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Deng Z, Zhou D. Mechanisms of Csp
3
‐H or Nsp
2
‐H functionalization of 2,3‐diaminoindoles with triplet O
2
: A density functional theory investigation. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Zhe‐Peng Deng
- Research Institute Lanzhou Jiaotong University Lanzhou China
| | - Da‐Gang Zhou
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, Institute of Synthesis and Application of Functional Materials, College of Chemistry and Chemical Engineering China West Normal University Nanchong China
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2
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He JP, Zhan ZZ, Luo N, Zhang MM, Huang GS. Direct synthesis of 2,3,5-trisubstituted pyrroles via copper-mediated one-pot multicomponent reaction. Org Biomol Chem 2020; 18:9831-9835. [PMID: 33245315 DOI: 10.1039/d0ob01952f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We have developed a copper-mediated one-pot synthesis of 2,3,5-trisubstituted pyrroles from 1,3-dicarbonyl compounds and acrylates using ammonium acetate as a nitrogen source. The reaction achieves C-C and C-N bond formation and provides an efficient approach to access highly functionalized pyrroles without further raw material preparation. This method is operationally simple, compatible with a wide range of functional groups, and provides the target products in moderate to good yields.
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Affiliation(s)
- Jian-Ping He
- State Key Laboratory of Applied Organic Chemistry, Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province, Department of Chemistry, Lanzhou University, Lanzhou 730000, China.
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3
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Geedkar D, Kumar A, Reen GK, Sharma P. Titania‐silica nanoparticles ensemblies assisted heterogeneous catalytic strategy for the synthesis of pharmacologically significant 2,3‐diaryl‐3,4‐dihydroimidazo[4,5‐
b
]indole scaffolds. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Deepika Geedkar
- School of Chemical SciencesDevi Ahilya University Indore India
| | - Ashok Kumar
- School of Chemical SciencesDevi Ahilya University Indore India
| | | | - Pratibha Sharma
- School of Chemical SciencesDevi Ahilya University Indore India
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Heinrich B, Vázquez O. 4-Methyltrityl-Protected Pyrrole and Imidazole Building Blocks for Solid Phase Synthesis of DNA-Binding Polyamides. Org Lett 2020; 22:533-536. [PMID: 31904984 DOI: 10.1021/acs.orglett.9b04288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-binding polyamides are synthetic oligomers of pyrrole/imidazole units with high specificity and affinity for double-stranded DNA. To increase their synthetic diversity, we report a mild methodology based on 4-methyltrityl (Mtt) solid phase peptide synthesis (SPPS), whose building blocks are more accessible than the standard Fmoc and Boc SPPS ones. We demonstrate the robustness of the approach by preparing and studying a hairpin with all precursors. Importantly, our strategy is orthogonal and compatible with sensitive molecules and could be readily automated.
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Affiliation(s)
- Benedikt Heinrich
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
| | - Olalla Vázquez
- Fachbereich Chemie , Philipps-Universität Marburg , Hans-Meerwein-Straße 4 , 35043 Marburg , Germany
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5
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Padroni G, Parkinson JA, Fox KR, Burley GA. Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides. Nucleic Acids Res 2019; 46:42-53. [PMID: 29194552 PMCID: PMC5758887 DOI: 10.1093/nar/gkx1211] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/28/2017] [Indexed: 01/05/2023] Open
Abstract
This manuscript reports the molecular basis for double-stranded DNA (dsDNA) binding of hairpin polyamides incorporating a 5-alkyl thiazole (Nt) unit. Hairpin polyamides containing an N-terminal Nt unit induce higher melting stabilisation of target dsDNA sequences relative to an archetypical hairpin polyamide incorporating an N-terminal imidazole (Im) unit. However, modification of the N-terminus from Im to Nt-building blocks results in an increase in dsDNA binding affinity but lower G-selectivity. A general G-selectivity trend is observed for Nt-containing polyamide analogues. G-selectivity increases as the steric bulk in the Nt 5-position increases. Solution-based NMR structural studies reveal differences in the modulation of the target DNA duplex of Nt-containing hairpin polyamides relative to the Im-containing archetype. A structural hallmark of an Nt polyamide•dsDNA complex is a more significant degree of major groove compression of the target dsDNA sequence relative to the Im-containing hairpin polyamide.
