Sequential treatment with flavopiridol synergistically enhances pyrrolo-1,5-benzoxazepine-induced apoptosis in human chronic myeloid leukaemia cells including those resistant to imatinib treatment

The Bcr-Abl kinase inhibitor, imatinib mesylate, is the front line treatment for chronic myeloid leukaemia (CML), but the emergence of imatinib resistance has led to the search for alternative drug treatments and the examination of combination therapies to overcome imatinib resistance. The pro-apoptotic PBOX compounds are a recently developed novel series of microtubule targeting agents (MTAs) that depolymerise tubulin. Recent data demonstrating enhanced MTA-induced tumour cell apoptosis upon combination with the cyclin dependent kinase (CDK)-1 inhibitor flavopiridol prompted us to examine whether this compound could similarly enhance the effect of the PBOX compounds. We thus characterised the apoptotic and cell cycle events associated with combination therapy of the PBOX compounds and flavopiridol and results showed a sequence dependent, synergistic enhancement of apoptosis in CML cells including those expressing the imatinib-resistant T315I mutant. Flavopiridol reduced the number of polyploid cells formed in response to PBOX treatment but only to a small extent, suggesting that inhibition of endoreplication was unlikely to play a major role in the mechanism by which flavopiridol synergistically enhanced PBOX-induced apoptosis. The addition of flavopiridol following PBOX-6 treatment did however result in an accelerated exit from the G2/M transition accompanied by an enhanced downregulation and deactivation of the CDK1/cyclin B1 complex and an enhanced degradation of the inhibitor of apoptosis protein (IAP) survivin. In conclusion, results from this study highlight the potential of these novel series of PBOX compounds, alone or in sequential combination with flavopiridol, as an effective therapy against CML.

Structural basis for inhibition of cyclin-dependent kinase 9 by flavopiridol

Flavopiridol has been shown to potently inhibit CDK1 and 2 (cyclin-dependent kinases 1 and 2) and most recently it has been found that it also inhibits CDK9. The complex CDK9-cyclin T1 controls the elongation phase of transcription by RNA polymerase II. The present work describes a molecular model for the binary complex CDK9-flavopiridol. This structural model indicates that the inhibitor strongly binds to the ATP-binding pocket of CDK9 and the structural comparison of the complex CDK2-flavopiridol correlates the structural differences with differences in inhibition of these CDKs by flavopiridol. This structure opens the possibility of testing new inhibitor families, in addition to new substituents for the already known leading structures such as flavones and adenine derivatives. © 2002 Elsevier Science (USA). All rights reserved.

Advances in the systemic therapy of malignant pleural mesothelioma

Malignant pleural mesothelioma is an aggressive thoracic malignancy associated with exposure to asbestos, and its incidence is anticipated to increase during the first half of this century. Chemotherapy is the mainstay of treatment, yet sufficiently robust evidence to substantiate the current standard of care has emerged only in the past 5 years. This Review summarizes the evidence supporting the clinical activity of chemotherapy, discusses the use of end points for its assessment and examines the influence of clinical and biochemical prognostic factors on the natural history of malignant pleural mesothelioma. Early-phase clinical trials of second-line and novel agents are emerging from an increased understanding of mesothelioma cell biology. Coupled with high-quality translational research, such developments have real potential to improve the outlook of patients at a time of increasing incidence.

Targeting histone deacetylases for the treatment of immune, endocrine and metabolic disorders

The 'histone code' is a well-established hypothesis describing the idea that specific patterns of post-translational modifications to histones act like a molecular "code" recognised and used by non-histone proteins to regulate specific chromatin functions. One modification which has received significant attention is that of histone acetylation. The enzymes which regulate this modification are described as histone acetyltransferases or HATs, and histone deacetylases or HDACs. Due to their conserved catalytic domain HDACs have been actively targeted as a therapeutic target. The proinflammatory environment is increasingly being recognised as a critical element for both degenerative diseases and cancer. The present review will discuss the current knowledge surrounding the clinical potential & current development of histone deacetylases for the treatment of diseases for which a proinflammatory environment plays important roles, and the molecular mechanisms by which such inhibitors may play important functions in modulating the proinflammatory environment. © 2009 Bentham Science Publishers Ltd.

