.org/10.1080/07391102.2023.2294171
  • Aldulmani, S. A. A., & Alaghaz, A.-N M. A. (2019). Synthesis, spectroscopic characterization, quantum chemical calculations, evaluation of biological and cytotoxic activities, and molecular docking studies of 2-hydroxy-N′-(4,5,6-trimethoxy-2,3-dihydro-1H-inden-1-ylidene) benzohydrazide and its Cu(II), Co(II), Ni(II), and Zn(II) complexes. Journal of the Chinese Chemical Society, 66(12), 1682–1699. https://doi.org/10.1002/jccs.201800465
  • Barthel, T., Wollenhaupt, J., Lima, G. M. A., Wahl, M. C., & Weiss, M. S. (2022). Large-scale crystallographic fragment screening expedites compound optimization and identifies putative protein-protein interaction sites. Journal of Medicinal Chemistry, 65(21), 14630–14641. https://doi.org/10.1021/acs.jmedchem.2c01165
  • Bolger, G. B. (2021). The PDE-Opathies: Diverse phenotypes produced by a functionally related multigene family. Trends in Genetics, 37(7), 669–681. https://doi.org/10.1016/j.tig.2021.03.002
  • Borchers, A., & Pieler, T. (2010). Programming pluripotent precursor cells derived from Xenopus embryos to generate specific tissues and organs. Genes, 1(3), 413–426. https://doi.org/10.3390/genes1030413
  • Buijnsters, P., De Angelis, M., Langlois, X., Rombouts, F. J. R., Sanderson, W., Tresadern, G., Ritchie, A., Trabanco, A. A., VanHoof, G., Roosbroeck, Y. V., & Andrés, J.-I. (2014). Structure-based design of a potent, selective, and brain penetrating PDE2 inhibitor with demonstrated target engagement. ACS Medicinal Chemistry Letters, 5(9), 1049–1053. https://doi.org/10.1021/ml500262u
  • Delhaye, S., & Bardoni, B. (2021). Role of phosphodiesterases in the pathophysiology of neurodevelopmental disorders. Molecular Psychiatry, 26(9), 4570–4582. https://doi.org/10.1038/s41380-020-00997-9
  • Dorner-Ciossek, C., Kroker, K. S., & Rosenbrock, H. (2017). Role of PDE9 in cognition. Advances in Neurobiology, 17, 231–254. https://doi.org/10.1007/978-3-319-58811-7_9
  • Dunkerly-Eyring, B., & Kass, D. A. (2020). Myocardial phosphodiesterases and their role in cGMP regulation. Journal of Cardiovascular Pharmacology, 75(6), 483–493. https://doi.org/10.1097/FJC.0000000000000773
  • Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
  • Ghulam, M., Javed, M., Qamar, M. A., Shariq, M., Ahmed, I. A., Alziyadi, K. B., Almutib, E., Azooz, R., Alaghaz, A.-N M. A., & Ali, S. K. (2023). Highly-efficient Ni@CuS/SGCN nanocomposite with superior bifunctional electrocatalytic activity for water splitting. Journal of the Electrochemical Society.170(11), 116506. https://iopscience.iop.org/article/10 .1149/1945-7111/ad0ebc
  • Gomez, L., Massari, M. E., Vickers, T., Freestone, G., Vernier, W., Ly, K., Xu, R., McCarrick, M., Marrone, T., Metz, M., Yan, Y. G., Yoder, Z. W., Lemus, R., Broadbent, N. J., Barido, R., Warren, N., Schmelzer, K., Neul, D., Lee, D., … Breitenbucher, J. G. (2017). Design and synthesis of Novel and selective phosphodiesterase 2 (PDE2a) inhibitors for the treatment of memory disorders. Journal of Medicinal Chemistry, 60(5), 2037–2051. https://doi.org/10.1021/acs.jmedchem.6b01793
  • Helal, C. J., Arnold, E. P., Boyden, T. L., Chang, C., Chappie, T. A., Fennell, K. F., Forman, M. D., Hajos, M., Harms, J. F., Hoffman, W. E., Humphrey, J. M., Kang, Z., Kleiman, R. J., Kormos, B. L., Lee, C. W., Lu, J., Maklad, N., McDowell, L., Mente, S., … Yang, E. X. (2017). Application of structure-based design and parallel chemistry to identify a potent, selective, and brain penetrant phosphodiesterase 2A inhibitor. Journal of Medicinal Chemistry, 60(13), 5673–5698. https://doi.org/10.1021/acs.jmedchem.7b00397
  • Hofmann, F. (2020). The cGMP system: Components and function. Biological Chemistry, 401(4), 447–469. https://doi.org/10.1515/hsz-2019-0386
  • Huang, M., Shao, Y., Hou, J., Cui, W., Liang, B., Huang, Y., Li, Z., Wu, Y., Zhu, X., Liu, P., Wan, Y., Ke, H., & Luo, H. B. (2015). Structural asymmetry of phosphodiesterase-9A and a unique pocket for selective binding of a potent enantiomeric inhibitor. Molecular Pharmacology, 88(5), 836–845. https://doi.org/10.1124/mol.115.099747
  • Jansen, C., Kooistra, A. J., Kanev, G. K., Leurs, R., de Esch, I. J., & de Graaf, C. (2016). PDEStrIAn: A phosphodiesterase structure and ligand interaction annotated database as a tool for structure-based drug design. Journal of Medicinal Chemistry, 59(15), 7029–7065. https://doi.org/10.1021/acs.jmedchem.5b01813
  • Kamel, R., Leroy, J., Vandecasteele, G., & Fischmeister, R. (2023). Cyclic nucleotide phosphodiesterases as therapeutic targets in cardiac hypertrophy and heart failure. Nature Reviews. Cardiology, 20(2), 90–108. https://doi.org/10.1038/s41569-022-00756-z
