1
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Gómez-González J, Bouzada D, Pérez-Márquez LA, Sciortino G, Maréchal JD, Vázquez López M, Vázquez ME. Stereoselective Self-Assembly of DNA Binding Helicates Directed by the Viral β-Annulus Trimeric Peptide Motif. Bioconjug Chem 2021; 32:1564-1569. [PMID: 34320309 PMCID: PMC8485332 DOI: 10.1021/acs.bioconjchem.1c00312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Combining
coordination chemistry and peptide engineering offers
extraordinary opportunities for developing novel molecular (supra)structures.
Here, we demonstrate that the β-annulus motif is capable of
directing the stereoselective assembly of designed peptides containing
2,2′-bipyridine ligands into parallel three-stranded chiral
peptide helicates, and that these helicates selectively bind with
high affinity to three-way DNA junctions.
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Affiliation(s)
- Jacobo Gómez-González
- 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
| | - David Bouzada
- 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
| | - Lidia A Pérez-Márquez
- 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
| | - Giuseppe Sciortino
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola, Spain
| | - Jean-Didier Maréchal
- Insilichem, Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola, Spain
| | - 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
| | - 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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2
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Abstract
An organometallic complex that mimics an amino acid, also known as an amino acid isostere, can be synthesized from a functionalized bipyridine ligand and a fac-[Re(CO)3]+ center. The reaction of an achiral ligand and metal results in a racemic mixture of chiral-at-metal complexes. These metal species have amine and carboxy termini, a side chain type unit that can be varied, as well as the chiral metal that is analogous to the α carbon of an amino acid. The racemic mixtures can be separated into enantiomers by chiral chromatography, and the metal complexes can be incorporated into peptides by using solid-phase peptide synthesis.
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Affiliation(s)
- Sanjay Gaire
- Department of Chemistry, University of Akron, Akron, Ohio 44312-3601, United States
| | - Briana R Schrage
- Department of Chemistry, University of Akron, Akron, Ohio 44312-3601, United States
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3
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Liu XY, Yin XM, Yang SL, Zhang L, Bu R, Gao EQ. Chromic and Fluorescence-Responsive Metal-Organic Frameworks Afforded by N-Amination Modification. ACS APPLIED MATERIALS & INTERFACES 2021; 13:20380-20387. [PMID: 33878258 DOI: 10.1021/acsami.1c03937] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Sensory materials that show color and/or fluorescence changes in response to specific gases or vapors have important applications in many fields. Here, we report the postsynthetic preparation of novel sensory metal-organic frameworks (MOFs) and their multiple responsive properties. Through postsynthetic N-amination, the 2,2'-bipyridyl spacers in a Zr(IV) MOF are partially transformed into N-aminobipyridinium. The new MOF (Zr-bpy-A) shows chromic behavior toward ammonia and amines because the electron-deficient pyridinium groups form charge-transfer complexes with amino moieties. It also shows a unique chromic response to formaldehyde owing to the Schiff-base condensation with the N-amino groups. Furthermore, the N-amino group can be used to graft different polycyclic aromatic hydrocarbons, which endow the MOF with strong fluorescence of variable colors and afford a high-contrast fluorescence response to ammonia/amines and formaldehyde associated with the chromic response. The presence of the unquaternized bipyridyl group also leads to a fluorescence response to HCl. The multiple responsive behaviors hold appeal for applications in sensing, switching, and antifake marking, which are illustrated with a test paper and writing ink.
