1
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Li Y, Grotewold E, Dudareva N. Enough is enough: feedback control of specialized metabolism. TRENDS IN PLANT SCIENCE 2024; 29:514-523. [PMID: 37625949 DOI: 10.1016/j.tplants.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 07/24/2023] [Accepted: 07/27/2023] [Indexed: 08/27/2023]
Abstract
Recent advances in our understanding of plant metabolism have highlighted the significance of specialized metabolites in the regulation of gene expression associated with biosynthetic networks. This opinion article focuses on the molecular mechanisms of small-molecule-mediated feedback regulation at the transcriptional level and its potential modes of action, including metabolite signal perception, the nature of the sensor, and the signaling transduction mechanisms leading to transcriptional and post-transcriptional regulation, based on evidence available from plants and other kingdoms of life. We also discuss the challenges associated with identifying the occurrences, effects, and localization of small molecule-protein interactions. Further understanding of small-molecule-controlled metabolic fluxes will enable rational design of transcriptional regulation systems in metabolic engineering to produce high-value specialized metabolites.
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Affiliation(s)
- Ying Li
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA.
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Natalia Dudareva
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA; Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
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2
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Hussain A, Yang H, Zhang M, Liu Q, Alotaibi G, Irfan M, He H, Chang J, Liang XJ, Weng Y, Huang Y. mRNA vaccines for COVID-19 and diverse diseases. J Control Release 2022; 345:314-333. [PMID: 35331783 PMCID: PMC8935967 DOI: 10.1016/j.jconrel.2022.03.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/11/2022] [Accepted: 03/17/2022] [Indexed: 12/24/2022]
Abstract
Since its outbreak in late 2019, the novel coronavirus disease 2019 (COVID-19) has spread to every continent on the planet. The global pandemic has affected human health and socioeconomic status around the world. At first, the global response to the pandemic was to isolate afflicted individuals to prevent the virus from spreading, while vaccine development was ongoing. The genome sequence was first presented in early January 2020, and the phase I clinical trial of the vaccine started in March 2020 in the United States using novel lipid-based nanoparticle (LNP), encapsulated with mRNA termed as mRNA-1273. Till now, various mRNA-based vaccines are in development, while one mRNA-based vaccine got market approval from US-FDA for the prevention of COVID-19. Previously, mRNA-based vaccines were thought to be difficult to develop, but the current development is a significant accomplishment. However, widespread production and global availability of mRNA-based vaccinations to combat the COVID-19 pandemic remains a major challenge, especially when the mutations continually occur on the virus (e.g., the recent outbreaks of Omicron variant). This review elaborately discusses the COVID-19 pandemic, the biology of SARS-CoV-2 and the progress of mRNA-based vaccines. Moreover, the review also highlighted a detailed description of mRNA delivery technologies and the application potential in controlling other life-threatening diseases. Therefore, it provides a comprehensive view and multidisciplinary insights into mRNA therapy for broader audiences.
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Affiliation(s)
- Abid Hussain
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, School of Medical Technology (Institute of Engineering Medicine), Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Haiyin Yang
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, School of Medical Technology (Institute of Engineering Medicine), Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Mengjie Zhang
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, School of Medical Technology (Institute of Engineering Medicine), Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Qing Liu
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, School of Medical Technology (Institute of Engineering Medicine), Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China.
| | - Ghallab Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Al-Dawadmi Campus, Shaqra University, Shaqra, Saudi Arabia
| | - Muhammad Irfan
- School of Management and Economics, Beijing Institute of Technology, Beijing 100081, China; School of Business Administration, Ilma University, Karachi 75190, Pakistan
| | - Huining He
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Jin Chang
- School of Life Sciences, Tianjin University, Tianjin Engineering Center of Micro Nano Biomaterials and Detection Treatment Technology, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 300072, China
| | - Xing-Jie Liang
- Chinese Academy of Sciences (CAS) Key Laboratory for Biomedical Effects of Nanomaterials and Nano safety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Yuhua Weng
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, School of Medical Technology (Institute of Engineering Medicine), Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yuanyu Huang
- Advanced Research Institute of Multidisciplinary Science, School of Life Science, School of Medical Technology (Institute of Engineering Medicine), Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing 100081, China.
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3
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Hancock EJ, Oyarzún DA. Stabilization of antithetic control via molecular buffering. J R Soc Interface 2022; 19:20210762. [PMID: 35259958 PMCID: PMC8905164 DOI: 10.1098/rsif.2021.0762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A key goal in synthetic biology is the construction of molecular circuits that robustly adapt to perturbations. Although many natural systems display perfect adaptation, whereby stationary molecular concentrations are insensitive to perturbations, its de novo engineering has proven elusive. The discovery of the antithetic control motif was a significant step towards a universal mechanism for engineering perfect adaptation. Antithetic control provides perfect adaptation in a wide range of systems, but it can lead to oscillatory dynamics due to loss of stability; moreover, it can lose perfect adaptation in fast growing cultures. Here, we introduce an extended antithetic control motif that resolves these limitations. We show that molecular buffering, a widely conserved mechanism for homeostatic control in Nature, stabilizes oscillations and allows for near-perfect adaptation during rapid growth. We study multiple buffering topologies and compare their performance in terms of their stability and adaptation properties. We illustrate the benefits of our proposed strategy in exemplar models for biofuel production and growth rate control in bacterial cultures. Our results provide an improved circuit for robust control of biomolecular systems.
