1
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Furka Á. Forty years of combinatorial technology. Drug Discov Today 2022; 27:103308. [PMID: 35760283 DOI: 10.1016/j.drudis.2022.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/24/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Combinatorial technology has been facilitating the synthesis and screening of large molecular libraries containing millions of organic compounds ever since its introduction 40 years ago. It has changed the paradigms of pharmaceutical research from focusing on single compounds to focusing on immense collections of compounds. It inspired the development of dynamic combinatorial libraries, fragment-based drug discovery and virtual library screening. Combinatorial technology was revitalized by the development of DNA encoding. Amplification of DNA oligomers plus next-generation sequencing has made it possible to successfully screen billions of compounds in a single process.
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Affiliation(s)
- Árpád Furka
- Eötvös Loránd University Budapest Hungary, 1077 Rozsa u. 23-25, Budapest, Hungary.
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2
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Casciuc I, Osypenko A, Kozibroda B, Horvath D, Marcou G, Bonachera F, Varnek A, Lehn JM. Toward in Silico Modeling of Dynamic Combinatorial Libraries. ACS CENTRAL SCIENCE 2022; 8:804-813. [PMID: 35756377 PMCID: PMC9228562 DOI: 10.1021/acscentsci.2c00048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Indexed: 06/15/2023]
Abstract
Dynamic combinatorial libraries (DCLs) display adaptive behavior, enabled by the reversible generation of their molecular constituents from building blocks, in response to external effectors, e.g., protein receptors. So far, chemoinformatics has not yet been used for the design of DCLs-which comprise a radically different set of challenges compared to classical library design. Here, we propose a chemoinformatic model for theoretically assessing the composition of DCLs in the presence and the absence of an effector. An imine-based DCL in interaction with the effector human carbonic anhydrase II (CA II) served as a case study. Support vector regression models for the imine formation constants and imine-CA II binding were derived from, respectively, a set of 276 imines synthesized and experimentally studied in this work and 4350 inhibitors of CA II from ChEMBL. These models predict constants for all DCL constituents, to feed software assessing equilibrium concentrations. They are publicly available on the dedicated website. Models rationally selected two amines and two aldehydes predicted to yield stable imines with high affinity for CA II and provided a virtual illustration on how effector affinity regulates DCL members.
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Affiliation(s)
- Iuri Casciuc
- Laboratoire
de Chémoinformatique UMR 7140 CNRS, Institut Le Bel 4, rue B. Pascal 67081 Strasbourg, France
- Laboratoire
de Chimie Supramoléculaire, Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), Université
de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Artem Osypenko
- Laboratoire
de Chimie Supramoléculaire, Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), Université
de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Bohdan Kozibroda
- Laboratoire
de Chimie Supramoléculaire, Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), Université
de Strasbourg, 8 allée Gaspard Monge, 67000 Strasbourg, France
- Institute
of High Technologies, Taras Shevchenko National
University of Kyiv, 4g
Hlushkova Avenue, 03022 Kyiv, Ukraine
| | - Dragos Horvath
- Laboratoire
de Chémoinformatique UMR 7140 CNRS, Institut Le Bel 4, rue B. Pascal 67081 Strasbourg, France
| | - Gilles Marcou
- Laboratoire
de Chémoinformatique UMR 7140 CNRS, Institut Le Bel 4, rue B. Pascal 67081 Strasbourg, France
| | - Fanny Bonachera
- Laboratoire
de Chémoinformatique UMR 7140 CNRS, Institut Le Bel 4, rue B. Pascal 67081 Strasbourg, France
| | - Alexandre Varnek
- Laboratoire
de Chémoinformatique UMR 7140 CNRS, Institut Le Bel 4, rue B. Pascal 67081 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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3
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Kravchenko A, Timmer BJJ, Inge AK, Biedermann M, Ramström O. Stable CAAC‐based Ruthenium Complexes for Dynamic Olefin Metathesis Under Mild Conditions. ChemCatChem 2021. [DOI: 10.1002/cctc.202101172] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alexander Kravchenko
- Department of Chemistry KTH – Royal Institute of Technology Teknikringen 36 S-10044 Stockholm Sweden
| | - Brian J. J. Timmer
- Department of Chemistry KTH – Royal Institute of Technology Teknikringen 36 S-10044 Stockholm Sweden
| | - A. Ken Inge
- Stockholm University Department of Materials and Environmental Chemistry Svante Arrhenius väg 16 C S-10691 Stockholm Sweden