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Affiliation(s)
- Xiao-Yan Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xue-Mei Yin
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Shuai-Liang Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Lin Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Ran Bu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - En-Qing Gao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
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4
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Gómez-González J, Pérez Y, Sciortino G, Roldan-Martín L, Martínez-Costas J, Maréchal JD, Alfonso I, Vázquez López M, Vázquez ME. Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells*. Angew Chem Int Ed Engl 2021; 60:8859-8866. [PMID: 33290612 DOI: 10.1002/anie.202013039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/12/2020] [Indexed: 01/03/2023]
Abstract
Although largely overlooked in peptide engineering, coordination chemistry offers a new set of interactions that opens unexplored design opportunities for developing complex molecular structures. In this context, we report new artificial peptide ligands that fold into chiral helicates in the presence of labile metal ions such as FeII and CoII . Heterochiral β-turn-promoting sequences encode the stereoselective folding of the peptide ligands and define the physicochemical properties of their corresponding metal complexes. Circular dichroism and NMR spectroscopy in combination with computational methods allowed us to identify and determine the structure of two isochiral ΛΛ-helicates, folded as topological isomers. Finally, in addition to the in-vitro characterization of their selective binding to DNA three-way junctions, cell-microscopy experiments demonstrated that a rhodamine-labeled FeII helicate was internalized and selectively stains DNA replication factories in functional cells.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Spain
| | - Yolanda Pérez
- NMR Facility, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain.,Institute of Chemical Research of Catalonia (ICIQ), Avgda. Països Catalans, 16, 43007, Tarragona, Spain
| | - Lorena Roldan-Martín
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - José Martínez-Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Bioquímica y Biología Molecular, Universidade de Santiago de Compostela, Spain
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193, Cerdanyola, Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de 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, Spain
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5
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Gómez‐González J, Pérez Y, Sciortino G, Roldan‐Martín L, Martínez‐Costas J, Maréchal J, Alfonso I, Vázquez López M, Vázquez ME. Dynamic Stereoselection of Peptide Helicates and Their Selective Labeling of DNA Replication Foci in Cells**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013039] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jacobo Gómez‐González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Orgánica Universidade de Santiago de Compostela Spain
| | - Yolanda Pérez
- NMR Facility Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Giuseppe Sciortino
- Departament de Química Universitat Autònoma de Barcelona 08193 Cerdanyola Spain
- Institute of Chemical Research of Catalonia (ICIQ) Avgda. Països Catalans, 16 43007 Tarragona Spain
| | | | - José Martínez‐Costas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Bioquímica y Biología Molecular Universidade de Santiago de Compostela Spain
| | | | - Ignacio Alfonso
- Department of Biological Chemistry Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Jordi Girona 18–26 08034 Barcelona Spain
| | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) Departamento de Química Inorgánica Universidade de 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 Spain
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6
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Song Y, Schaufelberger F, Ashbridge Z, Pirvu L, Vitorica-Yrezabal IJ, Leigh DA. Effects of turn-structure on folding and entanglement in artificial molecular overhand knots. Chem Sci 2020; 12:1826-1833. [PMID: 34163946 PMCID: PMC8179330 DOI: 10.1039/d0sc05897a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The length and constitution of spacers linking three 2,6-pyridinedicarboxamide units in a molecular strand influence the tightness of the resulting overhand (open-trefoil) knot that the strand folds into in the presence of lanthanide(iii) ions. The use of β-hairpin forming motifs as linkers enables a metal-coordinated pseudopeptide with a knotted tertiary structure to be generated. The resulting pseudopeptide knot has one of the highest backbone-to-crossing ratios (BCR)—a measure of knot tightness (a high value corresponding to looseness)—for a synthetic molecular knot to date. Preorganization in the crossing-free turn section of the knot affects aromatic stacking interactions close to the crossing region. The metal-coordinated pseudopeptide knot is compared to overhand knots with other linkers of varying tightness and turn preorganization, and the entangled architectures characterized by NMR spectroscopy, ESI-MS, CD spectroscopy and, in one case, X-ray crystallography. The results show how it is possible to program specific conformational properties into different key regions of synthetic molecular knots, opening the way to systems where knotting can be systematically incorporated into peptide-like chains through design. Spacers linking 2,6-pyridinedicarboxamide units influence the tightness of the corresponding lanthanide-coordinated overhand knot. β-Hairpin forming motifs generate a metal-coordinated pseudopeptide with a knotted tertiary structure.![]()
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Affiliation(s)
- Yiwei Song
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 PR China
| | | | - Zoe Ashbridge
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | - Lucian Pirvu
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | | | - David A Leigh
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 PR China .,Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
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7
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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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8
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Gong T, Li Y, Lv B, Wang H, Liu Y, Yang W, Wu Y, Jiang X, Gao H, Zheng X, Bu W. Full-Process Radiosensitization Based on Nanoscale Metal-Organic Frameworks. ACS NANO 2020; 14:3032-3040. [PMID: 32150395 DOI: 10.1021/acsnano.9b07898] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Full-process radiosensitization, that is, pre-increasing radiation sensitivity of cancer cells, magnifying •OH formation during ionizing irradiation, and intervention on the resultant DNA repair for final cells death, could enhance the overall radiotherapeutic effects, but has not yet been achieved. Herein, Hf-nMOFs with Fe3+ ions uniformly dispersed (Hf-BPY-Fe) were constructed to integratedly improve radiotherapeutic effects via a multifaceted mechanism. The in vitro experiments demonstrated that persistent reactive oxygen species stress from Hf-BPY-Fe-activated in situ Fenton reaction reassorted cell cycle distribution, consequently contributing to increased tumoral radiosensitivity to photon radiation. Upon irradiation during the course of radiation therapy, Hf4+ in Hf-BPY-Fe gave substantial amounts of high-energy electrons, which partially converted H2O to •OH and, meanwhile, relaxed to a low-energy state in nMOF pores, leading to an electron-rich environment. These aggregated electrons facilitated the reduction from Fe3+ to Fe2+ and further promoted the production of •OH in the Fenton process to attack DNA. The Hf-BPY-Fe postponed the DNA damage response process by interfering with certain proteins involved in the DNA repair signaling pathway. The in vivo experiments showed improved radiotherapeutic effects from integrated contributions from Fe3+-based Fenton reaction and Hf4+-induced X-ray energy conversion in tumors. This work provides a nMOFs-based full-process radiosensitizing approach for better radiotherapeutic efficacy.
