Perspectives for cancer therapies with cdk2 inhibitors

Characterization of lung adenocarcinoma based on immunophenotyping and constructing an immune scoring model to predict prognosis

Background: Lung cancer poses great threat to human health, and lung adenocarcinoma (LUAD) is the main subtype. Immunotherapy has become first line therapy for LUAD. However, the pathogenic mechanism of LUAD is still unclear. Methods: We scored immune-related pathways in LUAD patients using single sample gene set enrichment analysis (ssGSEA) algorithm, and further identified distinct immune-related subtypes through consistent clustering analysis. Next, immune signatures, Kaplan-Meier survival analysis, copy number variation (CNV) analysis, gene methylation analysis, mutational analysis were used to reveal differences between subtypes. pRRophetic method was used to predict the response to chemotherapeutic drugs (half maximal inhibitory concentration). Then, weighted gene co-expression network analysis (WGCNA) was performed to screen hub genes. Significantly, we built an immune score (IMscore) model to predict prognosis of LUAD. Results: Consensus clustering analysis identified three LUAD subtypes, namely immune-Enrich subtype (Immune-E), stromal-Enrich subtype (Stromal-E) and immune-Deprived subtype (Immune-D). Stromal-E subtype had a better prognosis, as shown by Kaplan-Meier survival analysis. Higher tumor purity and lower immune cell scores were found in the Immune-D subtype. CNV analysis showed that homologous recombination deficiency was lower in Stromal-E and higher in Immune-D. Likewise, mutational analysis found that the Stromal-E subtype had a lower mutation frequency in TP53 mutations. Difference in gene methylation (ZEB2, TWIST1, CDH2, CDH1 and CLDN1) among three subtypes was also observed. Moreover, Immune-E was more sensitive to traditional chemotherapy drugs Cisplatin, Sunitinib, Crizotinib, Dasatinib, Bortezomib, and Midostaurin in both the TCGA and GSE cohorts. Furthermore, a 6-gene signature was constructed to predicting prognosis, which performed better than TIDE score. The performance of IMscore model was successfully validated in three independent datasets and pan-cancer.

Upregulation of Excision Repair Cross-Complementation Group 6-Like (ERCC6L) Promotes Tumor Growth in Hepatocellular Carcinoma

BACKGROUND

Excision repair cross-complementation group 6-like (ERCC6L) is overexpressed in some malignancies; however, its role in hepatocellular carcinoma (HCC) remains to be further investigated.

AIMS

In the present study, we explored the expression and function of ERCC6L in HCC.

METHODS AND RESULTS

We investigated the expression of ERCC6L by microarray analysis, using the Cancer Genome Atlas database, and by HCC tissue microarray. The results showed that ERCC6L expression was upregulated in tumor specimens and HCC cell lines. High ERCC6L expression in tumor tissues was significantly correlated with poor prognosis and could serve as an independent prognostic indicator for HCC patients. Results of in vitro and in vivo assays revealed that ERCC6L substantially promoted cell proliferation, and our flow cytometry analysis revealed that this was accomplished by acceleration of the G1/S transition. Finally, gene set enrichment analysis and western blotting results indicated that ERCC6L might regulate HCC proliferation by activating p53 signaling.

CONCLUSIONS

Our study suggests that ERCC6L plays an important role in HCC proliferation and that it might serve as a promising therapeutic target in HCC.

Synthetic lethality of RB1 and aurora A is driven by stathmin-mediated disruption of microtubule dynamics

RB1 mutational inactivation is a cancer driver in various types of cancer including lung cancer, making it an important target for therapeutic exploitation. We performed chemical and genetic vulnerability screens in RB1-isogenic lung cancer pair and herein report that aurora kinase A (AURKA) inhibition is synthetic lethal in RB1-deficient lung cancer. Mechanistically, RB1^−/− cells show unbalanced microtubule dynamics through E2F-mediated upregulation of the microtubule destabilizer stathmin and are hypersensitive to agents targeting microtubule stability. Inhibition of AURKA activity activates stathmin function via reduced phosphorylation and facilitates microtubule destabilization in RB1^−/− cells, heavily impacting the bipolar spindle formation and inducing mitotic cell death selectively in RB1^−/− cells. This study shows that stathmin-mediated disruption of microtubule dynamics is critical to induce synthetic lethality in RB1-deficient cancer and suggests that upstream factors regulating microtubule dynamics, such as AURKA, can be potential therapeutic targets in RB1-deficient cancer.

Retinoblastoma susceptibility gene (RB1) is frequently mutated in lung cancers. Here the authors perform chemical and genetic vulnerability screens and identify aurora A kinase (AURKA) as a synthetic lethal candidate for RB1-deficient lung cancer cells and that AURKA inhibition sensitizes these cells to mitotic cell death.