| | - Maurice Biedermann
- Department of Chemistry KTH – Royal Institute of Technology Teknikringen 36 S-10044 Stockholm Sweden
| | - Olof Ramström
- Department of Chemistry KTH – Royal Institute of Technology Teknikringen 36 S-10044 Stockholm Sweden
- Department of Chemistry University of Massachusetts Lowell One University Ave. Lowell MA 01854 USA
- Department of Chemistry and Biomedical Sciences Linnaeus University SE-39182 Kalmar Sweden
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4
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Lutz E, Moulin E, Tchakalova V, Benczédi D, Herrmann A, Giuseppone N. Design of Stimuli-Responsive Dynamic Covalent Delivery Systems for Volatile Compounds (Part 1): Controlled Hydrolysis of Micellar Amphiphilic Imines in Water. Chemistry 2021; 27:13457-13467. [PMID: 34270124 DOI: 10.1002/chem.202102049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 12/29/2022]
Abstract
Despite their intrinsic hydrolysable character, imine bonds can become remarkably stable in water when self-assembled in amphiphilic micellar structures. In this work, we systematically studied some of these structures and the influence of various parameters that can be used to take control of their hydrolysis, including pH, concentration, the position of the imine function in the amphiphilic structure, relative lengths of the linked hydrophilic and hydrophobic moieties. Thermodynamic and kinetic data led us to the rational design of stable imines in water, partly based on the location of the imine function within the hydrophobic part of the amphiphile and on a predictable quantitative term that we define as the total hydrophilic-lipophilic balance (HLB). In addition, we show that such stable systems are also stimuli-responsive and therefore, of potential interest in trapping and releasing micellar components on demand.
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Affiliation(s)
- Eric Lutz
- SAMS Research Group, Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Emilie Moulin
- SAMS Research Group, Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Vera Tchakalova
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Daniel Benczédi
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Andreas Herrmann
- Firmenich SA, Corporate R&D Division, Rue de la Bergère 7, 1242, Satigny, Switzerland
| | - Nicolas Giuseppone
- SAMS Research Group, Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
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5
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Lloyd Williams OH, Rijs NJ. Reaction Monitoring and Structural Characterisation of Coordination Driven Self-Assembled Systems by Ion Mobility-Mass Spectrometry. Front Chem 2021; 9:682743. [PMID: 34169059 PMCID: PMC8217442 DOI: 10.3389/fchem.2021.682743] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/14/2021] [Indexed: 01/03/2023] Open
Abstract
Nature creates exquisite molecular assemblies, required for the molecular-level functions of life, via self-assembly. Understanding and harnessing these complex processes presents an immense opportunity for the design and fabrication of advanced functional materials. However, the significant industrial potential of self-assembly to fabricate highly functional materials is hampered by a lack of knowledge of critical reaction intermediates, mechanisms, and kinetics. As we move beyond the covalent synthetic regime, into the domain of non-covalent interactions occupied by self-assembly, harnessing and embracing complexity is a must, and non-targeted analyses of dynamic systems are becoming increasingly important. Coordination driven self-assembly is an important subtype of self-assembly that presents several wicked analytical challenges. These challenges are "wicked" due the very complexity desired confounding the analysis of products, intermediates, and pathways, therefore limiting reaction optimisation, tuning, and ultimately, utility. Ion Mobility-Mass Spectrometry solves many of the most challenging analytical problems in separating and analysing the structure of both simple and complex species formed via coordination driven self-assembly. Thus, due to the emerging importance of ion mobility mass spectrometry as an analytical technique tackling complex systems, this review highlights exciting recent applications. These include equilibrium monitoring, structural and dynamic analysis of previously analytically inaccessible complex interlinked structures and the process of self-sorting. The vast and largely untapped potential of ion mobility mass spectrometry to coordination driven self-assembly is yet to be fully realised. Therefore, we also propose where current analytical approaches can be built upon to allow for greater insight into the complexity and structural dynamics involved in self-assembly.