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Affiliation(s)
- Edward J Hancock
- School of Mathematics and Statistics, The University of Sydney, New South Wales 2006, Australia.,Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
| | - Diego A Oyarzún
- School of Informatics, The University of Edinburgh, Edinburgh, UK.,School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.,The Alan Turing Institute, London, UK
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4
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Yang J, Ding S. Chimeric RNA-binding protein-based killing switch targeting hepatocellular carcinoma cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:683-695. [PMID: 34589286 PMCID: PMC8463442 DOI: 10.1016/j.omtn.2021.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 08/13/2021] [Indexed: 11/09/2022]
Abstract
Cancer cell-specific killing switches are synthetic circuits developed as an intelligent weapon to specifically eliminate malignant cells. RNA-delivered synthetic circuits provide safer means to control oncolytic functions, in which proteolysis-responding capsid-cNOT7 is developed to enable logic computation and modular design. Unfortunately, although circuits containing these capsid-cNOT7s exhibited good performance when introduced as replicons, in modified mRNA (modRNA) delivery, the performance was not quite as good. To improve this situation, alternative modules suitable for modRNA delivery need to be developed. An attractive option is RNA-binding protein (RBP)/riboswitches. In this study, RBPs were engineered by fusing with degron and cleavage sites. The compatibility of these chimeric RBPs with proteolysis-based sensing units were tested. Eight two-input logic gates and four three-input logic gates were implemented. After building this chimeric RBP-based system, we constructed a hepatocellular carcinoma (HCC) cell-specific killing circuit using two proteolysis-based sensing units, a two-input logic OR gate, and a leakproof apoptosis-inducing actuator, which distinguished HCC cells and induced apoptosis in a mixed IMR90-PLC/PRF/5 population.
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Affiliation(s)
- Jiong Yang
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing 100191, China.,Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases, Beijing 100191, China
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5
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Chavali S, Singh AK, Santhanam B, Babu MM. Amino acid homorepeats in proteins. Nat Rev Chem 2020; 4:420-434. [PMID: 37127972 DOI: 10.1038/s41570-020-0204-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/16/2022]
Abstract
Amino acid homorepeats, or homorepeats, are polypeptide segments found in proteins that contain stretches of identical amino acid residues. Although abnormal homorepeat expansions are linked to pathologies such as neurodegenerative diseases, homorepeats are prevalent in eukaryotic proteomes, suggesting that they are important for normal physiology. In this Review, we discuss recent advances in our understanding of the biological functions of homorepeats, which range from facilitating subcellular protein localization to mediating interactions between proteins across diverse cellular pathways. We explore how the functional diversity of homorepeat-containing proteins could be linked to the ability of homorepeats to adopt different structural conformations, an ability influenced by repeat composition, repeat length and the nature of flanking sequences. We conclude by highlighting how an understanding of homorepeats will help us better characterize and develop therapeutics against the human diseases to which they contribute.
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Affiliation(s)
- Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India.
| | - Anjali K Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA.
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6
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Nair MS, Shukla A. Molecular modeling, simulation and principal component analysis of binding of resveratrol and its analogues with DNA. J Biomol Struct Dyn 2019; 38:3087-3097. [PMID: 31476951 DOI: 10.1080/07391102.2019.1662849] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structure-based drug designing has become a significant subject of research, and several clinically promising DNA binding compounds were evolved using this technique. The interaction of an octamer DNA sequence d(CCAATTGG)2 with a natural stilbene, resveratrol and its analogues have been studied using molecular docking method. Out of the ten compounds studied, seven compounds were found to bind to the minor groove of AATT segment of the sequence. Pterostilbene, a natural analogue of resveratrol, showed the lowest binding energy. Rhaponticin, a natural analogue of resveratrol and digalloylresveratrol, a synthetic ester of resveratrol bind to the major groove of the AATT segment while dihydroresveratrol binds to the minor groove of GC terminal base pair. ADMET (Absorption, distribution, metabolism, excretion and toxicity) study showed that all compounds obey Lipinski rule and are accepted as orally active drugs based on different physicochemical descriptors. Molecular dynamics simulations were performed for the complex with lowest binding energy and trajectory analysis were performed. Principal component analysis has been performed to underline the prominent motions in alone DNA and when it is bound to pterostilbene. AbbreviationsADMETAbsorption, distribution, metabolism, excretion and toxicityDIGDigalloyl resveratrolDNADeoxyribonucleic acidELElectrostatic energyENPOLARNonpolar solvation energyESURFSurface areaGBGeneralized BornHBAHydrogen bond acceptorsHBDHydrogen bond donorsLGALamarckian genetic algorithmMDMolecular dynamicsPBPoisson-BoltzmannPCAPrincipal component analysisPTPterostilbeneRMSDRoot mean square deviationSASimulated annealingTLX3T-cell leukemia homeobox 3VDWvan der WaalsCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maya S Nair
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Aishwarya Shukla
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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7
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Bauman KD, Li J, Murata K, Mantovani SM, Dahesh S, Nizet V, Luhavaya H, Moore BS. Refactoring the Cryptic Streptophenazine Biosynthetic Gene Cluster Unites Phenazine, Polyketide, and Nonribosomal Peptide Biochemistry. Cell Chem Biol 2019; 26:724-736.e7. [PMID: 30853419 PMCID: PMC6525064 DOI: 10.1016/j.chembiol.2019.02.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 01/02/2019] [Accepted: 01/31/2019] [Indexed: 11/28/2022]
Abstract
The disconnect between the genomic prediction of secondary metabolite biosynthetic potential and the observed laboratory production profile of microorganisms is well documented. While heterologous expression of biosynthetic gene clusters (BGCs) is often seen as a potential solution to bridge this gap, it is not immune to many challenges including impaired regulation, the inability to recruit essential building blocks, and transcriptional and/or translational silence of the biosynthetic genes. Here we report the discovery, cloning, refactoring, and heterologous expression of a cryptic hybrid phenazine-type BGC (spz) from the marine actinomycete Streptomyces sp. CNB-091. Overexpression of the engineered spz pathway resulted in increased production and chemical diversity of phenazine natural products belonging to the streptophenazine family, including bioactive members containing an unprecedented N-formylglycine attachment. An atypical discrete adenylation enzyme in the spz cluster is required to introduce the formylglycine moiety and represents a phylogenetically distinct class of adenylation proteins.
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Affiliation(s)
- Katherine D Bauman
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Jie Li
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Kazuya Murata
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Simone M Mantovani
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Samira Dahesh
- Department of Pediatrics, University of California at San Diego, La Jolla, CA, USA
| | - Victor Nizet
- Department of Pediatrics, University of California at San Diego, La Jolla, CA, USA; Collaborative to Halt Antibiotic Resistant Microbes, University of California at San Diego, La Jolla, CA, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA
| | - Hanna Luhavaya
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA.
| | - Bradley S Moore
- Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA.
