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Research Articles

Desmodin and isopongachromene as potential inhibitors of cyclin-dependent kinase 5: phytoconstituents targeting anticancer and neurological therapy

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Pages 8042-8052 | Received 22 Jul 2022, Accepted 20 Sep 2022, Published online: 02 Oct 2022

References

  • Ali, S., Khan, F. I., Mohammad, T., Lan, D., Hassan, M., & Wang, Y. (2019). Identification and evaluation of inhibitors of lipase from Malassezia restricta using virtual high-throughput screening and molecular dynamics studies. International Journal of Molecular Sciences, 20(4), 884. https://doi.org/10.3390/ijms20040884
  • Allnutt, A. B., Waters, A. K., Kesari, S., & Yenugonda, V. M. (2020). Physiological and pathological roles of cdk5: Potential directions for therapeutic targeting in neurodegenerative disease. ACS Chemical Neuroscience, 11(9), 1218–1230. https://doi.org/10.1021/acschemneuro.0c00096
  • Altis, A., Otten, M., Nguyen, P. H., Hegger, R., & Stock, G. (2008). Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis. The Journal of Chemical Physics, 128(24), 245102. https://doi.org/10.1063/1.2945165
  • Anjum, F., Ali, F., Mohammad, T., Shafie, A., Akhtar, O., Abdullaev, B., & Hassan, I. (2021). Discovery of natural compounds as potential inhibitors of human carbonic anhydrase II: An integrated virtual screening, docking, and molecular dynamics simulation study. OMICS: A Journal of Integrative Biology, 25(8), 513–524. https://doi.org/10.1089/omi.2021.0059
  • Anjum, F., Mohammad, T., Almalki, A. A., Akhtar, O., Abdullaev, B., & Hassan, M. I. (2021). Phytoconstituents and medicinal plants for anticancer drug discovery: Computational identification of potent inhibitors of Pim1 kinase. OMICS: A Journal of Integrative Biology, 25(9), 580–590. https://doi.org/10.1089/omi.2021.0107
  • Anwar, S., DasGupta, D., Shafie, A., Alhumaydhi, F. A., Alsagaby, S. A., Shahwan, M., Anjum, F., Al Abdulmonem, W., Sharaf, S. E., & Hassan, M. I. (2022). Implications of tempol in pyruvate dehydrogenase kinase 3 targeted anticancer therapeutics: Computational, spectroscopic, and calorimetric studies. Journal of Molecular Liquids, 350, 118581. https://doi.org/10.1016/j.molliq.2022.118581
  • Arnittali, M., Rissanou, A. N., & Harmandaris, V. (2019). Structure of biomolecules through molecular dynamics simulations. Procedia Computer Science, 156, 69–78. https://doi.org/10.1016/j.procs.2019.08.181
  • Baell, J. B. (2016). Feeling nature’s PAINS: Natural products, natural product drugs, and pan assay interference compounds (PAINS). Journal of Natural Products, 79(3), 616–628. https://doi.org/10.1021/acs.jnatprod.5b00947
  • Batool, M., Ahmad, B., & Choi, S. (2019). A structure-based drug discovery paradigm. International Journal of Molecular Sciences, 20(11), 2783. https://doi.org/10.3390/ijms20112783
  • Bhurta, D., & Bharate, S. B. (2022). Analyzing the scaffold diversity of cyclin‐dependent kinase inhibitors and revisiting the clinical and preclinical pipeline. Medicinal Research Reviews, 42(2), 654–709. https://doi.org/10.1002/med.21856
  • Borhani, D. W., & Shaw, D. E. (2012). The future of molecular dynamics simulations in drug discovery. Journal of Computer-Aided Molecular Design, 26(1), 15–26. https://doi.org/10.1007/s10822-011-9517-y
  • Camins, A., Verdaguer, E., Folch, J., Canudas, A. M., & Pallàs, M. (2006). The role of CDK5/P25 formation/inhibition in neurodegeneration. Drug News & Perspectives, 19(8), 453–460. https://doi.org/10.1358/dnp.2006.19.8.1043961
  • Cicenas, J., Kalyan, K., Sorokinas, A., Jatulyte, A., Valiunas, D., Kaupinis, A., & Valius, M. (2014). Highlights of the latest advances in research on CDK inhibitors. Cancers, 6(4), 2224–2242. https://doi.org/10.3390/cancers6042224
  • Cruz, J. C., Tseng, H.-C., Goldman, J. A., Shih, H., & Tsai, L.-H. (2003). Aberrant Cdk5 activation by p25 triggers pathological events leading to neurodegeneration and neurofibrillary tangles. Neuron, 40(3), 471–483. https://doi.org/10.1016/S0896-6273(03)00627-5
  • da Silva Rocha, S. F., Olanda, C. G., Fokoue, H. H., & Sant’Anna, C. M. (2019). Virtual screening techniques in drug discovery: Review and recent applications. Current Topics in Medicinal Chemistry, 19(19), 1751–1767. https://doi.org/10.2174/1568026619666190816101948
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 1–13. https://doi.org/10.1038/srep42717
  • DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40(1), 82–92.
