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Guo P, Farahat AA, Paul A, Boykin DW, Wilson WD. Engineered modular heterocyclic-diamidines for sequence-specific recognition of mixed AT/GC base pairs at the DNA minor groove. Chem Sci 2021; 12:15849-15861. [PMID: 35024109 PMCID: PMC8672716 DOI: 10.1039/d1sc04720e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
This report describes a breakthrough in a project to design minor groove binders to recognize any sequence of DNA. A key goal is to invent synthetic chemistry for compound preparation to recognize an adjacent GG sequence that has been difficult to target. After trying several unsuccessful compound designs, an N-alkyl-benzodiimidazole structure was selected to provide two H-bond acceptors for the adjacent GG-NH groups. Flanking thiophenes provide a preorganized structure with strong affinity, DB2831, and the structure is terminated by phenyl-amidines. The binding experimental results for DB2831 with a target AAAGGTTT sequence were successful and include a high ΔT m, biosensor SPR with a K D of 4 nM, a similar K D from fluorescence titrations and supporting competition mass spectrometry. MD analysis of DB2831 bound to an AAAGGTTT site reveals that the two unprotonated N of the benzodiimidazole group form strong H-bonds (based on distance) with the two central G-NH while the central -CH of the benzodiimidazole is close to the -C[double bond, length as m-dash]O of a C base. These three interactions account for the strong preference of DB2831 for a -GG- sequence. Surprisingly, a complex with one dynamic, interfacial water is favored with 75% occupancy.
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Affiliation(s)
- Pu Guo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - Abdelbasset A Farahat
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Ananya Paul
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - David W Boykin
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
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2
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Learte‐Aymamí S, Rodríguez J, Vázquez ME, Mascareñas JL. Assembly of a Ternary Metallopeptide Complex at Specific DNA Sites Mediated by an AT‐Hook Adaptor. Chemistry 2020; 26:8875-8878. [DOI: 10.1002/chem.202001277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Soraya Learte‐Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - Jéssica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) andDepartamento de Química OrgánicaUniversidade de Santiago de Compostela 15782 Santiago de Compostela Spain
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3
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Farahat AA, Guo P, Shoeib H, Paul A, Boykin DW, Wilson WD. Small Sequence-Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove. Chemistry 2020; 26:4539-4551. [PMID: 31884714 PMCID: PMC7265973 DOI: 10.1002/chem.201904396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/10/2019] [Indexed: 12/24/2022]
Abstract
A series of small diamidines with thiophene and modified N-alkylbenzimidazole σ-hole module represent specific binding to single G⋅C base pair (bp) DNA sequence. The variation of N-alkyl or aromatic rings were sensitive to microstructures of the DNA minor groove. Thirteen new compounds were synthesized to test their binding affinity and selectivity. The dicyanobenzimidazoles needed to synthesize the target diamidines were made via condensation/cyclization reactions of different aldehydes with different 3-amino-4-(alkyl- or phenyl-amino) benzonitriles. The final diamidines were synthesized using lithium bis-trimethylsilylamide (LiN[Si(CH3 )3 ]2 ) or Pinner methods. The newly synthesized compounds showed strong binding and selectivity to AAAGTTT compared to similar sequences AAATTT and AAAGCTTT investigated by several biophysical methods including biosensor-SPR, fluorescence spectroscopy, DNA thermal melting, ESI-MS spectrometry, circular dichroism, and molecular dynamics. The binding affinity results determined by fluorescence spectroscopy are in accordance with those obtained by biosensor-SPR. These small size single G⋅C bp highly specific binders extend the compound database for future biological applications.
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Affiliation(s)
- Abdelbasset A. Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Hadir Shoeib
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - David W. Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - W. David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
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4
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Sánchez MI, Rama G, Calo-Lapido R, Ucar K, Lincoln P, López MV, Melle-Franco M, Mascareñas JL, Vázquez ME. Canonical DNA minor groove insertion of bisbenzamidine-Ru(ii) complexes with chiral selectivity. Chem Sci 2019; 10:8668-8674. [PMID: 31803441 PMCID: PMC6849638 DOI: 10.1039/c9sc03053k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 07/30/2019] [Indexed: 11/24/2022] Open
Abstract
We report the first Ru(ii) coordination compounds that interact with DNA through a canonical minor groove insertion mode and with selectivity for A/T rich sites. This was made possible by integrating a bis-benzamidine minor groove DNA-binding agent with a ruthenium(ii) complex. Importantly, one of the enantiomers (Δ-[Ru(bpy)2 b4bpy]2+, Δ-4Ru) shows a considerably higher DNA affinity than the parent organic ligand and the other enantiomer, particularly for the AATT sequence, while the other enantiomer preferentially targets long AAATTT sites with overall lower affinity. Finally, we demonstrate that the photophysical properties of these new binders can be exploited for DNA cleavage using visible light.