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8
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Heaton BE, Kennedy EM, Dumm RE, Harding AT, Sacco MT, Sachs D, Heaton NS. A CRISPR Activation Screen Identifies a Pan-avian Influenza Virus Inhibitory Host Factor. Cell Rep 2018; 20:1503-1512. [PMID: 28813663 DOI: 10.1016/j.celrep.2017.07.060] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/17/2017] [Accepted: 07/21/2017] [Indexed: 02/02/2023] Open
Abstract
Influenza A virus (IAV) is a pathogen that poses significant risks to human health. It is therefore critical to develop strategies to prevent influenza disease. Many loss-of-function screens have been performed to identify the host proteins required for viral infection. However, there has been no systematic screen to identify the host factors that, when overexpressed, are sufficient to prevent infection. In this study, we used CRISPR/dCas9 activation technology to perform a genome-wide overexpression screen to identify IAV restriction factors. The major hit from our screen, B4GALNT2, showed inhibitory activity against influenza viruses with an α2,3-linked sialic acid receptor preference. B4GALNT2 overexpression prevented the infection of every avian influenza virus strain tested, including the H5, H9, and H7 subtypes, which have previously caused disease in humans. Thus, we have used CRISPR/dCas9 activation technology to identify a factor that can abolish infection by avian influenza viruses.
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Affiliation(s)
- Brook E Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Edward M Kennedy
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rebekah E Dumm
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alfred T Harding
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthew T Sacco
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - David Sachs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA.
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9
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Rodríguez J, Mosquera J, García-Fandiño R, Vázquez ME, Mascareñas JL. A designed DNA binding motif that recognizes extended sites and spans two adjacent major grooves. Chem Sci 2016; 7:3298-3303. [PMID: 27252825 PMCID: PMC4885664 DOI: 10.1039/c6sc00045b] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/01/2016] [Indexed: 12/28/2022] Open
Abstract
We report the rational design of a DNA-binding peptide construct composed of the DNA-contacting regions of two transcription factors (GCN4 and GAGA) linked through an AT-hook DNA anchor. The resulting chimera, which represents a new, non-natural DNA binding motif, binds with high affinity and selectivity to a long composite sequence of 13 base pairs (TCAT-AATT-GAGAG).
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Affiliation(s)
- Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - Rebeca García-Fandiño
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
; Fax: +34 981 595 012
; Tel: +34 981576541-14405
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11
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Sánchez MI, Mosquera J, Vázquez ME, Mascareñas JL. Reversible Supramolecular Assembly at Specific DNA Sites: Nickel-Promoted Bivalent DNA Binding with Designed Peptide and Bipyridyl-Bis(benzamidine) Components. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405726] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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Sánchez MI, Mosquera J, Vázquez ME, Mascareñas JL. Reversible Supramolecular Assembly at Specific DNA Sites: Nickel-Promoted Bivalent DNA Binding with Designed Peptide and Bipyridyl-Bis(benzamidine) Components. Angew Chem Int Ed Engl 2014; 53:9917-21. [DOI: 10.1002/anie.201405726] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Indexed: 01/20/2023]
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13
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Mosquera J, Rodríguez J, Vázquez ME, Mascareñas JL. Selective DNA-binding by designed bisbenzamidine-homeodomain chimeras. Chembiochem 2014; 15:1092-5. [PMID: 24764315 DOI: 10.1002/cbic.201400079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Indexed: 02/06/2023]
Abstract
We report the construction of conjugates between three variants of the helix 3 region of a Q50K engrailed homeodomain and bisbenzamidine minor-groove DNA binders. The hybrid featuring the sequence of the native protein failed to bind to DNA; however, modifications that increased the α-helical folding propensity of the peptide allowed specific DNA binding by a bipartite (major/minor groove) interaction.
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Affiliation(s)
- Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente sn, 15782 Santiago de Compostela (Spain)
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14
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Sánchez MI, Vázquez O, Vázquez ME, Mascareñas JL. Sequence-selective DNA recognition with peptide-bisbenzamidine conjugates. Chemistry 2013; 19:9923-9. [PMID: 23780839 DOI: 10.1002/chem.201300519] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Indexed: 12/15/2022]
Abstract
Transcription factors (TFs) are specialized proteins that play a key role in the regulation of genetic expression. Their mechanism of action involves the interaction with specific DNA sequences, which usually takes place through specialized domains of the protein. However, achieving an efficient binding usually requires the presence of the full protein. This is the case for bZIP and zinc finger TF families, which cannot interact with their target sites when the DNA binding fragments are presented as isolated monomers. Herein it is demonstrated that the DNA binding of these monomeric peptides can be restored when conjugated to aza-bisbenzamidines, which are readily accessible molecules that interact with A/T-rich sites by insertion into their minor groove. Importantly, the fluorogenic properties of the aza-benzamidine unit provide details of the DNA interaction that are eluded in electrophoresis mobility shift assays (EMSA). The hybrids based on the GCN4 bZIP protein preferentially bind to composite sequences containing tandem bisbenzamidine-GCN4 binding sites (TCAT⋅AAATT). Fluorescence reverse titrations show an interesting multiphasic profile consistent with the formation of competitive nonspecific complexes at low DNA/peptide ratios. On the other hand, the conjugate with the DNA binding domain of the zinc finger protein GAGA binds with high affinity (KD≈12 nM) and specificity to a composite AATTT⋅GAGA sequence containing both the bisbenzamidine and the TF consensus binding sites.
