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Targeting Oct1 genomic function inhibits androgen receptor signaling and castration-resistant prostate cancer growth. Oncogene 2016; 35:6350-6358. [PMID: 27270436 DOI: 10.1038/onc.2016.171] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/22/2016] [Accepted: 04/12/2016] [Indexed: 12/25/2022]
Abstract
Androgen receptor (AR) functions as a ligand-dependent transcription factor to regulate its downstream signaling for prostate cancer progression. AR complex formation by multiple transcription factors is important for enhancer activity and transcriptional regulation. However, the significance of such collaborative transcription factors has not been fully understood. In this study, we show that Oct1, an AR collaborative factor, coordinates genome-wide AR signaling for prostate cancer growth. Using global analysis by chromatin immunoprecipitation sequencing (ChIP-seq), we found that Oct1 is recruited to AR-binding enhancer/promoter regions and facilitates androgen signaling. Moreover, a major target of AR/Oct1 complex, acyl-CoA synthetase 3 (ACSL3), contributes to tumor growth in nude mice, and its high expression is associated with poor prognosis in prostate cancer patients. Next, we examined the therapeutic effects of pyrrole-imidazole polyamides that target the Oct1-binding sequence identified in the center of the ACSL3 AR-binding site. We observed that treatment with Oct1 polyamide severely blocked the Oct1 binding at the ACSL3 enhancer responsible for its transcriptional activity and ACSL3 induction. In addition, Oct1 polyamides suppressed castration-resistant tumor growth and specifically repressed global Oct1 chromatin association and androgen signaling in prostate cancer cells, with few nonspecific effects on basal promoter activity. Thus, targeting Oct1 binding could be a novel therapeutic strategy for AR-activated castration-resistant prostate cancer.
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Sawatani Y, Kashiwazaki G, Chandran A, Asamitsu S, Guo C, Sato S, Hashiya K, Bando T, Sugiyama H. Sequence-specific DNA binding by long hairpin pyrrole-imidazole polyamides containing an 8-amino-3,6-dioxaoctanoic acid unit. Bioorg Med Chem 2016; 24:3603-11. [PMID: 27301681 DOI: 10.1016/j.bmc.2016.05.070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 05/28/2016] [Accepted: 05/30/2016] [Indexed: 12/13/2022]
Abstract
With the aim of improving aqueous solubility, we designed and synthesized five N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides capable of recognizing 9-bp sequences. Their DNA-binding affinities and sequence specificities were evaluated by SPR and Bind-n-Seq analyses. The design of polyamide 1 was based on a conventional model, with three consecutive Py or Im rings separated by a β-alanine to match the curvature and twist of long DNA helices. Polyamides 2 and 3 contained an 8-amino-3,6-dioxaoctanoic acid (AO) unit, which has previously only been used as a linker within linear Py-Im polyamides or between Py-Im hairpin motifs for tandem hairpin. It is demonstrated herein that AO also functions as a linker element that can extend to 2-bp in hairpin motifs. Notably, although the AO-containing unit can fail to bind the expected sequence, polyamide 4, which has two AO units facing each other in a hairpin form, successfully showed the expected motif and a KD value of 16nM was recorded. Polyamide 5, containing a β-alanine-β-alanine unit instead of the AO of polyamide 2, was synthesized for comparison. The aqueous solubilities and nuclear localization of three of the polyamides were also examined. The results suggest the possibility of applying the AO unit in the core of Py-Im polyamide compounds.
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Affiliation(s)
- Yoshito Sawatani
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Gengo Kashiwazaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Anandhakumar Chandran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Chuanxin Guo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo, Kyoto 606-8501, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawaoiwakecho, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiyacho, Sakyo, Kyoto 606-8501, Japan.
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Esmaeili M, Jennek S, Ludwig S, Klitzsch A, Kraft F, Melle C, Baniahmad A. The tumor suppressor ING1b is a novel corepressor for the androgen receptor and induces cellular senescence in prostate cancer cells. J Mol Cell Biol 2016; 8:207-20. [PMID: 26993046 DOI: 10.1093/jmcb/mjw007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/10/2015] [Indexed: 12/28/2022] Open
Abstract
The androgen receptor (AR) signaling is critical for prostate cancer (PCa) progression to the castration-resistant stage with poor clinical outcome. Altered function of AR-interacting factors may contribute to castration-resistant PCa (CRPCa). Inhibitor of growth 1 (ING1) is a tumor suppressor that regulates various cellular processes including cell proliferation. Interestingly, ING1 expression is upregulated in senescent primary human prostate cells; however, its role in AR signaling in PCa was unknown. Using a proteomic approach by surface-enhanced laser desorption ionization-mass spectrometry (SELDI-MS) combined with immunological techniques, we provide here evidence that ING1b interacts in vivo with the AR. The interaction was confirmed by co-immunoprecipitation, in vitro GST-pull-down, and quantitative intracellular colocalization analyses. Functionally, ING1b inhibits AR-responsive promoters and endogenous key AR target genes in the human PCa LNCaP cells. Conversely, ING1b knockout (KO) mouse embryonic fibroblasts (MEFs) exhibit enhanced AR activity, suggesting that the interaction with ING1b represses the AR-mediated transcription. Also, data suggest that ING1b expression is downregulated in CRPCa cells compared with androgen-dependent LNCaP cells. Interestingly, its ectopic expression induces cellular senescence and reduces cell migration in both androgen-dependent and CRPCa cells. Intriguingly, ING1b can also inhibit androgen-induced growth in LNCaP cells in a similar manner as AR antagonists. Moreover, ING1b upregulates different cell cycle inhibitors including p27(KIP1), which is a novel target for ING1b. Taken together, our findings reveal a novel corepressor function of ING1b on various AR functions, thereby inhibiting PCa cell growth.
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Affiliation(s)
- Mohsen Esmaeili
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Susanne Jennek
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Susann Ludwig
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | | | - Florian Kraft
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Christian Melle
- Biomolecular Photonics Group, Jena University Hospital, Jena, Germany
| | - Aria Baniahmad
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
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Grabowska MM, Kelly SM, Reese AL, Cates JM, Case TC, Zhang J, DeGraff DJ, Strand DW, Miller NL, Clark PE, Hayward SW, Gronostajski RM, Anderson PD, Matusik RJ. Nfib Regulates Transcriptional Networks That Control the Development of Prostatic Hyperplasia. Endocrinology 2016; 157:1094-109. [PMID: 26677878 PMCID: PMC4769366 DOI: 10.1210/en.2015-1312] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A functional complex consisting of androgen receptor (AR) and forkhead box A1 (FOXA1) proteins supports prostatic development, differentiation, and disease. In addition, the interaction of FOXA1 with cofactors such as nuclear factor I (NFI) family members modulates AR target gene expression. However, the global role of specific NFI family members has yet to be described in the prostate. In these studies, chromatin immunoprecipitation followed by DNA sequencing in androgen-dependent LNCaP prostate cancer cells demonstrated that 64.3% of NFIB binding sites are associated with AR and FOXA1 binding sites. Interrogation of published data revealed that genes associated with NFIB binding sites are predominantly induced after dihydrotestosterone treatment of LNCaP cells, whereas NFIB knockdown studies demonstrated that loss of NFIB drives increased AR expression and superinduction of a subset of AR target genes. Notably, genes bound by NFIB only are associated with cell division and cell cycle. To define the role of NFIB in vivo, mouse Nfib knockout prostatic tissue was rescued via renal capsule engraftment. Loss of Nfib expression resulted in prostatic hyperplasia, which did not resolve in response to castration, and an expansion of an intermediate cell population in a small subset of grafts. In human benign prostatic hyperplasia, luminal NFIB loss correlated with more severe disease. Finally, some areas of intermediate cell expansion were also associated with NFIB loss. Taken together, these results show a fundamental role for NFIB as a coregulator of AR action in the prostate and in controlling prostatic hyperplasia.