A novel CDK-2 homolog identified in lamprey, Lampetra japonica, with roles in apoptosis

CDK-2, a member of the cyclin-dependent kinase family, plays an important role in many cell processes, such as cell cycle regulation, cell growth and differentiation, and cell apoptosis. Lampreys belong to the most primitive vertebrates, and there is no report about the CDK-2 gene in lampreys at present. In this study, a CDK-2-like gene sequence and deduced amino acid sequence were identified in Japanese lamprey (Lampetra japonica, L. japonica). The CDK-2-like gene has about 80% similarity with its homologs in jaw vertebrates. The polyclonal antibody against CDK-2-like was well prepared, and the results showed that CDK-2-like was highly expressed in the gonad tissue of lampreys. Apoptosis could reduce the expression of CDK-2-like in lymphocytes of lamprey, while overexpression of CDK-2-like could inhibit apoptosis. In addition, inhibition of CDK-2-like activity was able to trigger out apoptosis and also helped apoptotic inducer actinomycin D (Act-D) to induce apoptosis. These results suggest that CDK-2-like identified from lamprey may play a crucial role in apoptosis of jawless vertebrates.

Evidence that the human cell cycle is a series of uncoupled, memoryless phases

The cell cycle is canonically described as a series of four consecutive phases: G1, S, G2, and M. In single cells, the duration of each phase varies, but the quantitative laws that govern phase durations are not well understood. Using time-lapse microscopy, we found that each phase duration follows an Erlang distribution and is statistically independent from other phases. We challenged this observation by perturbing phase durations through oncogene activation, inhibition of DNA synthesis, reduced temperature, and DNA damage. Despite large changes in durations in cell populations, phase durations remained uncoupled in individual cells. These results suggested that the independence of phase durations may arise from a large number of molecular factors that each exerts a minor influence on the rate of cell cycle progression. We tested this model by experimentally forcing phase coupling through inhibition of cyclin-dependent kinase 2 (CDK2) or overexpression of cyclin D. Our work provides an explanation for the historical observation that phase durations are both inherited and independent and suggests how cell cycle progression may be altered in disease states.

Cyclin-Dependent Kinase 2 Inhibitors in Cancer Therapy: An Update

Cyclin-dependent kinase 2 (CDK2) drives the progression of cells into the S- and M-phases of the cell cycle. CDK2 activity is largely dispensable for normal development, but it is critically associated with tumor growth in multiple cancer types. Although the role of CDK2 in tumorigenesis has been controversial, emerging evidence proposes that selective CDK2 inhibition may provide a therapeutic benefit against certain tumors, and it continues to appeal as a strategy to exploit in anticancer drug development. Several small-molecule CDK2 inhibitors have progressed to the clinical trials. However, a CDK2-selective inhibitor is yet to be discovered. Here, we discuss the latest understandings of the role of CDK2 in normal and cancer cells, review the core pharmacophores used to target CDK2, and outline strategies for the rational design of CDK2 inhibitors. We attempt to provide an outlook on how CDK2-selective inhibitors may open new avenues for cancer therapy.

Halofuginone and artemisinin synergistically arrest cancer cells at the G1/G0 phase by upregulating p21Cip1 and p27Kip1

Combinational drug therapy is one of the most promising strategies in modern anticancer research. Traditional Chinese medicine (TCM) formulas represent a wealth of complex combinations proven successful over centuries of clinical application. One such formula used to treat a variety of diseases, including cancer, contains two herbs, whose main active components are Halofuginone (HF) and Artemisinin (ATS). Here we studied the anticancer synergism of HF and ATS in various cancer cell lines and in a xenograft nude mice model. We found that the HF-ATS combination arrested more cells at the G1/G0 phase than either one alone, with the concomitant increased levels of CDK2 inhibitors, p21^Cip1 and p27^Kip1. By knocking down p21^Cip1 and p27^Kip1 separately or simultaneously in HCT116 cells and MCF-7 cells, we found that p21^Cip1 was required for HF induced G1/G0 arrest, whereas p21^Cip1 and p27^Kip1 were both required for ATS or HF-ATS combination-mediated cell cycle arrest. Moreover, HF-ATS combination synergistically inhibited tumor growth in xenograft nude mice, and this was associated with the increased levels of p21^Cip1 and p27^Kip1. Collectively, these data indicate that the upregulation of p21^Cip1 and p27^Kip1 contributes to the synergistic anticancer effect of the HF-ATS combination.

Quercetin and Cisplatin combined treatment altered cell cycle and mitogen activated protein kinase expressions in malignant mesotelioma cells

Background

Malignant mesothelioma is a locally aggressive and highly lethal neoplasm of pleural, peritoneal and pericardial mesothelial cells without successful therapy. Previously, we reported that Quercetin in combination with Cisplatin inhibits cell proliferation and activates caspase-9 and -3 enzymes in different malignant mesothelioma cell lines. Moreover, Quercetin + Cisplatin lead to accumulation of both SPC111 and SPC212 cell lines in S phase.

Methods

In present work, 84 genes involved in cell growth and proliferation have analysed by using RT²-PCR array system and protein profile of mitogen activated protein kinase (MAPK) family proteins investigated by western blots.

Results

Our results showed that Quercetin and Quercetin + Cisplatin modulated gene expression of cyclins, cyclin dependent kinases and cyclin dependent kinases inhibitors. In addition genes involved in JNK, p38 and MAPK/ERK pathways were up regulated. Moreover, while p38 and JNK phosphorylations were increased, ERK phosphorylations were decreased after using Quercetin + Cisplatin.