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Affiliation(s)
- Mateo I Sánchez
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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15
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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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16
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Takagaki T, Bando T, Sugiyama H. Synthesis of pyrrole-imidazole polyamide seco-1-chloromethyl-5-hydroxy-1,2-dihydro-3h-benz[e]indole conjugates with a vinyl linker recognizing a 7 bp DNA sequence. J Am Chem Soc 2012; 134:13074-81. [PMID: 22799887 DOI: 10.1021/ja3044294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Convergent synthetic routes for N-methylpyrrole (P) and N-methylimidazole (I) seco-1-chloromethyl-5-hydroxy-1,2-dihydro-3H-benz[e]indole (CBI) conjugates with a vinyl linker were developed. New hairpin polyamide-seco-CBI conjugates, compounds 16-19, were synthesized, and their DNA sequence-specific alkylating activities were evaluated via high-resolution denaturing gel electrophoresis and high-performance liquid chromatography (HPLC) product analysis. The new synthetic route for PI conjugates with a vinyl linker consisted of the introduction of a vinylpyrrole unit (8-11) into the C terminal of a PI polyamide synthesized by (fluorenylmethoxy)carbonyl solid-phase peptide synthesis (SPPS), followed by liquid-phase coupling with seco-CBI. The yield of the conjugates was significantly improved compared with that of the method reported previously, which allows us to synthesize various substituted conjugates containing a vinyl linker. Conjugates 16-19 were designed to investigate the substituent effect of the vinyl linker, and conjugate 16S was synthesized to evaluate the reactivity between racemic and S enantiomers of the seco-CBI derivative. The results of high-resolution denaturing gel electrophoresis using 208 bp DNA fragments indicated that alkylation by compounds 16 and 17, in which the H of the vinyl linker of compound 16 was replaced with F, occurred predominantly at the A of the 5'-TTTGTCA-3' sequence at nanomolar concentrations. In clear contrast, compounds 18 and 19, which were methyl or Br derivatives of compound 16, did not exhibit any DNA alkylating activity. Moreover, HPLC product analysis using synthetic oligonucleotides demonstrated that alkylation occurred between the N3 of the adenine of the oligomer and the cyclopropane ring of 16S. Density functional calculation of substituted vinylpyrrole seco-CBI units indicated that methyl and Br substituents led to a significantly distorted geometry of the vinyl group with the pyrrole ring compared with H and F derivatives. Molecular modeling studies offered the additional information that steric hindrance reduced the DNA alkylating activity of these derivatives.
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Affiliation(s)
- Toshiki Takagaki
- Department of Chemistry, Graduate School of Science, Kyoto University , Sakyo, Kyoto 606-8502, Japan
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17
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Bahal R, Sahu B, Rapireddy S, Lee CM, Ly DH. Sequence-unrestricted, Watson-Crick recognition of double helical B-DNA by (R)-miniPEG-γPNAs. Chembiochem 2011; 13:56-60. [PMID: 22135012 DOI: 10.1002/cbic.201100646] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Indexed: 11/07/2022]
Affiliation(s)
- Raman Bahal
- Department of Chemistry and Center for Nucleic Acids Science and Technology (CNAST), Carnegie Mellon University, Pittsburgh, PA 15213, USA
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18
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Morinaga H, Bando T, Takagaki T, Yamamoto M, Hashiya K, Sugiyama H. Cysteine Cyclic Pyrrole–Imidazole Polyamide for Sequence-Specific Recognition in the DNA Minor Groove. J Am Chem Soc 2011; 133:18924-30. [DOI: 10.1021/ja207440p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Hiroshi Sugiyama
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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19
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Takagaki T, Bando T, Kitano M, Hashiya K, Kashiwazaki G, Sugiyama H. Evaluation of PI polyamide conjugates with eight-base pair recognition and improvement of the aqueous solubility by PEGylation. Bioorg Med Chem 2011; 19:5896-902. [PMID: 21903400 DOI: 10.1016/j.bmc.2011.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/04/2011] [Accepted: 08/05/2011] [Indexed: 11/15/2022]
Abstract
To investigate the effect of elongating base-pair (bp) recognition sequences, we synthesized N-methylpyrrole-N-methylimidazole (PI) polyamide conjugates with eight-bp recognition (3-5). The DNA alkylating activities of conjugates 3-5 were evaluated by high-resolution denaturing polyacrylamide gel electrophoresis with a 208-bp DNA fragment. Conjugates 3-5 showed high alkylating activities at nanomolar concentrations. We then addressed the following issue about PI conjugates. Generally, PI polyamide conjugates hardly dissolve in aqueous solution. To improve the aqueous solubility, by the introduction of hydrophilic groups, we synthesized PI polyamide conjugates that were modified with a seco-CBI moiety (6-11). Conjugates 9-11 that were modified by methoxypolyethylene glycol (PEG) 750 acquired moderate solubility and stability in aqueous solution. In addition, conjugates 10 and 11 had high cytotoxicity against A549 and DU145.