  • Demetrick, D., Zhang, H., & Beach, D. (1994). Chromosomal mapping of human CDK2, CDK4, and CDK5 cell cycle kinase genes. Cytogenetics & Cell Genetics, 66(1), 72–74. https://doi.org/10.1159/000133669
  • Dhavan, R., & Tsai, L.-H. (2001). A decade of CDK5. Nature Reviews: Molecular Cell Biology, 2(10), 749–759. https://doi.org/10.1038/35096019
  • Dixit, A. B., Banerjee, J., Tripathi, M., Sarkar, C., & Chandra, P. S. (2017). Synaptic roles of cyclin-dependent kinase 5 and its implications in epilepsy. The Indian Journal of Medical Research, 145(2), 179–188. https://doi.org/10.4103/ijmr.IJMR_1249_14
  • Guex, N., & Peitsch, M. C. (1997). SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling. Electrophoresis, 18(15), 2714–2723. https://doi.org/10.1002/elps.1150181505
  • Hubbard, R. E., & Haider, M. K. (2010). Hydrogen bonds in proteins: Role and strength. eLS, 1-7.
  • Jairajpuri, D. S., Mohammad, T., Adhikari, K., Gupta, P., Hasan, G. M., Alajmi, M. F., Rehman, M. T., Hussain, A., & Hassan, M. I. (2020). Identification of sphingosine kinase-1 inhibitors from bioactive natural products targeting cancer therapy. ACS Omega, 5(24), 14720–14729. https://doi.org/10.1021/acsomega.0c01511
  • Jin, X., Yang, C., Fan, P., Xiao, J., Zhang, W., Zhan, S., Liu, T., Wang, D., & Wu, H. (2017). CDK5/FBW7-dependent ubiquitination and degradation of EZH2 inhibits pancreatic cancer cell migration and invasion. The Journal of Biological Chemistry, 292(15), 6269–6280. https://doi.org/10.1074/jbc.M116.764407
  • Khan, A., Mohammad, T., Shamsi, A., Hussain, A., Alajmi, M. F., Husain, S. A., Iqbal, M. A., & Hassan, M. I. (2021). Identification of plant-based hexokinase 2 inhibitors: Combined molecular docking and dynamics simulation studies. Journal of Biomolecular Structure & Dynamics, 1–13. https://doi.org/10.1080/07391102.2021.1942217
  • Kim, S. H., & Ryan, T. A. (2010). CDK5 serves as a major control point in neurotransmitter release. Neuron, 67(5), 797–809. https://doi.org/10.1016/j.neuron.2010.08.003
  • Kumar, B., Mohammad, T., Hussain, A., Islam, A., Ahmad, F., Alajmi, M. F., Singh, S., Pandey, K. C., Hassan, M. I., & Abid, M. (2021). Targeting metacaspase-3 from Plasmodium falciparum towards antimalarial therapy: A combined approach of in-silico and in-vitro investigation. Journal of Biomolecular Structure & Dynamics, 39(2), 421–430. https://doi.org/10.1080/07391102.2019.1711194
  • Kumar, S. K., LaPlant, B., Chng, W. J., Zonder, J., Callander, N., Fonseca, R., Fruth, B., Roy, V., Erlichman, C., & Stewart, A. K, Mayo Phase 2 Consortium (2015). Dinaciclib, a novel CDK inhibitor, demonstrates encouraging single-agent activity in patients with relapsed multiple myeloma. Blood, The Journal of the American Society of Hematology, 125(3), 443–448. https://doi.org/10.1182/blood-2014-05-573741
  • Lagunin, A., Stepanchikova, A., Filimonov, D., & Poroikov, V. (2000). PASS: Prediction of activity spectra for biologically active substances. Bioinformatics (Oxford, England), 16(8), 747–748. https://doi.org/10.1093/bioinformatics/16.8.747
