1
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Cougnon FBL, Stefankiewicz AR, Ulrich S. Dynamic covalent synthesis. Chem Sci 2024; 15:879-895. [PMID: 38239698 PMCID: PMC10793650 DOI: 10.1039/d3sc05343a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/10/2023] [Indexed: 01/22/2024] Open
Abstract
Dynamic covalent synthesis aims to precisely control the assembly of simple building blocks linked by reversible covalent bonds to generate a single, structurally complex, product. In recent years, considerable progress in the programmability of dynamic covalent systems has enabled easy access to a broad range of assemblies, including macrocycles, shape-persistent cages, unconventional foldamers and mechanically-interlocked species (catenanes, knots, etc.). The reversibility of the covalent linkages can be either switched off to yield stable, isolable products or activated by specific physico-chemical stimuli, allowing the assemblies to adapt and respond to environmental changes in a controlled manner. This activatable dynamic property makes dynamic covalent assemblies particularly attractive for the design of complex matter, smart chemical systems, out-of-equilibrium systems, and molecular devices.
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Affiliation(s)
- Fabien B L Cougnon
- Department of Chemistry and Nanoscience Centre, University of Jyväskylä Jyväskylä Finland
| | - Artur R Stefankiewicz
- Centre for Advanced Technology and Faculty of Chemistry, Adam Mickiewicz University Poznań Poland
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM Montpellier France
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2
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Han X, Guo C, Xu C, Shi L, Liu B, Zhang Z, Bai Q, Song B, Pan F, Lu S, Zhu X, Wang H, Hao XQ, Song MP, Li X. Water-Soluble Metallo-Supramolecular Nanoreactors for Mediating Visible-Light-Promoted Cross-Dehydrogenative Coupling Reactions. ACS NANO 2023; 17:3723-3736. [PMID: 36757357 DOI: 10.1021/acsnano.2c10856] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Water-soluble metallo-supramolecular cages with well-defined nanosized cavities have a wide range of functions and applications. Herein, we design and synthesize two series of metallo-supramolecular octahedral cages based on the self-assembly of two congeneric truxene-derived tripyridyl ligands modified with two polyethylene glycol (PEG) chains, i.e., monodispersed tetraethylene glycol (TEG) and polydispersed PEG-1000, with four divalent transition metals (i.e., Pd, Cu, Ni, and Zn). The resulting monodispersed cages C1-C4 are fully characterized by electrospray ionization mass spectrometry (ESI-MS), nuclear magnetic resonance (NMR) spectroscopy, and single-crystal X-ray diffraction. The polydispersed cages C5-C8 display good water solubilities and can act as nanoreactors to mediate visible-light-promoted C(sp3)-C(sp2) cross-dehydrogenative coupling reactions in an aqueous phase. In particular, the most robust Pd(II)-linked water-soluble polydispersed nanoreactor C5 is characterized by ESI-MS and capable of mediating the reactions with the highest efficiencies. Detailed host-guest binding studies in conjunction with control studies suggest that these cages could encapsulate the substrates simultaneously inside its hydrophobic cavity while interacting with the photosensitizer (i.e., eosin Y).
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Affiliation(s)
- Xin Han
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, China
| | - Chenxing Guo
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, China
- School of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Chen Xu
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212003, China
| | - Linlin Shi
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Binghui Liu
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Zhe Zhang
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Qixia Bai
- Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Bo Song
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Fangfang Pan
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan, Hubei 430079, China
| | - Shuai Lu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, China
| | - Xinju Zhu
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Heng Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, China
| | - Xin-Qi Hao
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Mao-Ping Song
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xiaopeng Li
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong 518055, China
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3
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Tailored Supramolecular Cage for Efficient Bio-Labeling. Int J Mol Sci 2023; 24:ijms24032147. [PMID: 36768471 PMCID: PMC9916613 DOI: 10.3390/ijms24032147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/10/2022] [Accepted: 12/21/2022] [Indexed: 01/25/2023] Open
Abstract
Fluorescent chemosensors are powerful imaging tools used in a broad range of biomedical fields. However, the application of fluorescent dyes in bioimaging still remains challenging, with small Stokes shifts, interfering signals, background noise, and self-quenching on current microscope configurations. In this work, we reported a supramolecular cage (CA) by coordination-driven self-assembly of benzothiadiazole derivatives and Eu(OTf)3. The CA exhibited high fluorescence with a quantum yield (QY) of 38.57%, good photoluminescence (PL) stability, and a large Stokes shift (153 nm). Furthermore, the CCK-8 assay against U87 glioblastoma cells verified the low cytotoxicity of CA. We revealed that the designed probes could be used as U87 cells targeting bioimaging.
