1
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Schlosser J, Fedorova O, Fedorov Y, Ihmels H. Photoinduced in situ generation of DNA-targeting ligands: DNA-binding and DNA-photodamaging properties of benzo[ c]quinolizinium ions. Beilstein J Org Chem 2024; 20:101-117. [PMID: 38264449 PMCID: PMC10804566 DOI: 10.3762/bjoc.20.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/05/2024] [Indexed: 01/25/2024] Open
Abstract
The photoreactions of selected styrylpyridine derivatives to the corresponding benzo[c]quinolizinium ions are described. It is shown that these reactions are more efficient in aqueous solution (97-44%) than in organic solvents (78-20% in MeCN). The quinolizinium derivatives bind to DNA by intercalation with binding constants of 6-11 × 104 M-1, as shown by photometric and fluorimetric titrations as well as by CD- and LD-spectroscopic analyses. These ligand-DNA complexes can also be established in situ upon irradiation of the styrylpyridines and formation of the intercalator directly in the presence of DNA. In addition to the DNA-binding properties, the tested benzo[c]quinolizinium derivatives also operate as photosensitizers, which induce DNA damage at relative low concentrations and short irradiation times, even under anaerobic conditions. Investigations of the mechanism of the DNA damage revealed the involvement of intermediate hydroxyl radicals and C-centered radicals. Under aerobic conditions, singlet oxygen only contributes to marginal extent to the DNA damage.
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Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cµ), University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Olga Fedorova
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991 Moscow, Russia
| | - Yuri Fedorov
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991 Moscow, Russia
| | - Heiko Ihmels
- Department of Chemistry and Biology, and Center of Micro- and Nanochemistry and (Bio)Technology (Cµ), University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
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2
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Matsuura K, Inaba H. Photoresponsive peptide materials: Spatiotemporal control of self-assembly and biological functions. BIOPHYSICS REVIEWS 2023; 4:041303. [PMID: 38505425 PMCID: PMC10903425 DOI: 10.1063/5.0179171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/27/2023] [Indexed: 03/21/2024]
Abstract
Peptides work as both functional molecules to modulate various biological phenomena and self-assembling artificial materials. The introduction of photoresponsive units to peptides allows the spatiotemporal remote control of their structure and function upon light irradiation. This article overviews the photoresponsive peptide design, interaction with biomolecules, and applications in self-assembling materials over the last 30 years. Peptides modified with photochromic (photoisomerizable) molecules, such as azobenzene and spiropyran, reversibly photo-controlled the binding to biomolecules and nanostructure formation through self-assembly. Photocleavable molecular units irreversibly control the functions of peptides through cleavage of the main chain and deprotection by light. Photocrosslinking between peptides or between peptides and other biomolecules enhances the structural stability of peptide assemblies and complexes. These photoresponsive peptides spatiotemporally controlled the formation and dissociation of peptide assemblies, gene expressions, protein-drug interactions, protein-protein interactions, liposome deformation and motility, cytoskeleton structure and stability, and cell functions by appropriate light irradiation. These molecular systems can be applied to photo-control biological functions, molecular robots, artificial cells, and next-generation smart drug delivery materials.
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3
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Lin D, Ke Y, Chen H, Zhang Y, Tang X, Cui W, Li X, He Y, Wu L. Self-Assembly Nanostructure Induced by Regulation of G-Quadruplex DNA Topology via a Reduction-Sensitive Azobenzene Ligand on Cells. Biomacromolecules 2023; 24:5004-5017. [PMID: 37843895 DOI: 10.1021/acs.biomac.3c00657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
The control of DNA assembly systems on cells has increasingly shown great importance for precisely targeted therapies. Here, we report a controllable DNA self-assembly system based on the regulation of G-quadruplex DNA topology by a reduction-sensitive azobenzene ligand. Specifically, three azobenzene multiamines are developed, and AzoDiTren is identified as the best G4 binder, which displays high affinity and specificity for G4 DNA. Moreover, the reduction-sensitive nature of the azobenzene scaffold allows AzoDiTren to induce a complete change of the G4 topology in a tissue-specific manner, even at high metal cation concentrations. On this basis, the AzoDiTren-induced G4 conformational switch achieves control of the self-assembly of G4-functionalized DNAs on cells. This strategy enables the regulation of G4 and DNA self-assembly by the bioreductant-responsive ligand.
