1
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MCM2 in human cancer: functions, mechanisms, and clinical significance. Mol Med 2022; 28:128. [PMID: 36303105 PMCID: PMC9615236 DOI: 10.1186/s10020-022-00555-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 10/10/2022] [Indexed: 11/18/2022] Open
Abstract
Background Aberrant DNA replication is the main source of genomic instability that leads to tumorigenesis and progression. MCM2, a core subunit of eukaryotic helicase, plays a vital role in DNA replication. The dysfunction of MCM2 results in the occurrence and progression of multiple cancers through impairing DNA replication and cell proliferation. Conclusions MCM2 is a vital regulator in DNA replication. The overexpression of MCM2 was detected in multiple types of cancers, and the dysfunction of MCM2 was correlated with the progression and poor prognoses of malignant tumors. According to the altered expression of MCM2 and its correlation with clinicopathological features of cancer patients, MCM2 was thought to be a sensitive biomarker for cancer diagnosis, prognosis, and chemotherapy response. The anti-tumor effect induced by MCM2 inhibition implies the potential of MCM2 to be a novel therapeutic target for cancer treatment. Since DNA replication stress, which may stimulate anti-tumor immunity, frequently occurs in MCM2 deficient cells, it also proposes the possibility that MCM2 targeting improves the effect of tumor immunotherapy.
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2
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Yang N, Lu X, Jiang Y, Zhao L, Wang D, Wei Y, Yu Y, Kim MO, Laster KV, Li X, Yuan B, Dong Z, Liu K. Arbidol inhibits human esophageal squamous cell carcinoma growth in vitro and in vivo through suppressing ataxia telangiectasia and Rad3-related protein kinase. eLife 2022; 11:73953. [PMID: 36082941 PMCID: PMC9512399 DOI: 10.7554/elife.73953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 09/08/2022] [Indexed: 12/24/2022] Open
Abstract
Human esophageal cancer has a global impact on human health due to its high incidence and mortality. Therefore, there is an urgent need to develop new drugs to treat or prevent the prominent pathological subtype of esophageal cancer, esophageal squamous cell carcinoma (ESCC). Based upon the screening of drugs approved by the Food and Drug Administration, we discovered that Arbidol could effectively inhibit the proliferation of human ESCC in vitro. Next, we conducted a series of cell-based assays and found that Arbidol treatment inhibited the proliferation and colony formation ability of ESCC cells and promoted G1-phase cell cycle arrest. Phosphoproteomics experiments, in vitro kinase assays and pull-down assays were subsequently performed in order to identify the underlying growth inhibitory mechanism. We verified that Arbidol is a potential ataxia telangiectasia and Rad3-related (ATR) inhibitor via binding to ATR kinase to reduce the phosphorylation and activation of minichromosome maintenance protein 2 at Ser108. Finally, we demonstrated Arbidol had the inhibitory effect of ESCC in vivo by a patient-derived xenograft model. All together, Arbidol inhibits the proliferation of ESCC in vitro and in vivo through the DNA replication pathway and is associated with the cell cycle.