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Affiliation(s)
- Teng Gong
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Yanli Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Bin Lv
- Department of Radiation Oncology, Shanghai Huadong Hospital, Fudan University, Shanghai 200040, China
| | - Han Wang
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Science, Shanghai 200050, China
| | - Yanyan Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Wei Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Yelin Wu
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Xingwu Jiang
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Hongbo Gao
- Department of Radiation Oncology, Shanghai Huadong Hospital, Fudan University, Shanghai 200040, China
| | - Xiangpeng Zheng
- Department of Radiation Oncology, Shanghai Huadong Hospital, Fudan University, Shanghai 200040, China
| | - Wenbo Bu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Science, Shanghai 200050, China
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9
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Gonzalez MI, Turkiewicz AB, Darago LE, Oktawiec J, Bustillo K, Grandjean F, Long GJ, Long JR. Confinement of atomically defined metal halide sheets in a metal-organic framework. Nature 2019; 577:64-68. [PMID: 31739311 DOI: 10.1038/s41586-019-1776-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/26/2019] [Indexed: 11/09/2022]
Abstract
The size-dependent and shape-dependent characteristics that distinguish nanoscale materials from bulk solids arise from constraining the dimensionality of an inorganic structure1-3. As a consequence, many studies have focused on rationally shaping these materials to influence and enhance their optical, electronic, magnetic and catalytic properties4-6. Although a select number of stable clusters can typically be synthesized within the nanoscale regime for a specific composition, isolating clusters of a predetermined size and shape remains a challenge, especially for those derived from two-dimensional materials. Here we realize a multidentate coordination environment in a metal-organic framework to stabilize discrete inorganic clusters within a porous crystalline support. We show confined growth of atomically defined nickel(II) bromide, nickel(II) chloride, cobalt(II) chloride and iron(II) chloride sheets through the peripheral coordination of six chelating bipyridine linkers. Notably, confinement within the framework defines the structure and composition of these sheets and facilitates their precise characterization by crystallography. Each metal(II) halide sheet represents a fragment excised from a single layer of the bulk solid structure, and structures obtained at different precursor loadings enable observation of successive stages of sheet assembly. Finally, the isolated sheets exhibit magnetic behaviours distinct from those of the bulk metal halides, including the isolation of ferromagnetically coupled large-spin ground states through the elimination of long-range, interlayer magnetic ordering. Overall, these results demonstrate that the pore environment of a metal-organic framework can be designed to afford precise control over the size, structure and spatial arrangement of inorganic clusters.
