We report on the discovery of norbornyl moiety as a novel structural motif for cyclin-dependent kinase 2 (CDK2) inhibitors which was identified by screening a carbocyclic nucleoside analogue library. Three micromolar hits were expanded by the use of medicinal chemistry methods into a series of 16 novel compounds. They had prevailingly micromolar activities against CDK2 and the best compound of the series attained IC50 of 190 nM. The binding modes were explored in molecular details by modeling and docking. Quantum mechanics-based scoring was used to rationalize the affinities. In conclusion, the discovered 9-hydroxymethylnorbornyl moiety was shown by joint experimental-theoretical efforts to be able to serve as a novel substituent for CDK2 inhibitors. This finding opens door to the exploration of chemical space towards more effective derivatives targeting this important class of protein kinases.

Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 Czech Republic

Laboratory of Growth Regulators Faculty of Science Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences Olomouc Czech Republic

Regional Center of Advanced Technologies and Materials Department of Physical Chemistry Palacký University Olomouc Czech Republic

Zobrazit více v PubMed

Klein ME, Kovatcheva M, Davis LE, Tap WD, Koff A. CDK4/6 inhibitors: the mechanism of action may not be as simple as once thought. Cancer Cell. 2018;34:9-20.

Malumbres M. Cyclin-dependent kinases. Genome Biol. 2014;15:122.

Huwe A, Mazitschek R, Giannis A. Cyclin-dependent kinases small molecules as inhibitors of cyclin-dependent kinases. Angew Chem Int Ed. 2003;42:2122-2138.

Fanfrlík J, Bronowska AK, Řezáč J, Přenosil O, Konvalinka J, Hobza P. A reliable docking/scoring scheme based on the semiempirical quantum mechanical PM6-DH2 method accurately covering dispersion and H-bonding: HIV-1 protease with 22 ligands. J Phys Chem B. 2010;114:12666-12678.

Lepšík M, Řezáč J, Kolář M, Pecina A, Hobza P, Fanfrlík J. The semiempirical quantum mechanical scoring function for in silico drug design. ChemPlusChem. 2013;78:921-931.

Hylsová M, Carbain B, Fanfrlík J, et al. Explicit treatment of active-site waters enhances quantum mechanical/implicit solvent scoring: inhibition of CDK2 by new pyrazolo[1,5-a]pyrimidines. Eur J Med Chem. 2017;126:1118-1128.

Nekardová M, Vymětalová L, Khirsariya P, et al. Structural basis of the interaction of cyclin-dependent kinase 2 with roscovitine and its analogues having bioisosteric central heterocycles. ChemPhysChem. 2017;18:785-795.

Pecina A, Meier R, Fanfrlík J, et al. The SQM/COSMO filter: reliable native pose identification based on the quantum-mechanical description of protein-ligand interactions and implicit COSMO solvation. Chem Commun (Camb). 2016;52:3312-3315.

Pecina A, Brynda J, Vrzal L, et al. Ranking power of the SQM/COSMO scoring function on carbonic anhydrase II-inhibitor complexes. ChemPhysChem. 2018;19:873-879.

Pecina A, Haldar S, Fanfrlík J, et al. SQM/COSMO scoring function at the DFTB3-D3H4 level: unique identification of native protein-ligand poses. J Chem Inf Model. 2017;57:127-132.

Ajani, H., Pecina, A., Eyrilmez, S. M. et al. Superior performance of the SQM/COSMO scoring functions in native pose recognition of diverse protein−ligand complexes in cognate docking. 2017

Eyrilmez SM, Köprülüoğlu C, Řezáč J, Hobza P. Impressive enrichment of semiempirical quantum mechanics-based scoring function: HSP90 protein with 4541 inhibitors and decoys. ChemPhysChem. 2019;20:2759-2766.

Nencka R, Sala M, Dejmek M, Dracinsky M, Holy A, Hrebabecky H. Two convergent approaches toward novel carbocyclic C-nucleosides. Synthesis. 2010;23:4119-4130.

Šála M, De Palma AM, Hřebabecký H, et al. Design, synthesis, and biological evaluation of novel coxsackievirus B3 inhibitors. Bioorg Med Chem. 2010;18:4374-4384.

Hřebabecký H, Dejmek M, Dračínský M, et al. Synthesis of novel azanorbornylpurine derivatives. Tetrahedron. 2012;68:1286-1298.

Dejmek M, Hrebabecky H, Sala M, et al. From norbornane-based nucleotide analogs locked in south conformation to novel inhibitors of feline herpes virus. Bioorg Med Chem. 2014;22:2974-2983.

Šála M, Dejmek M, Procházková E, et al. Synthesis of locked cyclohexene and cyclohexane nucleic acids (LCeNA and LCNA) with modified adenosine units. Org Biomol Chem. 2015;13:2703-2715.

Hrebabecky H, Dracinsky M, Prochazkova E, Sala M, Mackman R, Nencka R. Control of alpha/beta Anomer formation by a 2′,5′ bridge: toward nucleoside derivatives locked in the south conformation. J Org Chem. 2017;82:11337-11347.

Hercik K, Kozak J, Sala M, et al. Adenosine triphosphate analogs can efficiently inhibit the Zika virus RNA-dependent RNA polymerase. Antiviral Res. 2017;137:131-133.

Enkvist E, Raidaru G, Vaasa A, Pehk T, Lavogina D, Uri A. Carbocyclic 3′-deoxyadenosine-based highly potent bisubstrate-analog inhibitor of basophilic protein kinases. Bioorg Med Chem Lett. 2007;17:5336-5339.