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Affiliation(s)
- Mateo I Sánchez
- 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 .
| | - Gustavo Rama
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) , Departamento de Química Inorgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Renata Calo-Lapido
- 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 .
| | - Kübra Ucar
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , SE 412 96 Gothenburg , Sweden
| | - Per Lincoln
- Department of Chemistry and Chemical Engineering , Chalmers University of Technology , SE 412 96 Gothenburg , Sweden
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) , Departamento de Química Inorgánica , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain
| | - Manuel Melle-Franco
- Ciceco - Aveiro Institute of Materials , University of Aveiro Campus Universitario de Santiago , Aveiro , 3810-193 , Portugal
| | - 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 .
| | - 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 .
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5
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A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context. Molecules 2019; 24:molecules24050946. [PMID: 30866557 PMCID: PMC6429135 DOI: 10.3390/molecules24050946] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/17/2022] Open
Abstract
We review the preparation of new compounds with good solution and cell uptake properties that can selectively recognize mixed A·T and G·C bp sequences of DNA. Our underlying aim is to show that these new compounds provide important new biotechnology reagents as well as a new class of therapeutic candidates with better properties and development potential than other currently available agents. In this review, entirely different ways to recognize mixed sequences of DNA by modifying AT selective heterocyclic cations are described. To selectively recognize a G·C base pair an H-bond acceptor must be incorporated with AT recognizing groups as with netropsin. We have used pyridine, azabenzimidazole and thiophene-N-methylbenzimidazole GC recognition units in modules crafted with both rational design and empirical optimization. These modules can selectively and strongly recognize a single G·C base pair in an AT sequence context. In some cases, a relatively simple change in substituents can convert a heterocyclic module from AT to GC recognition selectivity. Synthesis and DNA interaction results for initial example lead modules are described for single G·C base pair recognition compounds. The review concludes with a description of the initial efforts to prepare larger compounds to recognize sequences of DNA with more than one G·C base pairs. The challenges and initial successes are described along with future directions.
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6
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Liu B, Pett L, Kiakos K, Patil PC, Satam V, Hartley JA, Lee M, Wilson WD. DNA-Binding Properties of New Fluorescent AzaHx Amides: Methoxypyridylazabenzimidazolepyrroleimidazole/pyrrole. Chembiochem 2018; 19:1979-1987. [PMID: 29974647 DOI: 10.1002/cbic.201800273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Indexed: 11/11/2022]
Abstract
DNA minor groove binding polyamides have been extensively developed to control abnormal gene expression. The establishment of novel, inherently fluorescent 2-(p-anisyl)benzimidazole (Hx) amides has provided an alternative path for studying DNA binding in cells by direct observation of cell localization. Because of the 2:1 antiparallel stacking homodimer binding mode of these molecules to DNA, modification of Hx amides to 2-(p-anisyl)-4-azabenzimidazole (AzaHx) amides has successfully extended the DNA-recognition repertoire from central CG [recognized by Hx-I (I=N-methylimidazole)] to central GC [recognized by AzaHx-P (P=N-methylpyrrole)] recognition. For potential targeting of two consecutive GG bases, modification of the AzaHx moiety to 2- and 3-pyridyl-aza-benzimidazole (Pyr-AzaHx) moieties was explored. The newly designed molecules are also small-sized, fluorescent amides with the Pyr-AzaHx moiety connected to two conventional five-membered heterocycles. Complementary biophysical methods were performed to investigate the DNA-binding properties of these molecules. The results showed that neither 3-Pyr-AzaHx nor 2-Pyr-AzaHx was able to mimic I-I=N-methylimidazole-N-methylimidazole to target GG dinucleotides specifically. Rather, 3-Pyr-AzaHx was found to function like AzaHx, f-I (f=formamide), or P-I as an antiparallel stacked dimer. 3-Pyr-AzaHx-PI (2) binds 5'-ACGCGT'-3' with improved binding affinity and high sequence specificity in comparison to its parent molecule AzaHx-PI (1). However, 2-Pyr-AzaHx is detrimental to DNA binding because of an unfavorable steric clash upon stacking in the minor groove.