  • Lever, J., Krzywinski, M., & Altman, N. (2017). Points of significance: Principal component analysis. Nature Methods, 14(7), 641–642. https://doi.org/10.1038/nmeth.4346
  • Liu, W., Li, J., Song, Y.-S., Li, Y., Jia, Y.-H., & Zhao, H.-D. (2017). Cdk5 links with DNA damage response and cancer. Molecular Cancer, 16(1), 1–9. https://doi.org/10.1186/s12943-017-0611-1
  • Lobanov, M. Y., Bogatyreva, N., & Galzitskaya, O. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
  • Maisuradze, G. G., Liwo, A., & Scheraga, H. A. (2009). Principal component analysis for protein folding dynamics. Journal of Molecular Biology, 385(1), 312–329. https://doi.org/10.1016/j.jmb.2008.10.018
  • Malumbres, M. (2014). Cyclin-dependent kinases. Genome Biology, 15(6), 110–122. https://doi.org/10.1186/gb4184
  • Mark, P., & Nilsson, L. (2001). Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. The Journal of Physical Chemistry A, 105(43), 9954–9960. https://doi.org/10.1021/jp003020w
  • Mohammad, T., Khan, F. I., Lobb, K. A., Islam, A., Ahmad, F., & Hassan, M. I. (2019). Identification and evaluation of bioactive natural products as potential inhibitors of human microtubule affinity-regulating kinase 4 (MARK4). Journal of Biomolecular Structure & Dynamics, 37(7), 1813–1829. https://doi.org/10.1080/07391102.2018.1468282
  • Mohammad, T., Mathur, Y., & Hassan, M. I. (2021). InstaDock: A single-click graphical user interface for molecular docking-based virtual high-throughput screening. Briefings in Bioinformatics, 22(4), bbaa279. https://doi.org/10.1093/bib/bbaa279
  • Mohammad, T., Shamsi, A., Anwar, S., Umair, M., Hussain, A., Rehman, M. T., AlAjmi, M. F., Islam, A., & Hassan, M. I. (2020). Identification of high-affinity inhibitors of SARS-CoV-2 main protease: Towards the development of effective COVID-19 therapy. Virus Research, 288, 198102. https://doi.org/10.1016/j.virusres.2020.198102
  • Mohammad, T., Siddiqui, S., Shamsi, A., Alajmi, M. F., Hussain, A., Islam, A., Ahmad, F., & Hassan, M. (2020). Virtual screening approach to identify high-affinity inhibitors of serum and glucocorticoid-regulated kinase 1 among bioactive natural products: Combined molecular docking and simulation studies. Molecules, 25(4), 823. https://doi.org/10.3390/molecules25040823
  • Mohanraj, K., Karthikeyan, B. S., Vivek-Ananth, R., Chand, R. B., Aparna, S., Mangalapandi, P., & Samal, A. (2018). IMPPAT: A curated database of Indian medicinal plants, phytochemistry and therapeutics. Scientific Reports, 8(1), 1–17. https://doi.org/10.1038/s41598-018-22631-z
  • Naqvi, A. A., Mohammad, T., Hasan, G. M., & Hassan, M. (2018). Advancements in docking and molecular dynamics simulations towards ligand–receptor interactions and structure–function relationships. Current Topics in Medicinal Chemistry, 18(20), 1755–1768. https://doi.org/10.2174/1568026618666181025114157
  • Narwani, T. J., Craveur, P., Shinada, N. K., Floch, A., Santuz, H., Vattekatte, A. M., Srinivasan, N., Rebehmed, J., Gelly, J.-C., Etchebest, C., & de Brevern, A. G. (2020). Discrete analyses of protein dynamics. Journal of Biomolecular Structure & Dynamics, 38(10), 2988–3002. https://doi.org/10.1080/07391102.2019.1650112