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Affiliation(s)
- Magdalena M Grabowska
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Stephen M Kelly
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Amy L Reese
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Justin M Cates
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Tom C Case
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Jianghong Zhang
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - David J DeGraff
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Douglas W Strand
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Nicole L Miller
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Peter E Clark
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Simon W Hayward
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Richard M Gronostajski
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Philip D Anderson
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
| | - Robert J Matusik
- Department of Urologic Surgery (M.M.G., T.C.C., J.Z., N.L.M., P.E.C., S.W.H., R.J.M.), Department of Pathology, Microbiology, and Immunology (J.M.C.), and Vanderbilt-Ingram Cancer Center (P.E.C., R.J.M.), Vanderbilt University Medical Center, Nashville, Tennessee 37232; Department of Biological Sciences (S.M.K., A.L.R., P.D.A.), Salisbury University, Salisbury, Maryland 21801; Department of Pathology (D.J.G.), Penn State University College of Medicine, Hershey, Pennsylvania 17033; Department of Urology (D.W.S.), University of Texas Southwestern Medical Center, Dallas, Texas 75390; Department of Cancer Biology (S.W.H.), NorthShore HealthSystem Research Institute, Evanston, Illinois 60201; Department of Biochemistry, Genetics, Genomics and Bioinformatics Program (R.M.G.), University at Buffalo, Buffalo, New York 14203; and Department of Cell and Developmental Biology (R.J.M.), Vanderbilt University, Nashville, Tennessee 37235
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Erwin GS, Grieshop MP, Bhimsaria D, Eguchi A, Rodríguez-Martínez JA, Ansari AZ. Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin). J Vis Exp 2016:e53510. [PMID: 26863565 DOI: 10.3791/53510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The genome is the target of some of the most effective chemotherapeutics, but most of these drugs lack DNA sequence specificity, which leads to dose-limiting toxicity and many adverse side effects. Targeting the genome with sequence-specific small molecules may enable molecules with increased therapeutic index and fewer off-target effects. N-methylpyrrole/N-methylimidazole polyamides are molecules that can be rationally designed to target specific DNA sequences with exquisite precision. And unlike most natural transcription factors, polyamides can bind to methylated and chromatinized DNA without a loss in affinity. The sequence specificity of polyamides has been extensively studied in vitro with cognate site identification (CSI) and with traditional biochemical and biophysical approaches, but the study of polyamide binding to genomic targets in cells remains elusive. Here we report a method, the crosslinking of small molecules to isolate chromatin (COSMIC), that identifies polyamide binding sites across the genome. COSMIC is similar to chromatin immunoprecipitation (ChIP), but differs in two important ways: (1) a photocrosslinker is employed to enable selective, temporally-controlled capture of polyamide binding events, and (2) the biotin affinity handle is used to purify polyamide-DNA conjugates under semi-denaturing conditions to decrease DNA that is non-covalently bound. COSMIC is a general strategy that can be used to reveal the genome-wide binding events of polyamides and other genome-targeting chemotherapeutic agents.
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Affiliation(s)
- Graham S Erwin
- Department of Biochemistry, University of Wisconsin-Madison
| | | | - Devesh Bhimsaria
- Department of Biochemistry, University of Wisconsin-Madison; Department of Electrical and Computer Engineering, University of Wisconsin-Madison
| | - Asuka Eguchi
- Graduate Program in Cellular and Molecular Biology, University of Wisconsin-Madison
| | | | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin-Madison; The Genome Center, University of Wisconsin-Madison;
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56
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Han YW, Sugiyama H, Harada Y. The application of fluorescence-conjugated pyrrole/imidazole polyamides in the characterization of protein–DNA complex formation. Biomater Sci 2016; 4:391-9. [DOI: 10.1039/c5bm00214a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescent conjugates of Py–Im polyamides are used as sequence-specific fluorescent probes and applied to the characterisation of protein–DNA complex dynamics.
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Affiliation(s)
- Yong-Woon Han
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
- Department of Chemistry
| | - Yoshie Harada
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
- Graduate School of Biostudies
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57
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Szablowski JO, Raskatov JA, Dervan PB. An HRE-Binding Py-Im Polyamide Impairs Hypoxic Signaling in Tumors. Mol Cancer Ther 2015; 15:608-17. [PMID: 26719577 DOI: 10.1158/1535-7163.mct-15-0719] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 12/11/2015] [Indexed: 12/16/2022]
Abstract
Hypoxic gene expression contributes to the pathogenesis of many diseases, including organ fibrosis, age-related macular degeneration, and cancer. Hypoxia-inducible factor-1 (HIF1), a transcription factor central to the hypoxic gene expression, mediates multiple processes including neovascularization, cancer metastasis, and cell survival. Pyrrole-imidazole polyamide 1: has been shown to inhibit HIF1-mediated gene expression in cell culture but its activity in vivo was unknown. This study reports activity of polyamide 1: in subcutaneous tumors capable of mounting a hypoxic response and showing neovascularization. We show that 1: distributes into subcutaneous tumor xenografts and normal tissues, reduces the expression of proangiogenic and prometastatic factors, inhibits the formation of new tumor blood vessels, and suppresses tumor growth. Tumors treated with 1: show no increase in HIF1α and have reduced ability to adapt to the hypoxic conditions, as evidenced by increased apoptosis in HIF1α-positive regions and the increased proximity of necrotic regions to vasculature. Overall, these results show that a molecule designed to block the transcriptional activity of HIF1 has potent antitumor activity in vivo, consistent with partial inhibition of the tumor hypoxic response. Mol Cancer Ther; 15(4); 608-17. ©2015 AACR.
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Affiliation(s)
- Jerzy O Szablowski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Jevgenij A Raskatov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California.
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Fang L, Pan Z, Cullis PM, Burley GA, Su W. Pyrrole-Imidazole Polyamides: Automated Solid-Phase Synthesis. ACTA ACUST UNITED AC 2015; 63:8.11.1-8.11.14. [PMID: 26623976 DOI: 10.1002/0471142700.nc0811s63] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this unit, the fully automated solid-phase synthetic strategy of hairpin Py-Im polyamides is described using triphosgene (BTC) as a coupling agent. This automated methodology is compatible with all the typical building blocks, enabling the facile synthesis of polyamide libraries in 9% to 20% yield in 3 days.
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Affiliation(s)
- Lijing Fang
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, People's Republic of China
| | - Zhengyin Pan
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, People's Republic of China
| | - Paul M Cullis
- Department of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Wu Su
- Guangdong Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, People's Republic of China
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59
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Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide. PLoS One 2015; 10:e0143161. [PMID: 26571387 PMCID: PMC4646452 DOI: 10.1371/journal.pone.0143161] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 11/02/2015] [Indexed: 12/21/2022] Open
Abstract
Pyrrole-imidazole (Py-Im) polyamides are high affinity DNA-binding small molecules that can inhibit protein-DNA interactions. In VCaP cells, a human prostate cancer cell line overexpressing both AR and the TMPRSS2-ERG gene fusion, an androgen response element (ARE)-targeted Py-Im polyamide significantly downregulates AR driven gene expression. Polyamide exposure to VCaP cells reduced proliferation without causing DNA damage. Py-Im polyamide treatment also reduced tumor growth in a VCaP mouse xenograft model. In addition to the effects on AR regulated transcription, RNA-seq analysis revealed inhibition of topoisomerase-DNA binding as a potential mechanism that contributes to the antitumor effects of polyamides in cell culture and in xenografts. These studies support the therapeutic potential of Py-Im polyamides to target multiple aspects of transcriptional regulation in prostate cancers without genotoxic stress.