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Affiliation(s)
- Ning Yang
- Department of Pathophysiology, Zhengzhou University
| | - Xuebo Lu
- Department of Pathophysiology, Zhengzhou University
| | - Yanan Jiang
- Department of Pathophysiology, Zhengzhou University
| | - Lili Zhao
- Department of Pathophysiology, Zhengzhou University
| | - Donghao Wang
- Department of Pathophysiology, Zhengzhou University
| | - Yaxing Wei
- Department of Pathophysiology, Zhengzhou University
| | - Yin Yu
- Department of Pathophysiology, Zhengzhou University
| | - Myoung Ok Kim
- Department of Animal Science and Biotechnology, Kyungpook National University
| | | | - Xin Li
- Department of Pathophysiology, Zhengzhou University
| | - Baoyin Yuan
- Department of Pathophysiology, Zhengzhou University
| | - Zigang Dong
- Department of Pathophysiology, Zhengzhou University
| | - Kangdong Liu
- Department of Pathophysiology, Zhengzhou University
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3
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Single position substitution of hairpin pyrrole-imidazole polyamides imparts distinct DNA-binding profiles across the human genome. PLoS One 2020; 15:e0243905. [PMID: 33351840 PMCID: PMC7755219 DOI: 10.1371/journal.pone.0243905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/01/2020] [Indexed: 01/21/2023] Open
Abstract
Pyrrole–imidazole (Py–Im) polyamides are synthetic molecules that can be rationally designed to target specific DNA sequences to both disrupt and recruit transcriptional machinery. While in vitro binding has been extensively studied, in vivo effects are often difficult to predict using current models of DNA binding. Determining the impact of genomic architecture and the local chromatin landscape on polyamide-DNA sequence specificity remains an unresolved question that impedes their effective deployment in vivo. In this report we identified polyamide–DNA interaction sites across the entire genome, by covalently crosslinking and capturing these events in the nuclei of human LNCaP cells. This technique confirms the ability of two eight ring hairpin-polyamides, with similar architectures but differing at a single ring position (Py to Im), to retain in vitro specificities and display distinct genome-wide binding profiles.
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4
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Heinrich B, Vázquez O. 4-Methyltrityl-Protected Pyrrole and Imidazole Building Blocks for Solid Phase Synthesis of DNA-Binding Polyamides. Org Lett 2020; 22:533-536. [PMID: 31904984 DOI: 10.1021/acs.orglett.9b04288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-binding polyamides are synthetic oligomers of pyrrole/imidazole units with high specificity and affinity for double-stranded DNA. To increase their synthetic diversity, we report a mild methodology based on 4-methyltrityl (Mtt) solid phase peptide synthesis (SPPS), whose building blocks are more accessible than the standard Fmoc and Boc SPPS ones. We demonstrate the robustness of the approach by preparing and studying a hairpin with all precursors. Importantly, our strategy is orthogonal and compatible with sensitive molecules and could be readily automated.
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Affiliation(s)
- Benedikt Heinrich
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
| | - Olalla Vázquez
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
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5
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Yu Z, Pandian GN, Hidaka T, Sugiyama H. Therapeutic gene regulation using pyrrole-imidazole polyamides. Adv Drug Deliv Rev 2019; 147:66-85. [PMID: 30742856 DOI: 10.1016/j.addr.2019.02.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/22/2018] [Accepted: 02/04/2019] [Indexed: 12/13/2022]
Abstract
Recent innovations in cutting-edge sequencing platforms have allowed the rapid identification of genes associated with communicable, noncommunicable and rare diseases. Exploitation of this collected biological information has facilitated the development of nonviral gene therapy strategies and the design of several proteins capable of editing specific DNA sequences for disease control. Small molecule-based targeted therapeutic approaches have gained increasing attention because of their suggested clinical benefits, ease of control and lower costs. Pyrrole-imidazole polyamides (PIPs) are a major class of DNA minor groove-binding small molecules that can be predesigned to recognize specific DNA sequences. This programmability of PIPs allows the on-demand design of artificial genetic switches and fluorescent probes. In this review, we detail the progress in the development of PIP-based designer ligands and their prospects as advanced DNA-based small-molecule drugs for therapeutic gene modulation.
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6
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Kurmis AA, Dervan PB. Sequence specific suppression of androgen receptor-DNA binding in vivo by a Py-Im polyamide. Nucleic Acids Res 2019; 47:3828-3835. [PMID: 30838415 PMCID: PMC6486638 DOI: 10.1093/nar/gkz153] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/20/2019] [Accepted: 02/22/2019] [Indexed: 12/11/2022] Open
Abstract
The crucial role of androgen receptor (AR) in prostate cancer development is well documented, and its inhibition is a mainstay of prostate cancer treatment. Here, we analyze the perturbations to the AR cistrome caused by a minor groove binding molecule that is designed to target a sequence found in a subset of androgen response elements (ARE). We find treatment with this pyrrole-imidazole (Py-Im) polyamide exhibits sequence selectivity in its repression of AR binding in vivo. Differentially changed loci are enriched for sequences resembling ARE half-sites that match the Py-Im polyamide binding preferences determined in vitro. Comparatively, permutations of the ARE half-site bearing single or double mismatches to the Py-Im polyamide binding sequence are not enriched. This study confirms that the in vivo perturbation pattern caused by a sequence specific polyamide correlates with its in vitro binding preference genome-wide in an unbiased manner.