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Affiliation(s)
- Toshiki Takagaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo, Kyoto 606-8502, Japan
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20
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Li C, Du C, Tian H, Jiang C, Du M, Liu Y, Qiao RZ, Jia YX, Zhao YF. Artificial Transcription Factors which Mediate Double-Strand DNA Cleavage. Chemistry 2010; 16:12935-40. [DOI: 10.1002/chem.201000552] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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21
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Anticancer activities of alkylating pyrrole–imidazole polyamides with specific sequence recognition. Anticancer Drugs 2010; 21:228-42. [DOI: 10.1097/cad.0b013e328334d8f9] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Usai I, Krueger M, Einsiedel J, Hillen W, Gmeiner P. Click-Chemistry-Derived Tetracycline-Amino Acid Conjugates Exhibiting Exceptional Potency and Exclusive Recognition of the Reverse Tet Repressor. Chembiochem 2010; 11:703-12. [DOI: 10.1002/cbic.200900710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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23
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Babu B, Mackay H, Prast A, Dittenhafer K, Davis R, Tronrud C, Rice T, Chavda S, Lee M. Synthesis and biophysical studies of hairpin polyamides targeting the Brn-3b and GATA-3 transcriptional sites. HETEROCYCL COMMUN 2010. [DOI: 10.1515/hc.2010.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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24
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Kormann C, Pimenta I, Löber S, Wimmer C, Lanig H, Clark T, Hillen W, Gmeiner P. Diarylpropane-1,3-dione Derivatives as TetR-Inducing Tetracycline Mimetics: Synthesis and Biological Investigations. Chembiochem 2009; 10:2924-33. [DOI: 10.1002/cbic.200900564] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Zeng Z, Torriero AAJ, Belousoff MJ, Bond AM, Spiccia L. Synthesis, X-ray structure of ferrocene bearing bis(Zn-cyclen) complexes and the selective electrochemical sensing of TpT. Chemistry 2009; 15:10988-96. [PMID: 19746486 DOI: 10.1002/chem.200901639] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The new ligand, [Fc(cyclen)(2)] (5) (Fc=ferrocene, cyclen=1,4,7,10-tetraazacyclododecane), and corresponding Zn(II) complex receptor, [Fc{Zn(cyclen)(CH(3)OH)}(2)](ClO(4))(4) (1), consisting of a ferrocene moiety bearing one Zn(II)-cyclen complex on each cyclopentadienyl ring, have been designed and prepared through a multi-step synthesis. Significant shifts in the (1)H NMR signals of the ferrocenyl group, cf. ferrocene and a previously reported [Fc{Zn(cyclen)}](2+) derivative, indicated that the two Zn(II)-cyclen units in 1 significantly affect the electronic properties of the cyclopentadienyl rings. The X-ray crystal structure shows that the two positively charged Zn(II)-cyclen complexes are arranged in a trans like configuration, with respect to the ferrocene bridging unit, presumably to minimise electrostatic repulsion. Both 5 and 1 can be oxidized in 1:4 CH(2)Cl(2)/CH(3)CN and Tris-HCl aqueous buffer solution under conditions of cyclic voltammetry to give a well defined ferrocene-centred (Fc(0/+)) process. Importantly, 1 is a highly selective electrochemical sensor of thymidilyl(3'-5')thymidine (TpT) relative to other nucleobases and nucleotides in Tris-HCl buffer solution (pH 7.4). The electrochemical selectivity, detected as a shift in reversible potential of the Fc(0/+) component, is postulated to result from a change in the configuration of bis(Zn(II)-cyclen) units from a trans to a cis state. This is caused by the strong 1:1 binding of the two deprotonated thymine groups in TpT to different Zn(II) centres of receptor 1. UV-visible spectrophotometric titrations confirmed the 1:1 stoichiometry for the 1:TpT adduct and allowed the determination of the apparent formation constant of 0.89+/-0.10x10(6) M(-1) at pH 7.4.
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Affiliation(s)
- Zhanghua Zeng
- School of Chemistry, Monash University, Clayton, Victoria, Australia
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26
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Liu B, Kodadek T. Investigation of the relative cellular permeability of DNA-binding pyrrole-imidazole polyamides. J Med Chem 2009; 52:4604-12. [PMID: 19610652 DOI: 10.1021/jm9002999] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyrrole-imidazole (Py-Im) polyamides are a group of chemicals that are able to bind specifically to DNA sequences in vitro and in mammalian cells. Using a cell based reporter assay, we investigated the size and linker affects on the cellular permeability of polyamides. We found that the conventional beta-alanine-3,3'-diamino-N-methyldipropylamine (betaDa) linker strongly limited the cellular permeability. We discovered that a short ethylene diamine (Et) linker displayed high cellular permeability. With the improved Et linker, we found that the cellular permeability of polyamides was size-dependent.
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Affiliation(s)
- Bo Liu
- Department of Internal Medicine, Division of Translational Research, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA
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27
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Lee LW, Taylor CEC, Desaulniers JP, Zhang M, Højfeldt JW, Pan Q, Mapp AK. Inhibition of ErbB2(Her2) expression with small molecule transcription factor mimics. Bioorg Med Chem Lett 2009; 19:6233-6. [PMID: 19782563 DOI: 10.1016/j.bmcl.2009.08.090] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 08/21/2009] [Accepted: 08/24/2009] [Indexed: 10/20/2022]
Abstract
Small molecules that mimic the transcriptional activation domain of eukaryotic transcriptional activators have the potential to serve as effective inhibitors of transcriptional processes. Here we show that one class of transcriptional activation domain mimics, amphipathic isoxazolidines, can be converted into inhibitors of gene expression mediated by the transcriptional activator ESX through small structural modifications. Addition of the small molecules leads to decreased expression of the cell surface growth receptor ErbB2(Her2) in ErbB2-positive cancer cells and, correspondingly, decreased proliferation.
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Affiliation(s)
- Lori W Lee
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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28
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Buhrlage SJ, Bates CA, Rowe SP, Minter AR, Brennan BB, Majmudar CY, Wemmer DE, Al-Hashimi H, Mapp AK. Amphipathic small molecules mimic the binding mode and function of endogenous transcription factors. ACS Chem Biol 2009; 4:335-44. [PMID: 19348463 PMCID: PMC2744096 DOI: 10.1021/cb900028j] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Small molecules that reconstitute the binding mode(s) of a protein and in doing so elicit a programmed functional response offer considerable advantages in the control of complex biological processes. The development challenges of such molecules are significant, however. Many protein-protein interactions require multiple points of contact over relatively large surface areas. More significantly, several binding modes can be superimposed upon a single sequence within a protein, and a true small molecule replacement must be preprogrammed for such multimodal binding. This is the case for the transcriptional activation domain or TAD of transcriptional activators as these motifs utilize a poorly characterized multipartner binding profile in order to stimulate gene expression. Here we describe a unique class of small molecules that exhibit both function and a binding profile analogous to natural transcriptional activation domains. Of particular note, the small molecules are the first reported to bind to the KIX domain within the CREB binding protein (CBP) at a site that is utilized by natural activators. Further, a comparison of functional and nonfunctional small molecules indicates that an interaction with CBP is a key contributor to transcriptional activity. Taken together, the evidence suggests that the small molecule TADs mimic both the function and mechanism of their natural counterparts and thus present a framework for the broader development of small molecule transcriptional switches.