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Affiliation(s)
- Beibei Liu
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA, 30303, USA
| | - Luke Pett
- Cancer Research (UK) Drug-DNA Interactions Research Group, UCL Cancer Institute, Gower Street, London, WC1E 6BT, UK
| | - Konstantinos Kiakos
- Cancer Research (UK) Drug-DNA Interactions Research Group, UCL Cancer Institute, Gower Street, London, WC1E 6BT, UK
| | - Pravin C Patil
- Department of Chemistry, Hope College, 141 E 12th Street, Holland, MI, 49423, USA
| | - Vijay Satam
- Department of Chemistry, Hope College, 141 E 12th Street, Holland, MI, 49423, USA
| | - John A Hartley
- Cancer Research (UK) Drug-DNA Interactions Research Group, UCL Cancer Institute, Gower Street, London, WC1E 6BT, UK
| | - Moses Lee
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA, 30303, USA.,Department of Chemistry, Hope College, 141 E 12th Street, Holland, MI, 49423, USA.,Current address: M. J. Murdock Charitable Trust, 703 Broadway Street, Suite, 710, Vancouver, WA, 98660, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA, 30303, USA
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7
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Rodríguez J, Learte-Aymamí S, Mosquera J, Celaya G, Rodríguez-Larrea D, Vázquez ME, Mascareñas JL. DNA-binding miniproteins based on zinc fingers. Assessment of the interaction using nanopores. Chem Sci 2018; 9:4118-4123. [PMID: 29780541 PMCID: PMC5941273 DOI: 10.1039/c7sc05441f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/23/2018] [Indexed: 12/18/2022] Open
Abstract
We report a synthetic miniprotein that combines zinc finger modules of the transcription factor GAGA with the AT-hook peptide. This designed chimera binds to extended DNA sites with high affinity and selectivity, as shown by nanopore force spectroscopy.
Obtaining artificial proteins that mimic the DNA binding properties of natural transcription factors could open new ways of manipulating gene expression at will. In this context it is particularly interesting to develop simple synthetic systems. Inspired by the modularity of natural transcription factors, we have designed synthetic miniproteins that combine the zinc finger module of the transcription factor GAGA and AT-hook peptide domains. These constructs are capable of binding to composite DNA sequences of up to 14 base pairs with high affinity and good selectivity. In particular, we have synthesized three different chimeras and characterized their DNA binding properties by electrophoresis and fluorescence anisotropy. We have also used, for the first time in the study of peptide-based DNA binders, nanopore force spectroscopy to obtain further data on the DNA interaction.
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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 .
| | - Soraya Learte-Aymamí
- 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 .
| | - 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 .
| | - Garbiñe Celaya
- Biofisika Institute (CSIC, UPV/EHU) , Department of Biochemistry and Molecular Biology (UPV/EHU) , Leioa 48940 , Spain
| | - David Rodríguez-Larrea
- Biofisika Institute (CSIC, UPV/EHU) , Department of Biochemistry and Molecular Biology (UPV/EHU) , Leioa 48940 , Spain
| | - 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 .
| | - 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 .
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8
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Pinto LF, Correa J, Zhao L, Riguera R, Fernandez-Megia E. Fast NMR Screening of Macromolecular Complexes by a Paramagnetic Spin Relaxation Filter. ACS OMEGA 2018; 3:2974-2983. [PMID: 31458565 PMCID: PMC6641404 DOI: 10.1021/acsomega.7b02074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/28/2018] [Indexed: 05/09/2023]
Abstract
The paramagnetic spin relaxation filter is described for the rapid NMR screening of intermolecular interactions between ligands and macromolecular anionic receptors with large transverse relaxation enhancements (R 2p). The addition of micromolar concentrations of Gd3+ to the mixture produces the immediate broadening/suppression of the NMR signals of interacting species while leaving unaffected those of noncompetitive binders (one-dimensional and two-dimensional experiments). The method is highly sensitive, unveiling interactions that are too weak to generate changes in chemical shifts or relaxation times. It is operationally very simple and hence, it is amenable to ready implementation by nonspecialists. Examples of application such as detecting the formation of interpolymer complexes, cyclodextrin host-guest interactions, and the screening of DNA ligands are included that demonstrate the reliability and broad applicability of the method.