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Affiliation(s)
| | - Nicole J. Rijs
- School of Chemistry, UNSW Sydney, Sydney, NSW, Australia
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6
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Ren Y, Kravchenko O, Ramström O. Configurational and Constitutional Dynamics of Enamine Molecular Switches. Chemistry 2020; 26:15654-15663. [PMID: 33044767 PMCID: PMC7756271 DOI: 10.1002/chem.202003478] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Indexed: 12/11/2022]
Abstract
Dual configurational and constitutional dynamics in systems based on enamine molecular switches has been systematically studied. pH-responsive moieties, such as 2-pyridyl and 2-quinolinyl units, were required on the "stator" part, also providing enamine stability through intramolecular hydrogen-bonding (IMHB) effects. Upon protonation or deprotonation, forward and backward switching could be rapidly achieved. Extension of the stator π-system in the 2-quinolinyl derivative provided a higher E-isomeric equilibrium ratio under neutral conditions, pointing to a means to achieve quantitative forward/backward isomerization processes. The "rotor" part of the enamine switches exhibited constitutional exchange ability with primary amines. Interestingly, considerably higher exchange rates were observed with amines containing ester groups, indicating potential stabilization of the transition state through IMHB. Acids, particularly BiIII , were found to efficiently catalyze the constitutional dynamic processes. In contrast, the enamine and the formed dynamic enamine system showed excellent stability under basic conditions. This coupled configurational and constitutional dynamics expands the scope of dynamic C-C and C-N bonds and potentiates further studies and applications in the fields of molecular machinery and systems chemistry.
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Affiliation(s)
- Yansong Ren
- Department of ChemistryKTH—Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
| | - Oleksandr Kravchenko
- Department of ChemistryKTH—Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
| | - Olof Ramström
- Department of ChemistryKTH—Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
- Department of ChemistryUniversity of Massachusetts LowellOne University Ave.LowellMA01854USA
- Department of Chemistry and Biomedical SciencesLinnaeus University39182KalmarSweden
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7
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Karalius A, Zhang Y, Kravchenko O, Elofsson U, Szabó Z, Yan M, Ramström O. Formation and Out‐of‐Equilibrium, High/Low State Switching of a Nitroaldol Dynamer in Neutral Aqueous Media. Angew Chem Int Ed Engl 2020; 59:3434-3438. [DOI: 10.1002/anie.201911706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/19/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Antanas Karalius
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
| | - Yang Zhang
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
| | - Oleksandr Kravchenko
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
| | - Ulla Elofsson
- Bioscience and Materials divisionResearch Institutes of Sweden Box 5607 114 86 Stockholm Sweden
| | - Zoltán Szabó
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
| | - Mingdi Yan
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
- Department of ChemistryUniversity of Massachusetts Lowell One University Ave. Lowell MA 01854 USA
| | - Olof Ramström
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
- Department of ChemistryUniversity of Massachusetts Lowell One University Ave. Lowell MA 01854 USA
- Department of Chemistry and Biomedical SciencesLinnaeus University 39182 Kalmar Sweden
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8
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Karalius A, Zhang Y, Kravchenko O, Elofsson U, Szabó Z, Yan M, Ramström O. Formation and Out‐of‐Equilibrium, High/Low State Switching of a Nitroaldol Dynamer in Neutral Aqueous Media. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911706] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Antanas Karalius
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
| | - Yang Zhang
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
| | - Oleksandr Kravchenko
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
| | - Ulla Elofsson
- Bioscience and Materials divisionResearch Institutes of Sweden Box 5607 114 86 Stockholm Sweden
| | - Zoltán Szabó
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
| | - Mingdi Yan
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
- Department of ChemistryUniversity of Massachusetts Lowell One University Ave. Lowell MA 01854 USA
| | - Olof Ramström
- Department of ChemistryKTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
- Department of ChemistryUniversity of Massachusetts Lowell One University Ave. Lowell MA 01854 USA
- Department of Chemistry and Biomedical SciencesLinnaeus University 39182 Kalmar Sweden
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9
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Martinez-Amezaga M, Orrillo AG, Furlan RLE. Engineering multilayer chemical networks. Chem Sci 2019; 10:8338-8347. [PMID: 31803411 PMCID: PMC6844274 DOI: 10.1039/c9sc02166c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/28/2019] [Indexed: 12/19/2022] Open
Abstract
Dynamic multilevel systems emerged in the last few years as new platforms to study thermodynamic systems. In this work, unprecedented fully communicated three-level systems are studied. First, different conditions were screened to selectively activate thiol/dithioacetal, thiol/thioester, and thiol/disulfide exchanges, individually or in pairs. Some of those conditions were applied, sequentially, to build multilayer dynamic systems wherein information, in the form of relative amounts of building blocks, can be directionally transmitted between different exchange pools. As far as we know, this is the first report of one synthetic dynamic chemical system where relationships between layers can be changed through network operations.