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Affiliation(s)
| | - Caleb A. Bates
- Department of Medicinal Chemistry, University of Michigan
| | | | | | | | | | | | - Hashim Al-Hashimi
- Department of Chemistry, University of Michigan
- Department of Biophysics, University of Michigan
| | - Anna K. Mapp
- Department of Chemistry, University of Michigan
- Department of Medicinal Chemistry, University of Michigan
- Program in Chemical Biology, University of Michigan
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29
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Ansari KI, Grant JD, Kasiri S, Woldemariam G, Shrestha B, Mandal SS. Manganese(III)-salens induce tumor selective apoptosis in human cells. J Inorg Biochem 2009; 103:818-26. [DOI: 10.1016/j.jinorgbio.2009.02.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 02/11/2009] [Accepted: 02/12/2009] [Indexed: 11/26/2022]
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30
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Iron(III)-salen damages DNA and induces apoptosis in human cell via mitochondrial pathway. J Inorg Biochem 2008; 102:740-7. [DOI: 10.1016/j.jinorgbio.2007.11.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2007] [Revised: 11/14/2007] [Accepted: 11/19/2007] [Indexed: 11/20/2022]
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31
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Bando T, Minoshima M, Kashiwazaki G, Shinohara KI, Sasaki S, Fujimoto J, Ohtsuki A, Murakami M, Nakazono S, Sugiyama H. Requirement of β-alanine components in sequence-specific DNA alkylation by pyrrole–imidazole conjugates with seven-base pair recognition. Bioorg Med Chem 2008; 16:2286-91. [DOI: 10.1016/j.bmc.2007.11.064] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 11/25/2007] [Indexed: 10/22/2022]
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32
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Discovery of Novel Transcription Factor Inhibitors Using a Pyrazole-based Small Molecule Library. B KOREAN CHEM SOC 2008. [DOI: 10.5012/bkcs.2008.29.2.323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Affiliation(s)
- Daniel P Walsh
- Department of Chemistry, New York University, New York, New York 10003, USA
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34
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Xiao X, Yu P, Lim HS, Sikder D, Kodadek T. A cell-permeable synthetic transcription factor mimic. Angew Chem Int Ed Engl 2007; 46:2865-8. [PMID: 17351994 DOI: 10.1002/anie.200604485] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiangshu Xiao
- Division of Translational Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9185, USA
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35
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Xiao X, Yu P, Lim HS, Sikder D, Kodadek T. Design and synthesis of a cell-permeable synthetic transcription factor mimic. ACTA ACUST UNITED AC 2007; 9:592-600. [PMID: 17530904 PMCID: PMC2518654 DOI: 10.1021/cc070023a] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthetic molecules capable of activating the expression of specific genes are of great interest as tools for biological research and, potentially, as a novel class of pharmaceutical agents. It has been demonstrated previously that such synthetic transcription factor mimics (STFMs) can be constructed by connecting a sequence-specific DNA-binding module to a molecule capable of binding to the transcriptional machinery via a suitable linker. These chimeras mimic the two basic properties of native transcription factors, which are able to recognize a promoter sequence specifically and to recruit the transcriptional machinery to that promoter. However, none of the compounds of this type reported to date have been shown to function in living cells. We report here the first example of a cell-permeable STFM that activates the transcription of a reporter gene in mammalian cells. The compound is composed of a cell-permeable coactivator-binding peptoid fused to a DNA-binding hairpin polyamide. The peptoid was identified by screening a combinatorial library of approximately 50,000 compounds for binding to the KIX domain of the CREB-binding protein (CBP), a mammalian transcription coactivator. When incubated with cultured HeLa cells carrying a luciferase reporter plasmid bearing several hairpin polyamide-binding sites, a 5-fold increase in luciferase expression was observed. These experiments set the stage for the identification of hairpin polyamide-peptoid conjugates that are targeted to native genes.
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Affiliation(s)
| | | | | | | | - Thomas Kodadek
- To whom correspondence should be addressed. Phone: 214-648-1239. FAX: 214-648-4156. E-mail:
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36
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Xiao X, Yu P, Lim HS, Sikder D, Kodadek T. A Cell-Permeable Synthetic Transcription Factor Mimic. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604485] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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37
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Stafford RL, Arndt HD, Brezinski ML, Ansari AZ, Dervan PB. Minimization of a protein-DNA dimerizer. J Am Chem Soc 2007; 129:2660-8. [PMID: 17290996 PMCID: PMC3064071 DOI: 10.1021/ja067971k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A protein-DNA dimerizer constructed from a DNA-binding polyamide and the peptide FYPWMKG facilitates the binding of a natural transcription factor Exd to an adjacent DNA site. The Exd binding domain can be reduced to a dipeptide WM attached to the polyamide through an epsilon-aminohexanoic acid linker with retention of protein-DNA dimerizer activity. Screening a library of analogues indicated that the tryptophan indole moiety is more important than methionine's side chain or the N-terminal acetamide. Remarkably, switching the stereochemistry of the tryptophan residue (l to d) stabilizes the dimerizer*Exd*DNA ternary complex at 37 degrees C. These observations provide design principles for artificial transcription factors that may function in concert with the cellular regulatory circuitry.
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38
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39
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Bando T, Sugiyama H. Synthesis and biological properties of sequence-specific DNA-alkylating pyrrole-imidazole polyamides. Acc Chem Res 2006; 39:935-44. [PMID: 17176032 DOI: 10.1021/ar030287f] [Citation(s) in RCA: 178] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In recent years, many diseases including cancer and hereditary and viral diseases have been understood at the DNA sequence level. Direct control of the expression level of a specific gene would provide a promising approach for knowledge-based therapy. N-Methylpyrrole (Py) and N-methylimidazole (Im) polyamides are a new type of small compound that precisely bind to the minor groove of the DNA duplex in a sequence-specific fashion and recruit alkylating agents to the target sequence. We designed and synthesized a series of sequence-specific alkylating Py-Im polyamide conjugates that selectively alkylate predetermined DNA sequences. We have demonstrated that sequence-specific alkylating agents possess gene-silencing activities and a promising potency against human cancer cell lines as well as against xenografts of human cancer cell lines. In this Account, we focus on recent progress in alkylating Py-Im polyamides with regard to sequence specificity and biological activities and the future direction of rational molecular design of genetic switches in the postgenome era is described.
