1
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Komáromy D, Monzón DM, Marić I, Monreal Santiago G, Ottelé J, Altay M, Schaeffer G, Otto S. Generalist versus Specialist Self-Replicators. Chemistry 2024; 30:e202303837. [PMID: 38294075 DOI: 10.1002/chem.202303837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/01/2024]
Abstract
Darwinian evolution, including the selection of the fittest species under given environmental conditions, is a major milestone in the development of synthetic living systems. In this regard, generalist or specialist behavior (the ability to replicate in a broader or narrower, more specific food environment) are of importance. Here we demonstrate generalist and specialist behavior in dynamic combinatorial libraries composed of a peptide-based and an oligo(ethylene glycol) based building block. Three different sets of macrocyclic replicators could be distinguished based on their supramolecular organization: two prepared from a single building block as well as one prepared from an equimolar mixture of them. Peptide-containing hexamer replicators were found to be generalists, i. e. they could replicate in a broad range of food niches, whereas the octamer peptide-based replicator and hexameric ethyleneoxide-based replicator were proven to be specialists, i. e. they only replicate in very specific food niches that correspond to their composition. However, sequence specificity cannot be demonstrated for either of the generalist replicators. The generalist versus specialist nature of these replicators was linked to their supramolecular organization. Assembly modes that accommodate structurally different building blocks lead to generalist replicators, while assembly modes that are more restrictive yield specialist replicators.
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Affiliation(s)
- Dávid Komáromy
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Diego M Monzón
- Instituto de Bio-Orgánica "Antonio González" (IUBO-AG), Departamento de Química Orgánica, Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez, 38206, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Ivana Marić
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Guillermo Monreal Santiago
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jim Ottelé
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Meniz Altay
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Gaël Schaeffer
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Sijbren Otto
- University of Groningen, Centre for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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2
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Kassem S, McPhee SA, Berisha N, Ulijn RV. Emergence of Cooperative Glucose-Binding Networks in Adaptive Peptide Systems. J Am Chem Soc 2023; 145:9800-9807. [PMID: 37075194 DOI: 10.1021/jacs.3c01620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Minimalistic peptide-based systems that bind sugars in water are challenging to design due to the weakness of interactions and required cooperative contributions from specific amino-acid side chains. Here, we used a bottom-up approach to create peptide-based adaptive glucose-binding networks by mixing glucose with selected sets of input dipeptides (up to 4) in the presence of an amidase to enable in situ reversible peptide elongation, forming mixtures of up to 16 dynamically interacting tetrapeptides. The choice of input dipeptides was based on amino-acid abundance in glucose-binding sites found in the protein data bank, with side chains that can support hydrogen bonding and CH-π interactions. Tetrapeptide sequence amplification patterns, determined through LC-MS analysis, served as a readout for collective interactions and led to the identification of optimized binding networks. Systematic variation of dipeptide input revealed the emergence of two networks of non-covalent hydrogen bonding and CH-π interactions that can co-exist, are cooperative and context-dependent. A cooperative binding mode was determined by studying the binding of the most amplified tetrapeptide (AWAD) with glucose in isolation. Overall, these results demonstrate that the bottom-up design of complex systems can recreate emergent behaviors driven by covalent and non-covalent self-organization that are not observed in reductionist designs and lead to the identification of system-level cooperative binding motifs.