Novel microtubule-targeting agents, pyrrolo-1,5-benzoxazepines, induce cell cycle arrest and apoptosis in prostate cancer cells

Advanced hormone-refractory prostate cancer is associated with poor prognosis and limited treatment options. Members of the pyrrolo-1,5-benzoxazepine (PBOX) family of compounds exhibit anti-cancer properties in cancer cell lines (including multi-drug resistant cells), ex vivo patient samples and in vivo mouse tumour models with minimal toxicity to normal cells. Recently, they have also been found to possess anti-angiogenic properties in vitro. However, both the apoptotic pathways and the overall extent of the apoptotic response induced by PBOX compounds tend to be cell-type specific. Since the effect of the PBOX compounds on prostate cancer has not yet been elucidated, the purpose of this study was to investigate if PBOX compounds induce anti-proliferative effects on hormone-refractory prostate cancer cells. We examined the effect of two representative PBOX compounds, PBOX-6 and PBOX-15, on the androgen-independent human prostate adenocarcinoma cell line, PC3. PBOX-6 and -15 displayed anti-proliferative effects on PC3 cells, mediated initially through a sustained G2/M arrest. G2/M arrest, illustrated as DNA tetraploidy, was accompanied by microtubule depolymerisation and phosphorylation of anti-apoptotic proteins Bcl-2 and Bcl-xL and the mitotic spindle checkpoint protein BubR1. Phosphorylation of BubR1 is indicative of an active mitotic checkpoint and results in maintenance of cell cycle arrest. G2/M arrest was followed by apoptosis illustrated by DNA hypoploidy and PARP cleavage and was accompanied by degradation of BubR1, Bcl-2 and Bcl-xL. Furthermore, sequential treatment with the CDK1-inhibitor, flavopiridol, synergistically enhanced PBOX-induced apoptosis. In summary, this in vitro study indicates that PBOX compounds may be useful alone or in combination with other agents in the treatment of hormone-refractory prostate cancer.

Gamma-linolenic Acid Alters Ku80, E2F1, and Bax Expression and Induces Micronucleus Formation in C6 Glioma Cells In Vitro

Gamma-linolenic acid (GLA) is an inhibitor of tumor cell proliferation in both in vitro and in vivo conditions. The aim of this study was to investigate the effects of 150 mu M GLA on the expression of E2F1, cyclin D1, bax, bcl2, Ku70, and Ku80 in C6 rat glioma cells. The Ku proteins were chosen as previous studies have shown that loss or reduction in their expression causes increased DNA damage and micronucleus formation in the presence of radiation. The fact that GLA exposure is known to enhance the efficacy of radiation treatment raised the question whether the Ku proteins could be involved in this effect as seen for other molecules such as roscovitine and flavopiridol. GLA altered the mRNA expression of E2F1, cyclin D1, and bax, but no changes were found for bcl2, Ku70, and Ku80. Alterations in protein expression were observed for bax, Ku80, and E2F1. The 45% decrease in E2F1 expression was proportional to decreased cell proliferation (44%). Morphological analysis found a 25% decrease in mitotic activity in the GLA-treated cells, which was accompanied by a 49% decrease in S-phase by FACS analysis. A 39% increase in the number of micronuclei detected by Hoechst fluorescence points to GLA`s effects on cell division even at concentrations that do not produce significant increases in apoptosis. Most important was the finding that Ku80 expression, a critical protein involved in DNA repair as a heterodimer with Ku70, was decreased by 71%. It is probable that reduced Ku80 is responsible for the increase in micronucleus formation in GLA-treated cells in a similar manner to that found in Ku80 null cells exposed to radiation. The decreased expression of Ku80 and E2F1 could make cells more susceptible to radiotherapy and chemotherapy. (C) 2009 IUBMB

