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Rodriguez J, Battistini F, Learte-Aymamí S, Orozco M, Mascareñas JL. Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA. RSC Chem Biol 2023; 4:486-493. [PMID: 37415868 PMCID: PMC10320839 DOI: 10.1039/d3cb00053b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/09/2023] [Indexed: 07/08/2023] Open
Abstract
We report the modelling of the DNA complex of an artificial miniprotein composed of two zinc finger modules and an AT-hook linking peptide. The computational study provides for the first time a structural view of these types of complexes, dissecting interactions that are key to modulate their stability. The relevance of these interactions was validated experimentally. These results confirm the potential of this type of computational approach for studying peptide-DNA complexes and suggest that they could be very useful for the rational design of non-natural, DNA binding miniproteins.
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Affiliation(s)
- Jessica Rodriguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona Spain
| | - Soraya Learte-Aymamí
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), and Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 10-12 08028 Barcelona Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona 08028 Barcelona 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 Rúa Jenaro de la Fuente s/n 15782 Santiago de Compostela Spain
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2
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Łagiewka J, Girek T, Ciesielski W. Cyclodextrins-Peptides/Proteins Conjugates: Synthesis, Properties and Applications. Polymers (Basel) 2021; 13:1759. [PMID: 34072062 PMCID: PMC8198514 DOI: 10.3390/polym13111759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/24/2022] Open
Abstract
Cyclodextrins (CDs) are a family of macrocyclic oligosaccharides mostly composed of six, seven, or eight α-D-glucopyranose units with α-1,4-glycosidic bonds to form toroidal structures. The CDs possess a hydrophilic exterior and hydrophobic interior with the ability to form an inclusion complex, especially with hydrophobic molecules. However, most existing studies are about conjugation CDs with peptide/protein focusing on the formation of new systems. The CD-peptide/protein can possess new abilities; particularly, the cavity can be applied in modulation properties of more complexed proteins. Most studies are focused on drug delivery, such as targeted delivery in cell-penetrating peptides or co-delivery. The co-delivery is based mostly on polylysine systems; on the other hand, the CD-peptide allows us to understand biomolecular mechanisms such as fibryllation or stem cell behaviour. Moreover, the CD-proteins are more complexed systems with a focus on targeted therapy; these conjugates might be controllable with various properties due to changes in their stability. Finally, the studies of CD-peptide/protein are promising in biomedical application and provide new possibilities for the conjugation of simple molecules to biomolecules.
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Affiliation(s)
- Jakub Łagiewka
- Faculty of Mathematics and Natural Science, Jan Dlugosz University in Czestochowa, Armii Krajowej Ave., 13/15, 42 201 Czestochowa, Poland; (T.G.); (W.C.)
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3
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Jicsinszky L, Martina K, Cravotto G. Cyclodextrins in the antiviral therapy. J Drug Deliv Sci Technol 2021; 64:102589. [PMID: 34035845 PMCID: PMC8135197 DOI: 10.1016/j.jddst.2021.102589] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/30/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023]
Abstract
The main antiviral drug-cyclodextrin interactions, changes in physicochemical and physiological properties of the most commonly used virucides are summarized. The potential complexation of antiviral molecules against the SARS-Cov2 also pointed out the lack of detailed information in designing effective and general medicines against viral infections. The principal problem of the current molecules is the 3D structures of the currently active compounds. Improving the solubility or bioavailability of antiviral molecules is possible, however, there is no universal solution, and the complexation experiments dominantly use the already approved cyclodextrin derivatives. This review discusses the basic properties of the different cyclodextrin derivatives, their potential in antiviral formulations, and the prevention and treatment of viral infections. The biologically active new cyclodextrin derivatives are also discussed.