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4
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Caillaud K, Ladavière C. Water‐soluble (poly)acylhydrazones: Syntheses and Applications. MACROMOL CHEM PHYS 2022. [DOI: 10.1002/macp.202200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kilian Caillaud
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères Université Claude Bernard Lyon1, INSA Lyon, Université Jean Monnet Villeurbanne Cédex F‐69622 France
| | - Catherine Ladavière
- Univ Lyon, CNRS, UMR 5223, Ingénierie des Matériaux Polymères Université Claude Bernard Lyon1, INSA Lyon, Université Jean Monnet Villeurbanne Cédex F‐69622 France
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5
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Carbajo D, Pérez Y, Guerra-Rebollo M, Prats E, Bujons J, Alfonso I. Dynamic Combinatorial Optimization of In Vitro and In Vivo Heparin Antidotes. J Med Chem 2022; 65:4865-4877. [PMID: 35235323 PMCID: PMC8958503 DOI: 10.1021/acs.jmedchem.1c02054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Heparin-like macromolecules
are widely used in clinics as anticoagulant,
antiviral, and anticancer drugs. However, the search of heparin antidotes
based on small synthetic molecules to control blood coagulation still
remains a challenging task due to the physicochemical properties of
this anionic polysaccharide. Here, we use a dynamic combinatorial
chemistry approach to optimize heparin binders with submicromolar
affinity. The recognition of heparin by the most amplified members
of the dynamic library has been studied with different experimental
(SPR, fluorescence, NMR) and theoretical approaches, rendering a detailed
interaction model. The enzymatic assays with selected library members
confirm the correlation between the dynamic covalent screening and
the in vitro heparin inhibition. Moreover, both ex vivo and in vivo blood coagulation assays
with mice show that the optimized molecules are potent antidotes with
potential use as heparin reversal drugs. Overall, these results underscore
the power of dynamic combinatorial chemistry targeting complex and
elusive biopolymers.
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Affiliation(s)
| | | | - Marta Guerra-Rebollo
- Grup d'Enginyeria de Materials (Gemat), Institut Químic de Sarriá (IQS), Universitat Ramon Llull (URL), Via Augusta 390, 08017 Barcelona, Spain
| | - Eva Prats
- Research and Development Center (CID-CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
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6
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Coste M, Kotras C, Bessin Y, Gervais V, Dellemme D, Leclercq M, Fossépré M, Richeter S, Clément S, Surin M, Ulrich S. Synthesis, Self‐Assembly, and Nucleic Acid Recognition of an Acylhydrazone‐Conjugated Cationic Tetraphenylethene Ligand. European J Org Chem 2021. [DOI: 10.1002/ejoc.202001420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Maëva Coste
- IBMM Université de Montpellier, CNRS, ENSCM Montpellier France
| | - Clément Kotras
- ICGM Institut Charles Gerhardt Montpellier UMR 5253 Université de Montpellier CNRS, ENSCM Montpellier France
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Yannick Bessin
- IBMM Université de Montpellier, CNRS, ENSCM Montpellier France
| | - Virginie Gervais
- CNRS Institut de Pharmacologie et de Biologie Structurale (IPBS) Université de Toulouse, UPS 205 route de Narbonne 31077 Toulouse France
| | - David Dellemme
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Maxime Leclercq
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
| | - Sébastien Richeter
- ICGM Institut Charles Gerhardt Montpellier UMR 5253 Université de Montpellier CNRS, ENSCM Montpellier France
| | - Sébastien Clément
- ICGM Institut Charles Gerhardt Montpellier UMR 5253 Université de Montpellier CNRS, ENSCM Montpellier France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials Center of Innovation and Research in Materials and Polymers (CIRMAP) University of Mons-UMONS 7000 Mons Belgium
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7
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Kieffer M, Bilbeisi RA, Thoburn JD, Clegg JK, Nitschke JR. Guest Binding Drives Host Redistribution in Libraries of Co II 4 L 4 Cages. Angew Chem Int Ed Engl 2020; 59:11369-11373. [PMID: 32243707 PMCID: PMC7383889 DOI: 10.1002/anie.202004627] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Indexed: 12/29/2022]
Abstract
Two CoII 4 L4 tetrahedral cages prepared from similar building blocks showed contrasting host-guest properties. One cage did not bind guests, whereas the second encapsulated a series of anions, due to electronic and geometric effects. When the building blocks of both cages were present during self-assembly, a library of five CoII LA x LB 4-x cages was formed in a statistical ratio in the absence of guests. Upon incorporation of anions able to interact preferentially with some library members, the products obtained were redistributed in favor of the best anion binders. To quantify the magnitudes of these templation effects, ESI-MS was used to gauge the effect of each template upon library redistribution.
