335
Views
14
CrossRef citations to date
0
Altmetric
Research Articles

An insight from computational approach to explore novel, high-affinity phosphodiesterase 10A inhibitors for neurological disorders

, ORCID Icon, &
Pages 9424-9436 | Received 26 Aug 2022, Accepted 25 Oct 2022, Published online: 06 Nov 2022

References

  • Abdel-Magid, A. F. (2018). Potential of PDE10A inhibitors as treatment for schizophrenia and other neurological disorders. Acs Medicinal Chemistry Letters, 9(9), 866–867. https://doi.org/10.1021/acsmedchemlett.8b00341
  • Al-Nema, M., Gaurav, A., Lee, V. S., Gunasekaran, B., Lee, M. T., Okechukwu, P., & NimmaNPipug, P. (2022). Structure-based discovery and bio-evaluation of a cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one as a phosphodiesterase 10A inhibitor. RSC Advances, 12(3), 1576–1591. https://doi.org/10.1039/D1RA07649C
  • Amin, H. S., Parikh, P. K., & Ghate, M. D. (2021). Medicinal chemistry strategies for the development of phosphodiesterase 10A (PDE10A) inhibitors – An update of recent progress. European Journal of Medicinal Chemistry, 214, 113155. https://doi.org/10.1016/J.EJMECH.2021.113155
  • Arthur, D. E., & Uzairu, A. (2019). Molecular docking studies on the interaction of NCI anticancer analogues with human Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit. Journal of King Saud University – Science, 31(4), 1151–1166. https://doi.org/10.1016/j.jksus.2019.01.011
  • Azevedo, M. F., Faucz, F. R., Bimpaki, E., Horvath, A., Levy, I., De Alexandre, R. B., Ahmad, F., Manganiello, V., & Stratakis, C. A. (2014). Clinical and molecular genetics of the phosphodiesterases (PDEs). Endocrine Reviews, 35(2), 195–233. https://doi.org/10.1210/ER.2013-1053
  • Bhardwaj, V. K., & Purohit, R. (2021). Computer simulation to identify selective inhibitor for human phosphodiesterase10A. Journal of Molecular Liquids, 328, 115419. https://doi.org/10.1016/j.molliq.2021.115419
  • Bhattacherjee, D., Kovalev, I. S., Kopchuk, D. S., Rahman, M., Santra, S., Zyryanov, G. V., Das, P., Purohit, R., Rusinov, V. L., & Chupakhin, O. N. (2022). Cu salts-free mechanochemical approach towards multi-functionalized 1,2,3-triazoles and anti-seizure drug rufinamide analogs. https://doi.org/10.26434/CHEMRXIV-2022-50C3J
  • Boswell-Smith, V., Spina, D., & Page, C. P. (2006). Phosphodiesterase inhibitors. British Journal of Pharmacology, 147(S1), S252–S257. https://doi.org/10.1038/sj.bjp.0706495
  • Chappie, T. A., Helal, C. J., & Hou, X. (2012). Current landscape of phosphodiesterase 10A (PDE10A) inhibition. Journal of Medicinal Chemistry, 55(17), 7299–7331. https://doi.org/10.1021/JM3004976
  • Chappie, T. A., Humphrey, J. M., Allen, M. P., Estep, K. G., Fox, C. B., Lebel, L. A., Liras, S., Marr, E. S., Menniti, F. S., Pandit, J., Schmidt, C. J., Tu, M., Williams, R. D., & Yang, F. V. (2007). Discovery of a series of 6,7-dimethoxy-4-pyrrolidylquinazoline PDE10A inhibitors. Journal of Medicinal Chemistry, 50(2), 182–185. https://doi.org/10.1021/JM060653B/SUPPL_FILE/JM060653BSI20061129_015143.PDF
  • Chen, D., Oezguen, N., Urvil, P., Ferguson, C., Dann, S. M., & Savidge, T. C. (2016). Regulation of protein-ligand binding affinity by hydrogen bond pairing. Science Advances, 2(3), e1501240. https://doi.org/10.1126/sciadv.1501240
  • Chen, J., Wang, J., & Zhu, W. (2017a). Zinc ion-induced conformational changes in new Delphi metallo-β-lactamase 1 probed by molecular dynamics simulations and umbrella sampling. Physical Chemistry Chemical Physics: PCCP, 19(4), 3067–3075. https://doi.org/10.1039/C6CP08105C