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Affiliation(s)
- Salma Kassem
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Scott A McPhee
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Naxhije Berisha
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
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3
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Del Giudice D, Spatola E, Valentini M, Ercolani G, Di Stefano S. Dissipative Dynamic Libraries (DDLs) and Dissipative Dynamic Combinatorial Chemistry (DDCC). CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202200023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Daniele Del Giudice
- Dipartimento di Chimica Università di Roma La Sapienza and ISB-CNR Sede Secondaria di Roma – Meccanismi di Reazione P.le A. Moro 5 I-00185 Roma Italy
| | - Emanuele Spatola
- Dipartimento di Chimica Università di Roma La Sapienza and ISB-CNR Sede Secondaria di Roma – Meccanismi di Reazione P.le A. Moro 5 I-00185 Roma Italy
| | - Matteo Valentini
- Dipartimento di Chimica Università di Roma La Sapienza and ISB-CNR Sede Secondaria di Roma – Meccanismi di Reazione P.le A. Moro 5 I-00185 Roma Italy
| | - Gianfranco Ercolani
- Dipartimento di Scienze e Tecnologie Chimiche Università di Roma Tor Vergata Via della Ricerca Scientifica 00133 Roma Italy
| | - Stefano Di Stefano
- Dipartimento di Chimica Università di Roma La Sapienza and ISB-CNR Sede Secondaria di Roma – Meccanismi di Reazione P.le A. Moro 5 I-00185 Roma Italy
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4
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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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5
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Komáromy D, Tiemersma-Wegman T, Kemmink J, Portale G, Adamski PR, Blokhuis A, Aalbers FS, Marić I, Santiago GM, Ottelé J, Sood A, Saggiomo V, Liu B, van der Meulen P, Otto S. Stoichiometry alone can steer supramolecular systems on complex free energy surfaces with high selectivity. Chem 2021. [DOI: 10.1016/j.chempr.2021.05.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Wagner P, Rominger F, Zhang W, Gross JH, Elbert SM, Schröder RR, Mastalerz M. Chiral Self-sorting of Giant Cubic [8+12] Salicylimine Cage Compounds. Angew Chem Int Ed Engl 2021; 60:8896-8904. [PMID: 33476442 PMCID: PMC8048989 DOI: 10.1002/anie.202016592] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/21/2021] [Indexed: 12/13/2022]
Abstract
Chiral self-sorting is intricately connected to the complicated chiral processes observed in nature and no artificial systems of comparably complexity have been generated by chemists. However, only a few examples of purely organic molecules have been reported so far, where the self-sorting process could be controlled. Herein, we describe the chiral self-sorting of large cubic [8+12] salicylimine cage compounds based on a chiral TBTQ precursor. Out of 23 possible cage isomers only the enantiopure and a meso cage were observed to be formed, which have been unambiguously characterized by single crystal X-ray diffraction. Furthermore, by careful choice of solvent the formation of meso cage could be controlled. With internal diameters of din =3.3-3.5 nm these cages are among the largest organic cage compounds characterized and show very high specific surface areas up to approx. 1500 m2 g-1 after desolvation.
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Affiliation(s)
- Philippe Wagner
- Organisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Frank Rominger
- Organisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Wen‐Shan Zhang
- Centre for Advanced MaterialsRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 22569120HeidelbergGermany
| | - Jürgen H. Gross
- Organisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Sven M. Elbert
- Organisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
| | - Rasmus R. Schröder
- Centre for Advanced MaterialsRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 22569120HeidelbergGermany
| | - Michael Mastalerz
- Organisch-Chemisches InstitutRuprecht-Karls-Universität HeidelbergIm Neuenheimer Feld 27069120HeidelbergGermany
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7
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Wagner P, Rominger F, Zhang W, Gross JH, Elbert SM, Schröder RR, Mastalerz M. Chiral Self‐sorting of Giant Cubic [8+12] Salicylimine Cage Compounds. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Philippe Wagner
- Organisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Frank Rominger
- Organisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Wen‐Shan Zhang
- Centre for Advanced Materials Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 225 69120 Heidelberg Germany
| | - Jürgen H. Gross
- Organisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Sven M. Elbert
- Organisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Rasmus R. Schröder
- Centre for Advanced Materials Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 225 69120 Heidelberg Germany
| | - Michael Mastalerz
- Organisch-Chemisches Institut Ruprecht-Karls-Universität Heidelberg Im Neuenheimer Feld 270 69120 Heidelberg Germany
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8
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Solà J, Jimeno C, Alfonso I. Exploiting complexity to implement function in chemical systems. Chem Commun (Camb) 2020; 56:13273-13286. [DOI: 10.1039/d0cc04170j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This feature article reflects a personal overview of the importance of complexity as an additional parameter to be considered in chemical research, being illustrated with selected examples in molecular recognition and catalysis.
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Affiliation(s)
- Jordi Solà
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
| | - Ciril Jimeno
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
| | - Ignacio Alfonso
- Department of Biological Chemistry
- Institute of Advanced Chemistry of Catalonia
- IQAC-CSIC
- 08034 Barcelona
- Spain
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9
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Larsen D, Bjerre PM, Beeren SR. Light-controlled out-of-equilibrium assembly of cyclodextrins in an enzyme-mediated dynamic system. Chem Commun (Camb) 2019; 55:15037-15040. [PMID: 31782430 DOI: 10.1039/c9cc08452e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We show that the selective enzymatic synthesis of specific cyclodextrins can be modulated using light. We use enzyme-mediated dynamic combinatorial chemistry to generate a mixture of interconverting linear and cyclic α-1,4-glucans, and employ an azobenzene photoswitch as a template. Using UV or blue light to switch between photostationary states with different azobenzene cis/trans isomeric ratios, we can promote the out-of-equilibrium assembly of either α-cyclodextrin or β-cyclodextrin.