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Affiliation(s)
- Miguel I Gonzalez
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Ari B Turkiewicz
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Lucy E Darago
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Julia Oktawiec
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Karen Bustillo
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fernande Grandjean
- Department of Chemistry, Missouri University of Science and Technology, University of Missouri, Rolla, MO, USA
| | - Gary J Long
- Department of Chemistry, Missouri University of Science and Technology, University of Missouri, Rolla, MO, USA
| | - Jeffrey R Long
- Department of Chemistry, University of California, Berkeley, CA, USA. .,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA. .,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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10
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Embaby AM, Lelieveldt LPWM, Diness F, Meldal M. Metallo-Organozymes with Specific Proteolytic Activity. Chemistry 2018; 24:17424-17428. [DOI: 10.1002/chem.201803666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Ahmed M. Embaby
- Center for Evolutionary Chemical Biology and Nano-Science center, Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
| | - Lianne P. W. M. Lelieveldt
- Center for Evolutionary Chemical Biology and Nano-Science center, Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
- Current address: Department of Biomolecular Chemistry; Radboud University Nijmegen; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Frederik Diness
- Center for Evolutionary Chemical Biology and Nano-Science center, Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
| | - Morten Meldal
- Center for Evolutionary Chemical Biology and Nano-Science center, Department of Chemistry; University of Copenhagen; Universitetsparken 5 2100 Copenhagen Denmark
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11
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Gómez-González J, Peña DG, Barka G, Sciortino G, Maréchal JD, Vázquez López M, Vázquez ME. Directed Self-Assembly of Trimeric DNA-Bindingchiral Miniprotein Helicates. Front Chem 2018; 6:520. [PMID: 30425980 PMCID: PMC6218460 DOI: 10.3389/fchem.2018.00520] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
We propose that peptides are highly versatile platforms for the precise design of supramolecular metal architectures, and particularly, for the controlled assembly of helicates. In this context, we show that the bacteriophage T4 Fibritin foldon (T4Ff) can been engineered on its N-terminus with metal-chelating 2,2'-bipyridine units that stereoselectively assemble in the presence of Fe(II) into parallel, three-stranded peptide helicates with preferred helical orientation. Modeling studies support the proposed self-assembly and the stability of the final helicate. Furthermore, we show that these designed mini-metalloproteins selectively recognize three-way DNA junctions over double-stranded DNA.
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Affiliation(s)
- Jacobo Gómez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Diego G Peña
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ghofrane Barka
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, Cerdanyola, Spain.,Dipartimento di Chimica e Farmacia, Università di Sassari, Sassari, Italy
| | | | - Miguel Vázquez López
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Inorgánica, Universidade de Santiago de Compostela, 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, Santiago de Compostela, Spain
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12
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Kobayashi Y, Hoshino M, Kameda T, Kobayashi K, Akaji K, Inuki S, Ohno H, Oishi S. Use of a Compact Tripodal Tris(bipyridine) Ligand to Stabilize a Single-Metal-Centered Chirality: Stereoselective Coordination of Iron(II) and Ruthenium(II) on a Semirigid Hexapeptide Macrocycle. Inorg Chem 2018; 57:5475-5485. [PMID: 29634246 DOI: 10.1021/acs.inorgchem.8b00416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fe(II)-coordinating hexapeptides containing three 2,2'-bipyridine moieties as side chains were designed and synthesized. A cyclic hexapeptide having three [(2,2'-bipyridin)-5-yl]-d-alanine (d-Bpa5) residues, in which d-Bpa5 and Gly are alternately arranged with 3-fold rotational symmetry, coordinated with Fe(II) to form a 1:1 octahedral Fe(II)-peptide complex with a single facial-Λ configuration of the metal-centered chirality. NMR spectroscopy and molecular dynamics simulations revealed that the Fe(II)-peptide complex has an apparent C3-symmetric conformations on the NMR time scale, while the peptide backbone is subject to dynamic conformational exchange between three asymmetric β/γ conformations and one C3-symmetric γ/γ/γ conformation. The semirigid cyclic hexapeptide preferentially arranged these conformations of the small octahedral Fe(II)-bipyridine complex, as well as the Ru(II) congener, to underpin the single configuration of the metal-centered chirality.