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Affiliation(s)
- Alexis A Kurmis
- Division of Chemistry and Chemical Engineering, 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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7
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Fei L, Xu H. Role of MCM2-7 protein phosphorylation in human cancer cells. Cell Biosci 2018; 8:43. [PMID: 30062004 PMCID: PMC6056998 DOI: 10.1186/s13578-018-0242-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/17/2018] [Indexed: 01/12/2023] Open
Abstract
A heterohexameric complex composed of minichromosome maintenance protein 2–7 (MCM2–7), which acts as a key replicative enzyme in eukaryotes, is crucial for initiating DNA synthesis only once per cell cycle. The MCM complex remains inactive through the G1 phase, until the S phase, when it is activated to initiate replication. During the transition from the G1 to S phase, the MCM undergoes multisite phosphorylation, an important change that promotes subsequent assembly of other replisome members. Phosphorylation is crucial for the regulation of MCM activity and function. MCMs can be phosphorylated by multiple kinases and these phosphorylation events are involved not only in DNA replication but also cell cycle progression and checkpoint response. Dysfunctional phosphorylation of MCMs appears to correlate with the occurrence and development of cancers. In this review, we summarize the currently available data regarding the regulatory mechanisms and functional consequences of MCM phosphorylation and seek the probability that protein kinase inhibitor can be used therapeutically to target MCM phosphorylation in cancer.
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Affiliation(s)
- Liangru Fei
- Department of Pathology, College of Basic Medical Sciences and the First Affiliated Hospital, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122 Liaoning Province People's Republic of China
| | - Hongtao Xu
- Department of Pathology, College of Basic Medical Sciences and the First Affiliated Hospital, China Medical University, No.77 Puhe Road, Shenyang North New Area, Shenyang, 110122 Liaoning Province People's Republic of China
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8
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Diaz-Perez S, Kane N, Kurmis AA, Yang F, Kummer NT, Dervan PB, Nickols NG. Interference with DNA repair after ionizing radiation by a pyrrole-imidazole polyamide. PLoS One 2018; 13:e0196803. [PMID: 29715291 PMCID: PMC5929528 DOI: 10.1371/journal.pone.0196803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/19/2018] [Indexed: 11/28/2022] Open
Abstract
Pyrrole-imidazole (Py–Im) polyamides are synthetic non-genotoxic minor groove-binding small molecules. We hypothesized that Py–Im polyamides can modulate the cellular response to ionizing radiation. Pre-treatment of cells with a Py-Im polyamide prior to exposure to ionizing radiation resulted in a delay in resolution of phosphorylated γ-H2AX foci, increase in XRCC1 foci, and reduced cellular replication potential. RNA-sequencing of cell lines exposed to the polyamide showed induction of genes related to the ultraviolet radiation response. We observed that the polyamide is almost 10-fold more toxic to a cell line deficient in DNA ligase 3 as compared to the parental cell line. Alkaline single cell gel electrophoresis reveals that the polyamide induces genomic fragmentation in the ligase 3 deficient cell line but not the corresponding parental line. The polyamide interferes directly with DNA ligation in vitro. We conclude that Py-Im polyamides may be further explored as sensitizers to genotoxic therapies.