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Affiliation(s)
- Dennis Larsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark.
| | - Philip M Bjerre
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark.
| | - Sophie R Beeren
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark.
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10
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Larsen D, Beeren SR. Enzyme-mediated dynamic combinatorial chemistry allows out-of-equilibrium template-directed synthesis of macrocyclic oligosaccharides. Chem Sci 2019; 10:9981-9987. [PMID: 32055354 PMCID: PMC6979337 DOI: 10.1039/c9sc03983j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/02/2019] [Indexed: 12/16/2022] Open
Abstract
Artificial templates can control out-of-equilibrium self-assembly in an enzyme-mediated dynamic system of cyclodextrins, even allowing access to products not selected in Nature.
We show that the outcome of enzymatic reactions can be manipulated and controlled by using artificial template molecules to direct the self-assembly of specific products in an enzyme-mediated dynamic system. Specifically, we utilize a glycosyltransferase to generate a complex dynamic mixture of interconverting linear and macrocyclic α-1,4-d-glucans (cyclodextrins). We find that the native cyclodextrins (α, β and γ) are formed out-of-equilibrium as part of a kinetically trapped subsystem, that surprisingly operates transiently like a Dynamic Combinatorial Library (DCL) under thermodynamic control. By addition of different templates, we can promote the synthesis of each of the native cyclodextrins with 89–99% selectivity, or alternatively, we can amplify the synthesis of unusual large-ring cyclodextrins (δ and ε) with 9 and 10 glucose units per macrocycle. In the absence of templates, the transient DCL lasts less than a day, and cyclodextrins convert rapidly to short maltooligosaccharides. Templates stabilize the kinetically trapped subsystem enabling robust selective synthesis of cyclodextrins, as demonstrated by the high-yielding sequential interconversion of cyclodextrins in a single reaction vessel. Our results show that given the right balance between thermodynamic and kinetic control, templates can direct out-of-equilibrium self-assembly, and be used to manipulate enzymatic transformations to favor specific and/or alternative products to those selected in Nature.
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Affiliation(s)
- Dennis Larsen
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , DK-2800 Kongens Lyngby , Denmark .
| | - Sophie R Beeren
- Department of Chemistry , Technical University of Denmark , Kemitorvet 207 , DK-2800 Kongens Lyngby , Denmark .
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11
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Singha N, Das BK, Pramanik B, Das S, Das D. Freeze the dynamicity: charge transfer complexation assisted control over the reaction pathway. Chem Sci 2019; 10:10035-10039. [PMID: 32015816 PMCID: PMC6977459 DOI: 10.1039/c9sc03417j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/06/2019] [Indexed: 12/20/2022] Open
Abstract
Aqueous CT complexes of donor and acceptor molecules with reactive thiol groups were frozen and lyophilized to get alternate D–A assemblies in the solid state. Oxidation of the thiols resulted in asymmetric disulfides exclusively.
Charge transfer (CT) complexes between electron donor and acceptor molecules provide unique alternate D–A arrangements. However, these arrangements cannot be fully translated into chemo-selective organic transformations as the dynamicity of CT complexes in solution results in the co-existence of D–A assemblies and free monomers during the reaction time-scale. A conceptually new strategy to exploit CT complexes toward chemo-selective products by means of seizing the dynamicity of CT complexes is reported here. Aqueous CT complexes of donor and acceptor molecules bearing reactive thiol groups were frozen instantly and cryo-desiccated to get the alternate D–A assemblies intact in the solid state. Oxidation of reactive thiols in an oxygen rich solvent in the solid state resulted in the formation of the hetero-dimer exclusively. CT complexation and appropriate molecular arrangements are the key factors behind successful execution of this novel methodology. The strategy also paves the way to prepare unsymmetrical disulfide molecules from two dissimilar thiols.
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Affiliation(s)
- Nilotpal Singha
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
| | - Basab Kanti Das
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
| | - Bapan Pramanik
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
| | - Saurav Das
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
| | - Debapratim Das
- Department of Chemistry , Indian Institute of Technology Guwahati , Assam 781039 , India .