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Affiliation(s)
- Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto, Japan
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40
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Berens C, Lochner S, Löber S, Usai I, Schmidt A, Drueppel L, Hillen W, Gmeiner P. Subtype selective tetracycline agonists and their application for a two-stage regulatory system. Chembiochem 2006; 7:1320-4. [PMID: 16871602 DOI: 10.1002/cbic.200600226] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Christian Berens
- Department of Microbiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstrasse 5, 91058 Erlangen, Germany
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41
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Hooda J, Bednarski D, Irish L, Firestine SM. Synthesis and testing of a triaza-cyclopenta[b]phenanthrene scaffold as a DNA binding agent. Bioorg Med Chem 2006; 14:1902-9. [PMID: 16298133 DOI: 10.1016/j.bmc.2005.10.047] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2004] [Revised: 10/24/2005] [Accepted: 10/25/2005] [Indexed: 11/17/2022]
Abstract
A novel DNA binding agent based upon a triaza-cyclopenta[b]phenanthrene scaffold, compound 1, has been synthesized. dsDNA binding analysis of this compound using the ethidium bromide displacement assay indicated a preference for GC-rich sequences. However, equilibrium dialysis experiments against a variety of nucleic acids showed that the target compound bound about 20-fold tighter to G-quartet DNA than to dsDNA under physiological salt concentrations. The binding of 1 to G-quartet DNA was verified by the ability of the compound to promote the formation of the quartet and to compete with TmPyP4 for binding to the quadruplex. Given the importance of G-quartet binding agents in the treatment of cancer and in the understanding of drug-DNA interactions, 1 and its related analogs should find utility as a new class of G-quartet specific agents.
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Affiliation(s)
- Jaipal Hooda
- Wayne State University, Eugene Applebaum College of Pharmacy and Health Science, Department of Pharmaceutical Sciences, 259 Mack Avenue, Detroit, MI 48201, USA
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42
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Shinohara KI, Sasaki S, Minoshima M, Bando T, Sugiyama H. Alkylation of template strand of coding region causes effective gene silencing. Nucleic Acids Res 2006; 34:1189-95. [PMID: 16500890 PMCID: PMC1383623 DOI: 10.1093/nar/gkl005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 02/10/2006] [Accepted: 02/10/2006] [Indexed: 11/12/2022] Open
Abstract
We recently developed a new type of pyrrole (Py)-imidazole (Im) polyamide-tetrahydrocyclopropabenzindolone (CBI) conjugate with an indole linker as a stable sequence-specific alkylating agent. In this study, we investigated the gene silencing activities of polyamides A, B and C, which selectively alkylate specific sequences in the promoter region, non-coding strand and coding strand, respectively, of the green fluorescent protein (GFP) gene. GFP vectors were transfected into human colon carcinoma cells (HCT116), and the cells were treated with 100 nM of the polyamides for 24 h. Fluorescence microscopy indicated that a significant reduction of GFP fluorescence was only observed in the cells that were treated with polyamide C. In clear contrast, polyamides A and B did not show such activity. Moreover, real-time PCR demonstrated selective reduction of the expression of GFP mRNA following treatment with polyamide C. These results suggest that alkylating Py-Im polyamides that target the coding strand represent a novel approach for sequence-specific gene silencing.
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Affiliation(s)
- Ken-ichi Shinohara
- Department of Chemistry, Graduate School of Science, Kyoto UniversityKitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Shunta Sasaki
- Department of Chemistry, Graduate School of Science, Kyoto UniversityKitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Masafumi Minoshima
- Department of Chemistry, Graduate School of Science, Kyoto UniversityKitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto UniversityKitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto UniversityKitashirakawa-Oiwakecho, Sakyo, Kyoto, 606-8502, Japan
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43
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Alluri P, Liu B, Yu P, Xiao X, Kodadek T. Isolation and characterization of coactivator-binding peptoids from a combinatorial library. MOLECULAR BIOSYSTEMS 2006; 2:568-79. [PMID: 17216038 DOI: 10.1039/b608924k] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pharmacologic agents capable of activating the expression of specific genes would be valuable tools in biological research and could potentially be useful therapeutically. Efforts to develop a general solution to this problem have focused on the discovery of cell permeable mimics of native transcription factors comprised of linked DNA-binding and activation domain surrogates. Recently, we reported the isolation of a peptoid, called KBPo2, that binds a fragment of the mammalian coactivator CREB-binding protein (CBP). When delivered to a promoter-bound DNA-binding domain, this peptoid acted as a potent activation domain mimic in human cells. In this paper, we provide full details of the screening experiments and also report further characterization of this molecule as well as the other peptoids that came out of the screen. Of the three peptoids identified as putative CBP ligands, only KBPo2 demonstrated the necessary combination of binding affinity, specificity and cell permeability necessary to function as a potent activation domain mimic in cells. KBPo2 binds to CBP in a region different than that recognized by the native activation peptide from the transcription factor CREB.
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Affiliation(s)
- Prasanna Alluri
- Division of Translational Research, Department of Internal Medicine and Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9185, USA
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Tabassum S, Bhat IUH. Novel Bimetallic Complexes of Copper, Nickel and Manganese Derived from the Cobalt(III) Complex and their Interaction Studies with Calf Thymus DNA. TRANSIT METAL CHEM 2005. [DOI: 10.1007/s11243-005-6333-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Smolina IV, Demidov VV, Soldatenkov VA, Chasovskikh SG, Frank-Kamenetskii MD. End invasion of peptide nucleic acids (PNAs) with mixed-base composition into linear DNA duplexes. Nucleic Acids Res 2005; 33:e146. [PMID: 16204449 PMCID: PMC1243805 DOI: 10.1093/nar/gni151] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Peptide nucleic acid (PNA) is a synthetic DNA mimic with valuable properties and a rapidly growing scope of applications. With the exception of recently introduced pseudocomplementary PNAs, binding of common PNA oligomers to target sites located inside linear double-stranded DNAs (dsDNAs) is essentially restricted to homopurine-homopyrimidine sequence motifs, which significantly hampers some of the PNA applications. Here, we suggest an approach to bypass this limitation of common PNAs. We demonstrate that PNA with mixed composition of ordinary nucleobases is capable of sequence-specific targeting of complementary dsDNA sites if they are located at the very termini of DNA duplex. We then show that such targeting makes it possible to perform capturing of designated dsDNA fragments via the DNA-bound biotinylated PNA as well as to signal the presence of a specific dsDNA sequence, in the case a PNA beacon is employed. We also examine the PNA-DNA conjugate and prove that it can initiate the primer-extension reaction starting from the duplex DNA termini when a DNA polymerase with the strand-displacement ability is used. We thus conclude that recognition of duplex DNA by mixed-base PNAs via the end invasion has a promising potential for site-specific and sequence-unrestricted DNA manipulation and detection.