Conclusion

This research has clarified our previous results and detailed mechanism of anti-carcinogenic potential of Quercetin alone and incombination with Cisplatin on malignant mesothelioma cells.

Screening on human hepatoma cell line HepG-2 nucleus and cytoplasm protein after CDK2 silencing by RNAi

The activation of phase-specific cyclin-dependent kinases is associated with ordered cell cycle transitions. Among the mammalian Cdks, Cdk2 is essential for liver cancer cell proliferation. The related cycling protein CDK2 was analyzed by 2D-gel and MALDI-TOF/TOF MS mass assay in liver cancer cells, which CDK2 was silenced. The results showed four significantly different spots in cell ribonucleoprotein (similar to ribosomal protein S12, chaperonin 10-related protein, beta-actin and zinc finger protein 276) and four in plasmosin (aldolase A protein, hCG, anonymous protein and tubulin, gamma complex associated protein 2). In the plasmosin, aldolase A catalyzes the production of tublin and actin. Together they regulate the cell cycle and arrest the cell in the S phage. In the cell ribonucleoprotein, proteins with homology to ribosomal protein S12 and chaperonin 10 play a similar role in cell cycle regulation.

An in silico exploration of the interaction mechanism of pyrazolo[1,5-a]pyrimidine type CDK2 inhibitors

CDK2, which interacts with cyclin A and cyclin E, is an important member of the CDK family. Having been proved to be associated with many diseases for its vital role in cell cycle, CDK2 is a promising target of anti-cancer drugs dealing with cell cycle disorders. In the present work, a total of 111 pyrazolo[1,5-a]pyrimidines (PHTPPs) as CDK2/cyclin A inhibitors were studied to conduct three-dimensional quantitative structure-activity (3D-QSAR) analyses. The optimal comparative molecular similarity indices analysis (CoMSIA) model shows that Q(2) = 0.516, Rncv(2) = 0.912, Rpre(2) = 0.914, Rm(2) = 0.843, SEP = 0.812, SEE = 0.347 with 10 components using steric, hydrophobic and H-bond donor field descriptors, indicating its effective internal and external predictive capacity. The contour maps further indicate that (1) bulky substituents in R1 are beneficial while H-bond donor groups at this position are detrimental; (2) hydrophobic contributions in the R2 area are favorable; (3) large and hydrophilic groups are well tolerated at the R3 position (a close H-bond donor moiety is favorable while a distal H-bond donor moiety in this area is disfavored); (4) bulky and hydrophobic features in the R4 region are beneficial for the biological activities and (5) the 7-N-aryl substitution is crucial to boost the inhibitory activities of the PHTPP inhibitors. Finally, docking and MD simulations demostrate that PHTPP derivatives are stabilized in a 'flying bat' conformation mainly through the H-bond interactions and hydrophobic contacts. Comparative studies indicate that PHTPP derivatives fit well within the ATP binding cleft in CDK2, with the core heterocyclic ring overlapping significantly with the adenine group of ATP despite a small deflection. In comparison to numerous other inhibitors binding to the ATP pocket, PHTPP analogues follow the binding fashion of purine inhibitors of this kinase. It is anticipated that the binding mechanism and structural features of PHTPP inhibitors studied in the present work will benefit the discovery of more potent CDK2 inhibitors, and the valid pyrazolo[1,5-a]pyrimidine-7-N-yl inhibitors will soon emerge from the large number of screening programmes to enter in clinical studies.

Cyclin-dependent kinase 2-associated protein 1 suppresses growth and tumorigenesis of lung cancer

Cyclin-dependent kinase 2-associated protein 1 (CDK2AP1), a growth suppressor that negatively regulates CDK2 activity, has been implicated in various types of cancer; yet its role in lung cancer remains unclear. In the present study, a lentivirus-based system was used to specifically downregulate or upregulate CDK2AP1 expression. A549 lung cancer cells were treated with RNAi (RNA interference) or lentiviral vectors for overexpression. Ectopic overexpression of CDK2AP1 in A549 cells in vitro greatly impaired their proliferation and colony-forming ability and enhanced their chemosensitivity to cisplatin and paclitaxel and caused cell cycle arrest at G1/S transition accompanied by the reduction of expression of CDK4 and CDK7. Injection of the ectopically CDK2AP1-overexpressing A549 cells into nude mice resulted in growth arrest of solid lung cancer tumors in vivo. Knockdown of CDK2AP1 in A549 cells, however, gave rise to the opposite effects including promoting cell proliferation/growth, cell cycling in vitro and enhancing tumorigenesis in vivo. These results suggest that CDK2AP1 plays an important role in modulating the growth and tumorigenesis of lung cancer cells and also has significant effects on the chemosensitivity of pulmonary malignancies to chemotherapeutics. Hence, this study extends our knowledge on the relationship between CDK2AP1 and oncogenesis of lung cancer, indicating that CDK2AP1 may serve as a new molecular target for future lung cancer therapy.