  • Chen, J., Wang, J., & Zhu, W. (2017b). Mutation L1196M-induced conformational changes and the drug resistant mechanism of anaplastic lymphoma kinase studied by free energy perturbation and umbrella sampling. Physical Chemistry Chemical Physics: PCCP, 19(44), 30239–30248. https://doi.org/10.1039/C7CP05418A
  • Conti, M., & Beavo, J. (2007). Biochemistry and physiology of cyclic nucleotide phosphodiesterases: Essential components in cyclic nucleotide signaling. Annual Review of Biochemistry, 76, 481–511. https://doi.org/10.1146/ANNUREV.BIOCHEM.76.060305.150444
  • de Souza, O. N., & Ornstein, R. L. (1999). Molecular dynamics simulations of a protein-protein dimer: Particle-mesh Ewald electrostatic model yields far superior results to standard cutoff model. Journal of Biomolecular Structure & Dynamics, 16(6), 1205–1218. https://doi.org/10.1080/07391102.1999.10508328
  • Erro, R., Mencacci, N. E., & Bhatia, K. P. (2021). The emerging role of phosphodiesterases in movement disorders. Movement Disorders, 36(10), 2225–2243. https://doi.org/10.1002/MDS.28686
  • Francis, S. H., Blount, M. A., & Corbin, J. D. (2011). Mammalian cyclic nucleotide phosphodiesterases: molecular mechanisms and physiological functions. Physiological Reviews, 91(2), 651–690. https://doi.org/10.1152/PHYSREV.00030.2010
  • Gaussian, M. F. (2016). Gaussian 16. Gaussian, Inc.
  • Grauer, S. M., Pulito, V. L., Navarra, R. L., Kelly, M. P., Kelley, C., Graf, R., Langen, B., Logue, S., Brennan, J., Jiang, L., Charych, E., Egerland, U., Liu, F., Marquis, K. L., Malamas, M., Hage, T., Comery, T. A., & Brandon, N. J. (2009). Phosphodiesterase 10A inhibitor activity in preclinical models of the positive, cognitive, and negative symptoms of Schizophrenia. The Journal of Pharmacology and Experimental Therapeutics, 331(2), 574–590. https://doi.org/10.1124/JPET.109.155994
  • Guleria, V., Pal, T., Sharma, B., Chauhan, S., & Jaiswal, V. (2021). Pharmacokinetic and molecular docking studies to design antimalarial compounds targeting Actin I. International Journal of Health Sciences, 15(6), 4–15. /pmc/articles/PMC8589829/
  • Helal, C. J., Kang, Z., Hou, X., Pandit, J., Chappie, T. A., HumphRey, J. M., Marr, E. S., Fennell, K. F., Chenard, L. K., Fox, C., Schmidt, C. J., Williams, R. D., Chapin, D. S., Siuciak, J., Lebel, L., Menniti, F., Cianfrogna, J., Fonseca, K. R., Nelson, F. R., … Liras, S. (2011). Use of structure-based design to discover a potent, selective, in vivo active phosphodiesterase 10A inhibitor lead series for the treatment of schizophrenia. Journal of Medicinal Chemistry, 54(13), 4536–4547. https://doi.org/10.1021/JM2001508/SUPPL_FILE/JM2001508_SI_001.PDF
  • Höfgen, N., Stange, H., Schindler, R., Lankau, H. J., Grunwald, C., Langen, B., Egerland, U., Tremmel, P., Pangalos, M. N., Marquis, K. L., Hage, T., Harrison, B. L., Malamas, M. S., Brandon, N. J., & Kronbach, T. (2010). Discovery of imidazo[1,5-a]pyrido[3,2-e]pyrazines as a new class of phosphodiesterase 10A inhibitiors. Journal of Medicinal Chemistry, 53(11), 4399–4411. https://doi.org/10.1021/JM1002793
  • Jäger, R., Russwurm, C., Schwede, F., Genieser, H. G., Koesling, D., & Russwurm, M. (2012). Activation of PDE10 and PDE11 phosphodiesterases. The Journal of Biological Chemistry, 287(2), 1210–1219. https://doi.org/10.1074/JBC.M111.263806
  • Jansen, C., Kooistra, A. J., Kanev, G. K., Leurs, R., De Esch, I., J. P., & 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/SUPPL_FILE/JM5B01813_SI_001.ZIP
  • Kehler, J., & Nielsen, J. (2011). PDE10A inhibitors: Novel therapeutic drugs for Schizophrenia. Current Pharmaceutical Design, 17(2), 137–150. https://doi.org/10.2174/138161211795049624