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Affiliation(s)
- Marion Kieffer
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Rana A. Bilbeisi
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Department of Civil and Environmental EngineeringAmerican University of BeirutBeirutLebanon
| | - John D. Thoburn
- Department of ChemistryRandolph-Macon CollegeAshlandVA23005USA
| | - Jack K. Clegg
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLD4072Australia
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8
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9
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Jiao T, Wu G, Zhang Y, Shen L, Lei Y, Wang C, Fahrenbach AC, Li H. Self‐Assembly in Water with N‐Substituted Imines. Angew Chem Int Ed Engl 2020; 59:18350-18367. [DOI: 10.1002/anie.201910739] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/09/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Tianyu Jiao
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Guangcheng Wu
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Yang Zhang
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Libo Shen
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Ye Lei
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | - Cai‐Yun Wang
- Department of Chemistry Zhejiang University Hangzhou 310027 China
| | | | - Hao Li
- Department of Chemistry Zhejiang University Hangzhou 310027 China
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10
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11
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Su D, Coste M, Diaconu A, Barboiu M, Ulrich S. Cationic dynamic covalent polymers for gene transfection. J Mater Chem B 2020; 8:9385-9403. [DOI: 10.1039/d0tb01836h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Dynamic covalent polymers have revealed strong potential in gene delivery, thanks to their versatile self-assembly, adaptive and responsive behaviors.
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Affiliation(s)
- Dandan Su
- Institut Européen des Membranes
- Adaptive Supramolecular Nanosystems Group
- University of Montpellier
- ENSCM
- CNRS
| | - Maëva Coste
- Institut des Biomolécules Max Mousseron (IBMM)
- CNRS
- Université of Montpellier
- ENSCM
- Montpellier
| | - Andrei Diaconu
- Petru Poni” Institute of Macromolecular Chemistry of Romanian Academy
- Iasi
- Romania
| | - Mihail Barboiu
- Institut Européen des Membranes
- Adaptive Supramolecular Nanosystems Group
- University of Montpellier
- ENSCM
- CNRS
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM)
- CNRS
- Université of Montpellier
- ENSCM
- Montpellier
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12
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Osypenko A, Dhers S, Lehn JM. Pattern Generation and Information Transfer through a Liquid/Liquid Interface in 3D Constitutional Dynamic Networks of Imine Ligands in Response to Metal Cation Effectors. J Am Chem Soc 2019; 141:12724-12737. [DOI: 10.1021/jacs.9b05438] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Artem Osypenko
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Sébastien Dhers
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Jean-Marie Lehn
- Laboratoire de Chimie Supramoléculaire, Institut de Science et d’Ingénierie Supramoléculaires (ISIS), Université de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
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13
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Löw H, Mena-Osteritz E, von Delius M. Self-assembled orthoester cryptands: orthoester scope, post-functionalization, kinetic locking and tunable degradation kinetics. Chem Sci 2018; 9:4785-4793. [PMID: 29910929 PMCID: PMC5982201 DOI: 10.1039/c8sc01750f] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 04/26/2018] [Indexed: 01/01/2023] Open
Abstract
Dynamic adaptability and biodegradability are key features of functional, 21st century host-guest systems. We have recently discovered a class of tripodal supramolecular hosts, in which two orthoesters act as constitutionally dynamic bridgeheads. Having previously demonstrated the adaptive nature of these hosts, we now report the synthesis and characterization - including eight solid state structures - of a diverse set of orthoester cages, which provides evidence for the broad scope of this new host class. With the same set of compounds, we demonstrated that the rates of orthoester exchange and hydrolysis can be tuned over a remarkably wide range, from rapid hydrolysis at pH 8 to nearly inert at pH 1, and that the Taft parameter of the orthoester substituent allows an adequate prediction of the reaction kinetics. Moreover, the synthesis of an alkyne-capped cryptand enabled the post-functionalization of orthoester cryptands by Sonogashira and CuAAC "click" reactions. The methylation of the resulting triazole furnished a cryptate that was kinetically inert towards orthoester exchange and hydrolysis at pH > 1, which is equivalent to the "turnoff" of constitutionally dynamic imines by means of reduction. These findings indicate that orthoester cages may be more broadly useful than anticipated, e.g. as drug delivery agents with precisely tunable biodegradability or, thanks to the kinetic locking strategy, as ion sensors.
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Affiliation(s)
- Henrik Löw
- Institute of Organic Chemistry and Advanced Materials , University of Ulm , Albert-Einstein-Allee 11 , 89081 Ulm , Germany .
| | - Elena Mena-Osteritz
- Institute of Organic Chemistry and Advanced Materials , University of Ulm , Albert-Einstein-Allee 11 , 89081 Ulm , Germany .
| | - Max von Delius
- Institute of Organic Chemistry and Advanced Materials , University of Ulm , Albert-Einstein-Allee 11 , 89081 Ulm , Germany .