Extraction and validation of substructure profiles for enriching compound libraries

Compounds known to be potent against a specific protein target may potentially contain a signature profile of common substructures that is highly correlated to their potency. These substructure profiles may be useful in enriching compound libraries or for prioritizing compounds against a specific protein target. With this objective in mind, a set of compounds with known potency against six selected kinases (2 each from 3 kinase families) was used to generate binary molecular fingerprints. Each fingerprint key represents a substructure that is found within a compound and the frequency with which the fingerprint occurs was then tabulated. Thereafter, a frequent pattern mining technique was applied with the aim of uncovering substructures that are not only well represented among known potent inhibitors but are also unrepresented among known inactive compounds and vice versa. Substructure profiles that are representative of potent inhibitors against each of the 3 kinase families were thus extracted. Based on our validation results, these substructure profiles demonstrated significant enrichment for highly potent compounds against their respective kinase targets. The advantages of using our approach over conventional methods in analyzing such datasets and its application in the mining of substructures for enriching compound libraries are presented.

Water extract of Hedyotis Diffusa Willd suppresses proliferation of human HepG2 cells and potentiates the anticancer efficacy of low-dose 5-fluorouracil by inhibiting the CDK2-E2F1 pathway

Hedyotis Diffusa Willd (HDW), a Chinese herbal medicine, has been widely used as an adjuvant therapy against various cancers, including hepatocellular carcinoma (HCC). However, the underlying anticancer mechanisms are yet to be elucidated. In the present study, the anticancer effects of HDW were evaluated and the efficacy and safety of HDW combined with low-dose 5-fluorouracil (5-FU) were investigated. HepG2 cells were cultured in vitro and nude mouse xenografts were established in vivo. The proliferation of HepG2 cells was measured using the MTT method and flow cytometry. The mRNA and protein expression levels of cyclin-dependent kinase 2 (CDK2), cyclin E and E2F1 were examined using relative quantitative real-time PCR and western blot analysis, respectively. The results showed that water extract of HDW remarkably inhibited HepG2 cell proliferation in a dose-dependent manner via arrest of HepG2 cells at the G0/G1 phase and induction of S phase delay. This suppression was accompanied by a great decrease of E2F1 and CDK2 mRNA expression. In addition, HDW remarkably potentiated the anticancer effect of low-dose 5-FU in the absence of overt toxicity by downregulating the mRNA and protein levels of CDK2, cyclin E and E2F1. Our findings support the use of HDW as adjuvant therapy of chemotherapy and suggest that HDW may potentiate the efficiency of low-dose 5-FU in treating HCC.

SUPPLEMENTING THE PBSA APPROACH WITH QUANTUM MECHANICS TO STUDY THE BINDING BETWEEN CDK2 AND N2-SUBSTITUTED O6-CYCLOHEXYLMETHOXYGUANINE INHIBITORS

Because classical Poisson–Boltzman Surface Area (PBSA) model does not allow re-polarization of charges and does not account for charge transfer when a ligand binds to a protein, we have examined a hybrid approach in which we describe the protein–ligand interface by quantum mechanics and the rest of the system with the classical PBSA model. We found this approach to rank order the binding of five N2 -substituted O6 -cyclohexylmethoxyguanine inhibitors to CDK2 (cyclin-dependent kinase 2) properly. The calculated binding free energy correlated well with experimental Log(IC50) with a correlation coefficient of 0.94. A regression fit between experimental Log(IC50) and calculated binding free energy yielded a root-mean-square error of 0.48 when Log(IC50) spanned a range over three units. In addition, we observed charge transfer between the ligand and the protein at the interface — an effect not accounted for by the classical PBSA model. We also found that the direct interactions between the protein and the ligands provided the dominant factor to distinguish the binding affinity of the five ligands studied here. This hybrid approach can better prioritize derivatives of lead compounds for synthesis and biological evaluation.

Impact of cyclin E overexpression on Smad3 activity in breast cancer cell lines

Smad3, a component of the TGFβ signaling pathway, contributes to G1 arrest in breast cancer cells. Overexpression of the cell cycle mitogen, cyclin E, is associated with poor prognosis in breast cancer, and cyclin E/CDK2 mediated phosphorylation of Smad3 has been linked with inhibition of Smad3 activity. We hypothesized that the biological aggressiveness of cyclin E overexpressing breast cancer cells would be associated with CDK2 phosphorylation and inhibition of the tumor suppressant action of Smad3. Expression constructs containing empty vector, wild type (WT) Smad3, or Smad3 with CDK phosphorylation site mutations were co-transfected with a Smad3-responsive reporter construct into parental, vector control (A1), or cyclin E overexpressing (EL1) MCF7 cells. Smad3 function was evaluated by luciferase reporter assay and mRNA analysis. The impact of a Cdk2 inhibitor and cdk2 siRNA on Smad3 activity was also assessed. Cells expressing Smad3 containing mutations of the CDK phosphorylation sites had higher p15 and p21 and lower c-myc mRNA levels, as well as higher Smad3-responsive reporter activity, compared with controls or cells expressing WT Smad3. Transfection of cdk2 siRNA resulted in a significant increase in Smad3-responsive reporter activity compared with control siRNA; reporter activity was also increased after the treatment with a Cdk2 inhibitor. Thus, cyclin E-mediated inhibition of Smad3 is regulated by CDK2 phosphorylation of the Smad3 protein in MCF7 cells. Inhibition of CDK2 may lead to restoration of Smad3 tumor suppressor activity in breast cancer cells, and may represent a potential treatment approach for cyclin E overexpressing breast cancers.