  • Kayikci, M., Venkatakrishnan, A. J., Scott-Brown, J., Ravarani, C. N. J., Flock, T., & Babu, M. M. (2018). Visualization and analysis of non-covalent contacts using the Protein Contacts Atlas. Nature Structural & Molecular Biology, 25(2), 185–194. https://doi.org/10.1038/s41594-017-0019-z
  • Kim, G. E., & Kass, D. A. (2017). Cardiac phosphodiesterases and their modulation for treating heart disease. Handbook of Experimental Pharmacology, 243, 249–269. https://doi.org/10.1007/164_2016_82
  • Lee, D. I., Zhu, G., Sasaki, T., Cho, G. S., Hamdani, N., Holewinski, R., Jo, S. H., Danner, T., Zhang, M., Rainer, P. P., Bedja, D., Kirk, J. A., Ranek, M. J., Dostmann, W. R., Kwon, C., Margulies, K. B., Van Eyk, J. E., Paulus, W. J., Takimoto, E., & Kass, D. A. (2015). Phosphodiesterase 9A controls nitric-oxide-independent cGMP and hypertrophic heart disease. Nature, 519(7544), 472–476. https://doi.org/10.1038/nature14332
  • Li, J., Abel, R., Zhu, K., Cao, Y., Zhao, S., & Friesner, R. A. (2011). The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling. Proteins, 79(10), 2794–2812. https://doi.org/10.1002/prot.23106
  • Lu, C., Wu, C., Ghoreishi, D., Chen, W., Wang, L., Damm, W., Ross, G. A., Dahlgren, M. K., Russell, E., Von Bargen, C. D., Abel, R., Friesner, R. A., & Harder, E. D. (2021). OPLS4: Improving force field accuracy on challenging regimes of chemical space. Journal of Chemical Theory and Computation, 17(7), 4291–4300. https://doi.org/10.1021/acs.jctc.1c00302
  • Manhas, A., Lone, M. Y., & Jha, P. C. (2019). In search of the representative pharmacophore hypotheses of the enzymatic proteome of Plasmodium falciparum: A multicomplex-based approach. Molecular Diversity, 23(2), 453–470. https://doi.org/10.1007/s11030-018-9885-5
  • Meng, F., Hou, J., Shao, Y. X., Wu, P. Y., Huang, M., Zhu, X., Cai, Y., Li, Z., Xu, J., Liu, P., Luo, H. B., Wan, Y., & Ke, H. (2012). Structure-based discovery of highly selective phosphodiesterase-9A inhibitors and implications for inhibitor design. Journal of Medicinal Chemistry, 55(19), 8549–8558. https://doi.org/10.1021/jm301189c
  • Mikami, S., Nakamura, S., Ashizawa, T., Nomura, I., Kawasaki, M., Sasaki, S., Oki, H., Kokubo, H., Hoffman, I. D., Zou, H., Uchiyama, N., Nakashima, K., Kamiguchi, N., Imada, H., Suzuki, N., Iwashita, H., & Taniguchi, T. (2017). Discovery of clinical candidate N-((1S)-1-(3-Fluoro-4-(trifluoromethoxy)phenyl)-2-methoxyethyl)-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915): A highly potent, selective, and brain-penetrating phosphodiesterase 2A inhibitor for the treatment of cognitive disorders. Journal of Medicinal Chemistry, 60(18), 7677–7702. https://doi.org/10.1021/acs.jmedchem.7b00807
  • Patil, Y., Attarde, S., Dhake, R., Fegade, U., & Alaghaz, A.-N M. A. (2023). Adsorption of Congo red dye using metal oxide nano-adsorbents: Past, present, and future perspective. International Journal of Chemical Kinetics, 55(10), 579–605. https://doi.org/10.1002/kin.21675
  • Philipp, D. M., & Friesner, R. A. (1999). Mixedab initio QM/MM modeling using frozen orbitals and tests with alanine dipeptide and tetrapeptide. Journal of Computational Chemistry, 20(14), 1468–1494. https://doi.org/10.1002/(SICI)1096-987X(19991115)20:14<1468::AID-JCC2>3.0.CO;2-0
  • Solanki, P., Rana, N., Jha, P. C., & Manhas, A. N. U. (2023). A comprehensive analysis of the role of molecular docking in the development of anticancer agents against the cell cycle CDK enzyme. BIOCELL, 47(4), 707–729. https://doi.org/10.32604/biocell.2023.026615
  • Trabanco, A. A., Buijnsters, P., & Rombouts, F. J. (2016). Towards selective phosphodiesterase 2A (PDE2A) inhibitors: A patent review (2010 – present). Expert Opinion on Therapeutic Patents, 26(8), 933–946. https://doi.org/10.1080/13543776.2016.1203902
  • Tzeliou, C. E., Mermigki, M. A., & Tzeli, D. (2022). Review on the QM/MM methodologies and their application to metalloproteins. Molecules, 27(9), 2660. https://doi.org/10.3390/molecules27092660
  • Yang, X., Xu, Z., Hu, S., & Shen, J. (2023). Perspectives of PDE inhibitor on treating idiopathic pulmonary fibrosis. Frontiers in Pharmacology, 14, 1111393. https://doi.org/10.3389/fphar.2023.1111393
  • Zaccolo, M., Zerio, A., & Lobo, M. J. (2021). Subcellular Organization of the cAMP signaling pathway. Pharmacological Reviews, 73(1), 278–309. https://doi.org/10.1124/pharmrev.120.000086

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.