Dejmek M, Sala M, Hrebabecky H, et al. Norbornane-based nucleoside and nucleotide analogues locked in north conformation. Bioorg Med Chem. 2015;23:184-191.

Klima, M.; Baumlova, A.; Chalupska, D.; Hrebabecky, H.; Dejmek, M.; Nencka, R.; Boura, E. Crystal Structure of Phosphatidyl Inositol 4-Kinase II Alpha in Complex with Nucleotide Analog. Worldwide Protein Data Bank, 2015.

Holý A. Antiviral acyclic nucleoside phosphonates structure activity studies. Antiviral Res. 2006;71:248-253.

Eyer L, Nencka R, de Clercq E, Seley-Radtke K, Růžek D. Nucleoside analogs as a rich source of antiviral agents active against arthropod-borne flaviviruses. Antiviral Chem Chemother. 2018;26:2040206618761299.

Bettayeb K, Oumata N, Echalier A, et al. CR8, a potent and selective, roscovitine-derived inhibitor of cyclin-dependent kinases. Oncogene. 2008;27:5797-5807.

Gucký T, Jorda R, Zatloukal M, et al. A novel series of highly potent2,6,9-trisubstituted purine cyclin-dependent kinase inhibitors. J MedChem. 2013;56:6234-6247.

Martin MP, Olesen SH, Georg GI, Schönbrunn E. Cyclin-dependent kinase inhibitor dinaciclib interacts with the acetyl-lysine recognition site of bromodomains. ACS Chem Biol. 2013;8:2360-2365.

Jorda R, Havlíček L, Šturc A, et al. 3,5,7-substituted pyrazolo[4,3-d]pyrimidine inhibitors of cyclin-dependent kinases and their evaluation in lymphoma models. J Med Chem. 2019;62:4606-4623.

Jorda R, Paruch K, Krystof V. Cyclin-dependent kinase inhibitors inspired by roscovitine: purine bioisosteres. Curr Pharm des. 2012;18:2974-2980.

Dejmek M, Kovackova S, Zbornikova E, et al. One-pot build-up procedure for the synthesis of variously substituted purine derivatives. RSC Adv. 2012;2:6970-6980.

Mojzych M, Šubertová V, Bielawska A, et al. Synthesis and kinase inhibitory activity of new sulfonamide derivatives of pyrazolo[4,3-e][1,2,4]triazines. Eur J Med Chem. 2014;78:217-224.

Myers SM, Bawn RH, Bisset LC, et al. High-throughput screening and hit validation of extracellular-related kinase 5 (ERK5) inhibitors. ACS Comb Sci. 2016;18:444-455.

Di Gioia ML, Leggio A, Guarino IF, Leotta V, Romio E, Liguori A. A simple synthesis of anilines by LiAlH4/TiCl4 reduction of aromatic nitro compounds. Tetrahedron Lett. 2015;56:5341-5344.

Thomas AP, Breault GA, Beattie JF, Jewsbury PJ. Imidazo[1,2-a]pyridine and Pyrazolo[2,3-a]pyridine Derivatives, WO2001014375A1. 2001.

Legraverend M, Ludwig O, Bisagni E, et al. Synthesis and in vitro evaluation of novel 2,6,9-trisubstituted purines acting as cyclin-dependent kinase inhibitors. Bioorg Med Chem. 1999;7:1281-1293.

Lawrie AM, Noble MEM, Tunnah P, Brown NR, Johnson LN, Endicott JA. Protein kinase inhibition by staurosporine revealed in details of the molecular interaction with CDK2. Nat Struct Biol. 1997;4:796-801.

Friesner RA, Banks JL, Murphy RB, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004;47:1739-1749.

Fanfrlík J, Ruiz FX, Kadlčíková A, et al. The effect of halogen-to-hydrogen bond substitution on human aldose reductase inhibition. ACS Chem Biol. 2015;10:1637-1642.

Ajani H, Jansa J, Köprülüoğlu C, et al. Imidazo[1,2-c]pyrimidin-5(6H)-one as a novel core of cyclin-dependent kinase 2 inhibitors: synthesis, activity measurement, docking, and quantum mechanical scoring. J Mol Recognit. 2018;31:e2720.

Brahmkshatriya S, Dobes P, Fanfrlik J, et al. Quantum mechanical scoring: structural and energetic insights into cyclin-dependent kinase 2 inhibition by Pyrazolo[1,5-a]pyrimidines. Curr Comp Aided-Drug Design. 2013;9:118-129.

Stewart JJP. Application of the PM6 method to modeling proteins. J Mol Model. 2009;15:765-805.

Stewart JJP. MOPAC2012. Stewart Computational Chemistry, Version 7.263W web: HTTP://OpenMOPAC.net

Řezáč J. Cuby: an integrative framework for computational chemistry. J Comput Chem. 2016;37:1230-1237.

Harder E, Damm W, Maple J, et al. OPLS3: a force field providing broad coverage of drug-like small molecules and proteins. J Chem Theory Comput. 2016;12:281-296.

De Lano WL. The PyMOL Molecular Graphics System. San Carlos, CA: DeLano Scientific LLC; 2002.

Inhibition of FLT3-ITD Kinase in Acute Myeloid Leukemia by New Imidazo[1,2-b]pyridazine Derivatives Identified by Scaffold Hopping