230
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

Exploring multi-target inhibitors using in silico approach targeting cell cycle dysregulator–CDK proteins

, ORCID Icon, , ORCID Icon &
Pages 8825-8839 | Received 18 Nov 2020, Accepted 11 Apr 2021, Published online: 30 Apr 2021

References

  • Abate, A. A., Pentimalli, F., Esposito, L., & Giordano, A. (2013). ATP-noncompetitive CDK inhibitors for cancer therapy: An overview. Expert Opinion on Investigational Drugs, 22(7), 895–906. https://doi.org/10.1517/13543784.2013.798641
  • Bae, E., & Phillips, G. N. (2005). Identifying and engineering ion pairs in adenylate kinases insights from molecular dynamics simulations of thermophilic and mesophilic homologues. Journal of Biological Chemistry, 280(35), 30943–30948. https://doi.org/10.1074/jbc.M504216200
  • Berendsen, H. J., Postma, J. V., van Gunsteren, W. F., DiNola, A., & Haak, J. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
  • Brown, N. R., Korolchuk, S., Martin, M. P., Stanley, W. A., Moukhametzianov, R., Noble, M. E., Endicott, J. A. (2015). CDK1 structures reveal conserved and unique features of the essential cell cycle CDK. Nature Communications, 6(1), 1–12. https://doi.org/10.1038/ncomms7769
  • Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Onufriev, A., Simmerling, C., Wang, B., Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26(16), 1668–1688. https://doi.org/10.1002/jcc.20290
  • Case, D., Vb Jtb, B. R., Cai, Q., Cerutti, D., Cheatham III, T., Darden, T., Duke, R., Gohlke, H., Goetz, A., & Gusarov, S. (2014). The FF14SB force field. AMBER, 14, 29–31.
  • Cheatham, T. I., Miller, J., Fox, T., Darden, T., & Kollman, P. (1995). Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. Journal of the American Chemical Society, 117(14), 4193–4194. https://doi.org/10.1021/ja00119a045
  • De Bondt, H. L., Rosenblatt, J., Jancarik, J., Jones, H. D., Morgan, D. O., & Kim, S. H. (1993). Crystal structure of cyclin-dependent kinase 2. Nature, 363(6430), 595–602. https://doi.org/10.1038/363595a0
  • Finn, R. S., Aleshin, A., & Slamon, D. J. (2016). Targeting the cyclin-dependent kinases (CDK) 4/6 in estrogen receptor-positive breast cancers. Breast Cancer Research, 18(1), 17. https://doi.org/10.1186/s13058-015-0661-5
  • Gray, N., Detivaud, L., Doerig, C., & Meijer, L. (1999). ATP-site directed inhibitors of cyclin-dependent kinases. Current Medicinal Chemistry, 6(9), 859–876.
  • Horiuchi, D., E. Huskey, N., Kusdra, L., Wohlbold, L., Merrick, K. A., Zhang, C., Creasman, K. J., Shokat, K. M., Fisher, R. P., & Goga, A. ( 2012). Chemical–genetic analysis of cyclin dependent kinase 2 function reveals an important role in cellular transformation by multiple oncogenic pathways. Proceedings of the National Academy of Sciences, 109(17), E1019–E1027. https://doi.org/10.1073/pnas.1111317109
  • Jarrahpour, A., Ebrahimi, E., Sinou, V., Latour, C., & Brunel, J. M. (2014). Diastereoselective synthesis of potent antimalarial cis-β-lactam agents through a [2 + 2] cycloaddition of chiral imines with a chiral ketene. European Journal of Medicinal Chemistry, 87, 364–371. https://doi.org/10.1016/j.ejmech.2014.09.077
  • Johnson, N., Bentley, J., Wang, L. Z., Newell, D. R., Robson, C. N., Shapiro, G. I., Curtin, N. J. (2010). Pre-clinical evaluation of cyclin-dependent kinase 2 and 1 inhibition in anti-estrogen-sensitive and resistant breast cancer cells. British Journal of Cancer, 102(2), 342–350. https://doi.org/10.1038/sj.bjc.6605479
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
  • Khan, S., Farooq, U., & Kurnikova, M. ( 2017). Protein stability and dynamics influenced by ligands in extremophilic complexes – A molecular dynamics investigation. Molecular Biosystems, 13(9), 1874–1887. https://doi.org/10.1039/C7MB00210F
