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Peptide Regulation of Gene Expression: A Systematic Review. Molecules 2021; 26:molecules26227053. [PMID: 34834147 PMCID: PMC8619776 DOI: 10.3390/molecules26227053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/22/2022] Open
Abstract
Peptides are characterized by their wide range of biological activity: they regulate functions of the endocrine, nervous, and immune systems. The mechanism of such action of peptides involves their ability to regulate gene expression and protein synthesis in plants, microorganisms, insects, birds, rodents, primates, and humans. Short peptides, consisting of 2-7 amino acid residues, can penetrate into the nuclei and nucleoli of cells and interact with the nucleosome, the histone proteins, and both single- and double-stranded DNA. DNA-peptide interactions, including sequence recognition in gene promoters, are important for template-directed synthetic reactions, replication, transcription, and reparation. Peptides can regulate the status of DNA methylation, which is an epigenetic mechanism for the activation or repression of genes in both the normal condition, as well as in cases of pathology and senescence. In this context, one can assume that short peptides were evolutionarily among the first signaling molecules that regulated the reactions of template-directed syntheses. This situation enhances the prospects of developing effective and safe immunoregulatory, neuroprotective, antimicrobial, antiviral, and other drugs based on short peptides.
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2
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Surin M, Ulrich S. From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies. ChemistryOpen 2020; 9:480-498. [PMID: 32328404 PMCID: PMC7175023 DOI: 10.1002/open.202000013] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.
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Affiliation(s)
- Mathieu Surin
- Laboratory for Chemistry of Novel MaterialsCenter of Innovation and Research in Materials and Polymers (CIRMAP)University of Mons-UMONS7000MonsBelgium
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3
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Mosquera J, García I, Liz-Marzán LM. Cellular Uptake of Nanoparticles versus Small Molecules: A Matter of Size. Acc Chem Res 2018; 51:2305-2313. [PMID: 30156826 DOI: 10.1021/acs.accounts.8b00292] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The primary function of the cell membrane is to protect cells from their surroundings. This entails a strict regulation on controlling the exchange of matter between the cell and its environment. A key factor when considering potential biological applications of a particular chemical structure has to do with its ability to internalize into cells. Molecules that can readily cross cell membranes are frequently needed in biological research and medicine, since most therapeutic entities are designed to modulate intracellular components. However, the design of molecules that do not penetrate cells is also relevant toward, for example, extracellular contrast agents, which are most widely used in clinical diagnosis. Small molecules have occupied the forefront of biomedical research until recently, but the past few decades have seen an increasing use of larger chemical structures, such as proteins or nanoparticles, leading to unprecedented and often unexpectedly novel research. Great achievements have been made toward understanding the rules that govern cellular uptake, which show that cell internalization of molecules is largely affected by their size. For example, macromolecules such as proteins and nucleic acids are usually unable to internalize cells. Intriguingly, in the case of nanoparticles, larger sizes seem to facilitate internalization via endocytic pathways, through which the particles remain trapped in lysosomes and endosomes. In this Account, we aimed at presenting our personal view of how different chemical structures behave in terms of cell internalization due to their size, ranging from small drugs to large nanoparticles. We first introduce the properties of cell membranes and the main mechanisms involved in cellular uptake. We then discuss the cellular internalization of molecules, distinguishing between those with molecular weights below 1 kDa and biological macromolecules such as proteins and nucleic acids. In the last section, we review the biological behavior of nanoparticles, with a special emphasis on plasmonic nanoparticles, which feature a high potential in the biomedical field. For each group of chemical structures, we discuss the parameters affecting their cellular internalization but also strategies that can be applied to achieve the desired intracellular delivery. Particular attention is paid to approaches that allow conditional regulation of the cell internalization process using external triggers, such as activable cell penetrating peptides, due to the impact that these systems may have in drug delivery and sensing applications. The Account ends with a "Conclusions and Outlook" section, where general lessons and future directions toward further advancements are briefly presented.
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Affiliation(s)
- Jesús Mosquera
- CIC biomaGUNE and CIBER-BBN, Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Isabel García
- CIC biomaGUNE and CIBER-BBN, Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
| | - Luis M. Liz-Marzán
- CIC biomaGUNE and CIBER-BBN, Paseo de Miramón 182, 20014 Donostia-San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
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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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5
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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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6
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Bartolami E, Bouillon C, Dumy P, Ulrich S. Bioactive clusters promoting cell penetration and nucleic acid complexation for drug and gene delivery applications: from designed to self-assembled and responsive systems. Chem Commun (Camb) 2016; 52:4257-73. [DOI: 10.1039/c5cc09715k] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recent developments in the (self-)assembly of cationic clusters promoting nucleic acids complexation and cell penetration open the door to applications in drug and gene delivery.
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Affiliation(s)
- Eline Bartolami
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Camille Bouillon
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
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7
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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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8
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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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9
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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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