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Affiliation(s)
| | | | - Libo Zhao
- 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 s/n, 15782 Santiago de Compostela, Spain
| | - Ricardo Riguera
- 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 s/n, 15782 Santiago de Compostela, Spain
| | - Eduardo Fernandez-Megia
- 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 s/n, 15782 Santiago de Compostela, Spain
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9
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Facile Chemical Access to Biologically Active Norcantharidin Derivatives from Biomass. Molecules 2017; 22:molecules22122210. [PMID: 29231880 PMCID: PMC6149738 DOI: 10.3390/molecules22122210] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 11/30/2017] [Accepted: 12/07/2017] [Indexed: 01/21/2023] Open
Abstract
Reductive amination of 2,5-diformylfuran (DFF) was used to implement the transition from bio-derived 5-hydroxymethylfurfural (HMF) to pharmaceuticals. The synthesized bis(aminomethyl)furans were utilized as building blocks for the construction of new derivatives with structural cores of naturally occurring biologically active compounds. Using the one-pot procedure, which included the Diels–Alder reaction followed by hydrogenation of the double bond, bio-derived analogues of the anticancer drug norcantharidin were obtained. The cyclization process was diastereoselective, and resulted in the formation of tricyclic products with the endo configuration. Analysis of cytotoxycity for the resulting tricyclic amine-containing compounds showed an increase of anticancer activity as compared with the unsubstituted norcantharimide.
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10
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Boga S, Bouzada D, García Peña D, Vázquez López M, Vázquez ME. Sequence-Specific DNA Recognition with Designed Peptides. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700988] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sonia Boga
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - David Bouzada
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Diego García Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Inorgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS) and Departamento de Química Orgánica; Universidade de Santiago de Compostela; 15782 Santiago de Compostela Spain
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11
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Learte-Aymamí S, Curado N, Rodríguez J, Vázquez ME, Mascareñas JL. Metal-Dependent DNA Recognition and Cell Internalization of Designed, Basic Peptides. J Am Chem Soc 2017; 139:16188-16193. [PMID: 29056048 PMCID: PMC5741177 DOI: 10.1021/jacs.7b07422] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Indexed: 12/18/2022]
Abstract
A fragment of the DNA basic region (br) of the GCN4 bZIP transcription factor has been modified to include two His residues at designed i and i+4 positions of its N-terminus. The resulting monomeric peptide (brHis2) does not bind to its consensus target DNA site (5'-GTCAT-3'). However, addition of Pd(en)Cl2 (en, ethylenediamine) promotes a high-affinity interaction with exquisite selectivity for this sequence. The peptide-DNA complex is disassembled by addition of a slight excess of a palladium chelator, and the interaction can be reversibly switched multiple times by playing with controlled amounts of either the metal complex or the chelator. Importantly, while the peptide brHis2 fails to translocate across cell membranes on its own, addition of the palladium reagent induces an efficient cell internalization of this peptide. In short, we report (1) a designed, short peptide that displays highly selective, major groove DNA binding, (2) a reversible, metal-dependent DNA interaction, and (3) a metal-promoted cell internalization of this basic peptide.
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Affiliation(s)
- Soraya Learte-Aymamí
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Natalia Curado
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Jéssica Rodríguez
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M. Eugenio Vázquez
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José L. Mascareñas
- Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS)
and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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12
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Guo P, Paul A, Kumar A, Farahat AA, Kumar D, Wang S, Boykin DW, Wilson WD. The Thiophene "Sigma-Hole" as a Concept for Preorganized, Specific Recognition of G⋅C Base Pairs in the DNA Minor Groove. Chemistry 2016; 22:15404-15412. [PMID: 27624927 PMCID: PMC5214980 DOI: 10.1002/chem.201603422] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Indexed: 11/10/2022]
Abstract
In spite of its importance in cell function, targeting DNA is under-represented in the design of small molecules. A barrier to progress in this area is the lack of a variety of modules that recognize G⋅C base pairs (bp) in DNA sequences. To overcome this barrier, an entirely new design concept for modules that can bind to mixed G⋅C and A⋅T sequences of DNA is reported herein. Because of their successes in biological applications, minor-groove-binding heterocyclic cations were selected as the platform for design. Binding to A⋅T sequences requires hydrogen-bond donors whereas recognition of the G-NH2 requires an acceptor. The concept that we report herein uses pre-organized N-methylbenzimidazole (N-MeBI) thiophene modules for selective binding with mixed bp DNA sequences. The interaction between the thiophene sigma hole (positive electrostatic potential) and the electron-donor nitrogen of N-MeBI preorganizes the conformation for accepting an hydrogen bond from G-NH2 . The compound-DNA interactions were evaluated with a powerful array of biophysical methods and the results show that N-MeBI-thiophene monomer compounds can strongly and selectively recognize single G⋅C bp sequences. Replacing the thiophene with other moieties significantly reduces binding affinity and specificity, as predicted by the design concept. These results show that the use of molecular features, such as sigma-holes, can lead to new approaches for small molecules in biomolecular interactions.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Dhiraj Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - Siming Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, 30303-3083, USA.
