Circular RNAs (circRNAs) have played an essential role in cancer development. This study aimed to illustrate the impact and potential mechanism of circRACGAP1 action in NSCLC development. The expression patterns of circRACGAP1, miR-1296, and CDK2 in NSCLC tissues and cell lines were analysed by RT-qPCR. The function of circRACGAP1 in NSCLC cell proliferation and apoptosis was investigated using the CCK-8 assay, flow cytometry, TUNEL staining, and Western blot. The interaction among circRACGAP1, miR-1296, and CDK2 was clarified by dual-luciferase reporter assay while the correlation was confirmed by the Pearson correlation coefficient. The expression of circRACGAP1 and CDK2 was up-regulated in NSCLC tissues, while the expression of miR-1296 was down-regulated. Cell function studies further revealed that circRACGAP1 could promote NSCLC cell proliferation, accelerate the cell cycle process, up-regulate B-cell lymphoma 2 (Bcl2) expression, and down-regulate Bcl2-associated X (Bax) expression. miR-1296 was identified as a downstream target to reverse circRACGAP1-mediated cell proliferation. miR-1296 directly targeted the 3'-UTR of CDK2 to regulate proliferation and apoptosis of NSCLC cells. Additionally, the dual-luciferase reporter assay and Pearson correlation coefficient analysis proved that circRACGAP1 acted in NSCLC cells by negatively regulating miR-1296 expression and positively regulating CDK2 expression. In summary, our study revealed that circRACGAP1 promoted NSCLC cell proliferation by regulating the miR-1296/CDK2 pathway, providing potential diagnostic and therapeutic targets for NSCLC.
- MeSH
- apoptóza * genetika MeSH
- cyklin-dependentní kinasa 2 * metabolismus genetika MeSH
- kruhová RNA * genetika metabolismus MeSH
- lidé MeSH
- mikro RNA * genetika metabolismus MeSH
- nádorové buněčné linie MeSH
- nádory plic * genetika patologie metabolismus MeSH
- nemalobuněčný karcinom plic * genetika patologie metabolismus MeSH
- proliferace buněk * genetika MeSH
- proteiny aktivující GTPasu genetika metabolismus MeSH
- regulace genové exprese u nádorů MeSH
- signální transdukce genetika MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
3,5,7-Trisubstituted pyrazolo[4,3-d]pyrimidines have been identified as potent inhibitors of cyclin-dependent kinases (CDKs), which are established drug targets. Herein, we describe their further structural modifications leading to novel nanomolar inhibitors with strong antiproliferative activity. We determined the crystal structure of fully active CDK2/A2 with 5-(2-amino-1-ethyl)thio-3-cyclobutyl-7-[4-(pyrazol-1-yl)benzyl]amino-1(2)H-pyrazolo[4,3-d]pyrimidine (24) at 1.7 Å resolution, confirming the competitive mode of inhibition. Biochemical and cellular assays in lymphoma cell lines confirmed the expected mechanism of action through dephosphorylation of retinoblastoma protein and RNA polymerase II, leading to induction of apoptosis. Importantly, we also revealed an interesting ability of compound 24 to induce proteasome-dependent degradation of cyclin K both in vitro and in a patient-derived xenograft in vivo. We propose that 24 has a dual mechanism of action, acting as a kinase inhibitor and as a molecular glue inducing an interaction between CDK12 and DDB1 that leads to polyubiquitination of cyclin K and its subsequent degradation.
- MeSH
- antitumorózní látky * chemie farmakologie MeSH
- cyklin-dependentní kinasa 2 MeSH
- cyklin-dependentní kinasy * MeSH
- cykliny metabolismus MeSH
- inhibitory proteinkinas chemie MeSH
- lidé MeSH
- nádorové buněčné linie MeSH
- pyrimidiny chemie MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Cyclin-dependent kinases (CDKs) are key regulators of the cell cycle in eukaryotes. Assessing their activity is one of the basic methods used to analyze their function. This is particularly true in synchronized cultures of unicellular organisms, where the entire culture is in the same physiological state. In this chapter, I describe a simple biochemical method to assess CDK activity in algae. Although the results are easier to interpret in the context of synchronized cultures, the method is not limited to them. The protocol requires only standard laboratory equipment and access to a radioactivity working room. The method is applicable to any algal species, including newly developed ones, as it does not require any specific tools. The method can, therefore, be used to widen the portfolio of cell cycle regulatory models within algae.