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Affiliation(s)
- Maitena Martinez-Amezaga
- Farmacognosia , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario - CONICET , Suipacha 531 , Rosario , S2002SLRK , Argentina .
| | - A Gastón Orrillo
- Farmacognosia , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario - CONICET , Suipacha 531 , Rosario , S2002SLRK , Argentina .
| | - Ricardo L E Furlan
- Farmacognosia , Facultad de Ciencias Bioquímicas y Farmacéuticas , Universidad Nacional de Rosario - CONICET , Suipacha 531 , Rosario , S2002SLRK , Argentina .
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10
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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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11
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Abellán-Flos M, Timmer BJJ, Altun S, Aastrup T, Vincent SP, Ramström O. QCM sensing of multivalent interactions between lectins and well-defined glycosylated nanoplatforms. Biosens Bioelectron 2019; 139:111328. [PMID: 31136921 DOI: 10.1016/j.bios.2019.111328] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/29/2019] [Accepted: 05/14/2019] [Indexed: 12/29/2022]
Abstract
Quartz crystal microbalance (QCM) methodology has been adopted to unravel important factors contributing to the "cluster glycoside effect" observed in carbohydrate-lectin interactions. Well-defined, glycosylated nanostructures of precise sizes, geometries and functionalization patterns were designed and synthesized, and applied to analysis of the interaction kinetics and thermodynamics with immobilized lectins. The nanostructures were based on Borromean rings, dodecaamine cages, and fullerenes, each of which carrying a defined number of carbohydrate ligands at precise locations. The synthesis of the Borromeates and dodecaamine cages was easily adjustable due to the modular assembly of the structures, resulting in variations in presentation mode. The binding properties of the glycosylated nanoplatforms were evaluated using flow-through QCM technology, as well as hemagglutination inhibition assays, and compared with dodecaglycosylated fullerenes and a monovalent reference. With the QCM setup, the association and dissociation rate constants and the associated equilibrium constants of the interactions could be estimated, and the results used to delineate the multivalency effects of the lectin-nanostructure interactions.
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Affiliation(s)
- Marta Abellán-Flos
- University of Namur, Départment de Chimie, Laboratoire de Chimie Bio-Organique, rue de Bruxelles 61, B-5000, Namur, Belgium
| | - Brian J J Timmer
- KTH - Royal Institute of Technology, Department of Chemistry, Teknikringen 36, S-100 44, Stockholm, Sweden
| | - Samuel Altun
- Attana AB, Björnnäsvägen 21, SE-114, 19 Stockholm, Sweden
| | - Teodor Aastrup
- Attana AB, Björnnäsvägen 21, SE-114, 19 Stockholm, Sweden.
| | - Stéphane P Vincent
- University of Namur, Départment de Chimie, Laboratoire de Chimie Bio-Organique, rue de Bruxelles 61, B-5000, Namur, Belgium.
| | - Olof Ramström
- KTH - Royal Institute of Technology, Department of Chemistry, Teknikringen 36, S-100 44, Stockholm, Sweden; University of Massachusetts Lowell, Department of Chemistry, One University Ave., Lowell, MA, 01854, USA; Linnaeus University, Department of Chemical and Biomedical Sciences, SE-39182, Kalmar, Sweden.