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Affiliation(s)
- Silvia Diaz-Perez
- Department of Radiation Oncology, University of California, Los Angeles, California, United States of America
| | - Nathanael Kane
- Department of Radiation Oncology, University of California, Los Angeles, California, United States of America
| | - Alexis A. Kurmis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Fei Yang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Nicolas T. Kummer
- Department of Radiation Oncology, University of California, Los Angeles, California, United States of America
| | - Peter B. Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Nicholas G. Nickols
- Department of Radiation Oncology, University of California, Los Angeles, California, United States of America
- Department of Radiation Oncology, VA Greater Los Angeles Healthcare System, Los Angeles, California, United States of America
- * E-mail:
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9
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Gumpper RH, Li W, Castañeda CH, Scuderi MJ, Bashkin JK, Luo M. A Polyamide Inhibits Replication of Vesicular Stomatitis Virus by Targeting RNA in the Nucleocapsid. J Virol 2018; 92:e00146-18. [PMID: 29437970 PMCID: PMC5874401 DOI: 10.1128/jvi.00146-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 01/28/2018] [Indexed: 12/17/2022] Open
Abstract
Polyamides have been shown to bind double-stranded DNA by complementing the curvature of the minor groove and forming various hydrogen bonds with DNA. Several polyamide molecules have been found to have potent antiviral activities against papillomavirus, a double-stranded DNA virus. By analogy, we reason that polyamides may also interact with the structured RNA bound in the nucleocapsid of a negative-strand RNA virus. Vesicular stomatitis virus (VSV) was selected as a prototype virus to test this possibility since its genomic RNA encapsidated in the nucleocapsid forms a structure resembling one strand of an A-form RNA duplex. One polyamide molecule, UMSL1011, was found to inhibit infection of VSV. To confirm that the polyamide targeted the nucleocapsid, a nucleocapsid-like particle (NLP) was incubated with UMSL1011. The encapsidated RNA in the polyamide-treated NLP was protected from thermo-release and digestion by RNase A. UMSL1011 also inhibits viral RNA synthesis in the intracellular activity assay for the viral RNA-dependent RNA polymerase. The crystal structure revealed that UMSL1011 binds the structured RNA in the nucleocapsid. The conclusion of our studies is that the RNA in the nucleocapsid is a viable antiviral target of polyamides. Since the RNA structure in the nucleocapsid is similar in all negative-strand RNA viruses, polyamides may be optimized to target the specific RNA genome of a negative-strand RNA virus, such as respiratory syncytial virus and Ebola virus.IMPORTANCE Negative-strand RNA viruses (NSVs) include several life-threatening pathogens, such as rabies virus, respiratory syncytial virus, and Ebola virus. There are no effective antiviral drugs against these viruses. Polyamides offer an exceptional opportunity because they may be optimized to target each NSV. Our studies on vesicular stomatitis virus, an NSV, demonstrated that a polyamide molecule could specifically target the viral RNA in the nucleocapsid and inhibit viral growth. The target specificity of the polyamide molecule was proved by its inhibition of thermo-release and RNA nuclease digestion of the RNA bound in a model nucleocapsid, and a crystal structure of the polyamide inside the nucleocapsid. This encouraging observation provided the proof-of-concept rationale for designing polyamides as antiviral drugs against NSVs.
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Affiliation(s)
- Ryan H Gumpper
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
- Molecular Basis of Disease, Georgia State University, Atlanta, Georgia, USA
| | - Weike Li
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Carlos H Castañeda
- Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - M José Scuderi
- Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - James K Bashkin
- Department of Chemistry and Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
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10
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Poynton FE, Bright SA, Blasco S, Williams DC, Kelly JM, Gunnlaugsson T. The development of ruthenium(ii) polypyridyl complexes and conjugates for in vitro cellular and in vivo applications. Chem Soc Rev 2018; 46:7706-7756. [PMID: 29177281 DOI: 10.1039/c7cs00680b] [Citation(s) in RCA: 299] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Ruthenium(ii) [Ru(ii)] polypyridyl complexes have been the focus of intense investigations since work began exploring their supramolecular interactions with DNA. In recent years, there have been considerable efforts to translate this solution-based research into a biological environment with the intention of developing new classes of probes, luminescent imaging agents, therapeutics and theranostics. In only 10 years the field has expanded with diverse applications for these complexes as imaging agents and promising candidates for therapeutics. In light of these efforts this review exclusively focuses on the developments of these complexes in biological systems, both in cells and in vivo, and hopes to communicate to readers the diversity of applications within which these complexes have found use, as well as new insights gained along the way and challenges that researchers in this field still face.