CDK9 a potential target for drug development

The family of Cyclin-Dependent Kinases (CDKs) can be subdivided into two major functional groups based on their roles in cell cycle and/or transcriptional control. CDK9 is the catalytic subunit of positive transcription elongation factor b (P-TEFb). CDK9 is the kinase of the TAK complex (Tat-associated kinase complex), and binds to Tat protein of HIV, suggesting a possible role for CDK9 in AIDS progression. CDK9 complexed with its regulatory partner cyclin T1, serves as a cellular mediator of the transactivation function of the HIV Tat protein. P-TEFb is responsible for the phosphorylation of the carboxyl-terminal domain of RNA Pol II, resulting in stimulation of transcription. Furthermore, the complexes containing CDK9 induce the differentiation in distinct tissue. The CDK9/cyclin T1 complex is expressed at higher level in more differentiated primary neuroectodermal and neuroblastoma tumors, showing a correlation between the kinase expression and tumor differentiation grade. This may have clinical and therapeutical implications for these tumor types. Among the CDK inhibitors two have shown to be effective against CDK9: Roscovitine and Flavopiridol. These two inhibitors prevented the replication of human immunodeficiency virus (HIV) type 1 by blocking Tat transactivation of the HIV type 1 promoter. These compounds inhibit CDKs by binding to the catalytic domain in place of ATP, preventing transfer of a phosphate group to the substrate. More sensitive therapeutic agents of CDK9 can be designed, and structural studies can add information in the understanding of this kinase. The major features related to CDK9 inhibition will be reviewed in this article.

Structural bioinformatics study of cyclin-dependent kinases complexed with inhibitors

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Molecular models of cyclin-dependent kinase 1 complexed with inhibitors

Roscovitine and flavopiridol have been shown to potently inhibit cyclin-dependent kinase 1 and 2 (CDK1 and 2). The structures of CDK2 complexed with roscovitine and deschoroflavopiridol have been reported, however no crystallographic structure is available for complexes of CDK1 with inhibitors. The present work describes two molecular models for the binary complexes CDK1:roscovitine and CDK1:flavopiridol. These structural models indicate that both inhibitors strongly bind to the ATP-binding pocket of CDKI and structural comparison of the CDK complexes correlates the structures with differences in inhibition of these CDKs by flavopiridol and roscovitine. This article explains the structural basis for the observed differences in activity of these inhibitors. (C) 2004 Elsevier B.V. All rights reserved.

Structural Basis for Interaction of Inhibitors with Cyclin-Dependent Kinase 2

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Estudo estrutural de quinases dependentes de ciclinas por métodos de modelagem molecular comparativa

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Bioinformatische Identifizierung und Charakterisierung von Zyklin-abhängigen Kinasen und Zyklinen des Parasiten Eimeria tenella und deren Nutzung im rationalen Wirkstoffdesign

