A Novel Class of Cyclin-dependent Kinase Inhibitors Identified by Molecular Docking Act through a Unique Mechanism

Corsino, Patrick; Horenstein, Nicole A.; Ostrov, David A.; Rowe, Thomas C.; Law, Mary E.; Barrett, Amanda; Aslanidi, George; Cress, W. Douglas; Law, Brian K.

doi:10.1074/jbc.m109.055251

Cited by 19 publications

(12 citation statements)

References 33 publications

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“…S7) with structures previously unknown to be associated with inhibition of RNR are particularly interesting and truly unique as RNR inhibitors. The most potent of these (NSC130872) is a reported inhibitor of cyclin-dependent kinase (22), and therefore a possible competitive inhibitor with respect to nucleotides.…”

Section: Discussionmentioning

confidence: 99%

Discovery of antimicrobial ribonucleotide reductase inhibitors by screening in microwell format

Tholander

Sjöberg²

2012

Proc. Natl. Acad. Sci. U.S.A.

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Ribonucleotide reductase (RNR) catalyzes reduction of the four different ribonucleotides to their corresponding deoxyribonucleotides and is the rate-limiting enzyme in DNA synthesis. RNR is a wellestablished target for the antiproliferative drugs Gemzar and Hydrea, for antisense therapy, and in combination chemotherapies. Surprisingly, few novel drugs that target RNR have emerged, partly because RNR activity assays are laboratory-intense and exclude high-throughput methodologies. Here, we present a previously undescribed PCRbased assay for RNR activity measurements in microplate format. We validated the approach by screening a diverse library of 1,364 compounds for inhibitors of class I RNR from the opportunistic pathogen Pseudomonas aeruginosa, and we identified 27 inhibitors with IC 50 values from ∼200 nM to 30 μM. Interestingly, a majority of the identified inhibitors have been found inactive in human cell lines as well as in anticancer and in vivo tumor tests as reported by the PubChem BioAssay database. Four of the RNR inhibitors inhibited growth of P. aeruginosa, and two were also found to affect the transcription of RNR genes and to decrease the cellular deoxyribonucleotide pools. This unique PCR-based assay works with any RNR enzyme and any substrate nucleotide, and thus opens the door to high-throughput screening for RNR inhibitors in drug discovery.National Cancer Institute diversity set II | nucleotide metabolism | ribonucleotide reductase assay | high-throughput assay R ibonucleotide reductase (RNR) is an essential enzyme for de novo synthesis of DNA building blocks via reduction of the 2′-hydroxyl of ribonucleotides (1, 2). With its key role in the DNA synthesis pathway, RNR is an absolute requirement for cellular proliferation and a prerequisite for life. RNR is found in all freeliving organisms as well as in some dsDNA viruses. The only known exceptions to this ubiquitous presence are a few parasites and obligate intracellular endosymbionts (3) that rely on the host cell for production of DNA precursors. Thus, RNR is a potential antimicrobial drug target in a wide variety of organisms. RNR enzymes exist in three different classes, each with different cofactor requirements. Eukaryotes generally possess only one class, whereas bacteria possess any combination of RNR classes (3). Different oligomeric states of RNRs are known, and a common active form of the major variants of RNR is a dimer of dimers (α 2 β 2 ) (4). RNR exhibits a radical-based catalytical mechanism that involves redox cycling of cysteine residues, specific metal ion dependencies, essential subunit interactions, and sophisticated allosteric regulation (1). Thus, in addition to conventional competitive inhibition, pharmaceuticals may interfere with subunit interactions, binding to allosteric effector sites, metal chelation, radical formation and transfer, or inhibition of cysteine disulfide exchange. These sites of potential intervention offer a plethora of possibilities for the design of pathogen-specific antibiotics. Because sequence...

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Section: Discussionmentioning

confidence: 99%

Discovery of antimicrobial ribonucleotide reductase inhibitors by screening in microwell format

Tholander

Sjöberg²

2012

Proc. Natl. Acad. Sci. U.S.A.