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12
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Nguyen R, Jouault N, Zanirati S, Rawiso M, Allouche L, Buhler E, Giuseppone N. Autopoietic Behavior of Dynamic Covalent Amphiphiles. Chemistry 2018; 24:17125-17137. [PMID: 30144185 DOI: 10.1002/chem.201803833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Indexed: 01/06/2023]
Abstract
The condensation of aldehydes and amines in water to give amphiphilic imines can lead to a particular autocatalytic behavior known as autopoiesis, in which the closed micellar structure made by the amphiphile at the mesoscale can accelerate the condensation of its constituents. Herein, through a combination of analytical tools, including diffusion ordered spectroscopy (DOSY) as well as light, neutron, and X-ray scattering techniques, the thermodynamic and kinetic parameters were probed at both the level of dynamic covalent imine bond formation and the level of the resulting micellar self-assemblies. It was found that the autopoietic behavior was the result of a combination of several parameters, including solubilization of hydrophobic building blocks, template effect at the core-shell interface, and growth/division cycles of the micellar objects.
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Affiliation(s)
- Rémi Nguyen
- Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Nicolas Jouault
- Matière et Systèmes Complexes (MSC) Laboratory, UMR 7057, Sorbonne Paris Cité, University of Paris Diderot-Paris VII, Bâtiment Condorcet, 10 rue Alice Domon et Léonie Duquet., 75205, Paris Cedex 13, France
- Sorbonne Université, CNRS, Laboratoire PHysicochimie des, Electrolytes et des Nanosytèmes InterfaciauX, PHENIX, 75005, Paris, France
| | - Stefano Zanirati
- Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Michel Rawiso
- Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
| | - Lionel Allouche
- Institut de Chimie, Service de RMN, Université Louis Pasteur, 1 rue Blaise Pascal, 67008, Strasbourg Cedex, France
| | - Eric Buhler
- Matière et Systèmes Complexes (MSC) Laboratory, UMR 7057, Sorbonne Paris Cité, University of Paris Diderot-Paris VII, Bâtiment Condorcet, 10 rue Alice Domon et Léonie Duquet., 75205, Paris Cedex 13, France
| | - Nicolas Giuseppone
- Institut Charles Sadron, CNRS, University of Strasbourg, 23 rue du Loess, BP 84047, 67034, Strasbourg Cedex 2, France
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13
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Das M, Yang T, Dong J, Prasetya F, Xie Y, Wong KHQ, Cheong A, Woon ECY. Multiprotein Dynamic Combinatorial Chemistry: A Strategy for the Simultaneous Discovery of Subfamily-Selective Inhibitors for Nucleic Acid Demethylases FTO and ALKBH3. Chem Asian J 2018; 13:2854-2867. [PMID: 29917331 DOI: 10.1002/asia.201800729] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/12/2018] [Indexed: 12/18/2022]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful supramolecular approach for discovering ligands for biomolecules. To date, most, if not all, biologically templated DCC systems employ only a single biomolecule to direct the self-assembly process. To expand the scope of DCC, herein, a novel multiprotein DCC strategy has been developed that combines the discriminatory power of a zwitterionic "thermal tag" with the sensitivity of differential scanning fluorimetry. This strategy is highly sensitive and could differentiate the binding of ligands to structurally similar subfamily members. Through this strategy, it was possible to simultaneously identify subfamily-selective probes against two clinically important epigenetic enzymes: FTO (7; IC50 =2.6 μm) and ALKBH3 (8; IC50 =3.7 μm). To date, this is the first report of a subfamily-selective ALKBH3 inhibitor. The developed strategy could, in principle, be adapted to a broad range of proteins; thus it is of broad scientific interest.