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Affiliation(s)
- Dao Lin
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongqi Ke
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongjia Chen
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yinlong Zhang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Wei Cui
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangjun Li
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yujian He
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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4
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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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5
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Dohmen C, Ihmels H. Switching between DNA binding modes with a photo- and redox-active DNA-targeting ligand, part II: the influence of the substitution pattern. Org Biomol Chem 2023. [PMID: 37401249 DOI: 10.1039/d3ob00879g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
A disulfide-functionalized photoactive DNA ligand is presented that enables the control of its DNA-binding properties by a combination of a photocycloaddition reaction and the redox reactivity of the sulfide/disulfide functionalities. In particular, the initially applied ligand binds to DNA by a combination of intercalation and groove-binding of separate benzo[b]quinolizinium units. The association to DNA is interrupted by an intramolecular [4 + 4] photocycloaddition to the non-binding head-to-head cyclomers. In turn, the subsequent cleavage of these cyclomers with dithiothreitol (DTT) regains temporarily a DNA-intercalating benzoquinolizinium ligand that is eventually converted into a non-binding benzothiophene. As a special feature, this sequence of controlled deactivation, recovery and internal shut-off of DNA-binding properties can be performed directly in the presence of DNA.
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Affiliation(s)
- Christoph Dohmen
- Department of Chemistry - Biology, University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - Heiko Ihmels
- Department of Chemistry - Biology, University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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6
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Dohmen C, Ihmels H. Switching between DNA binding modes with a photo- and redox-active DNA-targeting ligand. Org Biomol Chem 2023; 21:1958-1966. [PMID: 36762516 DOI: 10.1039/d3ob00013c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A disulfide-functionalized bis-benzo[b]quinolizinium is presented that is transformed quantitatively into its cyclomers in a fast intramolecular [4 + 4] photocycloaddition. Both the bis-quinolizinium and the photocyclomers react with glutathione (GSH) or dithiothreitol (DTT) to give 9-(sulfanylmethyl)benzo[b]quinolizinium as the only product. As all components of this reaction sequence have different DNA-binding properties, it enables the external control and switching of DNA association. Hence, the bis-benzo[b]quinolizinium binds strongly to DNA and is deactivated upon photocycloaddition to the non-binding cyclomers. In turn, the subsequent cleavage of the cyclomers with DTT regains a DNA-intercalating benzoquinolizinium ligand. Notably, this sequence of controlled deactivation and recovery of DNA-binding properties can be performed directly in the presence of DNA.
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Affiliation(s)
- Christoph Dohmen
- Department of Chemistry and Biology, University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, and Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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7
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Ogbonna EN, Paul A, Ross Terrell J, Fang Z, Chen C, Poon GMK, Boykin DW, Wilson WD. Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines. Bioorg Med Chem 2022; 68:116861. [PMID: 35661929 DOI: 10.1016/j.bmc.2022.116861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
Abstract
The understanding of sequence-specific DNA minor groove interactions has recently made major steps forward and as a result, the goal of development of compounds that target the minor groove is an active research area. In an effort to develop biologically active minor groove agents, we are preparing and exploring the DNA interactions of diverse diamidine derivatives with a 5'-GAATTC-3' binding site using a powerful array of methods including, biosensor-SPR methods, and X-ray crystallography. The benzimidazole-thiophene module provides an excellent minor groove recognition component. A central thiophene in a benzimidazole-thiophene-phenyl aromatic system provides essentially optimum curvature for matching the shape of the minor groove. Comparison of that structure to one with the benzimidazole replaced with an indole shows that the two structures are very similar, but have some interesting and important differences in electrostatic potential maps, the DNA minor groove binding structure based on x-ray crystallographic analysis, and inhibition of the major groove binding PU.1 transcription factor complex. The binding KD for both compounds is under 10 nM and both form amidine H-bonds to DNA bases. They both have bifurcated H-bonds from the benzimidazole or indole groups to bases at the center of the -AATT- binding site. Analysis of the comparative results provides an excellent understanding of how thiophene compounds recognize the minor groove and can act as transcription factor inhibitors.