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“…p27 association with CDK2 produces a pocket that is not present in its absence. Molecules predicted by molecular docking to bind to this pocket cause the selective aggregation and downregulation of CDK2 and CDK4, and evidence was presented that these compounds induce the degradation of CDKs via aggresomes (Corsino et al, 2009).…”

Section: Creative Approaches To Cdk Inhibitionmentioning

confidence: 99%

“…This general strategy has been extended using REPLACE (REplacement with Partial Ligand Alternatives through Computational Enrichment; Andrews et al, 2006) to develop drug-like, peptidomimetic CDK2 inhibitors. A fifth approach to CDK2 inhibition includes efforts designed to mimic the conformational changes in CDK2 induced by p27 binding (Corsino et al, 2009). p27 association with CDK2 produces a pocket that is not present in its absence.…”

Section: Creative Approaches To Cdk Inhibitionmentioning

confidence: 99%

Cyclin-Dependent Kinase Inhibitors as Anticancer Therapeutics

et al. 2015

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Cyclin-dependent kinases (CDKs) have been considered promising drug targets for a number of years, but most CDK inhibitors have failed rigorous clinical testing. Recent studies demonstrating clear anticancer efficacy and reduced toxicity of CDK4/6 inhibitors such as palbociclib and multi-CDK inhibitors such as dinaciclib have rejuvenated the field. Favorable results with palbociclib and its recent U.S. Food and Drug Administration approval demonstrate that CDK inhibitors with narrow selectivity profiles can have clinical utility for therapy based on individual tumor genetics. A brief overview of results obtained with ATPcompetitive inhibitors such as palbociclib and dinaciclib is presented, followed by a compilation of new avenues that have been pursued toward the development of novel, non-ATPcompetitive CDK inhibitors. These creative ways to develop CDK inhibitors are presented along with crystal structures of these agents complexed with CDK2 to highlight differences in their binding sites and mechanisms of action. The recent successes of CDK inhibitors in the clinic, combined with the potential for structure-based routes to the development of non-ATP-competitive CDK inhibitors, and evidence that CDK inhibitors may have use in suppressing chromosomal instability and in synthetic lethal drug combinations inspire optimism that CDK inhibitors will become important weapons in the fight against cancer.

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“…The mammalian cell cycle is orchestrated by the activity of the cyclin-dependent kinases (CDKs), 3 and because of this they are considered important targets in cancer drug development (1)(2)(3). A key G1 target of the CDKs is pRB, the protein product of the RB tumor suppressor gene, which in turn regulates the E2F family of transcription factors.…”

Section: From the Molecular Oncology Program H Lee Moffitt Cancer Cmentioning

confidence: 99%

CDKN1C Negatively Regulates RNA Polymerase II C-terminal Domain Phosphorylation in an E2F1-dependent Manner

Ma¹,

Chen²,

Wright

et al. 2010

Journal of Biological Chemistry

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CDKN1C is a cyclin-dependent kinase inhibitor and is a candidate tumor suppressor gene. We previously found that the CDKN1C protein represses E2F1-driven transcription in an apparent negative feedback loop. Herein, we explore the mechanism by which CDKN1C represses transcription. We find that adenoviral-mediated overexpression of CDKN1C leads to a dramatic reduction in phosphorylation of the RNA polymerase II (pol II) C-terminal domain (CTD). RNA interference studies demonstrate that this activity is not an artifact of CDKN1C overexpression, because endogenous CDKN1C mediates an inhibition of RNA pol II CTD phosphorylation in HeLa cells upon treatment with dexamethasone. Surprisingly, we find that CDKN1C-mediated repression of RNA pol II phosphorylation is E2F1-dependent, suggesting that E2F1 may direct CDKN1C to chromatin. Chromatin immunoprecipitation assays demonstrate that CDKN1C is associated with E2F1-regulated promoters in vivo and that this association can dramatically reduce the level of RNA pol II CTD phosphorylation at both Ser-2 and Ser-5 of the C-terminal domain repeat. In addition, we show that CDKN1C interacts with both CDK7 and CDK9 (putative RNA pol II CTD kinases) and that CDKN1C blocks their ability to phosphorylate a glutathione S-transferase-CTD fusion protein in vitro. E2F1 and CDKN1C are found to form stable complexes both in vivo and in vitro. Molecular studies demonstrate that the E2F1-CDKN1C interaction is mediated by two E2F domains. A central E2F1 domain interacts directly with CDKN1C, whereas a C-terminal E2F1 domain interacts with CDKN1C via interaction with Rb. The results presented in this report highlight a novel mechanism of tumor suppression by CDKN1C.

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A Novel Class of Cyclin-dependent Kinase Inhibitors Identified by Molecular Docking Act through a Unique Mechanism

Cited by 19 publications

References 33 publications

Discovery of antimicrobial ribonucleotide reductase inhibitors by screening in microwell format

Discovery of antimicrobial ribonucleotide reductase inhibitors by screening in microwell format

Cyclin-Dependent Kinase Inhibitors as Anticancer Therapeutics

CDKN1C Negatively Regulates RNA Polymerase II C-terminal Domain Phosphorylation in an E2F1-dependent Manner

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