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12
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Affiliation(s)
- Shinji Yamada
- Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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13
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Wołczański G, Cal M, Waliczek M, Lisowski M, Stefanowicz P. Self-Synthesizing Models of Helical Proteins Based on Aromatic Disulfide Chemistry. Chemistry 2018; 24:12869-12878. [DOI: 10.1002/chem.201800187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Revised: 06/13/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Grzegorz Wołczański
- Faculty of Chemistry; University of Wrocław; F. Joliot-Curie 14 50-383 Wrocław Poland
| | - Marta Cal
- Faculty of Chemistry; University of Wrocław; F. Joliot-Curie 14 50-383 Wrocław Poland
- Institute of Organic and Biomolecular Chemistry; Georg-August University Göttingen; Tammannstrasse 2 D-37077 Göttingen Germany
| | - Mateusz Waliczek
- Faculty of Chemistry; University of Wrocław; F. Joliot-Curie 14 50-383 Wrocław Poland
| | - Marek Lisowski
- Faculty of Chemistry; University of Wrocław; F. Joliot-Curie 14 50-383 Wrocław Poland
| | - Piotr Stefanowicz
- Faculty of Chemistry; University of Wrocław; F. Joliot-Curie 14 50-383 Wrocław Poland
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14
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Batiste SM, Johnston JN. Evidence for Ion-Templation During Macrocyclooligomerization of Depsipeptides. J Am Chem Soc 2018; 140:4560-4568. [PMID: 29565576 PMCID: PMC5996984 DOI: 10.1021/jacs.7b13148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The ion-mediated Mitsunobu macrocyclooligomerization (M-MCO) reaction of hydroxy acid depsipeptides provides small collections of cyclic depsipeptides with good mass recovery. The approach can produce good yields of a single macrocycle or provide rapid access to multiple oligomeric macrocycles in good overall yield. While Lewis acidic alkali metal salts are known to play a role in the outcome of MCO reactions, it is unclear whether their effect is due to an organizational (e.g., templating) mechanism. Isothermal titration calorimetry (ITC) was used to study macrocycle-metal ion binding interactions, and this report correlates these thermodynamic measurements to the (kinetically determined) size distributions of depsipeptides formed during a Mitsunobu-based macrocyclooligomerization (MCO). Key trends have been identified in quantitative metal ion-cyclic depsipeptide binding affinity ( Ka), enthalpy of binding (Δ H), and stoichiometry of complexation across discrete series of macrocycles, and they provide the first analytical platform to rationally select a metal-ion template for a targeted size regime of cyclic oligomeric depsipeptides.
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Affiliation(s)
- Suzanne M Batiste
- Department of Chemistry and Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37235-1822 , United States
| | - Jeffrey N Johnston
- Department of Chemistry and Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37235-1822 , United States
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15
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Kosikova T, Philp D. Exploring the emergence of complexity using synthetic replicators. Chem Soc Rev 2018; 46:7274-7305. [PMID: 29099123 DOI: 10.1039/c7cs00123a] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A significant number of synthetic systems capable of replicating themselves or entities that are complementary to themselves have appeared in the last 30 years. Building on an understanding of the operation of synthetic replicators in isolation, this field has progressed to examples where catalytic relationships between replicators within the same network and the extant reaction conditions play a role in driving phenomena at the level of the whole system. Systems chemistry has played a pivotal role in the attempts to understand the origin of biological complexity by exploiting the power of synthetic chemistry, in conjunction with the molecular recognition toolkit pioneered by the field of supramolecular chemistry, thereby permitting the bottom-up engineering of increasingly complex reaction networks from simple building blocks. This review describes the advances facilitated by the systems chemistry approach in relating the expression of complex and emergent behaviour in networks of replicators with the connectivity and catalytic relationships inherent within them. These systems, examined within well-stirred batch reactors, represent conceptual and practical frameworks that can then be translated to conditions that permit replicating systems to overcome the fundamental limits imposed on selection processes in networks operating under closed conditions. This shift away from traditional spatially homogeneous reactors towards dynamic and non-equilibrium conditions, such as those provided by reaction-diffusion reaction formats, constitutes a key change that mimics environments within cellular systems, which possess obvious compartmentalisation and inhomogeneity.
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Affiliation(s)
- Tamara Kosikova
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
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16
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Morrow SM, Bissette AJ, Fletcher SP. Potential for minimal self-replicating systems in a dynamic combinatorial library of equilibrating imines. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.06.045] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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17
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Komáromy D, Stuart MCA, Monreal Santiago G, Tezcan M, Krasnikov VV, Otto S. Self-Assembly Can Direct Dynamic Covalent Bond Formation toward Diversity or Specificity. J Am Chem Soc 2017; 139:6234-6241. [PMID: 28398730 PMCID: PMC5423079 DOI: 10.1021/jacs.7b01814] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
With
the advent of reversible covalent chemistry the study of the
interplay between covalent bond formation and noncovalent interactions
has become increasingly relevant. Here we report that the interplay
between reversible disulfide chemistry and self-assembly can give
rise either to molecular diversity, i.e., the emergence of a unprecedentedly
large range of macrocycles or to molecular specificity, i.e., the
autocatalytic emergence of a single species. The two phenomena are
the result of two different modes of self-assembly, demonstrating
that control over self-assembly pathways can enable control over covalent
bond formation.