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Affiliation(s)
- Irina V Smolina
- Center for Advanced Biotechnology, Boston University, 36 Cummington Street, Boston, MA 02215, USA.
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Liu B, Alluri PG, Yu P, Kodadek T. A potent transactivation domain mimic with activity in living cells. J Am Chem Soc 2005; 127:8254-5. [PMID: 15941237 DOI: 10.1021/ja0515295] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transcriptional coactivator-binding peptoids were isolated from a large combinatorial library. One of these molecules is shown to function as a potent activation domain surrogate in mammalian cells. Up to a 900-fold increase in expression of a Gal4-responsive reporter gene is observed when a steroid conjugate of the peptoid is incubated with HeLa cells expressing a Gal4 DNA-binding domain (DBD)-glucocorticoid receptor ligand-binding domain (GRLBD) fusion protein.
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Affiliation(s)
- Bo Liu
- Departments of Internal Medicine and Molecular Biology and Center for Biomedical Inventions, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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Liu B, Yu P, Alluri PG, Kodadek T. Simple reporter gene-based assays for hairpin poly(amide) conjugate permeability and DNA-binding activity in living cells. MOLECULAR BIOSYSTEMS 2005; 1:307-17. [PMID: 16880996 DOI: 10.1039/b511514k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hairpin poly(amide)s (HPs) are sequence specific DNA-binding compounds that have engendered considerable interest as potential pharmacological agents to manipulate the expression of specific genes. However, recent reports have indicated that the ability of HP conjugates to pass through cell membranes is sensitive to the cell type employed and the nature of the conjugate. Furthermore, while binding of HPs to DNA sequences in vitro is relatively well understood, packing of DNA into chromatin in living cells makes predicting the efficiency with which a given poly(amide) will bind its cognate site less certain. Previous methods to evaluate HP permeability and binding in vivo, while effective, are somewhat tedious and qualitative. We report here two related reporter gene-based assays that provide a more convenient and quantitative measure of poly(amide) permeability and DNA binding activity in living cells. We anticipate that these methods will complement existing tools and facilitate the development of HP conjugates with the desired biological activity.
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Affiliation(s)
- Bo Liu
- Department of Internal Medicine and the Division for Translational Research, University of Texas Southwestern Medical Center, Dallas, TX 75390-8573, USA
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Dickinson LA, Burnett R, Melander C, Edelson BS, Arora PS, Dervan PB, Gottesfeld JM. Arresting Cancer Proliferation by Small-Molecule Gene Regulation. ACTA ACUST UNITED AC 2004; 11:1583-94. [PMID: 15556009 DOI: 10.1016/j.chembiol.2004.09.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Revised: 09/03/2004] [Accepted: 09/09/2004] [Indexed: 12/31/2022]
Abstract
A small library of pyrrole-imidazole polyamide-DNA alkylator (chlorambucil) conjugates was screened for effects on morphology and growth characteristics of a human colon carcinoma cell line, and a compound was identified that causes cells to arrest in the G2/M stage of the cell cycle. Microarray analysis indicates that the histone H4c gene is significantly downregulated by this polyamide. RT-PCR and Western blotting experiments confirm this result, and siRNA to H4c mRNA yields the same cellular response. Strikingly, reduction of H4 protein by >50% does not lead to widespread changes in global gene expression. Sequence-specific alkylation within the coding region of the H4c gene in cell culture was confirmed by LM-PCR. The compound is active in a wide range of cancer cell lines, and treated cells do not form tumors in nude mice. The compound is also active in vivo, blocking tumor growth in mice, without obvious animal toxicity.
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Affiliation(s)
- Liliane A Dickinson
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Liu B, Han Y, Ferdous A, Corey DR, Kodadek T. Transcription activation by a PNA-peptide chimera in a mammalian cell extract. ACTA ACUST UNITED AC 2004; 10:909-16. [PMID: 14583257 DOI: 10.1016/j.chembiol.2003.09.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Bo Liu
- Center for Biomedical Inventions, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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Shimogawa H, Kwon Y, Mao Q, Kawazoe Y, Choi Y, Asada S, Kigoshi H, Uesugi M. A wrench-shaped synthetic molecule that modulates a transcription factor-coactivator interaction. J Am Chem Soc 2004; 126:3461-71. [PMID: 15025473 DOI: 10.1021/ja038855+] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Development of synthetic molecules that provide external control over the transcription of a given gene represents a challenge in medicinal and bioorganic chemistry. Here we report design and analysis of wrenchnolol, a wrench-shaped synthetic molecule that impairs the transcription of the Her2 oncogene by disrupting association of transcription factor ESX with its coactivator Sur-2. The "jaw" part of the compound mimics the alpha-helical interface of the activation domain of ESX, and the "handle" region accepts chemical modifications for a range of analysis. A water-soluble handle permitted NMR study in aqueous solution; a biotinylated handle verified the selectivity of the interaction, and a fluorescent handle confirmed the cell permeability of the compound. The case study of wrenchnolol foreshadows the promise and the challenge of targeting protein-protein interactions in the nucleus and may lead to the development of unique synthetic modulators of gene transcription.
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Affiliation(s)
- Hiroki Shimogawa
- The Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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