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14
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Drożdż W, Bouillon C, Kotras C, Richeter S, Barboiu M, Clément S, Stefankiewicz AR, Ulrich S. Generation of Multicomponent Molecular Cages using Simultaneous Dynamic Covalent Reactions. Chemistry 2017; 23:18010-18018. [DOI: 10.1002/chem.201703868] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Wojciech Drożdż
- Faculty of Chemistry; Adam Mickiewicz University; Umultowska 89b 61-614 Poznań Poland
- Centre for Advanced Technologies; Adam Mickiewicz University; Umultowska 89c, 6 1-614 Poznań Poland
| | - Camille Bouillon
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 240 Avenue du Professeur Emile Jeanbrau 34296 Montpellier cedex 5 France
| | - Clément Kotras
- Institut Charles Gerhardt (ICGM), UMR 5253; Université de Montpellier, CNRS, ENSCM; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Sébastien Richeter
- Institut Charles Gerhardt (ICGM), UMR 5253; Université de Montpellier, CNRS, ENSCM; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Mihail Barboiu
- Institut Européen des Membranes (IEM), UMR 5635; Université de Montpellier, ENSCM, CNRS, Adaptive Supramolecular Nanosystems Group; Place Eugène Bataillon, CC 047 34095 Montpellier France
| | - Sébastien Clément
- Institut Charles Gerhardt (ICGM), UMR 5253; Université de Montpellier, CNRS, ENSCM; Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - Artur R. Stefankiewicz
- Faculty of Chemistry; Adam Mickiewicz University; Umultowska 89b 61-614 Poznań Poland
- Centre for Advanced Technologies; Adam Mickiewicz University; Umultowska 89c, 6 1-614 Poznań Poland
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 240 Avenue du Professeur Emile Jeanbrau 34296 Montpellier cedex 5 France
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15
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Bartolami E, Knoops J, Bessin Y, Fossépré M, Chamieh J, Dumy P, Surin M, Ulrich S. One-Pot Self-Assembly of Peptide-Based Cage-Type Nanostructures Using Orthogonal Ligations. Chemistry 2017; 23:14323-14331. [DOI: 10.1002/chem.201702974] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Eline Bartolami
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
- Present address: Department of Organic Chemistry; University of Geneva; 30 Quai Ernest Ansermet 1211 Geneva 4 Switzerland
| | - Jérémie Knoops
- Laboratory for Chemistry of Novel Materials; University of Mons-UMONS; 20, Place du Parc 7000 Mons Belgium
| | - Yannick Bessin
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials; University of Mons-UMONS; 20, Place du Parc 7000 Mons Belgium
| | - Joseph Chamieh
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials; University of Mons-UMONS; 20, Place du Parc 7000 Mons Belgium
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Université de Montpellier, ENSCM; Ecole Nationale Supérieure de Chimie de Montpellier; 8 Rue de l'Ecole Normale 34296 Montpellier cedex 5 France
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16
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Cvrtila I, Fanlo-Virgós H, Schaeffer G, Monreal Santiago G, Otto S. Redox Control over Acyl Hydrazone Photoswitches. J Am Chem Soc 2017; 139:12459-12465. [PMID: 28749147 PMCID: PMC5599877 DOI: 10.1021/jacs.7b03724] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 11/28/2022]
Abstract
Photoisomerization provides a clean and efficient way of reversibly altering physical properties of chemical systems and injecting energy into them. These effects have been applied in development of systems such as photoresponsive materials, molecular motors, and photoactivated drugs. Typically, switching from more to less stable isomer(s) is performed by irradiation with UV or visible light, while the reverse process proceeds thermally or by irradiation using another wavelength. In this work we developed a method of rapid and tunable Z→E isomerization of C═N bond in acyl hydrazones, using aromatic thiols as nucleophilic catalysts. As thiols can be oxidized into catalytically inactive disulfides, the isomerization rates can be controlled via the oxidation state of the catalyst, which, together with the UV irradiation, provides orthogonal means to control the E/Z state of the system. As a proof of this concept, we have applied this method to control the diversity of acyl hydrazone based dynamic combinatorial libraries.
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Affiliation(s)
- Ivica Cvrtila
- Centre for Systems Chemistry,
Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hugo Fanlo-Virgós
- Centre for Systems Chemistry,
Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gaël Schaeffer
- Centre for Systems Chemistry,
Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Guillermo Monreal Santiago
- Centre for Systems Chemistry,
Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry,
Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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17
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Jaegle M, Wong EL, Tauber C, Nawrotzky E, Arkona C, Rademann J. Proteintemplat-gesteuerte Fragmentligationen - von der molekularen Erkennung zur Wirkstofffindung. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 129:7464-7485. [PMID: 32313319 PMCID: PMC7159557 DOI: 10.1002/ange.201610372] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Indexed: 12/28/2022]
Abstract
AbstractProteintemplat‐gesteuerte Fragmentligationen sind ein neuartiges Konzept zur Unterstützung der Wirkstofffindung und können dazu beitragen, die Wirksamkeit von Proteinliganden zu verbessern. Es handelt sich dabei um chemische Reaktionen zwischen niedermolekularen Verbindungen (“Fragmenten”), die die Oberfläche eines Proteins als Reaktionsgefäß verwenden, um die Bildung eines Proteinliganden mit erhöhter Bindungsaffinität zu katalysieren. Die Methode nutzt die molekulare Erkennung kleiner reaktiver Fragmente durch die Proteine sowohl zur Assemblierung der Liganden als auch zur Identifizierung bioaktiver Fragmentkombinationen. Chemische Synthese und Bioassay werden dabei in einem Schritt vereint. Dieser Aufsatz diskutiert die biophysikalischen Grundlagen der reversiblen und irreversiblen Fragmentligationen und gibt einen Überblick über die Methoden, mit denen die durch das Proteintemplat gebildeten Ligationsprodukte detektiert werden können. Der chemische Reaktionsraum und aktuelle Anwendungen wie auch die Bedeutung dieses Konzeptes für die Wirkstofffindung werden erörtert.