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Affiliation(s)
- Edwin N Ogbonna
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - J Ross Terrell
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ziyuan Fang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Cen Chen
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
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8
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Simeth NA, de Mendoza P, Dubach VRA, Stuart MCA, Smith JW, Kudernac T, Browne WR, Feringa BL. Photoswitchable architecture transformation of a DNA-hybrid assembly at the microscopic and macroscopic scale. Chem Sci 2022; 13:3263-3272. [PMID: 35414864 PMCID: PMC8926171 DOI: 10.1039/d1sc06490h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/16/2022] [Indexed: 01/01/2023] Open
Abstract
Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks. Oligonucleotide-based nanotechnology and soft-materials benefit from the high information storage density, self-correction, and memory function of DNA. Here we control these beneficial properties with light in a photoresponsive biohybrid hydrogel, adding an extra level of function to the system. An ssDNA template was combined with a complementary photo-responsive unit to reversibly switch between various functional states of the supramolecular assembly using a combination of light and heat. We studied the structural response of the hydrogel at both the microscopic and macroscopic scale using a combination of UV-vis absorption and CD spectroscopy, as well as fluorescence, transmission electron, and atomic force microscopy. The hydrogels grown from these supramolecular self-assembly systems show remarkable shape-memory properties and imprinting shape-behavior while the macroscopic shape of the materials obtained can be further manipulated by irradiation. Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks.![]()
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Affiliation(s)
- Nadja A Simeth
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Paula de Mendoza
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Victor R A Dubach
- Groningen Biomolecular Sciences and Biotechnology, Faculty for Science and Engineering, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Marc C A Stuart
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands .,Groningen Biomolecular Sciences and Biotechnology, Faculty for Science and Engineering, University of Groningen Nijenborgh 7 9747 AG Groningen The Netherlands
| | - Julien W Smith
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Tibor Kudernac
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Wesley R Browne
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Ben L Feringa
- Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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9
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Rodríguez J, Pérez-González C, Martínez-Calvo M, Mosquera J, Mascareñas JL. Deactivation of a dimeric DNA-binding peptide through a palladium-mediated self-immolative cleavage. RSC Adv 2022; 12:3500-3504. [PMID: 35425354 PMCID: PMC8979313 DOI: 10.1039/d1ra09180h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 01/11/2022] [Indexed: 12/19/2022] Open
Abstract
Herein, we describe an approach for the on-demand disassembly of dimeric peptides using a palladium-mediated cleavage of a designed self-immolative linker. The utility of the strategy is demonstrated for the case of dimeric basic regions of bZIP transcription factors. While the dimer binds designed DNA sequences with good affinities, the peptide–DNA complex can be readily dismounted by addition of palladium reagents that trigger the cleavage of the spacer, and the release of unfunctional monomeric peptides. A metallic trigger for disassembling and cancelling function.![]()
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Affiliation(s)
- Jessica Rodríguez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n Santiago de Compostela 15782 Spain
| | - Cibrán Pérez-González
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n Santiago de Compostela 15782 Spain
| | - Miguel Martínez-Calvo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n Santiago de Compostela 15782 Spain
| | - Jesús Mosquera
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n Santiago de Compostela 15782 Spain
| | - José L Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela Rúa Jenaro de la Fuente s/n Santiago de Compostela 15782 Spain
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10
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Ramos-Soriano J, Galan MC. Photoresponsive Control of G-Quadruplex DNA Systems. JACS AU 2021; 1:1516-1526. [PMID: 34723256 PMCID: PMC8549047 DOI: 10.1021/jacsau.1c00283] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 05/14/2023]
Abstract