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Affiliation(s)
- Dávid Komáromy
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marc C A Stuart
- 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
| | - Meniz Tezcan
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Victor V Krasnikov
- Zernike Institute for Advanced Materials, 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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18
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Bartus É, Hegedüs Z, Wéber E, Csipak B, Szakonyi G, Martinek TA. De Novo Modular Development of a Foldameric Protein-Protein Interaction Inhibitor for Separate Hot Spots: A Dynamic Covalent Assembly Approach. ChemistryOpen 2017; 6:236-241. [PMID: 28413758 PMCID: PMC5390796 DOI: 10.1002/open.201700012] [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: 01/17/2017] [Indexed: 01/27/2023] Open
Abstract
Protein-protein interactions stabilized by multiple separate hot spots are highly challenging targets for synthetic scaffolds. Surface-mimetic foldamers bearing multiple recognition segments are promising candidate inhibitors. In this work, a modular bottom-up approach is implemented by identifying short foldameric recognition segments that interact with the independent hot spots, and connecting them through dynamic covalent library (DCL) optimization. The independent hot spots of a model target (calmodulin) are mapped with hexameric β-peptide helices using a pull-down assay. Recognition segment hits are subjected to a target-templated DCL ligation through thiol-disulfide exchange. The most potent derivative displays low nanomolar affinity towards calmodulin and effectively inhibits the calmodulin-TRPV1 interaction. The DCL assembly of the folded segments offers an efficient approach towards the de novo development of a high-affinity inhibitor of protein-protein interactions.
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Affiliation(s)
- Éva Bartus
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Zsófia Hegedüs
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Edit Wéber
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Brigitta Csipak
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Gerda Szakonyi
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
| | - Tamás A. Martinek
- Institute of Pharmaceutical Analysis, SZTE-MTA Lendület Foldamer Research GroupUniversity of Szeged4 Somogyi Str.6720SzegedHungary
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19
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Jędrzejewska H, Szumna A. Making a Right or Left Choice: Chiral Self-Sorting as a Tool for the Formation of Discrete Complex Structures. Chem Rev 2017; 117:4863-4899. [PMID: 28277655 DOI: 10.1021/acs.chemrev.6b00745] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This review discusses chiral self-sorting-the process of choosing an interaction partner with a given chirality from a complex mixture of many possible racemic partners. Chiral self-sorting (also known as chiral self-recognition or chiral self-discrimination) is fundamental for creating functional structures in nature and in the world of chemistry because interactions between molecules of the same or the opposite chirality are characterized by different interaction energies and intrinsically different resulting structures. However, due to the similarity between recognition sites of enantiomers and common conformational lability, high fidelity homochiral or heterochiral self-sorting poses a substantial challenge. Chiral self-sorting occurs among natural and synthetic molecules that leads to the amplification of discrete species. The review covers a variety of complex self-assembled structures ranging from aggregates made of natural and racemic peptides and DNA, through artificial functional receptors, macrocyles, and cages to catalytically active metal complexes and helix mimics. The examples involve a plethora of reversible interactions: electrostatic interactions, π-π stacking, hydrogen bonds, coordination bonds, and dynamic covalent bonds. A generalized view of the examples collected from different fields allows us to suggest suitable geometric models that enable a rationalization of the observed experimental preferences and establishment of the rules that can facilitate further design.