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MESH Headings
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/antagonists & inhibitors
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/chemistry
- AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics
- AlkB Homolog 5, RNA Demethylase/antagonists & inhibitors
- AlkB Homolog 5, RNA Demethylase/chemistry
- AlkB Homolog 5, RNA Demethylase/genetics
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/antagonists & inhibitors
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/chemistry
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics
- Catalysis
- Combinatorial Chemistry Techniques/methods
- Enzyme Inhibitors/chemistry
- Fluorometry/methods
- Humans
- Hydrazones/chemistry
- Kinetics
- Ligands
- Molecular Structure
- Oxidoreductases, O-Demethylating/antagonists & inhibitors
- Oxidoreductases, O-Demethylating/chemistry
- Oxidoreductases, O-Demethylating/genetics
- Peptides/chemistry
- Peptides/genetics
- Protein Denaturation
- Protein Engineering
- Protein Structure, Secondary
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Transition Temperature
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Affiliation(s)
- Mohua Das
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Tianming Yang
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Jinghua Dong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Fransisca Prasetya
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Yiming Xie
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Kendra H Q Wong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Adeline Cheong
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Esther C Y Woon
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
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14
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Ren Y, Svensson PH, Ramström O. A Multicontrolled Enamine Configurational Switch Undergoing Dynamic Constitutional Exchange. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yansong Ren
- Department of Chemistry KTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
| | - Per H. Svensson
- Department of Chemistry KTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
- Research Institutes of Sweden RISE Bioscience and Materials Forskargatan 18 15136 Södertälje Sweden
| | - Olof Ramström
- Department of Chemistry KTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
- Department of Chemistry University of Massachusetts Lowell 1 University Avenue Lowell MA 01854 USA
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15
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Ren Y, Svensson PH, Ramström O. A Multicontrolled Enamine Configurational Switch Undergoing Dynamic Constitutional Exchange. Angew Chem Int Ed Engl 2018; 57:6256-6260. [DOI: 10.1002/anie.201802994] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Yansong Ren
- Department of Chemistry KTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
| | - Per H. Svensson
- Department of Chemistry KTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
- Research Institutes of Sweden RISE Bioscience and Materials Forskargatan 18 15136 Södertälje Sweden
| | - Olof Ramström
- Department of Chemistry KTH—Royal Institute of Technology Teknikringen 36 10044 Stockholm Sweden
- Department of Chemistry University of Massachusetts Lowell 1 University Avenue Lowell MA 01854 USA
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16
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Schaufelberger F, Timmer BJJ, Ramström O. Resolving a Reactive Organometallic Intermediate from Dynamic Directing Group Systems by Selective C-H Activation. Chemistry 2018; 24:101-104. [PMID: 29149517 PMCID: PMC5836886 DOI: 10.1002/chem.201705273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Indexed: 12/12/2022]
Abstract
Catalyst discovery from systems of potential precursors is a challenging endeavor. Herein, a new strategy applying dynamic chemistry to the identification of catalyst precursors from C-H activation of imines is proposed and evaluated. Using hydroacylation of imines as a model reaction, the selection of an organometallic reactive intermediate from a dynamic imine system, involving many potential directing group/metal entities, is demonstrated. The identity of the amplified reaction intermediate with the best directing group could be resolved in situ by ESI-MS, and coupling of the procedure to an iterative deconvolution protocol generated a system with high screening efficiency.
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Affiliation(s)
- Fredrik Schaufelberger
- Department of ChemistryKTH–Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
| | - Brian J. J. Timmer
- Department of ChemistryKTH–Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
| | - Olof Ramström
- Department of ChemistryKTH–Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
- Department of ChemistryUniversity of Massachusetts Lowell1 University Ave.LowellMA01854USA
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17
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Ekström AG, Wang JT, Bella J, Campopiano DJ. Non-invasive 19F NMR analysis of a protein-templated N-acylhydrazone dynamic combinatorial library. Org Biomol Chem 2018; 16:8144-8149. [DOI: 10.1039/c8ob01918e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful tool to identify ligands for biological targets.
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Affiliation(s)
| | | | - Juraj Bella
- EaStCHEM School of Chemistry
- University of Edinburgh
- Edinburgh
- UK
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18
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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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19
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Zhang Y, Xie S, Yan M, Ramström O. Dynamic Covalent Chemistry of Aldehyde Enamines: Bi III - and Sc III -Catalysis of Amine-Enamine Exchange. Chemistry 2017; 23:11908-11912. [PMID: 28722305 PMCID: PMC5656824 DOI: 10.1002/chem.201702363] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Indexed: 01/09/2023]
Abstract
The dynamic exchange of enamines from secondary amines and enolizable aldehydes has been demonstrated in organic solvents. The enamine exchange with amines was efficiently catalyzed by Bi(OTf)3 and Sc(OTf)3 (2 mol %) and the equilibria (60 mm) could be attained within hours at room temperature. The formed dynamic covalent systems displayed high stabilities in basic environment with <2 % by-product formation within one week after complete equilibration. This study expands the scope of dynamic C-N bonds from imine chemistry to enamines, enabling further dynamic methodologies in exploration of this important class of structures in systems chemistry.