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Affiliation(s)
- Giacomo Padroni
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - John A Parkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Keith R Fox
- Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Southampton SO17 1BJ, UK
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
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Aman K, Padroni G, Parkinson JA, Welte T, Burley GA. Structural and Kinetic Profiling of Allosteric Modulation of Duplex DNA Induced by DNA-Binding Polyamide Analogues. Chemistry 2019; 25:2757-2763. [PMID: 30407668 PMCID: PMC6468288 DOI: 10.1002/chem.201805338] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Indexed: 12/20/2022]
Abstract
A combined structural and quantitative biophysical profile of the DNA binding affinity, kinetics and sequence‐selectivity of hairpin polyamide analogues is described. DNA duplexes containing either target polyamide binding sites or mismatch sequences are immobilized on a microelectrode surface. Quantitation of the DNA binding profile of polyamides containing N‐terminal 1‐alkylimidazole (Im) units exhibit picomolar binding affinities for their target sequences, whereas 5‐alkylthiazole (Nt) units are an order of magnitude lower (low nanomolar). Comparative NMR structural analyses of the polyamide series shows that the steric bulk distal to the DNA‐binding face of the hairpin iPr‐Nt polyamide plays an influential role in the allosteric modulation of the overall DNA duplex structure. This combined kinetic and structural study provides a foundation to develop next‐generation hairpin designs where the DNA‐binding profile of polyamides is reconciled with their physicochemical properties.
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Affiliation(s)
- Khalid Aman
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Giacomo Padroni
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - John A Parkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Thomas Welte
- Dynamic Biosensors GmbH, 82152, Planegg, Germany
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, UK
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8
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Polák P, Tobrman T. Dearomatization Strategy for the Synthesis of Arylated 2H-Pyrroles and 2,3,5-Trisubstituted 1H-Pyrroles. Org Lett 2017; 19:4608-4611. [DOI: 10.1021/acs.orglett.7b02219] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peter Polák
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
| | - Tomáš Tobrman
- Department of Organic Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28 Prague 6, Czech Republic
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9
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Raibaut L, Vasseur W, Shimberg GD, Saint-Pierre C, Ravanat JL, Michel SLJ, Sénèque O. Design of a synthetic luminescent probe from a biomolecule binding domain: selective detection of AU-rich mRNA sequences. Chem Sci 2016; 8:1658-1664. [PMID: 28451295 PMCID: PMC5364516 DOI: 10.1039/c6sc04086a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/02/2016] [Indexed: 12/12/2022] Open
Abstract
We report the design of a luminescent sensor based upon the zinc finger protein TIS11d, that allows for the selective time-resolved detection of the UUAUUUAUU sequence of the 3′-untranslated region of messenger RNA.
We report the design of a luminescent sensor based upon the zinc finger (ZF) protein TIS11d, that allows for the selective time-resolved detection of the UUAUUUAUU sequence of the 3′-untranslated region of messenger RNA. This sensor is composed of the tandem ZF RNA binding domain of TIS11d functionalized with a luminescent Tb3+ complex on one of the ZFs and a sensitizing antenna on the other. This work provides the proof of principle that an RNA binding protein can be re-engineered as an RNA sensor and, more generally, that tunable synthetic luminescent probes for biomolecules can be obtained by modifying biomolecule-binding domains.
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Affiliation(s)
- Laurent Raibaut
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France .
| | - William Vasseur
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France .
| | - Geoffrey D Shimberg
- Department of Pharmaceutical Sciences , School of Pharmacy , University of Maryland , Baltimore , Maryland 21201-1180 , USA .
| | - Christine Saint-Pierre
- Univ. Grenoble Alpes , INAC-SyMMES , F-38000 Grenoble , France.,CEA , INAC-SyMMES , F-38000 Grenoble , France
| | - Jean-Luc Ravanat
- Univ. Grenoble Alpes , INAC-SyMMES , F-38000 Grenoble , France.,CEA , INAC-SyMMES , F-38000 Grenoble , France
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences , School of Pharmacy , University of Maryland , Baltimore , Maryland 21201-1180 , USA .
| | - Olivier Sénèque
- Univ. Grenoble Alpes , LCBM/PMB , F-38000 Grenoble , France.,CNRS , LCBM/PMB , UMR 5249 , F-38000 Grenoble , France.,CEA , BIG-CBM , PMB , F-38000 Grenoble , France .
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