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Affiliation(s)
- Hanna Jędrzejewska
- Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Agnieszka Szumna
- Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland
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20
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Orrillo AG, Escalante AM, Furlan RLE. Host Amplification in a Dithioacetal-Based Dynamic Covalent Library. Org Lett 2017; 19:1446-1449. [DOI: 10.1021/acs.orglett.7b00401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. Gastón Orrillo
- Instituto de Investigaciones
para el Descubrimiento de Fármacos de Rosario (UNR-CONICET), Ocampo y Esmeralda, Rosario (2000), Argentina
| | - Andrea. M. Escalante
- Instituto de Investigaciones
para el Descubrimiento de Fármacos de Rosario (UNR-CONICET), Ocampo y Esmeralda, Rosario (2000), Argentina
| | - Ricardo L. E. Furlan
- Instituto de Investigaciones
para el Descubrimiento de Fármacos de Rosario (UNR-CONICET), Ocampo y Esmeralda, Rosario (2000), Argentina
- Farmacognosia,
Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario (2000), Argentina
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21
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Leclaire J, Poisson G, Ziarelli F, Pepe G, Fotiadu F, Paruzzo FM, Rossini AJ, Dumez JN, Elena-Herrmann B, Emsley L. Structure elucidation of a complex CO 2-based organic framework material by NMR crystallography. Chem Sci 2016; 7:4379-4390. [PMID: 30155085 PMCID: PMC6014084 DOI: 10.1039/c5sc03810c] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/22/2016] [Indexed: 12/23/2022] Open
Abstract
A three-dimensional structural model of a complex CO2-based organic framework made from high molecular weight, self-assembled, flexible and multi-functional oligomeric constituents has been determined de novo by solid-state NMR including DNP-enhanced experiments. The complete assignment of the 15N, 13C and 1H resonances was obtained from a series of two-dimensional through space and through bond correlation experiments. MM-QM calculations were used to generate different model structures for the material which were then evaluated by comparing multiple experimental and calculated NMR parameters. Both NMR and powder X-ray diffraction were evaluated as tools to determine the packing by crystal modelling, and at the level of structural modelling used here PXRD was found not to be a useful complement. The structure determined reveals a highly optimised H-bonding network that explains the unusual selectivity of the self-assembly process which generates the material. The NMR crystallography approach used here should be applicable for the structure determination of other complex solid materials.
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Affiliation(s)
- Julien Leclaire
- Univ Lyon , Université Claude Bernard , CNRS, INSA, CPE , ICBMS UMR 5246 , 69622 Villeurbanne , France .
- Aix Marseille Université , Centrale Marseille , CNRS , iSm2 UMR 7313 , 13397 Marseille , France
| | - Guillaume Poisson
- Univ Lyon , Université Claude Bernard , CNRS, INSA, CPE , ICBMS UMR 5246 , 69622 Villeurbanne , France .
- Aix Marseille Université , Centrale Marseille , CNRS , iSm2 UMR 7313 , 13397 Marseille , France
| | - Fabio Ziarelli
- Aix-Marseille Université , Fédération des Sciences Chimiques , Spectropôle , 13397 Marseille , France
| | - Gerard Pepe
- Aix-Marseille Université , CNRS , UMR 7325 CINaM , 13288 Marseille , France
| | - Frédéric Fotiadu
- Aix Marseille Université , Centrale Marseille , CNRS , iSm2 UMR 7313 , 13397 Marseille , France
| | - Federico M Paruzzo
- Institut des Sciences et Ingénierie Chimiques , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Aaron J Rossini
- Université de Lyon , Institut des Sciences Analytiques , Centre de RMN à très hauts champs , CNRS/ENS Lyon/UCBL , 69100 Villeurbanne , France .
- Institut des Sciences et Ingénierie Chimiques , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
| | - Jean-Nicolas Dumez
- Université de Lyon , Institut des Sciences Analytiques , Centre de RMN à très hauts champs , CNRS/ENS Lyon/UCBL , 69100 Villeurbanne , France .
| | - Bénédicte Elena-Herrmann
- Université de Lyon , Institut des Sciences Analytiques , Centre de RMN à très hauts champs , CNRS/ENS Lyon/UCBL , 69100 Villeurbanne , France .
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques , Ecole Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne , Switzerland
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22
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Teunissen AJP, Paffen TFE, Ercolani G, de Greef TFA, Meijer EW. Regulating Competing Supramolecular Interactions Using Ligand Concentration. J Am Chem Soc 2016; 138:6852-60. [DOI: 10.1021/jacs.6b03421] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | | | - Gianfranco Ercolani
- Dipartimento
di Scienze e Tecnologie Chimiche, Università di Roma Tor Vergata, Via della Ricerca Scientifica, 00133 Roma, Italy
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23
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Ulatowski F, Dąbrowa K, Jurczak J. Supramolecular detection of geometrical differences of azobenzene carboxylates. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.03.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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24
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Sadownik JW, Philp D. A recognition-mediated reaction drives amplification within a dynamic library. Org Biomol Chem 2015; 13:10392-401. [PMID: 26324766 DOI: 10.1039/c5ob01621e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A single, appropriately designed, recognition event targets and transforms one of two reactive members of an exchanging pool of compounds through a recognition-mediated irreversible cycloaddition reaction, altering dramatically the final composition and kinetic behaviour of the dynamic library.
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Affiliation(s)
- Jan W Sadownik
- School of Chemistry and EaStCHEM, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK.