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61
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Mishra R, Watanabe T, Kimura MT, Koshikawa N, Ikeda M, Uekusa S, Kawashima H, Wang X, Igarashi J, Choudhury D, Grandori C, Kemp CJ, Ohira M, Verma NK, Kobayashi Y, Takeuchi J, Koshinaga T, Nemoto N, Fukuda N, Soma M, Kusafuka T, Fujiwara K, Nagase H. Identification of a novel E-box binding pyrrole-imidazole polyamide inhibiting MYC-driven cell proliferation. Cancer Sci 2015; 106:421-9. [PMID: 25611295 PMCID: PMC4406810 DOI: 10.1111/cas.12610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/09/2015] [Accepted: 01/11/2015] [Indexed: 12/23/2022] Open
Abstract
The MYC transcription factor plays a crucial role in the regulation of cell cycle progression, apoptosis, angiogenesis, and cellular transformation. Due to its oncogenic activities and overexpression in a majority of human cancers, it is an interesting target for novel drug therapies. MYC binding to the E-box (5'-CACGTGT-3') sequence at gene promoters contributes to more than 4000 MYC-dependent transcripts. Owing to its importance in MYC regulation, we designed a novel sequence-specific DNA-binding pyrrole-imidazole (PI) polyamide, Myc-5, that recognizes the E-box consensus sequence. Bioinformatics analysis revealed that the Myc-5 binding sequence appeared in 5'- MYC binding E-box sequences at the eIF4G1, CCND1, and CDK4 gene promoters. Furthermore, ChIP coupled with detection by quantitative PCR indicated that Myc-5 has the ability to inhibit MYC binding at the target gene promoters and thus cause downregulation at the mRNA level and protein expression of its target genes in human Burkitt's lymphoma model cell line, P493.6, carrying an inducible MYC repression system and the K562 (human chronic myelogenous leukemia) cell line. Single i.v. injection of Myc-5 at 7.5 mg/kg dose caused significant tumor growth inhibition in a MYC-dependent tumor xenograft model without evidence of toxicity. We report here a compelling rationale for the identification of a PI polyamide that inhibits a part of E-box-mediated MYC downstream gene expression and is a model for showing that phenotype-associated MYC downstream gene targets consequently inhibit MYC-dependent tumor growth.
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Affiliation(s)
- Rajeev Mishra
- Division of Cancer Genetics, Department of Advanced Medical Science, Nihon University Research Institute of Medical Science, Tokyo, Japan; Department of Medicine, Cedars-Sinai Medical Center, Samuel Oschin Comprehensive Cancer Institute, Los Angeles, California, USA
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62
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Androgen receptor: structure, role in prostate cancer and drug discovery. Acta Pharmacol Sin 2015; 36:3-23. [PMID: 24909511 PMCID: PMC4571323 DOI: 10.1038/aps.2014.18] [Citation(s) in RCA: 541] [Impact Index Per Article: 60.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/05/2014] [Indexed: 12/15/2022] Open
Abstract
Androgens and androgen receptors (AR) play a pivotal role in expression of the male phenotype. Several diseases, such as androgen insensitivity syndrome (AIS) and prostate cancer, are associated with alterations in AR functions. Indeed, androgen blockade by drugs that prevent the production of androgens and/or block the action of the AR inhibits prostate cancer growth. However, resistance to these drugs often occurs after 2–3 years as the patients develop castration-resistant prostate cancer (CRPC). In CRPC, a functional AR remains a key regulator. Early studies focused on the functional domains of the AR and its crucial role in the pathology. The elucidation of the structures of the AR DNA binding domain (DBD) and ligand binding domain (LBD) provides a new framework for understanding the functions of this receptor and leads to the development of rational drug design for the treatment of prostate cancer. An overview of androgen receptor structure and activity, its actions in prostate cancer, and how structural information and high-throughput screening have been or can be used for drug discovery are provided herein.
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63
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Fang L, Yao G, Pan Z, Wu C, Wang HS, Burley GA, Su W. Fully Automated Synthesis of DNA-Binding Py-Im Polyamides Using a Triphosgene Coupling Strategy. Org Lett 2014; 17:158-61. [DOI: 10.1021/ol503388a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lijing Fang
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Guiyang Yao
- Key Laboratory for the Chemistry and Molecular Engineer of Medicinal Resources, School of Chemistry & Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, P. R. China
| | - Zhengyin Pan
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Chunlei Wu
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
| | - Heng-Shan Wang
- Key Laboratory for the Chemistry and Molecular Engineer of Medicinal Resources, School of Chemistry & Pharmaceutical Sciences of Guangxi Normal University, Guilin 541004, P. R. China
| | - Glenn A Burley
- Department of Pure & Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Wu Su
- Guangdong
Key Laboratory of Nanomedicine, Institute of Biomedicine and Biotechnology,
Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, P. R. China
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64
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Anandhakumar C, Kizaki S, Bando T, Pandian GN, Sugiyama H. Advancing Small-Molecule-Based Chemical Biology with Next-Generation Sequencing Technologies. Chembiochem 2014; 16:20-38. [DOI: 10.1002/cbic.201402556] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Indexed: 12/24/2022]
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65
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Obinata D, Fujiwara K, Yamaguchi K, Takayama KI, Urano T, Nagase H, Inoue S, Takahashi S, Fukuda N. Review of novel therapeutic medicines targeting androgen signaling in castration-resistant prostate cancer. World J Clin Urol 2014; 3:264-271. [DOI: 10.5410/wjcu.v3.i3.264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/26/2014] [Accepted: 07/29/2014] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer is the most common male malignant neoplasm. Androgens and the androgen receptor (AR) play a key role in the onset and progression of prostate cancer. The expression of the AR is still preserved in the majority of patients with castration-resistant prostate cancer (CRPC). CRPC is considered to be induced by the following mechanisms: (1) sustained AR activation by enhancing intracellular conversion of adrenal androgens to dehydrotestosterone via a de novo route; (2) AR hypersensitivity; (3) promiscuous activation of AR signaling; and (4) outlaw pathways. Recent advances in the treatment of CRPC include novel medicines targeting AR signaling pathways. In addition, functional molecular studies have shown that some of the AR-regulated genes and AR coregulators are prognostic markers and potential therapeutic targets for prostate cancer, particularly in the castration-resistant state. Therefore, identification of the AR signaling pathways responsible for establishment of CRPC is critical for developing new strategies for the treatment of CRPC.
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66
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Liang S, Bian X, Liang D, Sivils JC, Neckers LM, Cox MB, Xie H. Solution formulation development and efficacy of MJC13 in a preclinical model of castration-resistant prostate cancer. Pharm Dev Technol 2014; 21:121-6. [PMID: 25380396 DOI: 10.3109/10837450.2014.979946] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MJC13, a novel FKBP52 targeting agent, has potential use for the treatment of castration-resistant prostate cancer. The purpose of this work was to develop a solution formulation of MJC13, and obtain its efficacy profile in a human prostate cancer xenograft mouse model. Preformulation studies were conducted to evaluate the physicochemical properties. Co-solvent systems were evaluated for aqueous solubility and tolerance. A human prostate cancer xenograft mouse model was established by growing 22Rv1 prostate cancer cells in C.B-17 SCID mice. The optimal formulation was used to study the efficacy of MJC13 in this preclinical model of castrate-resistant prostate cancer. We found that MJC13 was stable (at least for 1 month), highly lipophilic (logP = 6.49), poorly soluble in water (0.28 µg/mL), and highly plasma protein bound (>98%). The optimal formulation consisting of PEG 400 and Tween 80 (1:1, v/v) allowed us to achieve a MJC13 concentration of 7.5 mg/mL, and tolerated an aqueous environment. After twice weekly intratumoral injection with 10 mg/kg MJC13 in this formulation for four consecutive weeks, tumor volumes were significantly reduced compared to vehicle-treated controls.
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Affiliation(s)
- Su Liang
- a Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences , Texas Southern University , Houston , TX , USA
| | - Xiaomei Bian
- a Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences , Texas Southern University , Houston , TX , USA
| | - Dong Liang
- a Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences , Texas Southern University , Houston , TX , USA
| | - Jeffrey C Sivils
- b Department of Biological Sciences, Border Biomedical Research Center , University of Texas at El Paso , El Paso , TX , USA , and
| | - Leonard M Neckers
- c Urologic Oncology Branch , National Cancer Institute , Bethesda , MD , USA
| | - Marc B Cox
- b Department of Biological Sciences, Border Biomedical Research Center , University of Texas at El Paso , El Paso , TX , USA , and
| | - Huan Xie
- a Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences , Texas Southern University , Houston , TX , USA
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67
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Raskatov JA, Szablowski JO, Dervan PB. Tumor xenograft uptake of a pyrrole-imidazole (Py-Im) polyamide varies as a function of cell line grafted. J Med Chem 2014; 57:8471-6. [PMID: 25238175 PMCID: PMC4207538 DOI: 10.1021/jm500964c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
Subcutaneous
xenografts represent a popular approach to evaluate
efficacy of prospective molecular therapeutics in vivo. In the present study, the C-14 labeled radioactive pyrrole–imidazole
(Py-Im) polyamide 1, targeted to the 5′-WGWWCW-3′
DNA sequence, was evaluated with regard to its uptake properties in
subcutaneous xenografts, derived from the human tumor cell lines LNCaP
(prostate), A549 (lung), and U251 (brain), respectively. Significant
variation in compound tumor concentrations was seen in xenografts
derived from these three cell lines. Influence of cell line grafted
on systemic polyamide elimination was established. With A549, a marked
variation in localization of 1 was determined between
Matrigel-negative and -positive xenografts. An extensive tissue distribution
analysis of 1 in wild-type animals was conducted, enabling
the comparison between the xenografts and the corresponding host organs
of origin.