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Affiliation(s)
- Mike Jaegle
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Ee Lin Wong
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Carolin Tauber
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Eric Nawrotzky
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Christoph Arkona
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Jörg Rademann
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
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18
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Jaegle M, Wong EL, Tauber C, Nawrotzky E, Arkona C, Rademann J. Protein-Templated Fragment Ligations-From Molecular Recognition to Drug Discovery. Angew Chem Int Ed Engl 2017; 56:7358-7378. [PMID: 28117936 PMCID: PMC7159684 DOI: 10.1002/anie.201610372] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Indexed: 12/14/2022]
Abstract
Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") utilizing a protein's surface as a reaction vessel to catalyze the formation of a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. In this way, chemical synthesis and bioassay are integrated in one single step. This Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products. The chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed.
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Affiliation(s)
- Mike Jaegle
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Ee Lin Wong
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Carolin Tauber
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Eric Nawrotzky
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Christoph Arkona
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Jörg Rademann
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
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19
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Li Z, Wang Q, Yang X, Wang K, Du S, Zhang H, Gao L, Zheng Y, Nie W. Evaluating the Effect of Lidocaine on the Interactions of C-reactive Protein with Its Aptamer and Antibody by Dynamic Force Spectroscopy. Anal Chem 2017; 89:3370-3377. [PMID: 28231708 DOI: 10.1021/acs.analchem.6b03960] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Effects of medicine on the biomolecular interaction have been given extensive attention in biochemistry and biomedicine because of the complexity of the environment in vivo and the increasing opportunity of exposure to medicine. Herein, the effect of lidocaine on the interactions of C-reactive protein (CRP) with its aptamer and antibody under different temperature was investigated through dynamic force spectroscopy (DFS). The results revealed that lidocaine could reduce the binding probabilities and binding affinities of the CRP-aptamer and the CRP-antibody. An interesting discovery was that lidocaine had differential influences on the dynamic force spectra of the CRP-aptamer and the CRP-antibody. The energy landscape of the CRP-aptamer turned from two activation barriers to one after the treatment of lidocaine, while the one activation barrier in energy landscape of the CRP-antibody almost remained unchanged. In addition, similar results were obtained for 25 and 37 °C. In accordance with the result of molecular docking, the reduction of binding probabilities might be due to the binding of lidocaine on CRP. Additionally, the alteration of the dissociation pathway of the CRP-aptamer and the change of binding affinities might be caused by the conformational change of CRP, which was verified through synchronous fluorescence spectroscopy. Furthermore, differential effects of lidocaine on the interactions of CRP-aptamer and CRP-antibody might be attributed to the different dissociation processes and binding sites of the CRP-aptamer and the CRP-antibody and different structures of the aptamer and the antibody. This work indicated that DFS provided information for further research and comprehensive applications of biomolecular interaction, especially in the design of biosensors in complex systems.
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Affiliation(s)
- Zhiping Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, P. R. China
| | - Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, P. R. China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, P. R. China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, P. R. China
| | - Shasha Du
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, P. R. China
| | - Hua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, P. R. China
| | - Lei Gao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, P. R. China
| | - Yan Zheng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, P. R. China
| | - Wenyan Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha 410082, P. R. China
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20
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Seifert HM, Ramirez Trejo K, Anslyn EV. Four Simultaneously Dynamic Covalent Reactions. Experimental Proof of Orthogonality. J Am Chem Soc 2016; 138:10916-24. [DOI: 10.1021/jacs.6b04532] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Helen M. Seifert
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Karina Ramirez Trejo
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Eric V. Anslyn
- Department
of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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21
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Schaufelberger F, Ramström O. Kinetic Self-Sorting of Dynamic Covalent Catalysts with Systemic Feedback Regulation. J Am Chem Soc 2016; 138:7836-9. [DOI: 10.1021/jacs.6b04250] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fredrik Schaufelberger
- Department of Chemistry, KTH−Royal Institute of Technology, Teknikringen 30, S-10044 Stockholm, Sweden
| | - Olof Ramström
- Department of Chemistry, KTH−Royal Institute of Technology, Teknikringen 30, S-10044 Stockholm, Sweden
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22
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Rohse P, Wittmann V. Mechanistic Insight into Nanomolar Binding of Multivalent Neoglycopeptides to Wheat Germ Agglutinin. Chemistry 2016; 22:9724-33. [DOI: 10.1002/chem.201600657] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Philipp Rohse
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; 78457 Konstanz Germany
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23
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Abstract
A network of reader proteins and enzymes precisely controls gene transcription through the dynamic addition, removal, and recognition of post-translational modifications (PTMs) of histone tails. Histone PTMs work in concert with this network to regulate gene transcription through the histone code, and the dysregulation of PTM maintenance is linked to a large number of diseases, including many types of cancer. A wealth of research aims to elucidate the functions of this code, but our understanding of the effects of PTMs, specifically the methylation of lysine (Lys) and arginine (Arg), is lacking. The development of new tools to study PTMs relies on a sophisticated understanding of the mechanisms that drive protein and small molecule recognition in water. In this review, we outline the physical organic concepts that drive the molecular recognition of Lys and Arg methylation by reader proteins and draw comparisons to the binding mechanisms of small molecule receptors for methylated Lys and Arg that have been developed recently.