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25
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Ulatowski F, Lichosyt D, Jurczak J. Introducing a static receptor to compete with a dynamic combinatorial library in template binding. Org Biomol Chem 2015; 13:10451-5. [DOI: 10.1039/c5ob01698c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Association constants can be obtained from HPLC analysis of a system comprising a dynamic combinatorial library and a static host.
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Affiliation(s)
- Filip Ulatowski
- Institute of Organic Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
| | - Dawid Lichosyt
- Institute of Organic Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
| | - Janusz Jurczak
- Institute of Organic Chemistry
- Polish Academy of Sciences
- Warsaw
- Poland
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26
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Ciaccia M, Tosi I, Baldini L, Cacciapaglia R, Mandolini L, Di Stefano S, Hunter CA. Applications of dynamic combinatorial chemistry for the determination of effective molarity. Chem Sci 2015; 6:144-151. [PMID: 28553463 PMCID: PMC5424495 DOI: 10.1039/c4sc02347a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 09/16/2014] [Indexed: 01/04/2023] Open
Abstract
A new strategy for determining thermodynamic effective molarities (EM) for macrocylisation reactions using dynamic combinatorial chemistry under dilute conditions is presented. At low concentrations, below the critical value, Dynamic Libraries (DLs) of bifunctional building blocks contain only cyclic species, so it is not possible to quantify the equilibria between linear and cyclic species. However, addition of a monofunctional chain stopper can be used to promote the formation of linear oligomers allowing measurement of EM for all cyclic species present in the DL. The effectiveness of this approach was demonstrated for DLs generated from mixtures of 1,3-diimine calix[4]arenes, linear diaminoalkanes and monoaminoalkanes. For macrocycles deriving from one bifunctional calixarene and one diamine, there is an alternating pattern of EM values with the number of methylene units in the diamine: odd numbers give significantly higher EMs than even numbers. For odd numbers of methylene units, the alkyl chain can adopt an extended all anti conformation, whereas for even numbers of methylene units, gauche conformations are required for cyclisation, and the associated strain reduces EM. The value of EM for the five-carbon linker indicates that this macrocycle is a strainless ring.
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Affiliation(s)
- Maria Ciaccia
- Dipartimento di Chimica and IMC/CNR , Università La Sapienza , P.le A. Moro 5 , 00185 Rome , Italy .
- Department of Chemistry , University of Sheffield , Sheffield , S3 7HF , UK
| | - Irene Tosi
- Dipartimento di Chimica , Università di Parma , Parco Area delle Scienze 17/A , 43124 , Parma , Italy
| | - Laura Baldini
- Dipartimento di Chimica , Università di Parma , Parco Area delle Scienze 17/A , 43124 , Parma , Italy
| | - Roberta Cacciapaglia
- Dipartimento di Chimica and IMC/CNR , Università La Sapienza , P.le A. Moro 5 , 00185 Rome , Italy .
| | - Luigi Mandolini
- Dipartimento di Chimica and IMC/CNR , Università La Sapienza , P.le A. Moro 5 , 00185 Rome , Italy .
| | - Stefano Di Stefano
- Dipartimento di Chimica and IMC/CNR , Università La Sapienza , P.le A. Moro 5 , 00185 Rome , Italy .
| | - Christopher A Hunter
- Department of Chemistry , University of Sheffield , Sheffield , S3 7HF , UK
- Department of Chemistry , University of Cambridge , Cambridge , CB2 1EW , UK .
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27
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He Z, Ye G, Jiang W. Imine Macrocycle with a Deep Cavity: Guest-Selected Formation ofsyn/antiConfiguration and Guest-Controlled Reconfiguration. Chemistry 2014; 21:3005-12. [DOI: 10.1002/chem.201405912] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Indexed: 12/15/2022]
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28
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Black SP, Sanders JKM, Stefankiewicz AR. Disulfide exchange: exposing supramolecular reactivity through dynamic covalent chemistry. Chem Soc Rev 2014; 43:1861-72. [PMID: 24132207 DOI: 10.1039/c3cs60326a] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A Tutorial Review of the subtle supramolecular interactions influencing the outcomes of equilibrating systems, focusing on the dynamic covalent chemistry (DCC) of disulfide exchange reactions, is presented. We discuss the topics of cation-π interactions (2.1), hydrophobic effects (2.2), hydrogen bonding interactions (2.3) aromatic donor-acceptor interactions (2.4), and metal-ligand interactions (2.5) in the context of dynamic disulfide chemistry.
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Affiliation(s)
- Samuel P Black
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, UKCB21EW
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29
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Herrmann A. Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures. Chem Soc Rev 2014; 43:1899-933. [PMID: 24296754 DOI: 10.1039/c3cs60336a] [Citation(s) in RCA: 277] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.