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Affiliation(s)
- Jevgenij A Raskatov
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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68
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Martínez TF, Phillips JW, Karanja KK, Polaczek P, Wang CM, Li BC, Campbell JL, Dervan PB. Replication stress by Py-Im polyamides induces a non-canonical ATR-dependent checkpoint response. Nucleic Acids Res 2014; 42:11546-59. [PMID: 25249630 PMCID: PMC4191428 DOI: 10.1093/nar/gku866] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Pyrrole–imidazole polyamides targeted to the androgen response element were cytotoxic in multiple cell lines, independent of intact androgen receptor signaling. Polyamide treatment induced accumulation of S-phase cells and of PCNA replication/repair foci. Activation of a cell cycle checkpoint response was evidenced by autophosphorylation of ATR, the S-phase checkpoint kinase, and by recruitment of ATR and the ATR activators RPA, 9-1-1, and Rad17 to chromatin. Surprisingly, ATR activation was accompanied by only a slight increase in single-stranded DNA, and the ATR targets RPA2 and Chk1, a cell cycle checkpoint kinase, were not phosphorylated. However, ATR activation resulted in phosphorylation of the replicative helicase subunit MCM2, an ATR effector. Polyamide treatment also induced accumulation of monoubiquitinated FANCD2, which is recruited to stalled replication forks and interacts transiently with phospho-MCM2. This suggests that polyamides induce replication stress that ATR can counteract independently of Chk1 and that the FA/BRCA pathway may also be involved in the response to polyamides. In biochemical assays, polyamides inhibit DNA helicases, providing a plausible mechanism for S-phase inhibition.
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Affiliation(s)
- Thomas F Martínez
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - John W Phillips
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Kenneth K Karanja
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Piotr Polaczek
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chieh-Mei Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Benjamin C Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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69
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Obinata D, Ito A, Fujiwara K, Takayama KI, Ashikari D, Murata Y, Yamaguchi K, Urano T, Fujimura T, Fukuda N, Soma M, Watanabe T, Nagase H, Inoue S, Takahashi S. Pyrrole-imidazole polyamide targeted to break fusion sites in TMPRSS2 and ERG gene fusion represses prostate tumor growth. Cancer Sci 2014; 105:1272-8. [PMID: 25088707 PMCID: PMC4462350 DOI: 10.1111/cas.12493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Revised: 07/18/2014] [Accepted: 07/23/2014] [Indexed: 12/29/2022] Open
Abstract
Aberrant overexpression of ERG induced by the TMPRSS2-ERG gene fusion is likely involved in the development of prostate cancer. Synthetic pyrrole–imidazole (PI) polyamides recognize and attach to the minor groove of DNA with high affinity and specificity. In the present study, we designed a PI polyamide targeting TMPRSS2-ERG translocation breakpoints and assessed its effect on human prostate cancer cells. Our study identified that this PI polyamide repressed the cell and tumor growth of androgen-sensitive LNCaP prostate cancer cells. Targeting of these breakpoint sequences by PI polyamides could be a novel approach for the treatment of prostate cancer.
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Affiliation(s)
- Daisuke Obinata
- Department of Urology, Nihon University School of Medicine, Tokyo, Japan; Department of Anti-Aging Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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70
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Syed J, Pandian GN, Sato S, Taniguchi J, Chandran A, Hashiya K, Bando T, Sugiyama H. Targeted suppression of EVI1 oncogene expression by sequence-specific pyrrole-imidazole polyamide. ACTA ACUST UNITED AC 2014; 21:1370-1380. [PMID: 25219965 DOI: 10.1016/j.chembiol.2014.07.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/11/2014] [Accepted: 07/15/2014] [Indexed: 01/13/2023]
Abstract
Human ectopic viral integration site 1 (EVI1) is an oncogenic transcription factor known to play a critical role in many aggressive forms of cancer. Its selective modulation is thought to alter the cancer-specific gene regulatory networks. Pyrrole-imidazole polyamides (PIPs) are a class of small DNA binders that can be designed to target any destined DNA sequence. Herein, we report a sequence-specific pyrrole-imidazole polyamide, PIP1, which can target specific base pairs of the REL/ELK1 binding site in the EVI1 minimal promoter. The designed PIP1 significantly inhibited EVI1 in MDA-MB-231 cells. Whole-transcriptome analysis confirmed that PIP1 affected a fraction of EVI1-mediated gene regulation. In vitro assays suggested that this polyamide can also effectively inhibit breast cancer cell migration. Taken together, these results suggest that EVI1-targeted PIP1 is an effective transcriptional regulator in cancer cells.
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Affiliation(s)
- Junetha Syed
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Ganesh N Pandian
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Shinsuke Sato
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Junichi Taniguchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Anandhakumar Chandran
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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71
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Nagle PS, McKeever C, Rodriguez F, Nguyen B, Wilson WD, Rozas I. Unexpected DNA affinity and sequence selectivity through core rigidity in guanidinium-based minor groove binders. J Med Chem 2014; 57:7663-72. [PMID: 25158031 DOI: 10.1021/jm5008006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this paper we report the design and biophysical evaluation of novel rigid-core symmetric and asymmetric dicationic DNA binders containing 9H-fluorene and 9,10-dihydroanthracene cores as well as the synthesis of one of these fluorene derivatives. First, the affinity toward particular DNA sequences of these compounds and flexible core derivatives was evaluated by means of surface plasmon resonance and thermal denaturation experiments finding that the position of the cations significantly influence the binding strength. Then their affinity and mode of binding were further studied by performing circular dichroism and UV studies and the results obtained were rationalized by means of DFT calculations. We found that the fluorene derivatives prepared have the ability to bind to the minor groove of certain DNA sequences and intercalate to others, whereas the dihydroanthracene compounds bind via intercalation to all the DNA sequences studied here.
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Affiliation(s)
- Padraic S Nagle
- School of Chemistry, Trinity College Dublin , Dublin 2, Ireland
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72
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Li H, Ban F, Dalal K, Leblanc E, Frewin K, Ma D, Adomat H, Rennie PS, Cherkasov A. Discovery of small-molecule inhibitors selectively targeting the DNA-binding domain of the human androgen receptor. J Med Chem 2014; 57:6458-67. [PMID: 25062331 DOI: 10.1021/jm500802j] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The human androgen receptor (AR) is considered as a master regulator in the development and progression of prostate cancer (PCa). As resistance to clinically used anti-AR drugs remains a major challenge for the treatment of advanced PCa, there is a pressing need for new anti-AR therapeutic avenues. In this study, we identified a binding site on the DNA binding domain (DBD) of the receptor and utilized virtual screening to discover a set of micromolar hits for the target. Through further exploration of the most potent hit (1), a structural analogue (6) was identified demonstrating 10-fold improved anti-AR potency. Further optimization resulted in a more potent synthetic analogue (25) with anti-AR potency comparable to a newly FDA-approved drug Enzalutamide. Site-directed mutagenesis demonstrated that the developed inhibitors do interact with the intended target site. Importantly, the AR DBD inhibitors could effectively inhibit the growth of Enzalutamide-resistant cells as well as block the transcriptional activity of constitutively active AR splice variants, such as V7.