Cyclin-dependent kinases (CDKs) play an important role in the cell-division cycle. Synthetic inhibitors of CDKs are based on 2,6,9-trisubstituted purines and are developed as potential anticancer drugs; however, they have low solubility in water. In this study, we proved that the pharmaco-chemical properties of purine-based inhibitors can be improved by appropriate substitution with the adamantane moiety. We prepared ten new purine derivatives with adamantane skeletons that were linked at position 6 using phenylene spacers of variable geometry and polarity. We demonstrated that the adamantane skeleton does not compromise the biological activity, and some of the new purines displayed even higher inhibition activity towards CDK2/cyclin E than the parental compounds. These findings were supported by a docking study, which showed an adamantane scaffold inside the binding pocket participating in the complex stabilisation with non-polar interactions. In addition, we demonstrated that β-cyclodextrin (CD) increases the drug's solubility in water, although this is at the cost of reducing the biochemical and cellular effect. Most likely, the drug concentration, which is necessary for target engagement, was decreased by competitive drug binding within the complex with β-CD.
- MeSH
- adamantan chemie MeSH
- antitumorózní látky chemie farmakologie MeSH
- beta-cyklodextriny chemie MeSH
- buňky K562 MeSH
- cyklin-dependentní kinasa 2 antagonisté a inhibitory MeSH
- inhibitory proteinkinas farmakologie MeSH
- lidé MeSH
- MFC-7 buňky MeSH
- puriny chemie MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Pharmacological inhibition of cyclin-dependent kinases has emerged as a possible treatment option for various cancer types. We recently identified substituted imidazo[1,2-c]pyrimidin-5(6H)-ones as inhibitors of cyclin-dependent kinase 2 (CDK2). Here, we report the synthesis of derivatives modified at positions 2, 3, 6 or 8 prepared using Suzuki-Miyaura cross-coupling, halogenation, Dimroth-type rearrangement and alkylation as the main synthetic methods. The compounds displayed micro- to submicromolar inhibition of CDK2/cyclin E activity. Binding of the most potent compound 3b to CDK2 was determined using isothermal titration calorimetry. The co-crystal structure of 3b in complex with fully active CDK2 was solved, revealing the binding mode of 3b in the ATP pocket and a hydrogen bonding interaction with hinge region residue Leu83. Evaluation against leukaemia cell lines revealed low cytotoxicity, which is in line with the high selectivity towards CDK2. This study demonstrates that substituted imidazo[1,2-c]pyrimidines can be exploited for future kinase inhibitor development.
- MeSH
- antitumorózní látky chemická syntéza metabolismus farmakologie MeSH
- cyklin-dependentní kinasa 2 antagonisté a inhibitory metabolismus MeSH
- imidazoly chemie metabolismus farmakologie MeSH
- inhibitory proteinkinas chemická syntéza metabolismus farmakologie MeSH
- kontrolní body buněčného cyklu účinky léků MeSH
- krystalografie rentgenová MeSH
- lidé MeSH
- nádorové buněčné linie MeSH
- proliferace buněk účinky léků MeSH
- pyrimidiny chemie metabolismus farmakologie MeSH
- simulace molekulární dynamiky MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- vodíková vazba MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Cyclin A2 is a key regulator of the cell cycle, implicated both in DNA replication and mitotic entry. Cyclin A2 participates in feedback loops that activate mitotic kinases in G2 phase, but why active Cyclin A2-CDK2 during the S phase does not trigger mitotic kinase activation remains unclear. Here, we describe a change in localisation of Cyclin A2 from being only nuclear to both nuclear and cytoplasmic at the S/G2 border. We find that Cyclin A2-CDK2 can activate the mitotic kinase PLK1 through phosphorylation of Bora, and that only cytoplasmic Cyclin A2 interacts with Bora and PLK1. Expression of predominately cytoplasmic Cyclin A2 or phospho-mimicking PLK1 T210D can partially rescue a G2 arrest caused by Cyclin A2 depletion. Cytoplasmic presence of Cyclin A2 is restricted by p21, in particular after DNA damage. Cyclin A2 chromatin association during DNA replication and additional mechanisms contribute to Cyclin A2 localisation change in the G2 phase. We find no evidence that such mechanisms involve G2 feedback loops and suggest that cytoplasmic appearance of Cyclin A2 at the S/G2 transition functions as a trigger for mitotic kinase activation.