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Affiliation(s)
- Yang Zhang
- Department of ChemistryKTH-Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
| | - Sheng Xie
- Department of ChemistryKTH-Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
| | - Mingdi Yan
- Department of ChemistryKTH-Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
- Department of ChemistryUniversity of Massachusetts Lowell1 University Ave.LowellMA01854USA
| | - Olof Ramström
- Department of ChemistryKTH-Royal Institute of TechnologyTeknikringen 3610044StockholmSweden
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20
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Valdivielso AM, Puig-Castellví F, Atcher J, Solà J, Tauler R, Alfonso I. Unraveling the Multistimuli Responses of a Complex Dynamic System of Pseudopeptidic Macrocycles. Chemistry 2017; 23:10789-10799. [DOI: 10.1002/chem.201701294] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Angel M. Valdivielso
- Department of Biological Chemistry and Molecular Modeling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | | | - Joan Atcher
- Department of Biological Chemistry and Molecular Modeling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Jordi Solà
- Department of Biological Chemistry and Molecular Modeling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Romà Tauler
- Department of Environmental Chemistry; IDAEA-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry and Molecular Modeling; IQAC-CSIC; Jordi Girona 18-26 08034 Barcelona Spain
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21
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Chung MK, White PS, Lee SJ, Gagné MR, Waters ML. Investigation of a Catenane with a Responsive Noncovalent Network: Mimicking Long-Range Responses in Proteins. J Am Chem Soc 2016; 138:13344-13352. [PMID: 27631725 PMCID: PMC5553285 DOI: 10.1021/jacs.6b07833] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a functional synthetic model for studying the noncovalent networks (NCNs) required for complex protein functions. The model [2]-catenane is self-assembled from dipeptide building blocks and contains an extensive network of hydrogen bonds and aromatic interactions. Perturbations to the catenane cause compensating changes in the NCNs structure and dynamics, resulting in long-distance changes reminiscent of a protein. Key findings include the notion that NCNs require regions of negative cooperativity, or "frustrated" noncovalent interactions, as a source of potential energy for driving the response. We refer to this potential energy as latent free energy and describe a mechanistic and energetic model for responsive systems.
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Affiliation(s)
| | | | - Stephen J. Lee
- U.S. Army Research Office, P.O. Box 12211, Research Triangle Park, North Carolina 27709, United States
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22
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Abstract
Rational and generalisable methods for engineering surface functionality will be crucial to realising the technological potential of nanomaterials. Nanoparticle-bound dynamic covalent exchange combines the error-correcting and environment-responsive features of equilibrium processes with the stability, structural precision, and vast diversity of covalent chemistry, defining a new and powerful approach for manipulating structure, function and properties at nanomaterial surfaces. Dynamic covalent nanoparticle (DCNP) building blocks thus present a whole host of possibilities for constructing adaptive systems, devices and materials that incorporate both nanoscale and molecular functional components. At the same time, DCNPs have the potential to reveal fundamental insights regarding dynamic and complex chemical systems confined to nanoscale interfaces.
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Affiliation(s)
- Euan R Kay
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
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23
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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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24
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Nowak P, Colomb-Delsuc M, Otto S, Li J. Template-Triggered Emergence of a Self-Replicator from a Dynamic Combinatorial Library. J Am Chem Soc 2015; 137:10965-9. [PMID: 26192814 DOI: 10.1021/jacs.5b04380] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Self-assembly of a specific member of a dynamic combinatorial library (DCL) may lead to self-replication of this molecule. However, if the concentration of the potential replicator in the DCL fails to exceed its critical aggregation concentration (CAC), then self-replication will not occur. We now show how addition of a template can raise the concentration of a library member-template complex beyond its CAC, leading to the onset of self-replication. Once in existence, the replicator aggregates promote further replication also in the absence of the template that induced the initial emergence of the replicator.