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Affiliation(s)
- Fergus E Poynton
- School of Chemistry and Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, The University of Dublin, Dublin 2, Ireland.
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11
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Kawamoto Y, Bando T, Sugiyama H. Sequence-specific DNA binding Pyrrole-imidazole polyamides and their applications. Bioorg Med Chem 2018; 26:1393-1411. [PMID: 29439914 DOI: 10.1016/j.bmc.2018.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrrole-imidazole polyamides (Py-Im polyamides) are cell-permeable compounds that bind to the minor groove of double-stranded DNA in a sequence-specific manner without causing denaturation of the DNA. These compounds can be used to control gene expression and to stain specific sequences in cells. Here, we review the history, structural variations, and functional investigations of Py-Im polyamides.
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Affiliation(s)
- Yusuke Kawamoto
- 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 Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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12
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Cucco F, Palumbo E, Camerini S, D’Alessio B, Quarantotti V, Casella ML, Rizzo IM, Cukrov D, Delia D, Russo A, Crescenzi M, Musio A. Separase prevents genomic instability by controlling replication fork speed. Nucleic Acids Res 2018; 46:267-278. [PMID: 29165708 PMCID: PMC5758895 DOI: 10.1093/nar/gkx1172] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/26/2017] [Accepted: 11/10/2017] [Indexed: 01/21/2023] Open
Abstract
Proper chromosome segregation is crucial for preserving genomic integrity, and errors in this process cause chromosome mis-segregation, which may contribute to cancer development. Sister chromatid separation is triggered by Separase, an evolutionary conserved protease that cleaves the cohesin complex, allowing the dissolution of sister chromatid cohesion. Here we provide evidence that Separase participates in genomic stability maintenance by controlling replication fork speed. We found that Separase interacted with the replication licensing factors MCM2-7, and genome-wide data showed that Separase co-localized with MCM complex and cohesin. Unexpectedly, the depletion of Separase increased the fork velocity about 1.5-fold and caused a strong acetylation of cohesin's SMC3 subunit and altered checkpoint response. Notably, Separase silencing triggered genomic instability in both HeLa and human primary fibroblast cells. Our results show a novel mechanism for fork progression mediated by Separase and thus the basis for genomic instability associated with tumorigenesis.
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Affiliation(s)
- Francesco Cucco
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
| | - Elisa Palumbo
- Department of Biology, University of Padua, Padua, Italy
| | - Serena Camerini
- Department of Cell Biology and Neurosciences, National Institute of Health, Rome, Italy
| | - Barbara D’Alessio
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
| | - Valentina Quarantotti
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
| | - Maria Luisa Casella
- Department of Cell Biology and Neurosciences, National Institute of Health, Rome, Italy
| | - Ilaria Maria Rizzo
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
| | - Dubravka Cukrov
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
| | - Domenico Delia
- Fondazione IRCCS Istituto Nazionale Tumori, Department of Experimental Oncology, Milan, Italy
| | - Antonella Russo
- Department of Biology, University of Padua, Padua, Italy
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Marco Crescenzi
- Department of Cell Biology and Neurosciences, National Institute of Health, Rome, Italy
| | - Antonio Musio
- Institute for Biomedical and Genetic Research, National Research Council, Pisa, Italy
- Tumour Institute of Tuscany, Florence, Italy
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13
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Castaneda CH, Scuderi MJ, Edwards TG, Harris GD, Dupureur CM, Koeller KJ, Fisher C, Bashkin JK. Improved Antiviral Activity of a Polyamide Against High-Risk Human Papillomavirus Via N-Terminal Guanidinium Substitution. MEDCHEMCOMM 2016; 7:2076-2082. [PMID: 27840672 DOI: 10.1039/c6md00371k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the synthesis of two novel pyrrole-imidazole polyamides with N-terminal guanidinium or tetramethylguanidinium groups and evaluate their antiviral activity against three cancer-causing human papillomavirus strains. Introduction of guanidinium improves antiviral activity when compared to an unsubstituted analog, especially in IC90 values. These substitutions change DNA-binding preferences, while binding affinity remains unchanged.