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Affiliation(s)
- Yuka Kobayashi
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku , Kyoto 606-8501 , Japan
| | - Masaru Hoshino
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku , Kyoto 606-8501 , Japan
| | - Tomoshi Kameda
- Artificial Intelligence Research Center , National Institute of Advanced Industrial Science and Technology (AIST) , 2-4-7 Aomi , Koutou-ku, Tokyo 135-0064 , Japan
| | - Kazuya Kobayashi
- Kyoto Pharmaceutical University , Yamashina-ku , Kyoto 607-8412 , Japan
| | - Kenichi Akaji
- Kyoto Pharmaceutical University , Yamashina-ku , Kyoto 607-8412 , Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku , Kyoto 606-8501 , Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku , Kyoto 606-8501 , Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences , Kyoto University , Sakyo-ku , Kyoto 606-8501 , Japan
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13
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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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14
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Gonzalez MI, Oktawiec J, Long JR. Ethylene oligomerization in metal–organic frameworks bearing nickel(ii) 2,2′-bipyridine complexes. Faraday Discuss 2017; 201:351-367. [DOI: 10.1039/c7fd00061h] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The metal–organic frameworks Zr6O4(OH)4(bpydc)6 (1; bpydc2− = 2,2′-bipyridine-5,5′-dicarboxylate) and Zr6O4(OH)4(bpydc)0.84(bpdc)5.16 (2; bpdc2− = biphenyl-4,4′-dicarboxylate) were readily metalated with Ni(DME)Br2 (DME = dimethoxyethane) to produce the corresponding metalated frameworks 1(NiBr2)6 and 2(NiBr2)0.84. Both nickel(ii)-containing frameworks catalyze the oligomerization of ethylene in the presence of Et2AlCl. In these systems, the pore environment around the active nickel sites significantly influences their selectivity for formation of oligomers over polymer. Specifically, the single-crystal structure of 1(NiBr2)5.64 reveals that surrounding metal–linker complexes enforce a steric environment on each nickel site that causes polymer formation to become favorable. Minimizing this steric congestion by isolating the nickel(ii) bipyridine complexes in the mixed-linker framework 2(NiBr2)0.84 markedly improves both the catalytic activity and selectivity for oligomers. Furthermore, both frameworks give product mixtures that are enriched in shorter olefins (C4–10), leading to deviations from the expected Schulz–Flory distribution of oligomers. Although these deviations indicate possible pore confinement effects on selectivity, control experiments using the nickel-treated biphenyl framework Zr6O4(OH)4(bpdc)6(NiBr2)0.14 (3(NiBr2)0.14) reveal that they likely arise at least in part from the presence of nickel species that are not ligated by bipyridine within 1(NiBr2)5.64 and 2(NiBr2)0.84.
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Affiliation(s)
| | - Julia Oktawiec
- Department of Chemistry
- University of California
- Berkeley
- USA
| | - Jeffrey R. Long
- Department of Chemistry
- University of California
- Berkeley
- USA
- Department of Chemical and Biomolecular Engineering
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15
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Engineering Short Preorganized Peptide Sequences for Metal Ion Coordination: Copper(II) a Case Study. Methods Enzymol 2016. [PMID: 27586340 DOI: 10.1016/bs.mie.2016.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Peptides are multidentate chiral ligands capable of coordinating different metal ions. Nowadays, they can be obtained with high yield and purity, thanks to the advances on peptide/protein chemistry as well as in equipment (peptide synthesizers). Based on the identity and length of their amino acid sequences, peptides can present different degrees of flexibility and folding. Although short peptide sequences (<20 amino acids) usually lack structure in solution, different levels of structural preorganization can be induced by introducing conformational constraints, such as β-turn/loop template sequences and backbone cyclization. For all these reasons, and the fact that one is not restricted to use proteinogenic amino acids, small peptidic scaffolds constitute a simple and versatile platform for the development of inorganic systems with tailor-made properties and functions. Here we outline a general approach to the design of short preorganized peptide sequences (10-16 amino acids) for metal ion coordination. Based on our experience, we present a general scheme for the design, synthesis, and characterization of these peptidic scaffolds and provide protocols for the study of their metal ion coordination properties.
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16
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Salvadó I, Gamba I, Montenegro J, Martínez-Costas J, Brea JM, Loza MI, Vázquez López M, Vázquez ME. Membrane-disrupting iridium(iii) oligocationic organometallopeptides. Chem Commun (Camb) 2016; 52:11008-11. [PMID: 27538788 DOI: 10.1039/c6cc05537k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of oligoarginine peptide derivatives containing cyclometallated iridium(iii) units display remarkable cytotoxicity, comparable to that of cisplatin. In vitro studies with unilamellar vesicles support a membrane-disrupting mechanism of action.
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Affiliation(s)
- Iria Salvadó
- 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.