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Affiliation(s)
- Huifang Li
- Vancouver Prostate Centre, University of British Columbia , 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
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73
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Dalal K, Roshan-Moniri M, Sharma A, Li H, Ban F, Hessein M, Hsing M, Singh K, LeBlanc E, Dehm S, Tomlinson Guns ES, Cherkasov A, Rennie PS. Selectively targeting the DNA-binding domain of the androgen receptor as a prospective therapy for prostate cancer. J Biol Chem 2014; 289:26417-26429. [PMID: 25086042 DOI: 10.1074/jbc.m114.553818] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The androgen receptor (AR) is a transcription factor that has a pivotal role in the occurrence and progression of prostate cancer. The AR is activated by androgens that bind to its ligand-binding domain (LBD), causing the transcription factor to enter the nucleus and interact with genes via its conserved DNA-binding domain (DBD). Treatment for prostate cancer involves reducing androgen production or using anti-androgen drugs to block the interaction of hormones with the AR-LBD. Eventually the disease changes into a castration-resistant form of PCa where LBD mutations render anti-androgens ineffective or where constitutively active AR splice variants, lacking the LBD, become overexpressed. Recently, we identified a surfaced exposed pocket on the AR-DBD as an alternative drug-target site for AR inhibition. Here, we demonstrate that small molecules designed to selectively bind the pocket effectively block transcriptional activity of full-length and splice variant AR forms at low to sub-micromolar concentrations. The inhibition is lost when residues involved in drug interactions are mutated. Furthermore, the compounds did not impede nuclear localization of the AR and blocked interactions with chromatin, indicating the interference of DNA binding with the nuclear form of the transcription factor. Finally, we demonstrate the inhibition of gene expression and tumor volume in mouse xenografts. Our results indicate that the AR-DBD has a surface site that can be targeted to inhibit all forms of the AR, including enzalutamide-resistant and constitutively active splice variants and thus may serve as a potential avenue for the treatment of recurrent and metastatic prostate cancer.
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Affiliation(s)
- Kush Dalal
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and.
| | - Mani Roshan-Moniri
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and
| | - Aishwariya Sharma
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and
| | - Huifang Li
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and
| | - Fuqiang Ban
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and
| | - Mohamed Hessein
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and
| | - Michael Hsing
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and
| | - Kriti Singh
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and
| | - Eric LeBlanc
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and
| | - Scott Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455
| | - Emma S Tomlinson Guns
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and
| | - Paul S Rennie
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H 3Z6, Canada and
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74
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O'Sullivan P, Rozas I. Understanding the guanidine-like cationic moiety for optimal binding into the DNA minor groove. ChemMedChem 2014; 9:2065-73. [PMID: 25087855 DOI: 10.1002/cmdc.201402264] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Indexed: 01/01/2023]
Abstract
Based on our previous positive results with bis-guanidine-like diaromatic compounds as DNA minor groove binders, we propose a new family: bis-2-amino-1,4,5,6-tetrahydropyrimidines. According to calculated parameters, these dicationic systems would have a more suitable size and lipophilicity for binding into the minor groove than previous series. Moreover, their DFT-optimised structures and docking into an AT oligomer model show that they would bind in the minor groove with good strength and without energy penalty. Hence, we prepared compounds 4 a-c and evaluated their binding to ssDNA and poly(dA-dT)2 by thermal denaturation experiments. The results showed that 4 a (CO) and 4 d (NH) were the best DNA binders. Compared to the previous series, 4 a-d are better binders than bis-guanidiniums but poorer than bis-2-aminoimidazolinium derivatives. Moreover, circular dichroism experiments using ssDNA and poly(dA-dT)2 confirmed binding into the minor groove. Based on our computational design as well as biophysical studies, we have been able to determine that the optimal interaction of guanidine-like dications in the minor grove occurs with bis-2-aminoimidazolinium systems.
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Affiliation(s)
- Patrick O'Sullivan
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College, University of Dublin, 152-160 Pearse St., Dublin 2 (Ireland)
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75
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Soares JA, Kiessling LL. A symposium in honor of Peter B. Dervan, the 2014 ACS Chemical Biology Lectureship Award Winner. ACS Chem Biol 2014; 9:1221-3. [PMID: 25120068 DOI: 10.1021/cb5003703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jitesh A Soares
- Department of Chemistry, University of Wisconsin, Madition , 433 Babcock Drive, Madison, Wisconsin 53706-1544, United States
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76
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Raskatov JA, Puckett JW, Dervan PB. A C-14 labeled Py-Im polyamide localizes to a subcutaneous prostate cancer tumor. Bioorg Med Chem 2014; 22:4371-5. [PMID: 24780272 DOI: 10.1016/j.bmc.2014.04.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/06/2014] [Indexed: 02/08/2023]
Abstract
In an effort to quantitate Py-Im polyamide concentrations in vivo, we synthesized the C-14 radioactively labeled compounds 1-3, and investigated their tumor localization in a subcutaneous xenograft model of prostate cancer (LNCaP). Tumor concentrations were compared with representative host tissues, and exhibited a certain degree of preferential localization to the xenograft. Compound accumulation upon repeated administration was measured. Py-Im polyamide 1 was found to accumulate in LNCaP tumors at concentrations similar to the IC50 value for this compound in cell culture experiments.
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Affiliation(s)
- Jevgenij A Raskatov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - James W Puckett
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, United States.
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77
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Yu Y, Zhang Y, Guan W, Huang T, Kang J, Sheng X, Qi J. Androgen receptor promotes the oncogenic function of overexpressed Jagged1 in prostate cancer by enhancing cyclin B1 expression via Akt phosphorylation. Mol Cancer Res 2014; 12:830-42. [PMID: 24574517 DOI: 10.1158/1541-7786.mcr-13-0545] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED The Jagged1, a Notch signaling pathway ligand, had been shown to have a positive correlation with prostate cancer development. Our study for Jagged1 expression in 218 prostate cancer tissue samples also supports this conclusion. However, the detailed molecular mechanism of Jagged1 in promoting the progression of prostate cancer is still unclear. Through cell proliferation examination, androgen receptor (AR) was found to promote the oncogenic function of Jagged1 to enhance the cell proliferation rate by comparing four prostate cancer cell lines, LNCaP, LAPC4, DU145, and PC3, which was further validated through analyzing the survival of 118 patients treated with androgen-deprivation therapy (ADT) with different expression levels of Jagged1 and AR. More importantly, our data showed that Jagged1 combined with AR could increase the phosphorylation level of Akt and, in turn, phosphorylated Akt plays an important role in regulating the expression level of cyclin B1 by interacting with AR and increasing the transcriptional activity of AR. These data indicate that prostate cancer progression regulated by Jagged1 can be dramatically enhanced by combining with AR through promoting Akt activity. IMPLICATIONS This study could benefit our clinical treatments for patients with prostate cancer with overexpressed Jagged1 by targeting AR and Akt.
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Affiliation(s)
| | | | - Wenbin Guan
- Pathology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tao Huang
- Authors' Affiliations: Departments of Urology
| | - Jian Kang
- Authors' Affiliations: Departments of Urology
| | - Xujun Sheng
- Authors' Affiliations: Departments of Urology
| | - Jun Qi
- Authors' Affiliations: Departments of Urology,
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78
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Han YW, Tsunaka Y, Yokota H, Matsumoto T, Kashiwazaki G, Morinaga H, Hashiya K, Bando T, Sugiyama H, Harada Y. Construction and characterization of Cy3- or Cy5-conjugated hairpin pyrrole–imidazole polyamides binding to DNA in the nucleosome. Biomater Sci 2014; 2:297-307. [DOI: 10.1039/c3bm60202h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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79
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Chan SC, Dehm SM. Constitutive activity of the androgen receptor. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2014; 70:327-66. [PMID: 24931201 DOI: 10.1016/b978-0-12-417197-8.00011-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Prostate cancer (PCa) is the most frequently diagnosed cancer in the United States. The androgen receptor (AR) signaling axis is central to all stages of PCa pathophysiology and serves as the main target for endocrine-based therapy. The most advanced stage of the disease, castration-resistant prostate cancer (CRPC), is presently incurable and accounts for most PCa mortality. In this chapter, we highlight the mechanisms by which the AR signaling axis can bypass endocrine-targeted therapies and drive progression of CRPC. These mechanisms include alterations in growth factor, cytokine, and inflammatory signaling pathways, altered expression or activity of transcriptional coregulators, AR point mutations, and AR gene amplification leading to AR protein overexpression. Additionally, we will discuss the mechanisms underlying the synthesis of constitutively active AR splice variants (AR-Vs) lacking the COOH-terminal ligand-binding domain, as well as the role and regulation of AR-Vs in supporting therapeutic resistance in CRPC. Finally, we summarize the ongoing development of inhibitors targeting discrete AR functional domains as well as the status of new biomarkers for monitoring the AR signaling axis in patients.