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13
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Rodríguez J, Mosquera J, Vázquez ME, Mascareñas JL. Nickel-Promoted Recognition of Long DNA Sites by Designed Peptide Derivatives. Chemistry 2016; 22:13474-7. [DOI: 10.1002/chem.201602783] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Indexed: 12/13/2022]
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
| | - 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
| | - 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
| | - 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
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14
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Gamba I, Salvadó I, Brissos RF, Gamez P, Brea J, Loza MI, Vázquez ME, López MV. High-affinity sequence-selective DNA binding by iridium(iii) polypyridyl organometallopeptides. Chem Commun (Camb) 2016; 52:1234-7. [DOI: 10.1039/c5cc07619f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We demonstrate the application of solid-phase peptide synthesis methods for assembling polynuclear Ir(iii) organometallopeptides that exhibit high DNA-binding affinity, sequence selectivity, and high cytotoxic effect towards a set of cancer cell lines.
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Affiliation(s)
- Ilaria Gamba
- Departamento de Química Inorgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Iria Salvadó
- Departamento de Química Inorgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Rosa F. Brissos
- Departament de Química Inorgánica
- QBI
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - Patrick Gamez
- Departament de Química Inorgánica
- QBI
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - José Brea
- Grupo de Investigación BioFarma/Plataforma de Screening USEF
- Centro de Investigación CIMUS
- Universidade de Santiago de Compostela
- Spain
| | - María Isabel Loza
- Grupo de Investigación BioFarma/Plataforma de Screening USEF
- Centro de Investigación CIMUS
- Universidade de Santiago de Compostela
- Spain
| | - M. Eugenio Vázquez
- 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
| | - Miguel Vázquez López
- Departamento de Química Inorgánica 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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Penas C, Sánchez MI, Guerra-Varela J, Sanchez L, Vázquez ME, Mascareñas JL. Light-Controlled Cellular Internalization and Cytotoxicity of Nucleic Acid-Binding Agents: Studies in Vitro and in Zebrafish Embryos. Chembiochem 2016; 17:37-41. [PMID: 26534774 PMCID: PMC4766732 DOI: 10.1002/cbic.201500455] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Indexed: 01/19/2023]
Abstract
We synthesized octa-arginine conjugates of DNA-binding agents (bisbenzamidine, acridine and Thiazole Orange) and demonstrated that their DNA binding and cell internalization can be inhibited by appending a (negatively charged) oligoglutamic tail through a photolabile linker. UV irradiation released the parent conjugates, thus restoring cell internalization and biological activity. Assays with zebrafish embryos demonstrates the potential of this prodrug strategy for controlling in vivo cytotoxicity.
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Affiliation(s)
- Cristina Penas
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais, Moleculares (CIQUS), Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, Campus Vida, 15782, Santiago de Compostela, Spain
| | - Mateo I Sánchez
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais, Moleculares (CIQUS), Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, Campus Vida, 15782, Santiago de Compostela, Spain
| | - Jorge Guerra-Varela
- Departmento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Av. Carballo Calero s/n, 27002, Lugo, Spain
| | - Laura Sanchez
- Departmento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Av. Carballo Calero s/n, 27002, Lugo, Spain
| | - M Eugenio Vázquez
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais, Moleculares (CIQUS), Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, Campus Vida, 15782, Santiago de Compostela, Spain.
| | - José L Mascareñas
- Departamento de Química Orgánica, Centro Singular de Investigación en Química Biolóxica e Materiais, Moleculares (CIQUS), Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, Campus Vida, 15782, Santiago de Compostela, Spain.