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17
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Gamba I, Rama G, Ortega-Carrasco E, Berardozzi R, Sánchez-Pedregal VM, Di Bari L, Maréchal JD, Vázquez ME, Vázquez López M. The folding of a metallopeptide. Dalton Trans 2016; 45:881-5. [PMID: 26523378 DOI: 10.1039/c5dt02797g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We have applied solid-phase synthesis methods for the construction of tris(bipyridyl) peptidic ligands that coordinate Fe(ii) ions with high affinity and fold into stable mononuclear metallopeptides. The main factors influencing the folding pathway and chiral control of the peptidic ligands around the metal ions have been studied both by experimental techniques (CD, UV-vis and NMR) and molecular modeling tools. Amongst the numerous molecular variables that have been studied, this study clearly illustrates how the chirality of a given set of aminoacids (proline in this case) of the peptide dictates the chirality of the metal center of the resulting metallopeptide. Moreover, the relatively hydrophobic peptidic models used in this work show that the most stable structures present reduced solvent contacts and, in counterpart, stabilize the cis configuration of the proline residues.
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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.
| | - Gustavo Rama
- 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.
| | | | - Roberto Berardozzi
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy
| | - Víctor M Sánchez-Pedregal
- 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.
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, 56124 Pisa, Italy
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola, 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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18
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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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19
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Synthesis and conformational behavior of metallacyclicdipeptides derived from coordination of side chain alkynylamino acids to tungsten. J Organomet Chem 2016. [DOI: 10.1016/j.jorganchem.2016.01.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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20
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Soler M, Feliu L, Planas M, Ribas X, Costas M. Peptide-mediated vectorization of metal complexes: conjugation strategies and biomedical applications. Dalton Trans 2016; 45:12970-82. [DOI: 10.1039/c5dt04529k] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The rich chemical and structural versatility of transition metal complexes provides numerous novel paths to be pursued in the design of molecules that exert particular chemical or physicochemical effects that could operate over specific biological targets.
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Affiliation(s)
- Marta Soler
- QBIS–CAT Research Group
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química
- Universitat de Girona
- E-17071 Girona
- Spain
| | - Lidia Feliu
- LIPPSO
- Departament de Química
- Universitat de Girona
- E-17071 Girona
- Spain
| | - Marta Planas
- LIPPSO
- Departament de Química
- Universitat de Girona
- E-17071 Girona
- Spain
| | - Xavi Ribas
- QBIS–CAT Research Group
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química
- Universitat de Girona
- E-17071 Girona
- Spain
| | - Miquel Costas
- QBIS–CAT Research Group
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química
- Universitat de Girona
- E-17071 Girona
- Spain
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21
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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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22
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Soler M, Figueras E, Serrano-Plana J, González-Bártulos M, Massaguer A, Company A, Martínez MÁ, Malina J, Brabec V, Feliu L, Planas M, Ribas X, Costas M. Design, Preparation, and Characterization of Zn and Cu Metallopeptides Based On Tetradentate Aminopyridine Ligands Showing Enhanced DNA Cleavage Activity. Inorg Chem 2015; 54:10542-58. [PMID: 26503063 DOI: 10.1021/acs.inorgchem.5b01680] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The conjugation of redox-active complexes that can function as chemical nucleases to cationic tetrapeptides is pursued in this work in order to explore the expected synergistic effect between these two elements in DNA oxidative cleavage. Coordination complexes of biologically relevant first row metal ions, such as Zn(II) or Cu(II), containing the tetradentate ligands 1,4-dimethyl-7-(2-pyridylmethyl)-1,4,7-triazacyclononane ((Me2)PyTACN) and (2S,2S')-1,1'-bis(pyrid-2-ylmethyl)-2,2'-bipyrrolidine ((S,S')-BPBP) have been linked to a cationic LKKL tetrapeptide sequence. Solid-phase synthesis of the peptide-tetradentate ligand conjugates has been developed, and the preparation and characterization of the corresponding metallotetrapeptides is described. The DNA cleavage activity of Cu and Zn metallopeptides has been evaluated and compared to their metal binding conjugates as well as to the parent complexes and ligands. Very interestingly, the oxidative Cu metallopeptides 1Cu and 2Cu show an enhanced activity compared to the parent complexes, [Cu(PyTACN)](2+) and [Cu(BPBP)](2+), respectively. Under optimized conditions, 1Cu displays an apparent pseudo first-order rate constant (kobs) of ∼0.16 min(-1) with a supercoiled DNA half-life time (t1/2) of ∼4.3 min. On the other hand, kobs for 2Cu has been found to be ∼0.11 min(-1) with t1/2 ≈ 6.4 min. Hence, these results point out that the DNA cleavage activities promoted by the metallopeptides 1Cu and 2Cu render ∼4-fold and ∼23 rate accelerations in comparison with their parent Cu complexes. Additional binding assays and mechanistic studies demonstrate that the enhanced cleavage activities are explained by the presence of the cationic LKKL tetrapeptide sequence, which induces an improved binding affinity to the DNA, thus bringing the metal ion, which is responsible for cleavage, in close proximity.