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Affiliation(s)
- C H Castaneda
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - M J Scuderi
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - T G Edwards
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - G D Harris
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - C M Dupureur
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - K J Koeller
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA
| | - C Fisher
- NanoVir, LLC, Kalamazoo, MI 49008 (USA)
| | - J K Bashkin
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, MO 63121, USA; NanoVir, LLC, Kalamazoo, MI 49008 (USA)
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14
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A sequence-specific DNA binding small molecule triggers the release of immunogenic signals and phagocytosis in a model of B-cell lymphoma. Q Rev Biophys 2016; 48:453-64. [PMID: 26537405 PMCID: PMC4743504 DOI: 10.1017/s0033583515000104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Means to cause an immunogenic cell death could lead to significant insight into how cancer escapes immune control. In this study, we screened a library of five pyrrole–imidazole polyamides coding for different DNA sequences in a model of B-cell lymphoma for the upregulation of surface calreticulin, a pro-phagocytosis signal implicated in immunogenic cell death. We found that hairpin polyamide 1 triggers the release of the damage-associated molecular patterns calreticulin, ATP and HMGB1 in a slow necrotic-type cell death. Consistent with this signaling, we observed an increase in the rate of phagocytosis by macrophages after the cancer cells were exposed to polyamide 1. The DNA sequence preference of polyamide 1 is 5′-WGGGTW-3′ (where W = A/T), indicated by the pairing rules and confirmed by the Bind-n-Seq method. The close correspondence of this sequence with the telomere-repeat sequence suggests a potential mechanism of action through ligand binding at the telomere. This study reveals a chemical means to trigger an inflammatory necrotic cell death in cancer cells.
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15
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Vasilieva E, Niederschulte J, Song Y, Harris GD, Koeller KJ, Liao P, Bashkin JK, Dupureur CM. Interactions of two large antiviral polyamides with the long control region of HPV16. Biochimie 2016; 127:103-14. [PMID: 27155361 DOI: 10.1016/j.biochi.2016.04.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 04/30/2016] [Indexed: 02/07/2023]
Abstract
PA1 and PA25 are large hairpin polyamides that are effective in nearly eliminating HPV16 episomes (DNA) in cell culture, and PA25 has broad spectrum activity against three cancer-causing forms of HPV (Edwards, T. G., Koeller, K. J., Slomczynska, U., Fok, K., Helmus, M., Bashkin, J. K., Fisher, C., Antiviral Res. 91 (2011) 177-186). Described here are the interactions of these PAs with sequences in the long control region (LCR) of HPV16 (7348-122). Using an FeEDTA conjugate of PA1 (designed to recognize 5'-W2GW7-3'; W = A or T), 34 affinity cleavage (AC) patterns were detected for this fragment. These sites can be rationalized with sequences featuring perfect, single, double, triple and quadruple mismatches. Quantitative DNase I footprinting analysis indicates that perfect sites bind PA1 with Kds between 0.7 and 2.2 nM. Kds for single, double, triple and quadruple mismatch sites range from 1-3 nM-20 nM. Using AC and EDTA conjugates, we report that unlike smaller 8-ring hairpin PAs, introduction of a chiral turn in this large polyamide has no effect on binding orientation (forward vs. reverse). Despite its design to recognize 5'-W2GW5GW4-3' via two Im residues, a motif not represented in this HPV sequence, a PA25-EDTA conjugate yielded 31 affinity cleavage sites on the region. Low nM Kds for PA25 without EDTA indicates a high tolerance for triple and quadruple mismatches. While there is extensive coverage of the sequence examined, AC cleavage patterns for the two PAs show discrete binding events and do not overlap significantly. This indicates that within the context of A/T rich sequences, these PAs do not recognize a simple shared sequence-related feature of the DNA. These insights continue to inform the complex nature of large hairpin PA-DNA interactions and antiviral behavior.