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Affiliation(s)
- Siu Chiu Chan
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA.
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80
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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81
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Yang F, Nickols NG, Li BC, Szablowski JO, Hamilton SR, Meier JL, Wang CM, Dervan PB. Animal toxicity of hairpin pyrrole-imidazole polyamides varies with the turn unit. J Med Chem 2013; 56:7449-57. [PMID: 24015881 PMCID: PMC3788622 DOI: 10.1021/jm401100s] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
A hairpin
pyrrole-imidazole polyamide (1) targeted
to the androgen receptor consensus half-site was found to exert antitumor
effects against prostate cancer xenografts. A previous animal study
showed that 1, which has a chiral amine at the α-position
of the γ-aminobutyric acid turn (γ-turn), did not exhibit
toxicity at doses less than 10 mg/kg. In the same study, a polyamide
with an acetamide at the β-position of the γ-turn resulted
in animal morbidity at 2.3 mg/kg. To identify structural motifs that
cause animal toxicity, we synthesized polyamides 1–4 with variations at the α- and β-positions in
the γ-turn. Weight loss, histopathology, and serum chemistry
were analyzed in mice post-treatment. While serum concentration was
similar for all four polyamides after injection, dose-limiting liver
toxicity was only observed for three polyamides. Polyamide 3, with an α-acetamide, caused no significant evidence of rodent
toxicity and retains activity against LNCaP xenografts.
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Affiliation(s)
- Fei Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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82
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Effect of single pyrrole replacement with β-alanine on DNA binding affinity and sequence specificity of hairpin pyrrole/imidazole polyamides targeting 5′-GCGC-3′. Bioorg Med Chem 2013; 21:5436-41. [DOI: 10.1016/j.bmc.2013.06.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 12/27/2022]
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83
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Singh PK, Nath S. Molecular Recognition Controlled Delivery of a Small Molecule from a Nanocarrier to Natural DNA. J Phys Chem B 2013; 117:10370-5. [DOI: 10.1021/jp402902k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Prabhat K. Singh
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
| | - Sukhendu Nath
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400 085, India
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84
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Suppression of tumor and metastasis progression through the scaffolding functions of SSeCKS/Gravin/AKAP12. Cancer Metastasis Rev 2013; 31:493-500. [PMID: 22684366 DOI: 10.1007/s10555-012-9360-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Scaffolding proteins such as SSeCKS/Gravin/AKAP12 ("AKAP12") are thought to control oncogenic signaling pathways by regulating key mediators in a spatiotemporal manner. The downregulation of AKAP12 in many human cancers, often associated with promoter hypermethylation, or the loss of its locus at 6q24-25.2, correlates with progression to malignancy and metastasis. The forced re-expression of AKAP12 in cancer cell lines suppresses in vitro parameters of oncogenic growth, invasiveness, and cell motility through its ability to scaffold protein kinase C (PKC), F-actin, cyclins, Src, and phosphoinositides, and possibly through additional scaffolding domains for PKA, calmodulin, β1,4-galactosyltransferase-polypeptide-1, β2-adrenergic receptors, and cAMP-specific 3',5'-cyclic phosphodiesterase 4D. Moreover, AKAP12 re-expression in tumor models results in metastasis suppression through the inhibition of Src-regulated, VEGF-mediated neovascularization at distal sites. The current review will describe the emerging understanding of how AKAP12 regulates cellular senescence and oncogenic progression at the level of tumor cells and tumor-associated microenvironment via its multiple scaffolding functions.
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85
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Lallous N, Dalal K, Cherkasov A, Rennie PS. Targeting alternative sites on the androgen receptor to treat castration-resistant prostate cancer. Int J Mol Sci 2013; 14:12496-519. [PMID: 23771019 PMCID: PMC3709796 DOI: 10.3390/ijms140612496] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 05/29/2013] [Accepted: 06/03/2013] [Indexed: 01/22/2023] Open
Abstract
Recurrent, metastatic prostate cancer continues to be a leading cause of cancer-death in men. The androgen receptor (AR) is a modular, ligand-inducible transcription factor that regulates the expression of genes that can drive the progression of this disease, and as a consequence, this receptor is a key therapeutic target for controlling prostate cancer. The current drugs designed to directly inhibit the AR are called anti-androgens, and all act by competing with androgens for binding to the androgen/ligand binding site. Unfortunately, with the inevitable progression of the cancer to castration resistance, many of these drugs become ineffective. However, there are numerous other regulatory sites on this protein that have not been exploited therapeutically. The regulation of AR activity involves a cascade of complex interactions with numerous chaperones, co-factors and co-regulatory proteins, leading ultimately to direct binding of AR dimers to specific DNA androgen response elements within the promoter and enhancers of androgen-regulated genes. As part of the family of nuclear receptors, the AR is organized into modular structural and functional domains with specialized roles in facilitating their inter-molecular interactions. These regions of the AR present attractive, yet largely unexploited, drug target sites for reducing or eliminating androgen signaling in prostate cancers. The design of small molecule inhibitors targeting these specific AR domains is only now being realized and is the culmination of decades of work, including crystallographic and biochemistry approaches to map the shape and accessibility of the AR surfaces and cavities. Here, we review the structure of the AR protein and describe recent advancements in inhibiting its activity with small molecules specifically designed to target areas distinct from the receptor’s androgen binding site. It is anticipated that these new classes of anti-AR drugs will provide an additional arsenal to treat castration-resistant prostate cancer.
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Affiliation(s)
- Nada Lallous
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
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86
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Abstract
Androgenic steroids are important for male development in utero and secondary sexual characteristics at puberty. In addition, androgens play a role in non-reproductive tissues, such as bone and muscle in both sexes. The actions of the androgens testosterone and dihydrotestosterone are mediated by a single receptor protein, the androgen receptor. Over the last 60–70 years there has been considerable research interest in the development of inhibitors of androgen receptor for the management of diseases such as prostate cancer. However, more recently, there is also a growing appreciation of the need for selective androgen modulators that would demonstrate tissue-selective agonist or antagonist activity. The chemistry and biology of selective agonists, antagonists and selective androgen receptor modulators will be discussed in this review.
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87
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Xeno-oestrogens bisphenol a and diethylstilbestrol selectively activating androgen receptor mediated AREs-TATA reporter system. Chem Res Chin Univ 2013. [DOI: 10.1007/s40242-013-2248-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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88
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Sheng J, Gan J, Huang Z. Structure-based DNA-targeting strategies with small molecule ligands for drug discovery. Med Res Rev 2013; 33:1119-73. [PMID: 23633219 DOI: 10.1002/med.21278] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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89
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Salvia MV, Addison F, Alniss HY, Buurma NJ, Khalaf AI, Mackay SP, Anthony NG, Suckling CJ, Evstigneev MP, Santiago AH, Waigh RD, Parkinson JA. Thiazotropsin aggregation and its relationship to molecular recognition in the DNA minor groove. Biophys Chem 2013; 179:1-11. [PMID: 23714424 DOI: 10.1016/j.bpc.2013.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 04/19/2013] [Accepted: 04/19/2013] [Indexed: 11/29/2022]
Abstract
Aggregated states have been alluded to for many DNA minor groove binders but details of the molecule-on-molecule relationship have either been under-reported or ignored. Here we report our findings from ITC and NMR measurements carried out with AIK-18/51, a compound representative of the thiazotropsin class of DNA minor groove binders. The free aqueous form of AIK-18/51 is compared with that found in its complex with cognate DNA duplex d(CGACTAGTCG)2. Molecular self-association of AIK-18/51 is consistent with anti-parallel, face-to-face dimer formation, the building block on which the molecule aggregates. This underlying structure is closely allied to the form found in the ligand's DNA complex. NMR chemical shift and diffusion measurements yield a self-association constant Kass=(61±19)×10(3)M(-1) for AIK-18/51 that fits with a stepwise self-assembly model and is consistent with ITC data. The deconstructed energetics of this assembly process are reported with respect to a design strategy for ligand/DNA recognition.