G-quadruplex (G4) oligonucleotide secondary structures have recently attracted significant attention as therapeutic targets owing to their occurrence in human oncogene promoter sequences and the genome of pathogenic organisms. G4s also demonstrate interesting catalytic activities in their own right, as well as the ability to act as scaffolds for the development of DNA-based materials and nanodevices. Owing to this diverse range of opportunities to exploit G4 in a variety of applications, several strategies to control G4 structure and function have emerged. Interrogating the role of G4s in biology requires the delivery of small-molecule ligands that promote its formation under physiological conditions, while exploiting G4 in the development of responsive nanodevices is normally achieved by the addition and sequestration of the metal ions required for the stabilization of the folded structure. Although these strategies prove successful, neither allows the system in question to be controlled externally. Meanwhile, light has proven to be an attractive means for the control of DNA-based systems as it is noninvasive, can be delivered with high spatiotemporal precision, and is orthogonal to many chemical and biological processes. A plethora of photoresponsive DNA systems have been reported to date; however, the vast majority deploy photoreactive moieties to control the stability and assembly of duplex DNA hybrids. Despite the unique opportunities afforded by the regulation of G-quadruplex formation in biology, catalysis, and nanotechnology, comparatively little attention has been devoted to the design of photoresponsive G4-based systems. In this Perspective, we consider the potential of photoresponsive G4 assemblies and examine the strategies that may be used to engineer these systems toward a variety of applications. Through an overview of the main developments in the field to date, we highlight recent progress made toward this exciting goal and the emerging opportunities that remain ripe for further exploration in the coming years.
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Affiliation(s)
- Javier Ramos-Soriano
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - M Carmen Galan
- School
of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
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11
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Berdnikova DV. Photoswitches for controllable RNA binding: a future approach in the RNA-targeting therapy. Chem Commun (Camb) 2021; 57:10819-10826. [PMID: 34585681 DOI: 10.1039/d1cc04241f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA is an emerging drug target that opens new perspectives in the treatment of viral and bacterial infections, cancer and a range of so far incurable genetic diseases. Among the various strategies towards the design and development of selective and efficient ligands for targeting and detection of therapeutically relevant RNA, photoswitchable RNA binders represent a very promising approach due to the possibility to control the ligand-RNA and protein-RNA interactions by light with high spatiotemporal resolution. However, the field of photoswitchable RNA binders still remains underexplored due to challenging design of lead structures that should combine high RNA binding selectivity with efficient photochemical performance. The aim of this highlight article is to describe the development of photoswitchable noncovalent RNA binders and to outline the current situation and perspectives of this emerging interdisciplinary field.
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Affiliation(s)
- Daria V Berdnikova
- Universität Siegen, Organische Chemie II, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany.
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12
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Feng Y, Zhang K, Wu Q, Huang SY. NLDock: a Fast Nucleic Acid-Ligand Docking Algorithm for Modeling RNA/DNA-Ligand Complexes. J Chem Inf Model 2021; 61:4771-4782. [PMID: 34468128 DOI: 10.1021/acs.jcim.1c00341] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nucleic acid-ligand interactions play an important role in numerous cellular processes such as gene function expression and regulation. Therefore, nucleic acids such as RNAs have become more and more important drug targets, where the structural determination of nucleic acid-ligand complexes is pivotal for understanding their functions and thus developing therapeutic interventions. Molecular docking has been a useful computational tool in predicting the complex structure between molecules. However, although a number of docking algorithms have been developed for protein-ligand interactions, only a few docking programs were presented for nucleic acid-ligand interactions. Here, we have developed a fast nucleic acid-ligand docking algorithm, named NLDock, by implementing our intrinsic scoring function ITScoreNL for nucleic acid-ligand interactions into a modified version of the MDock program. NLDock was extensively evaluated on four test sets and compared with five other state-of-the-art docking algorithms including AutoDock, DOCK 6, rDock, GOLD, and Glide. It was shown that our NLDock algorithm obtained a significantly better performance than the other docking programs in binding mode predictions and achieved the success rates of 73%, 36%, and 32% on the largest test set of 77 complexes for local rigid-, local flexible-, and global flexible-ligand docking, respectively. In addition, our NLDock approach is also computationally efficient and consumed an average of as short as 0.97 and 2.08 min for a local flexible-ligand docking job and a global flexible-ligand docking job, respectively. These results suggest the good performance of our NLDock in both docking accuracy and computational efficiency.