Parasiten der Apicomplexa umfassen sowohl humanpathogene, als auch tierpathogene Protozoen. Beispiele für wichtige Vertreter human- und tierpathogener Parasiten sind Plasmodium falciparum und Eimeria tenella. E. tenella verursacht die Kokzidiose des Hühnchens, eine Darmerkrankung die weltweit für Verluste in einer geschätzten Höhe von bis zu 3 Milliarden US$ verantwortlich zeichnet. Eine prophylaktische Vakzinierung gegen diese Krankheit ist ökonomisch meist ineffizient, und eine Behandlung mit Kokzidiostatika wird durch häufige Resistenzbildung gegen bekannte Wirkstoffe erschwert. Diese Situation erfordert die Entwicklung neuer kostengünstiger Alternativen. Geeignete Zielproteine für die Entwicklung neuartiger Arzneistoffe zur Behandlung der Kokzidiose sind die Zyklin-abhängigen Kinasen (CDKs), zu denen auch die CDK-related Kinase 2 (EtCRK2) aus E. tenella gehört. Diese Proteine sind maßgeblich an der Regulation des Zellzyklus beteiligt. Durch chemische Validierung mit dem CDK Inhibitor Flavopiridol konnte nachgewiesen werden, dass ein Funktionsverlust von CDKs in E. tenella die Vermehrung des Parasiten in Zellkultur inhibiert. E. tenella CDKs sind daher als Zielproteine für die Entwicklung einer Chemotherapie der Kokzidiose geeignet. Mittels bioinformatischer Tiefenanalysen sollten CDK Proteine im Parasiten E. tenella identifiziert werden. Das Genom von E. tenella liegt in Rohfassung vor [ftp://ftp.sanger.ac.uk]. Jedoch waren zum Zeitpunkt dieser Arbeiten viele Sequenzen des Genoms noch nicht annotiert. Homologe CDK Proteine von E. tenella konnten durch den Vergleich von Sequenzinformationen mit anderen Organismen der Apicomplexa identifiziert und analysiert werden. Durch diese Analysen konnten neben der bereits bekannten EtCRK2, drei weitere, bislang nicht annotierte CDKs in E. tenella identifiziert werden (EtCRK1, EtCRK3 sowie EtMRK). Darüber hinaus wurde eine Analyse der entsprechenden Zykline – der Aktivatoren der CDKs – bezüglich Funktion und Struktur, sowie eine Datenbanksuche nach bisher nicht beschriebenen Zyklinen in E. tenella durchgeführt. Diese Suchen ergaben vier neue potentielle Zykline für E. tenella, wovon EtCYC3a als Aktivator der EtCRK2 von María L. Suárez Fernández (Intervet Innovation GmbH, Schwabenheim) bestätigt werden konnte. Sequenzvergleiche lassen vermuten, dass auch EtCYC1 und EtCYC3b in der Lage sind, EtCRK2 zu aktivieren. Außerdem ist anzunehmen, dass EtCYC4 als Aktivator der EtCRK1 fungiert. Ein weiterer Schwerpunkt der vorliegenden Arbeit war die Suche und Optimierung nach neuen Inhibitoren von CDKs aus E. tenella. In vorangegangenen Arbeiten konnten bereits Inhibitoren der EtCRK2 gefunden werden [BEYER, 2007]. Mittels Substruktur- und Ähnlichkeitssuchen konnten im Rahmen dieser Arbeit weitere Inhibitoren der EtCRK2 identifiziert werden. Vier dieser Strukturklassen erfüllen die Kriterien einer Leitstruktur. Eine dieser Leitstrukturen gehört zur Strukturklasse der Benzimidazol-Carbonitrile und ist bislang nicht als Inhibitor anderer Kinasen beschrieben. Diese neu identifizierte Leitstruktur konnte in silico weiter optimiert werden. Im Rahmen dieser Arbeit wurden Bindungsenergien von Vertretern dieser Strukturklasse berechnet, um einen wahrscheinlichen Bindemodus vorherzusagen. Für die weiterführende in silico Optimierung wurde eine virtuelle kombinatorische Substanzbibliothek dieser Klasse erstellt. Die Auswahl geeigneter Verbindungen für eine chemische Synthese erfolgte durch molekulares Docking unter Nutzung von Homologiemodellen der EtCRK2. Darüber hinaus wurde ein in silico Screening nach potentiellen Inhibitoren der PfMRK und EtMRK durchgeführt. Dabei konnten weitere interessante virtuelle Hit-Strukturen aus einer Substanzdatenbank kommerziell erhältlicher Verbindungen gefunden werden. Durch dieses virtuelle Screening konnten jeweils sieben Verbindungen als virtuelle Hits der PfMRK sowie der EtMRK identifiziert werden. Die Häufung von Strukturklassen mit bekannter CDK Aktivität deutet darauf hin, dass während des virtuellen Screenings eine Anreicherung von CDK Inhibitoren stattgefunden hat. Diese Ergebnisse lassen auf eine Weiterentwicklung neuer Wirkstoffe gegen Kokzidiose und Malaria hoffen.