LoFT: similarity-driven multiobjective focused library design

We present LoFT, a tool for focused combinatorial library design. LoFT provides a set of algorithms, constructing a focused library from a chemical fragment space under optimization of multiple design criteria. A weighted multiobjective scoring function based on physicochemical descriptors is employed for traversing the chemical search space. The new aspect of LoFT is that a similarity-driven product-based library design approach is provided on fragment level. For this reason the feature tree descriptor is incorporated for similarity comparison of library compounds to given bioactive molecules as well as for diversifying the resulting libraries. The feature tree descriptor abstracts the molecular graph to a tree structure where the nodes are labeled with physicochemical properties. For comparison, the nodes of two trees are mapped onto each other. This strictly hierarchical mechanism is suitable for the efficient comparison of chemical fragments, allowing the evaluation of the resulting products on fragment level without explicitly enumerating them. LoFT was validated, applying three different data sets. Starting with a random reagent selection, we optimized the libraries using maximum similarity to known bioactive molecules and iteratively adding further criteria. Moreover, we compared these results with data we obtained with FTrees-FS.

Nuclear targeting of cyclin-dependent kinase 2 reveals essential roles of cyclin-dependent kinase 2 localization and cyclin E in vitamin D-mediated growth inhibition

1,25-Dihydroxyvitamin D(3) (1,25-(OH)(2)D(3)), inhibits proliferation of a variety of cell types including adenocarcinoma of the prostate. We have previously shown that 1,25-(OH)(2)D(3) increases the stability of the cyclin-dependent kinase inhibitor p27(KIP1), decreases cyclin-dependent kinase 2 (CDK2) activity, and promotes G(1) phase accumulation in human prostate cancer cells. These effects correlate with cytoplasmic relocalization of CDK2. In this study, we investigated the role of CDK2 cytoplasmic relocalization in the antiproliferative effects of 1,25-(OH)(2)D(3). CDK2 was found to be necessary for prostate cancer cell proliferation. Although induced by 1,25-(OH)(2)D(3), the cyclin-dependent kinase inhibitor p27(KIP1) was dispensable for 1,25-(OH)(2)D(3)-mediated growth inhibition. Reduction in CDK2 activity by 1,25-(OH)(2)D(3) was associated with decreased T160 phosphorylation, a residue whose phosphorylation in the nucleus is essential for CDK2 activity. Ectopic expression of cyclin E was sufficient to overcome 1,25-(OH)(2)D(3)-mediated cytoplasmic mislocalization of CDK2 and all antiproliferative effects of 1,25-(OH)(2)D(3), yet endogenous levels of cyclin E or binding to CDK2 were not affected by 1,25-(OH)(2)D(3). Similarly, knockdown of the CDK2 substrate retinoblastoma, which causes cyclin E up-regulation, resulted in resistance to 1,25-(OH)(2)D(3)-mediated growth inhibition. Human prostate cancer cells resistant to growth inhibition by 1,25-(OH)(2)D(3) but retaining fully functional vitamin D receptors were developed. These cells did not exhibit 1,25-(OH)(2)D(3)-mediated cytoplasmic relocalization of CDK2. Targeting CDK2 to the nucleus of 1,25-(OH)(2)D(3)-sensitive cancer cells blocked G(1) accumulation and growth inhibition by 1,25-(OH)(2)D(3). These data establish central roles for CDK2 nuclear-cytoplasmic trafficking and cyclin E in the mechanism of 1,25-(OH)(2)D(3)-mediated growth inhibition in prostate cancer cells.

Novel structural features of CDK inhibition revealed by an ab initio computational method combined with dynamic simulations

The rational development of specific inhibitors for the approximately 500 protein kinases encoded in the human genome is impeded by a poor understanding of the structural basis for the activity and selectivity of small molecules that compete for ATP binding. Combining classical dynamic simulations with a novel ab initio computational approach linear-scalable to molecular interactions involving thousands of atoms, we have investigated the binding of five distinct inhibitors to the cyclin-dependent kinase CDK2. We report here that polarization and dynamic hydrogen bonding effects, so far undetected by crystallography, affect both their activity and selectivity. The effects arise from the specific solvation patterns of water molecules in the ATP binding pocket or the intermittent formation of hydrogen bonds during the dynamics of CDK/inhibitor interactions and explain the unexpectedly high potency of certain inhibitors such as 3-(3H-imidazol-4-ylmethylene)-5-methoxy-1,3-dihydro-indol-2-one (SU9516). The Lys89 residue in the ATP-binding pocket of CDK2 is observed to form temporary hydrogen bonds with the three most potent inhibitors. This residue is replaced in CDK4 by Thr89, whose shorter side-chain cannot form similar bonds, explaining the relative selectivity of the inhibitors for CDK2. Our results provide a generally applicable computational method for the analysis of biomolecular structures and reveal hitherto unrecognized features of the interaction between protein kinases and their inhibitors.