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Affiliation(s)
- Joshua E. Beaver
- Department of Chemistry, University of North Carolina, CB 3290, Chapel Hill, North Carolina 27599, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina, CB 3290, Chapel Hill, North Carolina 27599, United States
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24
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Zhang Y, Jayawardena HSN, Yan M, Ramström O. Enzyme classification using complex dynamic hemithioacetal systems. Chem Commun (Camb) 2016; 52:5053-6. [PMID: 26987550 PMCID: PMC4820758 DOI: 10.1039/c6cc01823h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A complex dynamic hemithioacetal system was used in combination with pattern recognition methodology to classify lipases into distinct groups.
A complex dynamic hemithioacetal system was generated for the evaluation of lipase reactivities in organic media. In combination with pattern recognition methodology, twelve different lipases were successfully classified into four distinct groups following their reaction selectivities and reactivities. A probe lipase was further categorized using the training matrix with predicted reactivity.
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Affiliation(s)
- Yan Zhang
- Department of Chemistry, KTH - Royal Institute of Technology, Teknikringen 30, 10044 Stockholm, Sweden.
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25
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Bartolami E, Bouillon C, Dumy P, Ulrich S. Bioactive clusters promoting cell penetration and nucleic acid complexation for drug and gene delivery applications: from designed to self-assembled and responsive systems. Chem Commun (Camb) 2016; 52:4257-73. [DOI: 10.1039/c5cc09715k] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recent developments in the (self-)assembly of cationic clusters promoting nucleic acids complexation and cell penetration open the door to applications in drug and gene delivery.
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Affiliation(s)
- Eline Bartolami
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Camille Bouillon
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
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26
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Alfonso I. From simplicity to complex systems with bioinspired pseudopeptides. Chem Commun (Camb) 2016; 52:239-50. [DOI: 10.1039/c5cc07596c] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This feature article highlights some of the recent advances in creating complexity from simple pseudopeptidic molecules. The bioinspired approaches discussed here allowed an increase in the structural, chemical and interactional complexity (see figure).
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Affiliation(s)
- Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modelling
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- Jordi Girona
- 18-26
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27
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Han Y, Nowak P, Colomb-Delsuc M, Leal MP, Otto S. Instructable Nanoparticles Using Dynamic Combinatorial Chemistry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:12658-63. [PMID: 26514180 DOI: 10.1021/acs.langmuir.5b03673] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The application of nanoparticles to the multivalent recognition of biomacromolecules or programmed self-assembly requires control over the relative placement of chemical groups on their surface. We have developed a method to direct the functionalization of surfaces of aldehyde-equipped gold nanoparticles using a DNA template. An error-correction mechanism is built into the functionalization process thanks to the thermodynamic control enabled by the hydrazone exchange reaction. This reversible reaction can be conveniently switched off by removing the catalyst, preserving the functionalization.