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Affiliation(s)
- László Jicsinszky
- Dept. of Drug Science and Technology, University of Turin, Via Giuria 9, 10125, Torino, Italy
| | - Katia Martina
- Dept. of Drug Science and Technology, University of Turin, Via Giuria 9, 10125, Torino, Italy
| | - Giancarlo Cravotto
- Dept. of Drug Science and Technology, University of Turin, Via Giuria 9, 10125, Torino, Italy
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4
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Sortase-click strategy for defined protein conjugation on a heptavalent cyclodextrin scaffold. PLoS One 2019; 14:e0217369. [PMID: 31125361 PMCID: PMC6534326 DOI: 10.1371/journal.pone.0217369] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/09/2019] [Indexed: 01/05/2023] Open
Abstract
Multivalent proteins or protein dendrimers are useful for clinical and biotechnological applications. However, assembly of chemically defined protein dendrimers is a challenging endeavor. In the past, majority of protein dendrimers have been developed on branched lysine scaffolds and are usually limited to a valency of two to four. The naturally occurring cyclodextrin (CD) scaffold composed of 6–8 glucose units offers the possibility of expanding the valency. Here we have adapted a chemoenzymatic-click strategy for displaying heptavalent peptides and large proteins on the β-cyclodextrin (β-CD) scaffold. We demonstrate that recombinant proteins (engineered with a LPXTG pentapeptide motif at the carboxy terminus), labeled with an alkyne moiety by sortase-mediated ligation, can be easily clicked on to the azide-derivatized β-cyclodextrin through the Huisgen cycloaddition reaction yielding a well-defined heptavalent display of proteins.
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5
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Redondo-Gómez C, Abdouni Y, Becer CR, Mata A. Self-Assembling Hydrogels Based on a Complementary Host–Guest Peptide Amphiphile Pair. Biomacromolecules 2019; 20:2276-2285. [DOI: 10.1021/acs.biomac.9b00224] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | | | - C. Remzi Becer
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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6
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Ruiz García Y, Pabon-Martinez YV, Smith CIE, Madder A. Specific dsDNA recognition by a mimic of the DNA binding domain of the c-Myc/Max transcription factor. Chem Commun (Camb) 2018; 53:6653-6656. [PMID: 28585621 DOI: 10.1039/c7cc01705g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We here report on the synthesis of the first mimic of the DNA binding domain of the c-Myc/Max-bHLH-ZIP transcription factor able to selectively recognize its cognate E-box sequence 5'-CACGTG-3' through the major groove of the double-stranded DNA. The designed peptidosteroid conjugate was shown to be effective as DNA binder in the presence of excess competitor DNA.
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Affiliation(s)
- Yara Ruiz García
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, S4, B-9000, Gent, Belgium.
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Vurgun N, Nitz M. Highly Functionalized β-Cyclodextrins by Solid-Supported Synthesis. Chemistry 2018; 24:4459-4467. [PMID: 29389050 DOI: 10.1002/chem.201800028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Indexed: 12/26/2022]
Abstract
Using covalent capture, a high yielding selective mono-functionalization of heptakis-[6-deoxy-6-(2-aminoethylsulfanyl)]-β-CD with a 5-mercaptopentyl functional group has been achieved. Here, we demonstrate the immobilization of the mono-thiol functionalized β-CD on PEGA resin via a disulfide bond, enabling solid-phase elaboration of the remaining six primary amines. To showcase the potential of this method, the amines were elaborated to tripeptides through standard Fmoc-peptide chemistry. A small library of CD-tripeptide conjugates was generated which, when reduced from the solid support, could be tagged at the released thiol with an environmentally sensitive fluorophore. The resulting library of sensors showed potential for the differential sensing of various bile salts. The described methodology provides a rapid and versatile route to synthesize highly functionalized libraries of CD derivatives that may be tailored towards applications in sensing, catalysis, and multivalent displays.
