References
- Sánchez-Martínez C, Gelbert LM, Lallena MJ, et al. Cyclin dependent kinase (CDK) inhibitors as anticancer drugs. Cheminform 2015;46:3420–35.
- Hydbring P, Malumbres M, Sicinski P. Non-canonical functions of cell cycle cyclins and cyclin-dependent kinases. Nat Rev Mol Cell Biol 2016;17:280–92.
- Han SH, Chung JH, Kim J, et al. New role of human ribosomal protein S3: regulation of cell cycle via phosphorylation by cyclin-dependent kinase 2. Oncol Lett 2017;13:3681–7.
- Chen JZ, Pan Y, Qian H, et al. Cyclin-dependent kinase-2 as a target for cancer therapy: progress in the development of CDK2 inhibitors as anti-cancer agents. Curr Med Chem 2014;22:237–63.
- Roskoski R. Cyclin-dependent protein kinase inhibitors including palbociclib as anticancer drugs. Pharmacol Res 2016;107:249–75.
- Wu L, Sun J, Su X, et al. A review about the development of fucoidan in antitumor activity: progress and challenges. Carbohydr Polym 2016;154:96–111.
- Javier HJ, Michael P, Lindsay S, et al. Giving drugs a second chance: overcoming regulatory and financial hurdles in repurposing approved drugs as cancer therapeutics. Front Oncol 2017;7:273.
- Kontopidis G, Mcinnes C, Pandalaneni SR, et al. Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design. Chem Biol (Cambridge) 2006;13:201–11.
- Drwal MN, Griffith R. Combination of ligand- and structure-based methods in virtual screening. Drug Disc Today Technol 2013;10:e395.
- Kumar A, Zhang K. Hierarchical virtual screening approaches in small molecule drug discovery. Methods 2015;71:26–37.
- Lei DW, Li LL, Wang WJ, et al. Identification of CDK2 inhibitors with new scaffolds by a hybrid virtual screening approach based on Bayesian model; pharmacophore hypothesis and molecular docking. J Mol Graph Model 2012;36:42–7.
- Ren JX, Li LL, Zheng RL, et al. Discovery of novel Pim-1 kinase inhibitors by a hierarchical multistage virtual screening approach based on SVM model, pharmacophore, and molecular docking. J Chem Inf Model 2011;51:1364.
- Ceretomassagué A, Guasch L, Valls C, et al. DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets. Bioinformatics 2012;28:1661–2.
- Mysinger MM, Carchia M, Irwin JJ, et al. Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. J Med Chem 2012;55:6582.
- Wei D, Zheng H, Su N, et al. Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening. J Chem Inf Model 2010;50:1855–64.
- Rogers D, Hahn M. Extended-connectivity fingerprints. J Chem Inf Model 2010;50:742–54.
- Vilar S, Cozza G, Moro S. Medicinal chemistry and the molecular operating environment (MOE): application of QSAR and molecular docking to drug discovery. Curr Top Med Chem 2008;8:1555–72.
- Hou T, Wang J, Li Y, et al. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model 2011;51:69–82.
- Chang CC, Lin CJ. LIBSVM: a library for support vector machines. ACM Trans Intell Syst Technol 2011;2:1.
- Cotesta S, Giordanetto F, Trosset JY, et al. Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models. Proteins Struct Funct Genet 2005;60:629–43.
- Verdonk ML, Cole JC, Hartshorn MJ, et al. Improved protein-ligand docking using GOLD. Proteins Struct Funct Genet 2003;52:609–23.
- Ullah MZ, Aono M, Seddiqui MH. Estimating a ranked list of human hereditary diseases for clinical phenotypes by using weighted bipartite network. Conf Proc IEEE Eng Med Biol Soc 2013;2013:3475–8.
- Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:33–8.
- Phillips JC, Braun R, Wang W, et al. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26:1781–802.
- Bártová I, Otyepka M, Kríz Z, et al. The mechanism of inhibition of the cyclin-dependent kinase-2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK. Protein Sci 2010;14:445–51.
- Jiang W, Phillips JC, Huang L, et al. Generalized scalable multiple copy algorithms for biological molecular dynamics simulations in NAMD. Comput Phys Commun 2014;185:908–16.
- Rastelli G, Del Rio A, Degliesposti G, et al. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. J Comput Chem 2010;31:797–810.
- Schonbrunn E, Betzi S, Alam R, et al. Development of highly potent and selective diaminothiazole inhibitors of cyclin-dependent kinases. J Med Chem 2013;56:3768–82.
- Richardson CM, Nunns CL, Williamson DS, et al. Discovery of a potent CDK2 inhibitor with a novel binding mode, using virtual screening and initial, structure-guided lead scoping. Bioorg Med Chem Lett 2007;17:3880–5.
- Betzi S, Alam R, Martin M, et al. Discovery of a potential allosteric ligand binding site in CDK2. ACS Chem Biol 2011;6:492–501.
- Kryštof V, McNae IW, Walkinshaw MD, et al. Antiproliferative activity of olomoucine II, a novel 2,6,9-trisubstituted purine cyclin-dependent kinase inhibitor. Cell Mol Life Sci 2005;62:1763–71.
- Su YW, Mcnae I, Kontopidis G, et al. Discovery of a novel family of CDK inhibitors with the program LIDAEUS: structural basis for ligand-induced disordering of the activation loop. Structure 2003;11:399–410.