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Affiliation(s)
- Marta Soler
- QBIS-CAT Research Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain.,LIPPSO, Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Eduard Figueras
- LIPPSO, Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Joan Serrano-Plana
- QBIS-CAT Research Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Marta González-Bártulos
- Biochemistry of Cancer Group, Biochemistry and Molecular Biology Unit, Department de Química and Department of Biology, Universitat de Girona , Campus Montilivi, 17071 Girona, Catalunya, Spain
| | - Anna Massaguer
- Biochemistry of Cancer Group, Biochemistry and Molecular Biology Unit, Department de Química and Department of Biology, Universitat de Girona , Campus Montilivi, 17071 Girona, Catalunya, Spain
| | - Anna Company
- QBIS-CAT Research Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Ma Ángeles Martínez
- Biochemistry of Cancer Group, Biochemistry and Molecular Biology Unit, Department de Química and Department of Biology, Universitat de Girona , Campus Montilivi, 17071 Girona, Catalunya, Spain
| | - Jaroslav Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic , v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic , v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Lidia Feliu
- LIPPSO, Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Marta Planas
- LIPPSO, Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Xavi Ribas
- QBIS-CAT Research Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
| | - Miquel Costas
- QBIS-CAT Research Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona , Campus Montilivi, E-17071 Girona, Catalonia, Spain
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23
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Oheix E, Peacock AFA. Metal-ion-regulated miniature DNA-binding proteins based on GCN4 and non-native regulation sites. Chemistry 2014; 20:2829-39. [PMID: 24478111 DOI: 10.1002/chem.201303747] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Indexed: 02/06/2023]
Abstract
The design of artificial peptide dimers containing polypyridine switching domains, for which metal-ion coordination is shown to regulate DNA binding, is reported. Short peptides, based on the basic domain of the GCN4 transcription factor (GCN4bd), dimerised with either 2,2'-bipyridine (bipy(GCN4bd)2 ) or 2,2':6',2''-terpyridine (terpy(GCN4bd)2 ) linker units, undergo a conformational rearrangement on Cu(II) and Zn(II) coordination. Depending on the linker substitution pattern, this is proposed to alter the relative alignment of the two peptide moieties, and in turn regulate DNA binding. Circular dichroism and UV-visible spectroscopy reveal that Cu(II) and Zn(II) coordination promotes binding to DNA containing the CRE target site, but to a differing and opposite degree for the two linkers, and that the metal-ion affinity for terpy(GCN4bd)2 is enhanced in the presence of CRE DNA. Binding to DNA containing the shorter AP1 target site, which lacks a single nucleobase pair compared to CRE, as well as half-CRE, which contains only half of the CRE target site, was also investigated. Cu(II) and Zn(II) coordination to terpy(GCN4bd)2 promotes binding to AP1 DNA, and to a lesser extent half-CRE DNA. Whereas, bipy(GCN4bd)2 , for which interpeptide distances are largely independent of metal-ion coordination and less suitable for binding to these shorter sites, displays allosteric ineffective behaviour in these cases. These findings for the first time demonstrate that biomolecular recognition, and specifically sequence-selective DNA binding, can be controlled by metal-ion coordination to designed switching units, non-native regulation sites, in artificial biomolecules. We believe that in the future these could find a wide range of applications in biotechnology.
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Affiliation(s)
- Emmanuel Oheix
- School of Chemistry, University of Birmingham, Edgbaston, B15 2TT (UK)
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24
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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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25
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Gamble AJ, Peacock AFA. De novo design of peptide scaffolds as novel preorganized ligands for metal-ion coordination. Methods Mol Biol 2014; 1216:211-31. [PMID: 25213418 DOI: 10.1007/978-1-4939-1486-9_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This chapter describes how de novo designed peptides can be used as novel preorganized ligands for metal ion coordination. The focus is on the design of peptides which are programmed to spontaneously self-assemble into α-helical coiled coils in aqueous solution, and how metal ion binding sites can be engineered onto and into these structures. In addition to describing the various design principles, some key examples are covered illustrating the success of this approach, including a more detailed example in the case study.