Induction of cell apoptosis in non-small cell lung cancer cells by cyclin A1 small interfering RNA

Cyclin A1 and cyclin B1 are overexpressed in various tumors but are present at low levels in normal tissues. Cyclin A1 is restricted to germ cells undergoing meiosis. In order to explore the possibility of using cyclin A1 and cyclin B1 as anticancer targets, we knocked them down in two lung cancer cell lines, H157 and H596, using siRNA. As with cyclin A1 siRNA in lung cancer cell lines, cyclin B1, Cdc2 and CDK2 were all significantly downregulated. The S phase fraction increased significantly, and they eventually underwent apoptosis by way of downregulated intrinsic apoptotic pathways and modulators with upregulated extrinsic apoptotic pathways. Our study suggests that cyclin A1 might be a promising anticancer target specific to lung cancer.

Mouse models of cell cycle regulators: new paradigms

In yeast, a single cyclin-dependent kinase (Cdk) is able to regulate diverse cell cycle transitions (S and M phases) by associating with multiple stage-specific cyclins. The evolution of multicellular organisms brought additional layers of cell cycle regulation in the form of numerous Cdks, cyclins and Cdk inhibitors to reflect the higher levels of organismal complexity. Our current knowledge about the mammalian cell cycle emerged from early experiments using human and rodent cell lines, from which we built the current textbook model of cell cycle regulation. In this model, the functions of different cyclin/Cdk complexes were thought to be specific for each cell cycle phase. In the last decade, studies using genetically engineered mice in which cell cycle regulators were targeted revealed many surprises. We discovered the in vivo functions of cell cycle proteins within the context of a living animal and whether they are essential for animal development. In this review, we discuss first the textbook model of cell cycle regulation, followed by a global overview of data obtained from different mouse models. We describe the similarities and differences between the phenotypes of different mouse models including embryonic lethality, sterility, hematopoietic, pancreatic, and placental defects. We also describe the role of key cell cycle regulators in the development of tumors in mice, and the implications of these data for human cancer. Furthermore, animal models in which two or more genes are ablated revealed which cell cycle regulators interact genetically and functionally complement each other. We discuss for example the interaction of cyclin D1 and p27 and the compensation of Cdk2 by Cdc2. We also focus on new functions discovered for certain cell cycle regulators such as the regulation of S phase by Cdc2 and the role of p27 in regulating cell migration. Finally, we conclude the chapter by discussing the limitations of animal models and to what extent can the recent findings be reconciled with the past work to come up with a new model for cell cycle regulation with high levels of redundancy among the molecular players.

Loss of Cyclin B1 followed by downregulation of Cyclin A/Cdk2, apoptosis and antiproliferation in Hela cell line

Recent studies have shown that Cyclin B1 is overexpressed in various tumor types but present at low levels in normal tissues. To explore the possibility of employing Cyclin B1 as an anticancer target, we knocked down Cyclin B1 in an HeLa cell line using RNA interference (RNAi). Subsequently, we monitored cell cycle-related molecules by Western blot together with immunofluorescence and determined cell cycle distribution by flow cytometry. XTT and soft agar colony growth experiments were performed to detect cell viability and proliferation. Furthermore, we analyzed cell apoptosis by measuring Bcl-2 and Bax protein level and DNA-ladder assay. After performing Cyclin B1 RNAi, Cyclin B1, Cyclin A and Cdk2 protein levels were found to be markedly downregulated, whereas Cdc2 was almost unaffected; S-phase fraction increased significantly; HeLa cell viability and cell colony forming ability were markedly diminished after the RNAi; Bcl-2 was noticeably attenuated but Bax was hardly changed; and HeLa cells displayed typical DNA ladder. The loss of Cyclin B1 resulted in the downregulation of Cyclin A and Cdk2, S-phase delay and eventually led to cell apoptosis and the decrease of cell viability and proliferation. Our studies suggest that Cyclin B1 may be a promising anticancer target.

Novel therapeutics in colorectal cancer

Colorectal cancer is an excellent tumor model for evaluating novel therapeutic strategies. Development of a mechanistic understanding of how this cancer develops, spreads, and grows allows a tailored approach to all stages of treatment: prevention, adjuvant treatment, and therapy of advanced disease. We focus on therapy in the advanced disease setting, although progress in this area could lend itself to treatment of early or premalignant disease. In the last 20 years, information has been generated about the intracellular pathways of tumor formation, invasion, and metastasis. As a result, specific molecular processes have been targeted for therapeutic intervention, including cell surface growth factor receptors, proliferation signaling, cell cycling, apo-ptosis, angiogenesis, and matrix metalloproteinases. We review the scientific rationale for recently developed novel therapeutics in colorectal cancer, and the results of clinical trials to date. We also suggest appropriate clinical settings for specific targets and outline future directions of research.

Measuring CAMD technique performance: a virtual screening case study in the design of validation experiments

The dynamic nature and comparatively young age of computational chemistry is such that novel algorithms continue to be developed at a rapid pace. Such efforts are often wrought at the expense of extensive experimental validations of said techniques, preventing a deeper understanding of their potential utility and limitations. Here we address this issue for ligand-based virtual screening descriptors through design of validation experiments that better reflect the aims of real world application. Applying the newly defined chemotype enrichment approach, a variety of two- and three-dimensional (2D/3D) similarity descriptors have been compared extensively across data sets from four diverse target types. The inhibitors within said data sets contain molecules exhibiting a wide array of substructure functionality, size and flexibility, permitting descriptor comparison in myriad settings. Relative descriptor performance under these conditions is examined, including results obtained using more typical virtual screening validation experiments. Guidelines for optimal application of said descriptors are also discussed in the context of the results obtained, as is the potential utility of fingerprint filtering.