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Affiliation(s)
- Yang Han
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Piotr Nowak
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Mathieu Colomb-Delsuc
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Manuel Pernia Leal
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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28
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Ren Y, You L. Dynamic Signaling Cascades: Reversible Covalent Reaction-Coupled Molecular Switches. J Am Chem Soc 2015; 137:14220-8. [DOI: 10.1021/jacs.5b09912] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yulong Ren
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, P. R. China
- College
of Chemistry, Fuzhou University, Fuzhou 350116, P. R. China
| | - Lei You
- State
Key Laboratory of Structural Chemistry, Fujian Institute of Research
on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, P. R. China
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29
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Berrocal JA, Albano S, Mandolini L, Di Stefano S. A CuI-Based Metallo-Supramolecular Gel-Like Material Built from a Library of Oligomeric Ligands Featuring Exotopic 1,10-Phenanthroline Units. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501201] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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30
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Di Stefano S, Ercolani G. Catenation Equilibria Between Ring Oligomers and Their Relation to Effective Molarities: Models From Theories and Simulations. MACROMOL THEOR SIMUL 2015. [DOI: 10.1002/mats.201500050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefano Di Stefano
- Dipartimento di Chimica, Sapienza Università di Roma and Istituto CNR di Metodologie Chimiche (IMC-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica; Università di Roma La Sapienza; P.le A. Moro 5 00185 Roma Italy
| | - Gianfranco Ercolani
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma Tor Vergata; Via della Ricerca Scientifica 00133 Roma Italy
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31
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Harnessing dynamic combinatorial chemistry in the search for new ligands for protein targets. Future Med Chem 2015; 7:2095-8. [DOI: 10.4155/fmc.15.146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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32
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Zhang Y, Barboiu M. Constitutional Dynamic Materials—Toward Natural Selection of Function. Chem Rev 2015; 116:809-34. [DOI: 10.1021/acs.chemrev.5b00168] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan Zhang
- Adaptive Supramolecular Nanosystems
Group, Institut Européen des Membranes—UMR CNRS 5635, Place Eugène
Bataillon, CC 047, F-34095 Montpellier, France
| | - Mihail Barboiu
- Adaptive Supramolecular Nanosystems
Group, Institut Européen des Membranes—UMR CNRS 5635, Place Eugène
Bataillon, CC 047, F-34095 Montpellier, France
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33
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Bartolami E, Bessin Y, Gervais V, Dumy P, Ulrich S. Dynamic Expression of DNA Complexation with Self-assembled Biomolecular Clusters. Angew Chem Int Ed Engl 2015; 54:10183-7. [DOI: 10.1002/anie.201504047] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/11/2015] [Indexed: 12/18/2022]
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34
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Bartolami E, Bessin Y, Gervais V, Dumy P, Ulrich S. Dynamic Expression of DNA Complexation with Self-assembled Biomolecular Clusters. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504047] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Zhou Y, Yuan Y, You L, Anslyn EV. Dynamic Aminal-Based TPA Ligands. Chemistry 2015; 21:8207-13. [DOI: 10.1002/chem.201500105] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Indexed: 12/21/2022]
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36
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Bartolami E, Gilles A, Dumy P, Ulrich S. Synthesis of α-PNA containing a functionalized triazine as nucleobase analogue. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.03.072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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Shi J, Du X, Yuan D, Haburcak R, Wu D, Zhou N, Xu B. Enzyme transformation to modulate the ligand-receptor interactions between small molecules. Chem Commun (Camb) 2015; 51:4899-901. [PMID: 25703347 PMCID: PMC4352935 DOI: 10.1039/c4cc10374b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymatic transformation is a fundamental process to control ligand-receptor interactions among proteins for signal transduction in cells. Here we report the first example of enzymatic transformation regulated ligand-receptor interactions of small molecules, in which enzymatic reaction changes the stoichiometry of the ligand-receptor binding from 1 : 1 to 1 : 2. We also show that this unique integration of enzymatic transformation and ligand-receptor interactions of small molecules is able to affect the fate of cells.
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Affiliation(s)
- Junfeng Shi
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454, USA.
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38
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Paolantoni D, Cantel S, Dumy P, Ulrich S. A dynamic combinatorial approach for identifying side groups that stabilize DNA-templated supramolecular self-assemblies. Int J Mol Sci 2015; 16:3609-25. [PMID: 25667976 PMCID: PMC4346916 DOI: 10.3390/ijms16023609] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/16/2015] [Accepted: 01/23/2015] [Indexed: 12/16/2022] Open
Abstract
DNA-templated self-assembly is an emerging strategy for generating functional supramolecular systems, which requires the identification of potent multi-point binding ligands. In this line, we recently showed that bis-functionalized guanidinium compounds can interact with ssDNA and generate a supramolecular complex through the recognition of the phosphodiester backbone of DNA. In order to probe the importance of secondary interactions and to identify side groups that stabilize these DNA-templated self-assemblies, we report herein the implementation of a dynamic combinatorial approach. We used an in situ fragment assembly process based on reductive amination and tested various side groups, including amino acids. The results reveal that aromatic and cationic side groups participate in secondary supramolecular interactions that stabilize the complexes formed with ssDNA.
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Affiliation(s)
- Delphine Paolantoni
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Sonia Cantel
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université de Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, Montpellier Cedex 5 34296, France.