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Affiliation(s)
- Marie-Virginie Salvia
- WestCHEM Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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90
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Hua S, Yao M, Vignarajan S, Witting P, Hejazi L, Gong Z, Teng Y, Niknami M, Assinder S, Richardson D, Dong Q. Cytosolic phospholipase A2α sustains pAKT, pERK and AR levels in PTEN-null/mutated prostate cancer cells. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:1146-57. [PMID: 23500889 DOI: 10.1016/j.bbalip.2013.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 02/03/2013] [Accepted: 02/27/2013] [Indexed: 10/27/2022]
Abstract
Constitutive phosphorylation of protein kinase B (AKT) is a common feature of cancer caused by genetic alteration in the phosphatase and tensin homolog (PTEN) gene and is associated with poor prognosis. This study determined the role of cytosolic phospholipase A2α (cPLA2α) in AKT, extracellular signal-regulated kinase (ERK) and androgen receptor (AR) signaling in PTEN-null/mutated prostate cancer cells. Doxycycline (Dox)-induced expression of cPLA2α led to an increase in pAKT, pGSK3β and cyclin D1 levels in LNCaP cells that possess a PTEN frame-shift mutation. In contrast, silencing cPLA2α expression with siRNA decreased pAKT, pGSK3β and cyclin D1 levels in both PC-3 (PTEN deletion) and LNCaP cells. Silencing of cPLA2α decreased pERK and AR protein levels. The inhibitory effect of cPLA2α siRNA on pAKT and AR protein levels was reduced by the addition of arachidonic acid (AA), whereas the stimulatory effect of AA on pAKT, pERK and AR levels was decreased by an inhibitor of 5-hydroxyeicosatetraenoic acid production. Pharmacological blockade of cPLA2α with Efipladib reduced pAKT and AR levels with a concomitant inhibition of PC-3 and LNCaP cell proliferation. These results demonstrate an important role for cPLA2α in sustaining AKT, ERK and AR signaling in PTEN-null/mutated prostate cancer cells and provide a potential molecular target for treating prostate cancer.
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Affiliation(s)
- Sheng Hua
- The University of Sydney, Sydney, Australia
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91
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Dubey R, Levin MD, Szabo LZ, Laszlo CF, Kushal S, Singh JB, Oh P, Schnitzer JE, Olenyuk BZ. Suppression of Tumor Growth by Designed Dimeric Epidithiodiketopiperazine Targeting Hypoxia-Inducible Transcription Factor Complex. J Am Chem Soc 2013; 135:4537-49. [DOI: 10.1021/ja400805b] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Ramin Dubey
- Department of Pharmacology and
Pharmaceutical Sciences, University of Southern California, 1985 Zonal Ave., PSC B15C, HSC 9121, Los Angeles, California 90089,
United States
| | - Michael D. Levin
- Proteogenomics Research Institute
for Systems Medicine, 11107 Roselle St., San Diego, California 92121,
United States
| | - Lajos Z. Szabo
- Department
of Chemistry and
Biochemistry, University of Arizona, 1306
East University Blvd., Tucson, Arizona 85721, United States
| | - Csaba F. Laszlo
- Department
of Chemistry and
Biochemistry, University of Arizona, 1306
East University Blvd., Tucson, Arizona 85721, United States
| | - Swati Kushal
- Department of Pharmacology and
Pharmaceutical Sciences, University of Southern California, 1985 Zonal Ave., PSC B15C, HSC 9121, Los Angeles, California 90089,
United States
| | - Jason B. Singh
- Department
of Chemistry and
Biochemistry, University of Arizona, 1306
East University Blvd., Tucson, Arizona 85721, United States
| | - Philip Oh
- Proteogenomics Research Institute
for Systems Medicine, 11107 Roselle St., San Diego, California 92121,
United States
| | - Jan E. Schnitzer
- Proteogenomics Research Institute
for Systems Medicine, 11107 Roselle St., San Diego, California 92121,
United States
| | - Bogdan Z. Olenyuk
- Department of Pharmacology and
Pharmaceutical Sciences, University of Southern California, 1985 Zonal Ave., PSC B15C, HSC 9121, Los Angeles, California 90089,
United States
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92
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Nickols NG, Szablowski JO, Hargrove AE, Li BC, Raskatov JA, Dervan PB. Activity of a Py-Im polyamide targeted to the estrogen response element. Mol Cancer Ther 2013; 12:675-84. [PMID: 23443804 DOI: 10.1158/1535-7163.mct-12-1040] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pyrrole-imidazole (Py-Im) polyamides are a class of programmable DNA minor groove binders capable of modulating the activity of DNA-binding proteins and affecting changes in gene expression. Estrogen receptor alpha (ERα) is a ligand-activated hormone receptor that binds as a homodimer to estrogen response elements (ERE) and is a driving oncogene in a majority of breast cancers. We tested a selection of structurally similar Py-Im polyamides with differing DNA sequence specificity for activity against 17β-estadiol (E2)-induced transcription and cytotoxicity in ERα positive, E2-stimulated T47DKBluc cells, which express luciferase under ERα control. The most active polyamide targeted the sequence 5'-WGGWCW-3' (W = A or T), which is the canonical ERE half site. Whole transcriptome analysis using RNA-Seq revealed that treatment of E2-stimulated breast cancer cells with this polyamide reduced the effects of E2 on the majority of those most strongly affected by E2 but had much less effect on the majority of E2-induced transcripts. In vivo, this polyamide circulated at detectable levels following subcutaneous injection and reduced levels of ER-driven luciferase expression in xenografted tumors in mice after subcutaneous compound administration without significant host toxicity.
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Affiliation(s)
- Nicholas G Nickols
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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93
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Abstract
Many cancer therapeutics target DNA and exert cytotoxicity through the induction of DNA damage and inhibition of transcription. We report that a DNA minor groove binding hairpin pyrrole-imidazole (Py-Im) polyamide interferes with RNA polymerase II (RNAP2) activity in cell culture. Polyamide treatment activates p53 signaling in LNCaP prostate cancer cells without detectable DNA damage. Genome-wide mapping of RNAP2 binding shows reduction of occupancy, preferentially at transcription start sites, but occupancy at enhancer sites is unchanged. Polyamide treatment results in a time- and dose-dependent depletion of the RNAP2 large subunit RPB1 that is preventable with proteasome inhibition. This polyamide demonstrates antitumor activity in a prostate tumor xenograft model with limited host toxicity.
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94
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Hou T, Wang X, Liu X, Liu S, Du Z, Li F. A label-free and colorimetric turn-on assay for coralyne based on coralyne-induced formation of peroxidase-mimicking split DNAzyme. Analyst 2013; 138:4728-31. [DOI: 10.1039/c3an01024d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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95
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Caboni L, Lloyd DG. Beyond the ligand-binding pocket: targeting alternate sites in nuclear receptors. Med Res Rev 2012; 33:1081-118. [PMID: 23344935 DOI: 10.1002/med.21275] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Nuclear receptors (NRs) are a family of ligand-modulated transcription factors with significant therapeutic relevance from metabolic disorders and inflammation to cancer, neurodegenerative, and psychiatric disorders. Drug discovery efforts are typically concentrated on modulating the natural ligand action within the ligand-binding pocket (LBP) in the C-terminal ligand-binding domain (LBD). Drawbacks of LBP-based strategies include physiological alterations due to disruption of ligand binding and difficulties in achieving tissue specificity. Furthermore, the lack of a "pure" and predictable mechanism of action predisposes such intervention toward drug resistance. Recent outstanding progress in our understanding of NR biology has shifted the focus of drug discovery efforts from inside to outside the LBP, affording consideration to the interaction between NRs and coactivator proteins, the interaction between NRs and DNA and the NRs' ligand-independent functions. This review encompasses such currently available NR non-LBP-based interventions and their potential application in therapy or as specific tools to probe NR biology.