  • Oostenbrink, C., Villa, A., Mark, A. E., & Van Gunsteren, W. F. (2004). A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6. Journal of Computational Chemistry, 25(13), 1656–1676. https://doi.org/10.1002/jcc.20090
  • Pao, P.-C., & Tsai, L.-H. (2021). Three decades of Cdk5. Journal of Biomedical Science, 28(1), 79. https://doi.org/10.1186/s12929-021-00774-y
  • Patrick, G. N., Zukerberg, L., Nikolic, M., de la Monte, S., Dikkes, P., & Tsai, L.-H. (1999). Conversion of p35 to p25 deregulates Cdk5 activity and promotes neurodegeneration. Nature, 402(6762), 615–622. https://doi.org/10.1038/45159
  • Peyressatre, M., Prével, C., Pellerano, M., & Morris, M. C. (2015). Targeting cyclin-dependent kinases in human cancers: From small molecules to peptide inhibitors. Cancers, 7(1), 179–237. https://doi.org/10.3390/cancers7010179
  • Pires, D. E., 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
  • Plattner, F., & Bibb, J. A. (2012). Chapter 25—Serine and threonine phosphorylation. In S. T. Brady, G. J. Siegel, R. W. Albers, and D. L. Price (Eds.), Basic neurochemistry (8th ed., pp. 467–492). Academic Press.
  • Pozo, K., & Bibb, J. A. (2016). The emerging role of Cdk5 in cancer. Trends in Cancer, 2(10), 606–618. https://doi.org/10.1016/j.trecan.2016.09.001
  • Rawlins, M. D. (2004). Cutting the cost of drug development? Nature Reviews: Drug Discovery, 3(4), 360–364. https://doi.org/10.1038/nrd1347
  • Richmond, T. J. (1984). Solvent accessible surface area and excluded volume in proteins: Analytical equations for overlapping spheres and implications for the hydrophobic effect. Journal of Molecular Biology, 178(1), 63–89. https://doi.org/10.1016/0022-2836(84)90231-6
  • Roufayel, R., & Murshid, N. (2019). CDK5: key regulator of apoptosis and cell survival. Biomedicines, 7(4), 88. https://doi.org/10.3390/biomedicines7040088
  • Salsbury, F. R. Jr. (2010). Molecular dynamics simulations of protein dynamics and their relevance to drug discovery. Current Opinion in Pharmacology, 10(6), 738–744. https://doi.org/10.1016/j.coph.2010.09.016
  • Schüttelkopf, A. W., & Van Aalten, D. M. (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
  • Shamsi, A., DasGupta, D., Alhumaydhi, F. A., Khan, M. S., Alsagaby, S. A., Al Abdulmonem, W., Hassan, M. I., & Yadav, D. K. (2022). Inhibition of MARK4 by serotonin as an attractive therapeutic approach to combat Alzheimer’s disease and neuroinflammation. RSC Medicinal Chemistry, 13(6), 737–745. https://doi.org/10.1039/D2MD00053A
  • Shamsi, A., Shahwan, M., Khan, M. S., Alhumaydhi, F. A., Alsagaby, S. A., Al Abdulmonem, W., Abdullaev, B., & Yadav, D. K. (2022). Mechanistic insight into binding of huperzine a with human serum albumin: Computational and spectroscopic approaches. Molecules, 27(3), 797. https://doi.org/10.3390/molecules27030797