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16
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Stefanucci A, Mosquera J, Vázquez E, Mascareñas JL, Novellino E, Mollica A. Synthesis, Characterization, and DNA Binding Profile of a Macrocyclic β-Sheet Analogue of ARC Protein. ACS Med Chem Lett 2015; 6:1220-4. [PMID: 26713108 DOI: 10.1021/acsmedchemlett.5b00363] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 10/29/2015] [Indexed: 12/29/2022] Open
Abstract
ARC repressor (apoptosis repressor with caspase recruitment domain) is a protein which binds selectively to a specific sequence of DNA. In humans, ARC is primarily expressed in striated muscle tissue, which normally does not undergo rapid cell turnover. This suggests that ARC may play a protective role in the prevention against Duchenne Muscular Dystrophy and several types of tumors. In this Letter we report the synthesis, characterization, and conformational analysis of a β-sheet ARC repressor mimetic, based on the amino acid sequence of the β-sheet domain in the ARC protein. The ability of this β-sheet macrocycle to bind to double-stranded DNA was also evaluated using spectroscopic methods. Our data show that the synthetic peptide has a defined conformation and is able to bind DNA with reasonable affinity. These initial results lay the groundwork for the design of novel β-sheets folded peptides as valuable substitutes of transcription factor proteins in drug therapy.
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Affiliation(s)
- Azzurra Stefanucci
- Dipartimento
di Chimica, Sapienza, Università di Roma, P.le A. Moro
5, 00187 Rome, Italy
| | - 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
| | - Eugènio 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
| | - 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
| | - Ettore Novellino
- Dipartimento
di Farmacia, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Naples, Italy
| | - Adriano Mollica
- Dipartimento
di Farmacia, Università di Chieti-Pescara “G. d’Annunzio”, Via dei Vestini 31, 66100 Chieti, Italy
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17
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Rodríguez J, Mosquera J, Couceiro JR, Vázquez ME, Mascareñas JL. The AT-Hook motif as a versatile minor groove anchor for promoting DNA binding of transcription factor fragments. Chem Sci 2015; 6:4767-4771. [PMID: 26290687 PMCID: PMC4538796 DOI: 10.1039/c5sc01415h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022] Open
Abstract
We report the development of chimeric DNA binding peptides comprising a DNA binding fragment of natural transcription factors (the basic region of a bZIP protein or a monomeric zinc finger module) and an AT-Hook peptide motif. The resulting peptide conjugates display high DNA affinity and excellent sequence selectivity. Furthermore, the AT-Hook motif also favors the cell internalization of the conjugates.
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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: +34 981 576541 ext. 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: +34 981 576541 ext. 14405
| | - Jose R. Couceiro
- 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: +34 981 576541 ext. 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: +34 981 576541 ext. 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: +34 981 576541 ext. 14405
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18
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Mosquera J, Sánchez MI, Valero J, Mendoza JD, Vázquez ME, Mascareñas JL. Sequence-selective DNA binding with cell-permeable oligoguanidinium–peptide conjugates. Chem Commun (Camb) 2015; 51:4811-4. [DOI: 10.1039/c4cc09525a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Conjugation of a short peptide fragment from a bZIP protein to an oligoguanidinium tail results in a DNA-binding miniprotein that selectively interacts with composite sequences containing the peptide-binding site next to an A/T-rich tract.
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Affiliation(s)
- Jesús Mosquera
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- C/ Jenaro de la Fuente s/n
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Mateo I. Sánchez
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- C/ Jenaro de la Fuente s/n
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - Julián Valero
- Institute of Chemical Research of Catalonia (ICIQ)
- 43007 Tarragona
- Spain
| | - Javier de Mendoza
- Institute of Chemical Research of Catalonia (ICIQ)
- 43007 Tarragona
- Spain
| | - M. Eugenio Vázquez
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- C/ Jenaro de la Fuente s/n
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
| | - José L. Mascareñas
- Departamento de Química Orgánica and Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
- C/ Jenaro de la Fuente s/n
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela
- Spain
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19
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Sánchez MI, Martínez-Costas J, Mascareñas JL, Vázquez ME. MitoBlue: a nontoxic and photostable blue-emitting dye that selectively labels functional mitochondria. ACS Chem Biol 2014; 9:2742-7. [PMID: 25325672 PMCID: PMC4306598 DOI: 10.1021/cb500552f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We report the discovery of a fluorogenic
dye, N1,N3-di(2-aminidonaphthalen-6-yl)
propane-1,3-diamine, MitoBlue, which selectively stains functional
mitochondria while displaying low toxicity, bright blue emission,
and high resistance to photobleaching. Additionally, we show that
a biotin-labeled MitoBlue derivative can be used as a handle for the
delivery of streptavidin-tagged species to the mitochondria.