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Affiliation(s)
- Laura Caboni
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
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96
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Yan C, Higgins PJ. Drugging the undruggable: transcription therapy for cancer. Biochim Biophys Acta Rev Cancer 2012; 1835:76-85. [PMID: 23147197 DOI: 10.1016/j.bbcan.2012.11.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 10/30/2012] [Accepted: 11/01/2012] [Indexed: 11/19/2022]
Abstract
Transcriptional regulation is often the convergence point of oncogenic signaling. It is not surprising, therefore, that aberrant gene expression is a hallmark of cancer. Transformed cells often develop a dependency on such a reprogramming highlighting the therapeutic potential of rectifying cancer-associated transcriptional abnormalities in malignant cells. Although transcription is traditionally considered as undruggable, agents have been developed that target various levels of transcriptional regulation including DNA binding by transcription factors, protein-protein interactions, and epigenetic alterations. Some of these agents have been approved for clinical use or entered clinical trials. While artificial transcription factors have been developed that can theoretically modulate expression of any given gene, the emergence of reliable reporter assays greatly facilitates the search for transcription-targeted agents. This review provides a comprehensive overview of these developments, and discusses various strategies applicable for developing transcription-targeted therapeutic agents.
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Affiliation(s)
- Chunhong Yan
- Center for Cell Biology and Cancer Research, Albany Medical College, MC-165, 47 New Scotland Avenue, Albany, NY 12208, USA.
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97
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Abstract
Nuclear receptor (NR)-targeted therapies comprise a large class of clinically employed drugs. A number of drugs currently being used against this protein class were designed as structural analogs of the endogenous ligand of these receptors. In recent years, there has been significant interest in developing newer strategies to target NRs, especially those that rely on mechanistic pathways of NR function. Prominent among these are noncanonical means of targeting NRs, which include selective NR modulation, NR coactivator interaction inhibition, inhibition of NR DNA binding, modulation of NR cellular localization, modulation of NR ligand biosynthesis and downregulation of NR levels in target tissues. This article reviews each of these promising emerging strategies for NR drug development and highlights some of most significant successes achieved in using them.
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98
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Abstract
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Cyclic Py-Im polyamides containing two GABA turn units
exhibit
enhanced DNA binding affinity, but extensive studies of their biological
properties have been hindered due to synthetic inaccessibility. A
facile modular approach toward cyclic polyamides has been developed
via microwave-assisted solid-phase synthesis of hairpin amino acid
oligomer intermediates followed by macrocyclization. A focused library
of cyclic polyamides 1–7 targeted
to the androgen response element (ARE) and the estrogen response element
(ERE) were synthesized in 12–17% overall yield. The Fmoc protection
strategy also allows for selective modifications on the GABA turn
units that have been shown to improve cellular uptake properties.
The DNA binding affinities of a library of cyclic polyamides were
measured by DNA thermal denaturation assays and compared to the corresponding
hairpin polyamides. Fluorescein-labeled cyclic polyamides have been
synthesized and imaged via confocal microscopy in A549 and T47D cell
lines. The IC50 values of compounds 1–7 and 9–11 were determined,
revealing remarkably varying levels of cytotoxicity.
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Affiliation(s)
- Benjamin C Li
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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99
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Levine PM, Lee E, Greenfield A, Bonneau R, Logan SK, Garabedian MJ, Kirshenbaum K. Androgen receptor antagonism by divalent ethisterone conjugates in castrate-resistant prostate cancer cells. ACS Chem Biol 2012; 7:1693-701. [PMID: 22871957 DOI: 10.1021/cb300332w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Sustained treatment of prostate cancer with androgen receptor (AR) antagonists can evoke drug resistance, leading to castrate-resistant disease. Elevated activity of the AR is often associated with this highly aggressive disease state. Therefore, new therapeutic regimens that target and modulate AR activity could prove beneficial. We previously introduced a versatile chemical platform to generate competitive and non-competitive multivalent peptoid oligomer conjugates that modulate AR activity. In particular, we identified a linear and a cyclic divalent ethisterone conjugate that exhibit potent anti-proliferative properties in LNCaP-abl cells, a model of castrate-resistant prostate cancer. Here, we characterize the mechanism of action of these compounds utilizing confocal microscopy, time-resolved fluorescence resonance energy transfer, chromatin immunoprecipitation, flow cytometry, and microarray analysis. The linear conjugate competitively blocks AR action by inhibiting DNA binding. In addition, the linear conjugate does not promote AR nuclear localization or co-activator binding. In contrast, the cyclic conjugate promotes AR nuclear localization and induces cell-cycle arrest, despite its inability to compete against endogenous ligand for binding to AR in vitro. Genome-wide expression analysis reveals that gene transcripts are differentially affected by treatment with the linear or cyclic conjugate. Although the divalent ethisterone conjugates share extensive chemical similarities, we illustrate that they can antagonize the AR via distinct mechanisms of action, establishing new therapeutic strategies for potential applications in AR pharmacology.
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Affiliation(s)
- Paul M. Levine
- Department
of Chemistry and §Center for Genomics and Systems Biology, New York University, New York, New York 10003, United
States
- Department
of Biochemistry and Molecular Pharmacology, ⊥Department of Urology, and ∥Department of
Microbiology, NYU Langone School of Medicine, New York, New York 10016, United States
| | - Eugine Lee
- Department
of Chemistry and §Center for Genomics and Systems Biology, New York University, New York, New York 10003, United
States
- Department
of Biochemistry and Molecular Pharmacology, ⊥Department of Urology, and ∥Department of
Microbiology, NYU Langone School of Medicine, New York, New York 10016, United States
| | - Alex Greenfield
- Department
of Chemistry and §Center for Genomics and Systems Biology, New York University, New York, New York 10003, United
States
- Department
of Biochemistry and Molecular Pharmacology, ⊥Department of Urology, and ∥Department of
Microbiology, NYU Langone School of Medicine, New York, New York 10016, United States
| | - Richard Bonneau
- Department
of Chemistry and §Center for Genomics and Systems Biology, New York University, New York, New York 10003, United
States
- Department
of Biochemistry and Molecular Pharmacology, ⊥Department of Urology, and ∥Department of
Microbiology, NYU Langone School of Medicine, New York, New York 10016, United States
| | - Susan K. Logan
- Department
of Chemistry and §Center for Genomics and Systems Biology, New York University, New York, New York 10003, United
States
- Department
of Biochemistry and Molecular Pharmacology, ⊥Department of Urology, and ∥Department of
Microbiology, NYU Langone School of Medicine, New York, New York 10016, United States
| | - Michael J. Garabedian
- Department
of Chemistry and §Center for Genomics and Systems Biology, New York University, New York, New York 10003, United
States
- Department
of Biochemistry and Molecular Pharmacology, ⊥Department of Urology, and ∥Department of
Microbiology, NYU Langone School of Medicine, New York, New York 10016, United States
| | - Kent Kirshenbaum
- Department
of Chemistry and §Center for Genomics and Systems Biology, New York University, New York, New York 10003, United
States
- Department
of Biochemistry and Molecular Pharmacology, ⊥Department of Urology, and ∥Department of
Microbiology, NYU Langone School of Medicine, New York, New York 10016, United States
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100
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Meier JL, Yu AS, Korf I, Segal DJ, Dervan PB. Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing. J Am Chem Soc 2012; 134:17814-22. [PMID: 23013524 PMCID: PMC3483022 DOI: 10.1021/ja308888c] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Genomic applications of DNA-binding molecules require
an unbiased
knowledge of their high affinity sites. We report the high-throughput
analysis of pyrrole-imidazole polyamide DNA-binding specificity in
a 1012-member DNA sequence library using affinity purification
coupled with massively parallel sequencing. We find that even within
this broad context, the canonical pairing rules are remarkably predictive
of polyamide DNA-binding specificity. However, this approach also
allows identification of unanticipated high affinity DNA-binding sites
in the reverse orientation for polyamides containing β/Im pairs.
These insights allow the redesign of hairpin polyamides with different
turn units capable of distinguishing 5′-WCGCGW-3′ from
5′-WGCGCW-3′. Overall, this study displays the power
of high-throughput methods to aid the optimal targeting of sequence-specific
minor groove binding molecules, an essential underpinning for biological
and nanotechnological applications.
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Affiliation(s)
- Jordan L Meier
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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