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Affiliation(s)
- Yuyu Feng
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Keqiong Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Qilong Wu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
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13
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Simeth NA, Kobayashi S, Kobauri P, Crespi S, Szymanski W, Nakatani K, Dohno C, Feringa BL. Rational design of a photoswitchable DNA glue enabling high regulatory function and supramolecular chirality transfer. Chem Sci 2021; 12:9207-9220. [PMID: 34276952 PMCID: PMC8261765 DOI: 10.1039/d1sc02194j] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/22/2021] [Indexed: 01/02/2023] Open
Abstract
Short, complementary DNA single strands with mismatched base pairs cannot undergo spontaneous formation of duplex DNA (dsDNA). Mismatch binding ligands (MBLs) can compensate this effect, inducing the formation of the double helix and thereby acting as a molecular glue. Here, we present the rational design of photoswitchable MBLs that allow for reversible dsDNA assembly by light. Careful choice of the azobenzene core structure results in excellent band separation of the E and Z isomers of the involved chromophores. This effect allows for efficient use of light as an external control element for duplex DNA formation and for an in-depth study of the DNA-ligand interaction by UV-Vis, SPR, and CD spectroscopy, revealing a tight mutual interaction and complementarity between the photoswitchable ligand and the mismatched DNA. We also show that the configuration of the switch reversibly dictates the conformation of the DNA strands, while the dsDNA serves as a chiral clamp and translates its chiral information onto the ligand inducing a preference in helical chirality of the Z isomer of the MBLs.
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Affiliation(s)
- Nadja A Simeth
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Shotaro Kobayashi
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Piermichele Kobauri
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Stefano Crespi
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
- Department of Radiology, Medical Imaging Center, University of Groningen, University Medical Centre Groningen Hanzeplein 1 9713 GZ Groningen The Netherlands
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, Faculty for Science and Engineering, University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands
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Ditopic Aza-Scorpiand Ligands Interact Selectively with ds-RNA and Modulate the Interaction upon Formation of Zn 2+ Complexes. Molecules 2021; 26:molecules26133957. [PMID: 34203562 PMCID: PMC8272215 DOI: 10.3390/molecules26133957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/10/2021] [Accepted: 06/22/2021] [Indexed: 11/17/2022] Open
Abstract
Nucleic acids are essential biomolecules in living systems and represent one of the main targets of chemists, biophysics, biologists, and nanotechnologists. New small molecules are continuously developed to target the duplex (ds) structure of DNA and, most recently, RNA to be used as therapeutics and/or biological tools. Stimuli-triggered systems can promote and hamper the interaction to biomolecules through external stimuli such as light and metal coordination. In this work, we report on the interaction with ds-DNA and ds-RNA of two aza-macrocycles able to coordinate Zn2+ metal ions and form binuclear complexes. The interaction of the aza-macrocycles and the Zn2+ metal complexes with duplex DNA and RNA was studied using UV thermal and fluorescence indicator displacement assays in combination with theoretical studies. Both ligands show a high affinity for ds-DNA/RNA and selectivity for ds-RNA. The ability to interact with these duplexes is blocked upon Zn2+ coordination, which was confirmed by the low variation in the melting temperature and poor displacement of the fluorescent dye from the ds-DNA/RNA. Cell viability assays show a decrease in the cytotoxicity of the metal complexes in comparison with the free ligands, which can be associated with the observed binding to the nucleic acids.
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