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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), and ‡Departamento de
Bioquímica y Biología Molecular and Centro Singular
de Investigación en Química Biolóxica e Materiais
Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | | | - José L. Mascareñas
- Departamento
de Química Orgánica and Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS), and ‡Departamento de
Bioquímica y Biología Molecular and Centro Singular
de Investigación en Química Biolóxica e Materiais
Moleculares (CIQUS), Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - M. Eugenio Vázquez
- Departamento
de Química Orgánica and Centro Singular de Investigación
en Química Biolóxica e Materiais Moleculares (CIQUS), and ‡Departamento de
Bioquímica y Biología Molecular 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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20
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Bordello J, Sánchez MI, Vázquez ME, Mascareñas JL, Al-Soufi W, Novo M. Fluorescence-labeled bis-benzamidines as fluorogenic DNA minor-groove binders: photophysics and binding dynamics. Chemistry 2014; 21:1609-19. [PMID: 25418429 DOI: 10.1002/chem.201404926] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Indexed: 01/19/2023]
Abstract
In recent decades there has been great interest in the design of highly sensitive sequence-specific DNA binders. The eligibility of the binder depends on the magnitude of the fluorescence increase upon binding, related to its photophysics, and on its affinity and specificity, which is, in turn, determined by the dynamics of the binding process. Therefore, progress in the design of DNA binders requires both thorough photophysical studies and precise determination of the association and dissociation rate constants involved. We have studied two bis-benzamidine (BBA) derivatives labeled by linkers of various lengths with the dye Oregon Green (OG). These fluorogenic binders show a dramatic fluorescence enhancement upon binding to the minor groove of double-stranded (ds) DNA, as well as significant improvement in their sequence specificity versus the parent BBA, although with decreased affinity constants. Detailed photophysical analysis shows that static and dynamic quenching of the OG fluorescence by BBA through photoinduced electron transfer is suppressed upon insertion of BBA into the minor groove of DNA. Fluorescence correlation spectroscopy yields precise dynamic rate constants that prove that the association process of these fluorogenic binders to dsDNA is very similar to that of BBA alone and that their lower affinity is mainly a consequence of their weaker attachment to the minor groove and the resultant faster dissociation process. The conclusions of this study will allow us to go one step further in the design of new DNA binders with tunable fluorescence and binding properties.
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Affiliation(s)
- Jorge Bordello
- Department of Physical Chemistry, Faculty of Science, Campus Lugo, University of Santiago de Compostela, 27002 Lugo (Spain), Fax: (+34) 982824001
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21
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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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22
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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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23
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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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24
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Sánchez MI, Penas C, Vázquez ME, Mascareñas JL. Metal-catalyzed uncaging of DNA-binding agents in living cells†Electronic supplementary information (ESI) available: Synthesis and characterization of the studied molecules and required precursors. NMR, UV, and fluorescence spectra, titrations, control experiments, and detailed procedures for cell uptake and co-staining experiments. See DOI: 10.1039/c3sc53317dClick here for additional data file. Chem Sci 2014; 5:1901-1907. [PMID: 25632343 PMCID: PMC4304260 DOI: 10.1039/c3sc53317d] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/30/2014] [Indexed: 12/27/2022] Open
Abstract
Ruthenium-catalyzed activation of DNA-binding compounds in aqueous buffers and in cellular environments.
Attachment of alloc protecting groups to the amidine units of fluorogenic DNA-binding bisbenzamidines or to the amino groups of ethidium bromide leads to a significant reduction of their DNA affinity. More importantly, the active DNA-binding species can be readily regenerated by treatment with ruthenium catalysts in aqueous conditions, even in cell cultures. The catalytic chemical uncaging can be easily monitored by fluorescence microscopy, because the protected products display both different emission properties and cell distribution to the parent compounds.
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Affiliation(s)
- Mateo I Sánchez
- Departamento de Química Orgánica e Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Tel: +34 881 81 44 05
| | - Cristina Penas
- Departamento de Química Orgánica e Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Tel: +34 881 81 44 05
| | - M Eugenio Vázquez
- Departamento de Química Orgánica e Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Tel: +34 881 81 44 05
| | - José L Mascareñas
- Departamento de Química Orgánica e Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS) , Universidade de Santiago de Compostela , 15782 Santiago de Compostela , Spain . ; Tel: +34 881 81 44 05
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25
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Rodríguez J, Mosquera J, Vázquez O, Vázquez ME, Mascareñas JL. The ββα fold of zinc finger proteins as a “natural” protecting group. Chemoselective synthesis of a DNA-binding zinc finger derivative. Chem Commun (Camb) 2014; 50:2258-60. [DOI: 10.1039/c3cc47599a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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Gamba I, Rama G, Ortega-Carrasco E, Maréchal JD, Martínez-Costas J, Eugenio Vázquez M, López MV. Programmed stereoselective assembly of DNA-binding helical metallopeptides. Chem Commun (Camb) 2014; 50:11097-100. [DOI: 10.1039/c4cc03606a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have applied solid phase peptide synthesis methods for the construction of peptide ligands that coordinate Fe(ii) ions and fold into chiral peptide helicates that show great affinity and chiral selectivity for three-way DNA junctions and promising cell-internalization properties.