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Affiliation(s)
- Piotr Nowak
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Mathieu Colomb-Delsuc
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jianwei Li
- Centre for Systems Chemistry, Stratingh Insitute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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25
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Jouault N, Moulin E, Giuseppone N, Buhler E. Light Scattering Strategy for the Investigation of Time-Evolving Heterogeneous Supramolecular Self-Assemblies. PHYSICAL REVIEW LETTERS 2015; 115:085501. [PMID: 26340192 DOI: 10.1103/physrevlett.115.085501] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Indexed: 06/05/2023]
Abstract
Supramolecular self-assembly is a multiple length-scale and time-dependent process involving many coexisting components. Such complexity requires suitable strategies to extract quantitative dynamical and structural information on all involved species. Here, we detail an original light scattering method to study the kinetics of tailored triarylamine molecules capable of self-assembling in supramolecular highly conductive nanowires upon light exposure. These micrometric assemblies cause the emergence of intermittences in the scattered intensity and the construction of a predominant slow mode in the correlation function making separation between small-and large-size species impossible using conventional treatments. Our strategy is based on the time monitoring of intermittences and allows us to determine the fraction of nanowires as well as those of small critical nuclei and triarylamine building blocks as a function of time and light exposure, in good agreement with recent theoretical predictions.
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Affiliation(s)
- Nicolas Jouault
- Sorbonne Universités, UPMC Université Paris 06, CNRS, Laboratoire PHENIX, Case 51, 4 place Jussieu, F-75005 Paris, France
- Matière et Systèmes Complexes (MSC) Laboratory, UMR CNRS 7057, Sorbonne Paris Cité, University of Paris Diderot-Paris VII, Bâtiment Condorcet, 75205 Paris Cedex 13, France
| | - Emilie Moulin
- Université de Strasbourg, Institut Charles Sadron, CNRS, 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2, France
| | - Nicolas Giuseppone
- Université de Strasbourg, Institut Charles Sadron, CNRS, 23 rue du Loess, BP 84047, 67034 Strasbourg Cedex 2, France
| | - Eric Buhler
- Matière et Systèmes Complexes (MSC) Laboratory, UMR CNRS 7057, Sorbonne Paris Cité, University of Paris Diderot-Paris VII, Bâtiment Condorcet, 75205 Paris Cedex 13, France
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26
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Schaufelberger F, Hu L, Ramström O. trans-Symmetric Dynamic Covalent Systems: Connected Transamination and Transimination Reactions. Chemistry 2015; 21:9776-83. [PMID: 26044061 PMCID: PMC4517097 DOI: 10.1002/chem.201500520] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Indexed: 11/08/2022]
Abstract
The development of chemical transaminations as a new type of dynamic covalent reaction is described. The key 1,3-proton shift is under complete catalytic control and can be conducted orthogonally to, or simultaneous with, transimination in the presence of an amine to rapidly yield two-dimensional dynamic systems with a high degree of complexity evolution. The transamination-transimination systems are proven to be fully reversible, stable over several days, compatible with a range of functional groups, and highly tunable. Kinetic studies show transamination to be the rate-limiting reaction in the network. Furthermore, it was discovered that readily available quinuclidine is a highly potent catalyst for aldimine transaminations. This study demonstrates how connected dynamic reactions give rise to significantly larger systems than the unconnected counterparts, and shows how reversible isomerizations can be utilized as an effective diversity-generating element.
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Affiliation(s)
- Fredrik Schaufelberger
- Department of Chemistry, KTH - Royal Institute of TechnologyTeknikringen 30, 10044 Stockholm (Sweden) E-mail:
| | - Lei Hu
- Department of Chemistry, KTH - Royal Institute of TechnologyTeknikringen 30, 10044 Stockholm (Sweden) E-mail:
| | - Olof Ramström
- Department of Chemistry, KTH - Royal Institute of TechnologyTeknikringen 30, 10044 Stockholm (Sweden) E-mail:
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27
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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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28
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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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29
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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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30
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Ziach K, Obrocka-Hrycyna A, Jurczak J. Dynamic Combinatorial Libraries of 2,5-Diformylfuran-Derived Macrocycles. J Org Chem 2014; 79:10334-41. [DOI: 10.1021/jo501966q] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Krzysztof Ziach
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | | | - Janusz Jurczak
- Institute
of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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31
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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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