  • Kleiman, R. J., Kimmel, L. H., Bove, S. E., Lanz, T. A., Harms, J. F., Romegialli, A., Miller, K. S., Willis, A., Des Etages, S., Kuhn, M., & Schmidt, C. J. (2011). Chronic suppression of phosphodiesterase 10A alters striatal expression of genes responsible for neurotransmitter synthesis, neurotransmission, and signaling pathways implicated in Huntington’s disease. The Journal of Pharmacology and Experimental Therapeutics, 336(1), 64–76. https://doi.org/10.1124/JPET.110.173294
  • Kumar Bhardwaj, V., Das, P., & Purohit, R. (2022). Identification and comparison of plant-derived scaffolds as selective CDK5 inhibitors against standard molecules: Insights from umbrella sampling simulations. Journal of Molecular Liquids, 348, 118015. https://doi.org/10.1016/j.molliq.2021.118015
  • Kumar, S., Bhardwaj, V. K., Singh, R., Das, P., & Purohit, R. (2022). Evaluation of plant-derived semi-synthetic molecules against BRD3-BD2 protein: A computational strategy to combat breast cancer. Molecular Systems Design & Engineering, 7(4), 381–391. https://doi.org/10.1039/D1ME00183C
  • Kumari, R., Kumar, R., & Lynn, A. (2014). G-mmpbsa – A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/CI500020M/SUPPL_FILE/CI500020M_SI_001.PDF
  • Lagorce, D., Douguet, D., Miteva, M. A., & Villoutreix, B. O. (2017). Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors. Scientific reports, 7(1),46277–15. https://doi.org/10.1038/srep46277
  • Le, L., Lee, E. H., Hardy, D. J., Truong, T. N., & Schulten, K. (2010). Molecular dynamics simulations suggest that electrostatic funnel directs binding of tamiflu to influenza N1 neuraminidases. PLoS Computational Biology, 6(9), e1000939. https://doi.org/10.1371/journal.pcbi.1000939
  • Lesitha Jeeva Kumari, J., Jesu Jaya Sudan, R., & Sudandiradoss, C. (2017). Evaluation of peptide designing strategy against subunit reassociation in mucin 1: A steered molecular dynamics approach. PloS One, 12(8), e0183041. https://doi.org/10.1371/JOURNAL.PONE.0183041
  • Li, Z., Fichthorn, K. A., & Milner, S. T. (2016). Surfactant binding to polymer-water interfaces in atomistic simulations. Langmuir: The ACS Journal of Surfaces and Colloids, 32(30), 7519–7529. https://doi.org/10.1021/ACS.LANGMUIR.6B01393/SUPPL_FILE/LA6B01393_SI_003.PDF
  • Mai, B. K., & Li, M. S. (2011). Neuraminidase inhibitor R-125489 – A promising drug for treating influenza virus: Steered molecular dynamics approach. Biochemical and Biophysical Research Communications, 410(3), 688–691. https://doi.org/10.1016/J.BBRC.2011.06.057
  • Majumder, R., & Mandal, M. (2022). Screening of plant-based natural compounds as a potential COVID-19 main protease inhibitor: an in silico docking and molecular dynamics simulation approach. Journal of Biomolecular Structure and Dynamics, 40(2), 696–711. https://doi.org/10.1080/07391102.2020.1817787
  • Manallack, D. T., Hughes, R. A., & Thompson, P. E. (2005). The next generation of phosphodiesterase inhibitors: structural clues to ligand and substrate selectivity of phosphodiesterases. Journal of Medicinal Chemistry, 48(10), 3449–3462. https://doi.org/10.1021/JM040217U
  • Menniti, F. S., Chappie, T. A., & Schmidt, C. J. (2020). PDE10A inhibitors—Clinical failure or window into antipsychotic drug action? Frontiers in Neuroscience, 14, 600178. https://doi.org/10.3389/FNINS.2020.600178/BIBTEX
  • Modestia, S. M., Malta De Sá, M., Auger, E., Trossini, G. H. G., Krieger, J. E., & Rangel-Yagui, C. D. O. (2019). Biased agonist TRV027 determinants in AT1R by molecular dynamics simulations. Journal of Chemical Information and Modeling, 59(2), 797–808. https://doi.org/10.1021/ACS.JCIM.8B00628/SUPPL_FILE/CI8B00628_SI_001.PDF