Biochemische Charakterisierung der Zyklin-abhängigen Kinase 2,Aktivator-Komplexe des Parasiten Eimeria tenella sowie deren Nutzung in der Wirkstoffforschung

Der Stamm der Apicomplexa ist eine artenreiche Gruppe, der einzellige, meist obligat intrazelluläre Parasiten angehören, darunter auch erstzunehmende Krankheitserreger wie Plasmodium sp. sowie tierpathogene Vertreter wie Eimeria sp. und Theileria sp. Eimeria sp. verursacht die Kokzidiose beim Huhn. Diese Krankheit bedingt weltweite Verluste in der Geflügelindustrie von etwa 3 Milliarden US$ pro Jahr [DALLOUL & LILLEHOJ, 2006; SHIRLEY et al., 2007; LUCIUS & LOOS-FRANK, 2008]. Die Parasiten weisen eine hohe Resistenzbildungsrate gegen vorhandene Wirkstoffe auf. Zudem ist der Einsatz von Vakzinen mit Nebenwirkungen verbunden und für hohe Produktionskosten verantwortlich. Daher ist die Entwicklung von neuen, kostengünstigen und effektiven Kokzidiostatika eine dringend notwendige Herausforderung [KINNAIRD et al., 2004]. rnAuf Grund ihrer essentiellen, regulatorischen Funktion im eukaryotischen Zellzyklus sind Zyklin-abhängige Kinasen (CDKs) validierte Zielproteine [LEHNINGER et al., 2005]. Auch Eimeria tenella CDC2-related kinase 2 (EtCRK2) wurde bereits mittels des bekannten CDK-Inhibitors Flavopiridol als Zielprotein chemisch validiert [ENGELS et al., 2010]. Wie bei allen CDKs ist die Aktivität von EtCRK2 abhängig von der Bindung eines Aktivators, der zur Zyklin-Proteinfamilie gehört. Dieser natürliche EtCRK2-Aktivator war jedoch bislang nicht bekannt. Deshalb war ein Teil dieser Arbeit die Identifizierung des natürlichen EtCRK2-Aktivators. Bioinformatische Analysen identifizierten vier E. tenella Zyklin-ähnliche Proteine (EtCYC1, EtCYC3a, EtCYC3b und EtCYC4), die nah verwandt zu den Plasmodium falciparum-Zyklinen sind [ENGELS et al., 2010; SUÁREZ FERNÁNDEZ et al., bislang unveröffentlichte Daten]. Im Rahmen dieser Arbeit konnten zwei neue Aktivatoren identifiziert und biochemisch charakterisiert werden: der bekannte CDK-Aktivator XlRINGO und das neue E. tenella-Zyklin EtCYC3a. Nachdem der nicht-radioaktive TR-FRET-Assay für die EtCRK2 etabliert und optimiert wurde, konnte die EtCRK2-Aktivität im Komplex mit beiden Aktivatoren und weitere wichtige kinetische Parameter bestimmt werden.rnZusätzlich wurde dieser Assay zum in vitro Screening einer kommerziellen Chemikalienbibliothek auf die EtCRK2 eingesetzt, um potentielle Inhibitoren für EtCRK2 zu identifizieren. Dieses in vitro Screening gefolgt von einer in silico Hit-Anreicherung identifizierte 19 aktive Verbindungen für die durch EtCYC3a und XlRINGO aktivierte EtCRK2. Zudem wurden drei Struktur-Cluster definiert: Naphthoquinone, 8-Hydroxyquinoline und 2-Pyrimidinyl-aminopiperidin-propan-2-ole. rnDie aktivsten Vertreter von jedem Cluster wurden als Leitstrukturen ausgewählt und auf EtCRK2 und HsCDK2 getestet. Aufgrund ihrer inhibierenden Wirkung auf EtCRK2 stellen diese Verbindungen viel versprechende Leitstrukturen für die Entwicklung eines neuen Antikokzidiums dar. Hiermit konnte auch gezeigt werden, dass BES124764, der Vertreter des 2-Pyrimidinyl-aminopiperidin-propan-2-ol-Clusters, in der Lage ist, die EtCRK2 selektiv zu inhibieren. rnDaher wird BES124764 sowie einige Derivate in den Leitstruktur-Optimierungsprozess für die Auffindung eines neuen Arzneimittelkandidaten gegen Kokzidiose eingehen.rn