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Affiliation(s)
- Ilaria Gamba
- Departamento de Química Inorgánica
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela, Spain
| | - Gustavo Rama
- Departamento de Química Inorgánica
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela, Spain
| | | | | | - José Martínez-Costas
- Departamento de Bioquímica y Biología Molecular
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela, Spain
| | - M. Eugenio Vázquez
- Departamento de Química Orgánica
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS)
- Universidade de Santiago de Compostela
- 15782 Santiago de Compostela, Spain
| | - Miguel Vázquez López
- Departamento de Química Inorgánica
- 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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27
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Mosquera J, Zarra S, Nitschke JR. Aqueous Anion Receptors through Reduction of Subcomponent Self-Assembled Structures. Angew Chem Int Ed Engl 2013; 53:1556-9. [DOI: 10.1002/anie.201308117] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/31/2013] [Indexed: 12/28/2022]
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Mosquera J, Zarra S, Nitschke JR. Aqueous Anion Receptors through Reduction of Subcomponent Self-Assembled Structures. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308117] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Chai Y, Munde M, Kumar A, Mickelson L, Lin S, Campbell NH, Banerjee M, Akay S, Liu Z, Farahat AA, Nhili R, Depauw S, David-Cordonnier MH, Neidle S, Wilson WD, Boykin DW. Structure-dependent binding of arylimidamides to the DNA minor groove. Chembiochem 2013; 15:68-79. [PMID: 24323836 DOI: 10.1002/cbic.201300622] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Indexed: 12/12/2022]
Abstract
Heterocyclic diamidines are strong DNA minor-groove binders and have excellent antiparasitic activity. To extend the biological activity of these compounds, a series of arylimidamides (AIAs) analogues, which have better uptake properties in Leishmania and Trypanosoma cruizi than diamidines, was prepared. The binding of the AIAs to DNA was investigated by Tm , fluorescence displacement titration, circular dichroism, DNase I footprinting, biosensor surface plasmon resonance, X-ray crystallography and molecular modeling. These compounds form 1:1 complexes with AT sequences in the DNA minor groove, and the binding strength varies with substituent size, charge and polarity. These substituent-dependent structure and properties provide a SAR that can be used to estimate K values for binding to DNA in this series. The structural results and molecular modeling studies provide an explanation for the differences in binding affinities for AIAs.
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Affiliation(s)
- Yun Chai
- Department of Chemistry, Georgia State University, 50 Decatur St. SE., Atlanta, GA 30303 (USA)
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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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Xie X, Choi B, Largy E, Guillot R, Granzhan A, Teulade-Fichou MP. Asymmetric Distyrylpyridinium Dyes as Red-Emitting Fluorescent Probes for Quadruplex DNA. Chemistry 2013; 19:1214-26. [DOI: 10.1002/chem.201203710] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Indexed: 11/06/2022]
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MoradpourHafshejani S, Hedley JH, Haigh AO, Pike AR, Tuite EM. Synthesis and binding of proflavine diazides as functional intercalators for directed assembly on DNA. RSC Adv 2013. [DOI: 10.1039/c3ra43090a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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Bordello J, Sánchez MI, Vázquez ME, Mascareñas JL, Al-Soufi W, Novo M. Single-Molecule Approach to DNA Minor-Groove Association Dynamics. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Bordello J, Sánchez MI, Vázquez ME, Mascareñas JL, Al-Soufi W, Novo M. Single-molecule approach to DNA minor-groove association dynamics. Angew Chem Int Ed Engl 2012; 51:7541-4. [PMID: 22700034 DOI: 10.1002/anie.201201099] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/26/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Jorge Bordello
- Departamento de Química Física, Universidade de Santiago de Compostela, Facultade de Ciencias, 27001 Lugo, Spain
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van Dongen SFM, Janvore J, van Berkel SS, Marie E, Piel M, Tribet C. Reactive protein-repellent surfaces for the straightforward attachment of small molecules up to whole cells. Chem Sci 2012. [DOI: 10.1039/c2sc20652h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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