- MeSH
- aktivace enzymů genetika MeSH
- buněčné jádro metabolismus MeSH
- chromatin metabolismus MeSH
- cyklin A2 genetika metabolismus MeSH
- cyklin-dependentní kinasa 2 nedostatek genetika MeSH
- cytoplazma metabolismus MeSH
- fosforylace genetika MeSH
- G2 fáze genetika MeSH
- HeLa buňky MeSH
- lidé MeSH
- mitóza genetika MeSH
- poškození DNA genetika MeSH
- protein-serin-threoninkinasy metabolismus MeSH
- proteinkinasa CDC2 nedostatek genetika MeSH
- proteiny buněčného cyklu metabolismus MeSH
- protoonkogenní proteiny metabolismus MeSH
- S fáze genetika MeSH
- signální transdukce genetika MeSH
- transfekce MeSH
- vazba proteinů MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
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.
- MeSH
- cyklin-dependentní kinasa 2 antagonisté a inhibitory MeSH
- inhibitory proteinkinas farmakologie MeSH
- norbornany farmakologie MeSH
- nukleosidy analogy a deriváty MeSH
- simulace molekulového dockingu MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Pharmacophore models are widely used for the identification of promising primary hits in compound large libraries. Recent studies have demonstrated that pharmacophores retrieved from protein-ligand molecular dynamic trajectories outperform pharmacophores retrieved from a single crystal complex structure. However, the number of retrieved pharmacophores can be enormous, thus, making it computationally inefficient to use all of them for virtual screening. In this study, we proposed selection of distinct representative pharmacophores by the removal of pharmacophores with identical three-dimensional (3D) pharmacophore hashes. We also proposed a new conformer coverage approach in order to rank compounds using all representative pharmacophores. Our results for four cyclin-dependent kinase 2 (CDK2) complexes with different ligands demonstrated that the proposed selection and ranking approaches outperformed the previously described common hits approach. We also demonstrated that ranking, based on averaged predicted scores obtained from different complexes, can outperform ranking based on scores from an individual complex. All developments were implemented in open-source software pharmd.
- MeSH
- cyklin-dependentní kinasa 2 chemie metabolismus MeSH
- inhibitory proteinkinas chemie farmakologie MeSH
- knihovny malých molekul chemie farmakologie MeSH
- lidé MeSH
- ligandy MeSH
- objevování léků metody MeSH
- počítačová simulace MeSH
- simulace molekulární dynamiky * MeSH
- simulace molekulového dockingu metody MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Several studies have revealed that cyclin-dependent kinases (CDK) can mediate phosphorylation of steroid receptors at multiple sites, including serine 81 of the androgen receptor (AR). Phosphorylation of S81 is required for AR nuclear translocation, an association with chromatin and also regulates endogenous AR-regulated transcription in response to hormones. Up to date, S81-phosphorylation has been studied using different CDK inhibitors. Nevertheless, most inhibitors are non-selective or have unknown selectivity. We investigated the selectivity of commercially available CDK inhibitors and identified compounds that will be suitable for further studies to identify the CDKs responsible for S81-AR phosphorylation. We confirmed the positive impact of CDK1 and CDK9 on phosphorylation of S81-AR and its transcriptional activity. Although CDK1-mediated phosphorylation was previously shown to occur during mitosis, our experiments did not confirm this finding. By using chemical and genetic inhibition techniques, we identified that CDK2 contributes to S81-AR phosphorylation and transactivation while CDK4 was not shown to be involved in this process.
A series of new pyrimidine-pyrazole hybrid molecules were designed as inhibitors of cyclin-dependent kinase 2. Designed compounds were docked using Glide and the compounds showing good score values and encouraging interactions with the residues were selected for synthesis. They were then evaluated using CDK2-CyclinA2 enzyme inhibition by a luminescent ADP detection assay. We show that of the 26 compounds synthesized and evaluated, at least 5 compounds were found to be highly potent (IC50 < 20 nm); which can be further optimized to have selectivity over other kinase isoforms.
- MeSH
- cyklin-dependentní kinasa 2 antagonisté a inhibitory metabolismus MeSH
- inhibiční koncentrace 50 MeSH
- inhibitory proteinkinas chemická syntéza metabolismus MeSH
- lidé MeSH
- protein - isoformy antagonisté a inhibitory metabolismus MeSH
- pyrazoly chemie metabolismus MeSH
- pyrimidiny chemie MeSH
- racionální návrh léčiv * MeSH
- simulace molekulového dockingu MeSH
- terciární struktura proteinů MeSH
- vazebná místa MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