  • Law, M. E., Corsino, P. E., Narayan, S., & Law, B. K. (2015). Cyclin-dependent kinase inhibitors as anticancer therapeutics. Molecular Pharmacology, 88(5), 846–852. https://doi.org/10.1124/mol.115.099325
  • Lees, E. (1995). Cyclin dependent kinase regulation. Current Opinion in Cell Biology, 7(6), 773–780. https://doi.org/10.1016/0955-0674(95)80060-3
  • Li, Y., Gao, W., Li, F., Wang, J., Zhang, J., Yang, Y., Zhang, S., & Yang, L. (2013). An in silico exploration of the interaction mechanism of pyrazolo[1,5-a]pyrimidine type CDK2 inhibitors. Molecular BioSystems, 9(9), 2266–2281. https://doi.org/10.1039/c3mb70186g
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and 497 computational approaches to estimate solubility and permeability in drug discovery and 498 development settings. Advanced Drug Delivery Reviews, 64, 4–17. https://doi.org/10.1016/j.addr.2012.09.019
  • Mapelli, M., Massimiliano, L., Crovace, C., Seeliger, M. A., Tsai, L.-H., Meijer, L., & Musacchio, A. (2005). Mechanism of CDK5/p25 binding by CDK inhibitors. Journal of Medicinal Chemistry, 48(3), 671–679. https://doi.org/10.1021/jm049323m
  • Matsuura, I., Denissova, N. G., Wang, G., He, D., Long, J., & Liu, F. ( 2004). Cyclin-dependent kinases regulate the antiproliferative function of Smads. Nature, 430 (6996), 226–231. https://doi.org/10.1038/nature02650
  • McInnes, C., Wang, S., Anderson, S., O'Boyle, J., Jackson, W., Kontopidis, G., Meades, C., Mezna, M., Thomas, M., Wood, G., Lane, D. P., & Fischer, P. M. (2004). Structural determinants of CDK4 inhibition and design of selective ATP competitive inhibitors. Chemistry & Biology, 11(4), 525–534. https://doi.org/10.1016/j.chembiol.2004.03.022
  • Miller III, B. R., McGee Jr., T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). Mmpbsa py: An efficient program for end-state free energy calculations. Journal of Chemical Theory & Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
  • Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
  • Tadesse, S., Caldon, C., Tilley, W., & Wang, S. (2019). Cyclin-dependent kinase 2 inhibitors in cancer therapy: An update. Journal of Medicinal Chemistry, 62( 9), 4233–4251. https://doi.org/10.1021/acs.jmedchem.8b01469
  • Takaki, T., Echalier, A., Brown, N., Hunt, T., Endicott, J., & Noble, M. (2009). The structure of CDK4/cyclin D3 has implications for models of CDK activation. Proceedings of the National Academy of Sciences, 106(11), 4171–4176. https://doi.org/10.1073/pnas.0809674106
  • Ubersax, J. A., Woodbury, E. L., Quang, P. N., Paraz, M., Blethrow, J. D., Shah, K., Shokat, K. M., & Morgan, D. O. (2003). Targets of the cyclin-dependent kinase Cdk1. Nature, 425(6960), 859–864. https://doi.org/10.1038/nature02062
  • Vilar, S., Cozza, G., & Moro, S. (2008). Medicinal chemistry and the molecular operating environment (MOE): Application of QSAR and molecular docking to drug discovery. Current Topics in Medicinal Chemistry, 8(18), 1555–1572. https://doi.org/10.2174/156802608786786624
  • Walker, R. C., Crowley, M. F., & Case, D. A. (2008). The implementation of a fast and accurate QM/MM potential method in Amber. Journal of Computational Chemistry, 29(7), 1019–1031. https://doi.org/10.1002/jcc.20857
  • Wang, H., Zhou, Y., & Fowke, L. C. (2006). The emerging importance of cyclin-dependent kinase inhibitors in the regulation of the plant cell cycle and related processes. This review is one of a selection of papers published in the Special Issue on Plant Cell Biology. Canadian Journal of Botany, 84(4), 640–650. https://doi.org/10.1139/b06-043
  • Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics & Modelling, 25(2), 247–260. https://doi.org/10.1016/j.jmgm.2005.12.005
  • Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035

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.