CDC2/CDK1 expression in esophageal adenocarcinoma and precursor lesions serves as a diagnostic and cancer progression marker and potential novel drug target

Esophageal adenocarcinoma arises through well-defined precursor lesions (Barrett esophagus), although only a subset of these lesions advances to invasive adenocarcinoma. The lack of markers predicting progression in Barrett esophagus, typical presentation at advanced stage, and limitations of conventional chemotherapy result in >90% mortality for Barrett-associated adenocarcinomas. To identify potential prognostic markers and therapeutic targets, we compared gene expression profiles from Barrett-associated esophageal adenocarcinoma cell lines (BIC1, SEG1, KYAE, OE33) and normal esophageal epithelial scrapings utilizing the Affymetrix U133_A gene expression platform. We identified 560 transcripts with >3-fold up-regulation in the adenocarcinoma cell lines compared with normal epithelium. Utilizing tissue microarrays composed of normal esophageal squamous mucosa (n = 20), Barrett esophagus (n = 10), low-grade dysplasia (n = 14), high-grade dysplasia (n = 27), adenocarcinoma (n = 59), and node metastases (n = 27), we confirmed differential up-regulation of three proteins (Cdc2/Cdk1, Cdc5, and Igfbp3) in adenocarcinomas and Barrett lesions. Protein expression mirrored histologic progression; thus, 87% of low-grade dysplasias had at least focal surface Cdc2/Cdk1 and 20% had >5% surface staining; 96% of high-grade dysplasias expressed abundant surface Cdc2/Cdk1, while invasive adenocarcinoma and metastases demonstrated ubiquitous expression. Esophageal adenocarcinoma cell lines treated with the novel CDC2/CDK1 transcriptional inhibitor, tetra-O-methyl nordihydroguaiaretic acid (EM-1421, formerly named M4N) demonstrated a dose-dependent reduction in cell proliferation, paralleling down-regulation of CDC2/CDK1 transcript and protein levels. These findings suggest a role for CDC2/CDK1 in esophageal adenocarcinogenesis, both as a potential histopathologic marker of dysplasia and a putative treatment target.

Effect of cell cycle inhibition on Cisplatin-induced cytotoxicity

Pharmacological inhibitors of cyclin-dependent kinase (CDK)2 are currently in preclinical and clinical development. The purpose of our work was to evaluate a series of guanine derivatives for their ability to inhibit CDK2, affect cell cycle progression, and enhance the cytotoxic and apoptotic effects of cisplatin. A panel of guanine derivatives, including O(6)-benzylguanine (O(6)-BG), S(6)-benzyl-6-thioguanine (S(6)-BG), S(6)-[(cyclohexyl)methyl]-6-thioguanine (S(6)-CMG), O(6)-[(cyclohexyl)methyl]guanine (O(6)-CMG), O(6)-benzyl-9-methylguanine (9-CH(3)-BG), O(6)-[(cyclohexyl)methyl]-9-methyl-guanine (9-CH(3)-CMG), and 7-benzylguanine (N7-BG), exhibited varying degrees of CDK2 inhibition with O(6)-CMG being the most potent and 9-CH(3)-BG, 9-CH(3)-CMG, and N7-BG the least potent compounds. Treatment with S(6)-CMG and O(6)-CMG significantly decreased the percentage of cells in S phase. In SQ20b and SCC61 head and neck cancer cell lines, the most potent CDK2 inhibitor, O(6)-CMG, was also the most effective at enhancing cisplatin-induced cytotoxicity and apoptosis. Cisplatin-induced DNA platination increased in SQ20b cells pretreated with S(6)-BG, S(6)-CMG, and O(6)-CMG. Treatment with both O(6)-BG and trichostatin A, an indirect cell cycle inhibitor, demonstrated additive effects on cisplatin-induced cytotoxicity. In summary, we have identified a group of guanine derivatives that were effective modulators of cisplatin-induced cytotoxicity and apoptosis.

Modulating protein kinase C (PKC) to increase the efficacy of chemotherapy: stepping into darkness

The identification of molecules that promote chemotherapeutic resistance would allow rationally designed approaches to abrogate this resistance, thereby possibly improving clinical outcomes for patients with cancer. In this regard, the PKC family is attractive for targeting, because it is comprised of a family of isoforms that play key roles in multiple cellular processes and can contribute to cellular transformation. Encouraging in vitro data originally showed that approaches to modulate PKC activity through small-molecule inhibitors or genetic manipulation could affect tumor cell survival. Recently, some of these approaches have begun clinical testing. Early-stage clinical trials revealed scattered clinical responses to these agents, but the most recent clinical trials have shown that combining modulators of PKC with standard chemotherapy does not improve outcome over chemotherapy alone. In this review, we will trace the development of these approaches, and discuss possible explanations for the recent negative results. Importantly, we will suggest guidelines for the clinical evaluation of PKC modulators.