The survival role and the potential therapeutic targeting of MET in multiple myeloma

Multiple myeloma (MM) is a debilitating and incurable B-cell malignancy. Previous studies have documented that the hepatocyte growth factor (HGF) plays a role in the pathobiology of MM. The receptor tyrosine kinase MET induced signaling initiates when its ligand HGF binds to the MET receptor. However, the direct importance of MET in MM has not been elucidated. The present work used three different but complementary approaches to reduce MET protein levels or its activity to demonstrate the importance of MET in MM. ^ In the first approach, MET transcript and protein levels were reduced by directly targeting the cellular MET transcripts using shRNA retroviral infection techniques. This direct reduction of MET mRNA leads to a reduction of MET protein levels, which caused an inhibition of growth and induction of cell death. ^ In the second approach, a global transcription inhibitor flavopiridol was used as a potential pharmacological tool to reduce MET levels. MET has a short half-life of 30 min for mRNA and 4 hours for protein; therefore using a RNA pol II inhibitor such as flavopiridol would be a viable option to reduce MET levels. When using flavopiridol in MM cell lines, there was a reduction of MET transcript and protein levels, which was associated with the induction of cell death. ^ Finally in the last strategy, MET kinase activity was suppressed by MP470, a small molecule inhibitor that binds to the ATP binding pocket in the kinase domain. At concentrations where phosphorylation of MET was inhibited there was induction of cell death in MM cell lines and primary cells from patients. In addition, in MM cell lines there was a decrease in phosphorylation of AKT (ser473) and caspase-9 (ser196); downstream of MET, suggesting that the mechanism of action for survival may be through these cascade of events. ^ Overall, this study provides a proof-of-principle that MET is important for the survival of MM cell lines as well as primary plasma cells obtained from patients. Therefore, targeting MET therapeutically may be a possible strategy to treat patients with this debilitating disease of MM. ^

Structural basis for specificity and potency of a flavonoid inhibitor of human CDK2, a cell cycle kinase.

The central role of cyclin-dependent kinases (CDKs) in cell cycle regulation makes them a promising target for studying inhibitory molecules that can modify the degree of cell proliferation. The discovery of specific inhibitors of CDKs such as polyhydroxylated flavones has opened the way to investigation and design of antimitotic compounds. A novel flavone, (-)-cis-5,7-dihydroxyphenyl-8-[4-(3-hydroxy-1-methyl)piperidinyl] -4H-1-benzopyran-4-one hydrochloride hemihydrate (L868276), is a potent inhibitor of CDKs. A chlorinated form, flavopiridol, is currently in phase I clinical trials as a drug against breast tumors. We determined the crystal structure of a complex between CDK2 and L868276 at 2.33 angstroms resolution and refined to an Rfactor 20.3%. The aromatic portion of the inhibitor binds to the adenine-binding pocket of CDK2, and the position of the phenyl group of the inhibitor enables the inhibitor to make contacts with the enzyme not observed in the ATP complex structure. The analysis of the position of this phenyl ring not only explains the great differences of kinase inhibition among the flavonoid inhibitors but also explains the specificity of L868276 to inhibit CDK2 and CDC2.