  • Sharif Siam, M. K., A., Sarker, & M. M. S., Sayeem. (2021). In silico drug design and molecular docking studies targeting Akt1 (RAC-alpha serine/threonine-protein kinase) and Akt2 (RAC-beta serine/threonine-protein kinase) proteins and investigation of CYP (cytochrome P450) inhibitors against MAOB (monoamine oxidase B) for OSCC (oral squamous cell carcinoma) treatment. Journal of Biomolecular Structure & Dynamics, 39(17), 6467–6479. https://doi.org/10.1080/07391102.2020.1802335
  • Shupp, A., Casimiro, M. C., & Pestell, R. G. (2017). Biological functions of CDK5 and potential CDK5 targeted clinical treatments. Oncotarget, 8(10), 17373–17382. https://doi.org/10.18632/oncotarget.14538
  • Studio, D. (2008). "Discovery Studio." Accelrys [2.1]
  • Teli, M. K., Kumar, S., Yadav, D. K., & Kim, M-h (2021). In silico identification of hydantoin derivatives: a novel natural prolyl hydroxylase inhibitor. Journal of Biomolecular Structure & Dynamics, 39(2), 703–717. https://doi.org/10.1080/07391102.2020.1714480
  • Turkson, J. (2017). Cancer drug discovery and anticancer drug development. The molecular basis of human cancer (pp. 695–707). Springer.
  • 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), 1701–1718. https://doi.org/10.1002/jcc.20291
  • Vlachakis, D., Bencurova, E., Papangelopoulos, N., & Kossida, S. (2014). Current state-of-the-art molecular dynamics methods and applications. Advances in Protein Chemistry & Structural Biology, 94, 269–313.
  • Walser, R., & van Gunsteren, W. F. (2001). Viscosity dependence of protein dynamics. Proteins: Structure, Function, & Genetics, 42(3), 414–421. https://doi.org/10.1002/1097-0134(20010215)42:3<414::AID-PROT110>3.0.CO;2-4
  • Williams, M., & Ladbury, J. (2003). Hydrogen bonds in protein–ligand complexes. Methods and Principles in Medicinal Chemistry, 19, 137–137.
  • Woll, K. A., Weiser, B. P., Liang, Q., Meng, T., McKinstry-Wu, A., Pinch, B., Dailey, W. P., Gao, W. D., Covarrubias, M., & Eckenhoff, R. G. (2015). Role for the propofol hydroxyl in anesthetic protein target molecular recognition. ACS Chemical Neuroscience, 6(6), 927–935. https://doi.org/10.1021/acschemneuro.5b00078
  • Yadav, D. K., Kumar, S., Choi, E.-H., Chaudhary, S., & Kim, M.-H. (2020). Computational modeling on aquaporin-3 as skin cancer target: A virtual screening study. Frontiers in Chemistry, 8, 250. https://doi.org/10.3389/fchem.2020.00250
  • Yadav, D. K., Kumar, S., Teli, M. K., & Kim, M. H. (2020). Ligand‐based pharmacophore modeling and docking studies on vitamin D receptor inhibitors. Journal of Cellular Biochemistry, 121(7), 3570–3583. https://doi.org/10.1002/jcb.29640
  • Yoo, C., & Shahlaei, M. (2018). The applications of PCA in QSAR studies: A case study on CCR5 antagonists. Chemical Biology & Drug Design, 91(1), 137–152. https://doi.org/10.1111/cbdd.13064
  • Zheng, Y.-L., Amin, N. D., Hu, Y.-F., Rudrabhatla, P., Shukla, V., Kanungo, J., Kesavapany, S., Grant, P., Albers, W., & Pant, H. C. (2010). A 24-residue peptide (p5), derived from p35, the Cdk5 neuronal activator, specifically inhibits Cdk5–p25 hyperactivity and tau hyperphosphorylation. The Journal of Biological Chemistry, 285(44), 34202–34212. https://doi.org/10.1074/jbc.M110.134643

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