  • Nittinger, E., Inhester, T., Bietz, S., Meyder, A., Schomburg, K. T., Lange, G., Klein, R., & Rarey, M. (2017). Large-scale analysis of hydrogen bond interaction patterns in protein–ligand interfaces. Journal of Medicinal Chemistry, 60(10), 4245-57. https://doi.org/10.1021/ACS.JMEDCHEM.7B00101
  • Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
  • Peng, T., Gong, J., Jin, Y., Zhou, Y., Tong, R., Wei, X., Bai, L., & Shi, J. (2018). Inhibitors of phosphodiesterase as cancer therapeutics. European Journal of Medicinal Chemistry, 150, 742–756. https://doi.org/10.1016/J.EJMECH.2018.03.046
  • Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/ACS.JMEDCHEM.5B00104/SUPPL_FILE/JM5B00104_SI_001.PDF
  • Rifai, E. A., Van Dijk, M., Vermeulen, N. P. E., Yanuar, A., & Geerke, D. P. (2019). A comparative linear interaction energy and MM/PBSA study on SIRT1–Ligand binding free energy calculation. Journal of Chemical Information and Modeling, 59(9), 4018–4033. https://doi.org/10.1021/ACS.JCIM.9B00609
  • Rodriguez, R. A., Yu, L., & Chen, L. Y. (2015). Computing protein-protein association affinity with hybrid steered molecular dynamics. Journal of Chemical Theory and Computation, 11(9), 4427–4438. https://doi.org/10.1021/ACS.JCTC.5B00340
  • Russo, S., Li, N., Lee, K., Xi, Y., Zhu, B., Gary, B., Ramirez, V., Gurpinar, E., Canzeroni, J., FajaRdo, A., Sigler, S., Piazza, J. T., Chen, X., Andrews, J., Li, Y., Eberhardt, B., Yet, L., Keeton, A., Grizzle, W. E., & Piazza, G. (2014). Phosphodiesterase 10, a novel target in colon cancer. Journal of Clinical Oncology, 32(3_suppl), 503–503. https://doi.org/10.1200/Jco.2014.32.3_suppl.503
  • Sack, J. S., Gao, M., Kiefer, S. E., Myers, J. E., Newitt, J. A., Wu, S., & Yan, C. (2016). Crystal structure of microtubule affinity-regulating kinase 4 catalytic domain in complex with a pyrazolopyrimidine inhibitor. Acta Crystallographica Section: F Structural Biology Communications, 72(2), 129–134. https://doi.org/10.1107/S2053230X15024747/TT5077SUP1.PDF
  • Schlitter, J. (1993). Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chemical Physics Letters, 215(6), 617–621. https://doi.org/10.1016/0009-2614(93)89366-P
  • Schüttelkopf, A. W., & Van Aalten, D. M. F. (2004). PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica. Section D, Biological Crystallography, 60(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
  • Sharma, J., Kumar Bhardwaj, V., & Purohit, R. (2021). Recognition of distinct chemical molecules as inhibitors for KIT receptor mutants D816H/Y/V: A simulation approach. Journal of Molecular Liquids, 339, 116317. https://doi.org/10.1016/j.molliq.2021.116317
  • Singam, A., Ramaprasad, E., Raman Subramanian, S., Subramanian, V., Muvva, C., Singam, E. R. A., Sundar, S., Ab, R., & Subramanian, V. (2014). Structure-based virtual screening of novel, high-affinity BRD4 inhibitors. Molecular bioSystems, 10(9), 2384–2397. https://doi.org/10.1039/c4mb00243a
  • Singh, R., Bhardwaj, V. K., Das, P., & Purohit, R. (2021). New ecdysone receptor agonists: A computational approach for rational discovery of insecticides for crop protection. Molecular Systems Design & Engineering, 6(11), 936–945. https://doi.org/10.1039/D1ME00047K
  • Singh, V. K., Chang, H. H., Kuo, C. C., Shiao, H. Y., Hsieh, H. P., & Coumar, M. S. (2017). Drug repurposing for chronic myeloid leukemia: in silico and in vitro investigation of DrugBank database for allosteric Bcr-Abl inhibitors. Journal of Biomolecular Structure & Dynamics, 35(8), 1833–1848. https://doi.org/10.1080/07391102.2016.1196462
  • Siuciak, J. A., McCarthy, S. A., Chapin, D. S., Fujiwara, R. A., James, L. C., Williams, R. D., Stock, J. L., McNeish, J. D., Strick, C. A., Menniti, F. S., & Schmidt, C. J. (2006). Genetic deletion of the striatum-enriched phosphodiesterase PDE10A: Evidence for altered striatal function. Neuropharmacology, 51(2), 374–385. https://doi.org/10.1016/J.NEUROPHARM.2006.01.012