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Affiliation(s)
- Nesrin Vurgun
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
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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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10
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Al Temimi AHK, Boltje TJ, Zollinger D, Rutjes FPJT, Feiters MC. Peptide-Appended Permethylated β-Cyclodextrins with Hydrophilic and Hydrophobic Spacers. Bioconjug Chem 2017; 28:2160-2166. [PMID: 28697600 PMCID: PMC5561536 DOI: 10.1021/acs.bioconjchem.7b00319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A novel
synthetic methodology, employing a combination of the strain-promoted
azide–alkyne cycloaddition and maleimide–thiol reactions,
for the preparation of permethylated β-cyclodextrin-linker-peptidyl
conjugates is reported. Two different bifunctional maleimide cross-linking
probes, the polyethylene glycol containing hydrophilic linker bicyclo[6.1.0]
nonyne-maleimide and the hydrophobic 5′-dibenzoazacyclooctyne-maleimide,
were attached to azide-appended permethylated β-cyclodextrin. The successfully introduced maleimide function was
exploited to covalently graft a cysteine-containing peptide (Ac-Tyr-Arg-Cys-Amide)
to produce the target conjugates. The final target compounds were
isolated in high purity after purification by isocratic preparative
reverse-phase high-performance liquid chromatography. This novel synthetic
approach is expected to give access to many different cyclodextrin–linker
peptides.
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Affiliation(s)
- Abbas H K Al Temimi
- Institute for Molecules and Materials, Radboud University , Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Thomas J Boltje
- Institute for Molecules and Materials, Radboud University , Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Daniel Zollinger
- Okklo Life Sciences BV , Pivot Park, Molenstraat 110, 5349 TD Oss, The Netherlands.,QareFree , Blauwoogvlinder 2, 4814 ST Breda, The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University , Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Martin C Feiters
- Institute for Molecules and Materials, Radboud University , Heijendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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Ruiz García Y, Iyer A, Van Lysebetten D, Pabon YV, Louage B, Honcharenko M, De Geest BG, Smith CIE, Strömberg R, Madder A. Sequence-selective DNA recognition and enhanced cellular up-take by peptide-steroid conjugates. Chem Commun (Camb) 2016; 51:17552-5. [PMID: 26477302 DOI: 10.1039/c5cc07097j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Several GCN4 bZIP TF models have previously been designed and synthesized. However, the synthetic routes towards these constructs are typically tedious and difficult. We here describe the substitution of the Leucine zipper domain of the protein by a deoxycholic acid derivative appending the two GCN4 binding region peptides through an optimized double azide-alkyne cycloaddition click reaction. In addition to achieving sequence specific dsDNA binding, we have investigated the potential of these compounds to enter cells. Confocal microscopy and flow cytometry show the beneficial influence of the steroid on cell uptake. This unique synthetic model of the bZIP TF thus combines sequence specific dsDNA binding properties with enhanced cell-uptake. Given the unique properties of deoxycholic acid and the convergent nature of the synthesis, we believe this work represents a key achievement in the field of TF mimicry.
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Affiliation(s)
- Yara Ruiz García
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 (S4), B-9000 Ghent, Belgium.
| | - Abhishek Iyer
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 (S4), B-9000 Ghent, Belgium.
| | - Dorien Van Lysebetten
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 (S4), B-9000 Ghent, Belgium.
| | - Y Vladimir Pabon
- Clinical Research Center, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, SE-141 86, Stockholm, Sweden.
| | - Benoit Louage
- Department of Pharmaceutics, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium.
| | - Malgorzata Honcharenko
- Department of Biosciences and Nutrition (BioNut), H2. Karolinska Institutet, Novum 141 83 Huddinge, Stockholm, Sweden.
| | - Bruno G De Geest
- Department of Pharmaceutics, Ghent University, Harelbekestraat 72, 9000 Ghent, Belgium.
| | - C I Edvard Smith
- Clinical Research Center, Department of Laboratory Medicine, Karolinska University Hospital Huddinge, SE-141 86, Stockholm, Sweden.
| | - Roger Strömberg
- Department of Biosciences and Nutrition (BioNut), H2. Karolinska Institutet, Novum 141 83 Huddinge, Stockholm, Sweden.
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281 (S4), B-9000 Ghent, Belgium.
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12
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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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13
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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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