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39
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Nowak P, Saggiomo V, Salehian F, Colomb-Delsuc M, Han Y, Otto S. Localized Template-Driven Functionalization of Nanoparticles by Dynamic Combinatorial Chemistry. Angew Chem Int Ed Engl 2015; 54:4192-7. [DOI: 10.1002/anie.201409667] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/21/2015] [Indexed: 12/18/2022]
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40
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Nowak P, Saggiomo V, Salehian F, Colomb-Delsuc M, Han Y, Otto S. Localized Template-Driven Functionalization of Nanoparticles by Dynamic Combinatorial Chemistry. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409667] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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41
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Wang Q, Liu L, Yang X, Wang K, Chen N, Zhou C, Luo B, Du S. Evaluation of medicine effects on the interaction of myoglobin and its aptamer or antibody using atomic force microscopy. Anal Chem 2015; 87:2242-8. [PMID: 25615803 DOI: 10.1021/ac503885e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The effects of medicine on the biomolecular interaction have been given increasing attention in biochemistry and affinity-based analytics since the environment in vivo is complex especially for the patients. Herein, myoglobin, a biomarker of acute myocardial infarction, was used as a model, and the medicine effects on the interactions of myoglobin/aptamer and myoglobin/antibody were systematically investigated using atomic force microscopy (AFM) for the first time. The results showed that the average binding force and the binding probability of myoglobin/aptamer almost remained unchanged after myoglobin-modified gold substrate was incubated with promazine, amoxicillin, aspirin, and sodium penicillin, respectively. These parameters were changed for myoglobin/antibody after the myoglobin-modified gold substrate was treated with these medicines. For promazine and amoxicillin, they resulted in the change of binding force distribution of myoglobin/antibody (i.e., from unimodal distribution to bimodal distribution) and the increase of binding probability; for aspirin, it only resulted in the change of the binding force distribution, and for sodium penicillin, it resulted in the increase of the average binding force and the binding probability. These results may be attributed to the different interaction modes and binding sites between myoglobin/aptamer and myoglobin/antibody, the different structures between aptamer and antibody, and the effects of medicines on the conformations of myoglobin. These findings could enrich our understanding of medicine effects on the interactions of aptamer and antibody to their target proteins. Moreover, this work will lay a good foundation for better research and extensive applications of biomolecular interaction, especially in the design of biosensors in complex systems.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha, Hunan 410082, P. R. China
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Kanfar N, Bartolami E, Zelli R, Marra A, Winum JY, Ulrich S, Dumy P. Emerging trends in enzyme inhibition by multivalent nanoconstructs. Org Biomol Chem 2015; 13:9894-906. [DOI: 10.1039/c5ob01405k] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This review highlights the recent implementation of multivalent nanoconstructs in enzyme inhibition and discusses the emerging trends in their design and identification.
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Affiliation(s)
- Nasreddine Kanfar
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Eline Bartolami
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Renaud Zelli
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Alberto Marra
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
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Oueis E, Sabot C, Renard PY. New insights into the kinetic target-guided synthesis of protein ligands. Chem Commun (Camb) 2015; 51:12158-69. [DOI: 10.1039/c5cc04183j] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review describes the recent applications of the kinetic target guided synthesis and highlights the new advances of this strategy.
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Affiliation(s)
- Emilia Oueis
- Biomedical Sciences Research Council
- University of St. Andrews
- St. Andrews KY16 9ST
- UK
| | - Cyrille Sabot
- Normandie University
- COBRA
- UMR 6014 & FR 3038; Univ Rouen; INSA Rouen; CNRS
- Cedex
- France
| | - Pierre-Yves Renard
- Normandie University
- COBRA
- UMR 6014 & FR 3038; Univ Rouen; INSA Rouen; CNRS
- Cedex
- France
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Li J, Nowak P, Otto S. An Allosteric Receptor by Simultaneous “Casting” and “Molding” in a Dynamic Combinatorial Library. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Li J, Nowak P, Otto S. An allosteric receptor by simultaneous "casting" and "molding" in a dynamic combinatorial library. Angew Chem Int Ed Engl 2014; 54:833-7. [PMID: 25430978 DOI: 10.1002/anie.201408907] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/31/2014] [Indexed: 01/13/2023]
Abstract
Allosteric synthetic receptors are difficult to access by design. Herein we report a dynamic combinatorial strategy towards such systems based on the simultaneous use of two different templates. Through a process of simultaneous casting (the assembly of a library member around a template) and molding (the assembly of a library member inside the binding pocket of a template), a Russian-doll-like termolecular complex was obtained with remarkable selectivity. Analysis of the stepwise formation of the complex indicates that binding of the two partners by the central macrocycle exhibits significant positive cooperativity. Such allosteric systems represent hubs that may have considerable potential in systems chemistry.
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Affiliation(s)
- Jianwei Li
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands) http://www.otto-lab.com
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Li J, Cvrtila I, Colomb-Delsuc M, Otten E, Otto S. An “Ingredients” Approach to Functional Self-Synthesizing Materials: A Metal-Ion-Selective, Multi-Responsive, Self-Assembled Hydrogel. Chemistry 2014; 20:15709-14. [DOI: 10.1002/chem.201404977] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Indexed: 12/22/2022]
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Bouillon C, Paolantoni D, Rote JC, Bessin Y, Peterson LW, Dumy P, Ulrich S. Degradable Hybrid Materials Based on Cationic Acylhydrazone Dynamic Covalent Polymers Promote DNA Complexation through Multivalent Interactions. Chemistry 2014; 20:14705-14. [DOI: 10.1002/chem.201403695] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 12/28/2022]
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