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Affiliation(s)
- Aimee J Gamble
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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26
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Gamba I, Salvadó I, Rama G, Bertazzon M, Sánchez MI, Sánchez-Pedregal VM, Martínez-Costas J, Brissos RF, Gamez P, Mascareñas JL, Vázquez López M, Vázquez ME. Custom-fit ruthenium(II) metallopeptides: a new twist to DNA binding with coordination compounds. Chemistry 2013; 19:13369-75. [PMID: 23943195 DOI: 10.1002/chem.201301629] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Indexed: 12/20/2022]
Abstract
A new bipyridine building block has been used for the solid-phase synthesis of dinuclear DNA-binding ruthenium(II) metallopeptides. Detailed spectroscopic studies suggest that these compounds bind to the DNA by insertion into the DNA minor groove. Moreover, the potential of the solid-phase peptide synthesis approach is demonstrated by the straightforward synthesis of an octaarginine derivative that shows effective cellular internalization and cytotoxicity linked with strong DNA interaction, as evidenced by steady-state fluorescence spectroscopy and AFM studies.
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Affiliation(s)
- Ilaria Gamba
- Departamento de Química Inorgánica y Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares, Universidade de Santiago de Compostela, 15782 Santiago de Compostela (Spain)
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27
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Oheix E, Spencer N, Gethings LA, Peacock AFA. Conformational Study of an Artificial Metal-Dependent Regulation Site for Use in Designer Proteins. Z Anorg Allg Chem 2013; 639:1370-1383. [PMID: 25995524 PMCID: PMC4431501 DOI: 10.1002/zaac.201300131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/21/2013] [Indexed: 11/07/2022]
Abstract
This report describes the dimerisation of glutathione, and by extension, other cysteine-containing peptides or protein fragments, with a 5, 5'-disubstituted-2, 2'-bipyridine or 6, 6"-disubstituted-2, 2':6',2"-terpyridine unit. The resulting bipy-GS2 and terpy-GS2 were investigated as potential metal ion dependent switches in aqueous solution, and were found to predominantly adopt the transoïd conformation at physiological pH. Metal complexation with CuII and ZnII at this pH has been studied by UV/Vis, CD, NMR and ion-mobility mass spectrometry. ZnII titrations are consistent with the formation of a 1:1 ZnII:terpy-GS2 complex at pH 7.4, but bipy-GS2 was shown to form both 1:1 and 1:2 complexes with the former being predominant under dilute micromolar conditions. Formation constants for the resulting 1:1 complexes were determined to be log KM 6.86 (bipy-GS2 ) and 6.22 (terpy-GS2 ), consistent with a higher affinity for the unconstrained bipyridine, compared to the strained terpyridine. CuII coordination involves the initial formation of 1:1 complexes, followed by 1.5Cu:1bipy-GS2 and 2Cu:1terpy-GS2 complexes at micromolar concentrations. Binding constants for formation of the 1:1 complexes (log KM 12.5 (bipy-GS2 ); 8.04 and 7.14 (terpy-GS2 )) indicate a higher affinity for CuII than ZnII. Finally, ion-mobility MS studies detected the free ligands in their protonated form, and were consistent with the formation of two different Cu adducts with different conformations in the gas-phase. We illustrate that the bipyridine and terpyridine dimerisation units can behave like conformational switches in response to Cu/Zn complexation, and propose that in future these can be employed in synthetic biology with larger peptide or protein fragments, to control large scale folding and related biological function.
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Affiliation(s)
- Emmanuel Oheix
- School of Chemistry, University of BirminghamEdgbaston, B15 2TT, UK
| | - Neil Spencer
- School of Chemistry, University of BirminghamEdgbaston, B15 2TT, UK
| | - Lee A Gethings
- Waters CorporationAtlas Park, Simonsway, Wythenshawe, Manchester, M22 5PP, UK
| | - Anna F A Peacock
- School of Chemistry, University of BirminghamEdgbaston, B15 2TT, UK
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Seo MS, Kim K, Kim H. Controlling helical chirality of cobalt complexes by chirality transfer from vicinal diamines. Chem Commun (Camb) 2013; 49:11623-5. [DOI: 10.1039/c3cc46887a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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