The discovery of a new structural class of cyclin-dependent kinase inhibitors, aminoimidazo[1,2-a]pyridines

The protein kinase family represents an enormous opportunity for drug development. However, the current limitation in structural diversity of kinase inhibitors has complicated efforts to identify effective treatments of diseases that involve protein kinase signaling pathways. We have identified a new structural class of protein serine/threonine kinase inhibitors comprising an aminoimidazo[1,2-a]pyridine nucleus. In this report, we describe the first successful use of this class of aza-heterocycles to generate potent inhibitors of cyclin-dependent kinases that compete with ATP for binding to a catalytic subunit of the protein. Co-crystal structures of CDK2 in complex with lead compounds reveal a unique mode of binding. Using this knowledge, a structure-based design approach directed this chemical scaffold toward generating potent and selective CDK2 inhibitors, which selectively inhibited the CDK2-dependent phosphorylation of Rb and induced caspase-3-dependent apoptosis in HCT 116 tumor cells. The discovery of this new class of ATP-site-directed protein kinase inhibitors, aminoimidazo[1,2-a]pyridines, provides the basis for a new medicinal chemistry tool to be used in the search for effective treatments of cancer and other diseases that involve protein kinase signaling pathways.

Flavopiridol downregulates the expression of both the inducible NO synthase and p27(kip1) in malignant cells from B-cell chronic lymphocytic leukemia

Flavopiridol, an inhibitor of cyclin-dependent kinases and other protein kinases, induces in vitro apoptosis of malignant cells from B-cell chronic lymphocytic leukemia (B-CLL). Previously, we reported that nitric oxide (NO), produced by an inducible NO synthase (iNOS), spontaneously expressed by the B-CLL cells, contributed to their deficiency in apoptosis. In the present work, we show that ex vivo treatment of leukemic cells from B-CLL patients with flavopiridol results in the inhibition of iNOS expression, as determined by immunofluorescence and Western blotting, and in a marked inhibition of NO production measured in situ with a specific fluorescent probe (DAF-2 DA). These effects are accompanied by membrane, mitochondrial and nuclear events of apoptosis. Flavopiridol exposure also results in the stimulation of caspase 3 activity and in caspase-dependent cleavage of p27(kip1), a negative regulator of the cell cycle, which is overexpressed in B-CLL. Thus, flavopiridol is capable of downregulating both iNOS and p27(kip1) expression in B-CLL cells. Furthermore, flavopiridol-promoted apoptosis is partly reverted by an NO donor, suggesting that inhibition of the NO pathway could participate in the apoptotic effects of flavopiridol on the leukemic cells.

The cell cycle, chromatin and cancer: mechanism-based therapeutics come of age

Tumour cells grow and divide in an uncontrolled fashion. Recent advances in the cell cycle have uncovered new mechanisms that integrate growth and division with chromatin and gene expression control. Small-molecule drugs that target key enzyme classes involved in these pathways, the cyclin-dependent kinases (Cdk) in the cell cycle and histone deacetylases (HDAC) in chromatin control, have entered clinical studies, with emerging clinical efficacy. These new mechanism-based approaches could provide significant improvements over many current chemotherapeutics.

The use of cyclin-dependent kinase inhibitors alone or in combination with established cytotoxic drugs in cancer chemotherapy

Cyclin-dependent kinase (CDK) inhibitors are small molecule inhibitors of the kinases required for the orderly progression of cells, both normal and neoplastic, through the cell cycle. Because cell cycle dysregulation is such a common occurrence in neoplasia, the search for agents that might block cell cycle traverse has been the focus of intense interest. These efforts have led to the identification of a broad array of compounds that interfere directly with the function of CDKs. Two of these agents (flavopiridol and UCN-01) have now entered the clinical arena, and others are scheduled to do so in the near future. In preclinical studies, CDK inhibitors have shown the ability not only to block neoplastic cell proliferation, but also to induce, through a variety of mechanisms, programmed cell death. The latter capacity may stem from the diverse effects that CDK inhibitors exert on multiple kinases and apoptotic regulatory molecules. In addition, there is abundant preclinical evidence that CDK inhibitors can potentiate, generally in a dose- and sequence-dependent manner, the anti-tumor effects of many established cytotoxic agents. In clinical studies in humans, flavopiridol and UCN-01 have been shown to be tolerable, although clear evidence of single agent activity or enhancement of the efficacy of established agents has not yet emerged. This may reflect a failure to optimize drug schedules/pharmacokinetics, or to identify the critical molecular targets of these agents. Finally, in recent years, a rationale has emerged for combining CDK inhibitors with other molecularly targeted agents (i.e. differentiation-inducers and signal transduction modulators). Current research has basically two goals: (a). to identify CDK inhibitor concentrations and schedules that inhibit the growth of and induce apoptosis in specific tumor cell types; and (b). to establish a rational basis for combining CDK inhibitors with more conventional cytotoxic agents to enhance antitumor efficacy. This review gives a brief summary of such efforts, with an emphasis on agents and combinations that are in or near clinical development.