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Affiliation(s)
- Elena Vasilieva
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - Jacquelyn Niederschulte
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - Yang Song
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - George Davis Harris
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - Kevin J Koeller
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - Puhong Liao
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - James K Bashkin
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA
| | - Cynthia M Dupureur
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121, USA.
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16
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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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17
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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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18
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Satam V, Babu B, Patil P, Brien KA, Olson K, Savagian M, Lee M, Mepham A, Jobe LB, Bingham JP, Pett L, Wang S, Ferrara M, Bruce CD, Wilson WD, Lee M, Hartley JA, Kiakos K. AzaHx, a novel fluorescent, DNA minor groove and G·C recognition element: Synthesis and DNA binding properties of a p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (azaHx-PI) polyamide. Bioorg Med Chem Lett 2015; 25:3681-5. [PMID: 26122210 DOI: 10.1016/j.bmcl.2015.06.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/09/2015] [Accepted: 06/11/2015] [Indexed: 11/30/2022]
Abstract
The design, synthesis, and DNA binding properties of azaHx-PI or p-anisyl-4-aza-benzimidazole-pyrrole-imidazole (5) are described. AzaHx, 2-(p-anisyl)-4-aza-benzimidazole-5-carboxamide, is a novel, fluorescent DNA recognition element, derived from Hoechst 33258 to recognize G·C base pairs. Supported by theoretical data, the results from DNase I footprinting, CD, ΔT(M), and SPR studies provided evidence that an azaHx/IP pairing, formed from antiparallel stacking of two azaHx-PI molecules in a side-by-side manner in the minor groove, selectively recognized a C-G doublet. AzaHx-PI was found to target 5'-ACGCGT-3', the Mlu1 Cell Cycle Box (MCB) promoter sequence with specificity and significant affinity (K(eq) 4.0±0.2×10(7) M(-1)).
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Affiliation(s)
- Vijay Satam
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Balaji Babu
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Pravin Patil
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Kimberly A Brien
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Kevin Olson
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Mia Savagian
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Megan Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Andrew Mepham
- Department of Chemistry, Hope College, Holland, MI 49423, United States
| | - Laura Beth Jobe
- Department of Chemistry, Erskine College, Due West, SC 29639, United States
| | - John P Bingham
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
| | - Luke Pett
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
| | - Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Maddi Ferrara
- Department of Chemistry, John Carroll University, University Heights, OH 44118, United States
| | - Chrystal D Bruce
- Department of Chemistry, John Carroll University, University Heights, OH 44118, United States
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Moses Lee
- Department of Chemistry, Hope College, Holland, MI 49423, United States; Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States.
| | - John A Hartley
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
| | - Konstantinos Kiakos
- Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, UK
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19
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Fisher C. Recent Insights into the Control of Human Papillomavirus (HPV) Genome Stability, Loss, and Degradation. J Clin Med 2015; 4:204-30. [PMID: 25798290 PMCID: PMC4366058 DOI: 10.3390/jcm4020204] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Most human papillomavirus (HPV) antiviral strategies have focused upon inhibiting viral DNA replication, but it is increasingly apparent that viral DNA levels can be chemically controlled by approaches that promote its instability. HPVs and other DNA viruses have a tenuous relationship with their hosts. They must replicate and hide from the DNA damage response (DDR) and innate immune systems, which serve to protect cells from foreign or “non-self” DNA, and yet they draft these same systems to support their life cycles. DNA binding antiviral agents promoting massive viral DNA instability and elimination are reviewed. Mechanistic studies of these agents have identified genetic antiviral enhancers and repressors, antiviral sensitizers, and host cell elements that protect and stabilize HPV genomes. Viral DNA degradation appears to be an important means of controlling HPV DNA levels in some cases, but the underlying mechanisms remain poorly understood. These findings may prove useful not only for understanding viral DNA persistence but only in devising future antiviral strategies.
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Affiliation(s)
- Chris Fisher
- NanoVir, 4717 Campus, Kalamazoo, MI 49008, USA; ; Tel.: +1-269-372-3261
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