  • Tirado-Rives, J., & Jorgensen, W. L. (2008). Performance of B3LYP density functional methods for a large set of organic molecules. Journal of Chemical Theory and Computation, 4(2), 297–306. https://doi.org/10.1021/CT700248K/SUPPL_FILE/CT700248K-FILE002.PDF
  • Tung, Ngo, S., Vu, K. B., Minh, Bui, L., & Vu, V. V. (2019). Effective estimation of ligand-binding affinity using biased sampling method. ACS omega, 4(2), 3887-93. https://doi.org/10.1021/acsomega.8b03258
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., Berendsen, H., & J., C. (2005). GROMACS: Fast, flexible, and free: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/JCC.20291
  • Verhoest, P. R., Chapin, D. S., Corman, M., Fonseca, K., Harms, J. F., Hou, X., Marr, E. S., Menniti, F. S., Nelson, F., O’Connor, R., Pandit, J., Proulx-LaFrance, C., Schmidt, A. W., Schmidt, C. J., SuICiak, J. A., & Liras, S. (2009). Discovery of a novel class of phosphodiesterase 10A inhibitors and identification of clinical candidate 2-[4-(1-methyl-4-pyridin-4-yl-1H-pyrazol-3-yl)-phenoxymethyl]-quinoline (PF-2545920) for the treatment of schizophrenia. Journal of Medicinal Chemistry, 52(16), 5188–5196. https://doi.org/10.1021/JM900521K/SUPPL_FILE/JM900521K_SI_001.PDF
  • Wu, G., Robertson, D. H., Brooks, C. L., & Vieth, M. (2003). Detailed analysis of grid-based molecular docking: A case study of CDOCKER—A CHARMm-based MD docking algorithm. Journal of Computational Chemistry, 24(13), 1549–1562. https://doi.org/10.1002/JCC.10306
  • Xi, M., Sun, T., Chai, S., Xie, M., Chen, S., Deng, L., Du, K., Shen, R., & Sun, H. (2022). Therapeutic potential of phosphodiesterase inhibitors for cognitive amelioration in Alzheimer’s disease. European Journal of Medicinal Chemistry, 232, 114170. https://doi.org/10.1016/J.EJMECH.2022.114170
  • Yadav, S., Pandey, S. K., Singh, V. K., Goel, Y., Kumar, A., & Singh, S. M. (2017). Molecular docking studies of 3-bromopyruvate and its derivatives to metabolic regulatory enzymes: Implication in designing of novel anticancer therapeutic strategies. PLoS One, 12(5), e0176403. https://doi.org/10.1371/journal.pone.0176403
  • Yang, Y., Zhang, S., Zhou, Q., Zhang, C., Gao, Y., Wang, H., Li, Z., Wu, D., Wu, Y., Huang, Y. Y., Guo, L., & Luo, H. B. (2020). Discovery of highly selective and orally available benzimidazole-based phosphodiesterase 10 inhibitors with improved solubility and pharmacokinetic properties for treatment of pulmonary arterial hypertension. Acta Pharmaceutica Sinica. B, 10(12), 2339–2347. https://doi.org/10.1016/J.APSB.2020.04.003
  • Zhu, B., Lee, K., Canzoneri, J., Ramirez-Alcantara, V., Sigler, S., Gary, B., Butler, E., Keeton, A., Chen, X., Boyd, M., & Piazza, G. (2015). Abstract 4372: Phosphodiesterase 10A inhibition suppresses lung tumor cell growth by activating PKG to inhibit RAS and WNT signaling. Cancer Research, 75(15_Supplement), 4372–4372. https://doi.org/10.1158/1538-7445.AM2015-4372
  • Zhu, B., Lindsey, A., Li, N., Lee, K., Ramirez-Alcantara, V., Canzoneri, J. C., Fajardo, A., Madeira da Silva, L., Thomas, M., Piazza, J. T., Yet, L., Eberhardt, B. T., Gurpinar, E., Otali, D., Grizzle, W., Valiyaveettil, J., Chen, X., Keeton, A. B., & Piazza, G. A. (2017). Phosphodiesterase 10A is overexpressed in lung tumor cells and inhibitors selectively suppress growth by blocking β-catenin and MAPK signaling. Oncotarget, 8(41), 69264–69280. https://doi.org/10.18632/ONCOTARGET.20566

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.