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Affiliation(s)
- Andreas Herrmann
- Firmenich SA, Division Recherche et Développement, Route des Jeunes 1, B. P. 239, CH-1211 Genève 8, Switzerland.
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30
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Mahon CS, Fulton DA. Mimicking nature with synthetic macromolecules capable of recognition. Nat Chem 2014; 6:665-72. [PMID: 25054935 DOI: 10.1038/nchem.1994] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 05/30/2014] [Indexed: 02/06/2023]
Abstract
Nature has, through billions of years of evolution, assembled a multitude of polymeric macromolecules capable of exquisite molecular recognition. This functionality arises from the precise control exerted over their biosynthesis that results in key residues being anchored in the appropriate positions to interact with target substrates. Developing 'wholly synthetic' macromolecular analogues that can mimic this behaviour presents a considerable challenge to chemists, who lack the 'biological machinery' used in nature to assemble polymers with such precision. In addressing this challenge, familiar chemical concepts, such as combinatorial methods and supramolecular interactions, have been adapted for application in the macromolecular arena. Working from a limited set of residues, synthetic macromolecules have been produced that display surprisingly high binding affinities towards target proteins, even possessing useful in vivo activities. These observations are all the more surprising when one considers the heterogeneity inherent within these synthetic macromolecular receptors, and provoke intriguing questions regarding our assumptions about the design of receptors.
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Affiliation(s)
- Clare S Mahon
- Chemical Nanoscience Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - David A Fulton
- Chemical Nanoscience Laboratory, School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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31
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Ulatowski F, Sadowska-Kuzioła A, Jurczak J. "Choose-a-size" approach in dynamic combinatorial chemistry: a single substrate dynamic combinatorial library of oligomacrocycles that adapts to the size and shape of carboxylates. J Org Chem 2014; 79:9762-70. [PMID: 25280250 DOI: 10.1021/jo501956h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A neutral anion binding receptor based on dipicolinic acid diamide was equipped with thiol groups in the amidic side arms. After the thiol was oxidized to disulfide groups with I2, a mixture of cyclic oligomers (a library) was obtained. The distribution of macrocycles can be controlled kinetically during the oxidation process or thermodynamically at basic conditions via disulfide bond exchange. The library proved to be very sensitive to templation with various carboxylates in DMSO. The amplification pattern reflects the structural features of the anionic template and is sensitive to changes in the template's geometry. The application of carboxylates with multiple functional groups resulted in very strong amplification of the large penta- and hexameric macrocycles. The thermodynamic parameters of some templation effects were rationalized using a simple model and confirmed using competitive NMR titration.
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Affiliation(s)
- Filip Ulatowski
- Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland
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32
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Evans NH, Beer PD. Advances in anion supramolecular chemistry: from recognition to chemical applications. Angew Chem Int Ed Engl 2014; 53:11716-54. [PMID: 25204549 DOI: 10.1002/anie.201309937] [Citation(s) in RCA: 415] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Indexed: 12/11/2022]
Abstract
Since the start of this millennium, remarkable progress in the binding and sensing of anions has been taking place, driven in part by discoveries in the use of hydrogen bonding, as well as the previously under-exploited anion-π interactions and halogen bonding. However, anion supramolecular chemistry has developed substantially beyond anion recognition, and now encompasses a diverse range of disciplines. Dramatic advance has been made in the anion-templated synthesis of macrocycles and interlocked molecular architectures, while the study of transmembrane anion transporters has flourished from almost nothing into a rapidly maturing field of research. The supramolecular chemistry of anions has also found real practical use in a variety of applications such as catalysis, ion extraction, and the use of anions as stimuli for responsive chemical systems.
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Affiliation(s)
- Nicholas H Evans
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB (UK).
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33
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Evans NH, Beer PD. Supramolekulare Chemie von Anionen: von der Erkennung zur chemischen Anwendung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309937] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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34
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Matache M, Bogdan E, Hădade ND. Selective Host Molecules Obtained by Dynamic Adaptive Chemistry. Chemistry 2014; 20:2106-31. [DOI: 10.1002/chem.201303504] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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35
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Li J, Nowak P, Fanlo-Virgós H, Otto S. Catenanes from catenanes: quantitative assessment of cooperativity in dynamic combinatorial catenation. Chem Sci 2014. [DOI: 10.1039/c4sc01998a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A series of dynamic combinatorial [2] and [3]catenanes have been prepared. Formation of the [3]catenanes occurs with positive or negative cooperativity, depending on the cyclodextrin homologue. Systems level analysis allows cooperativity to be quantified and MD simulations reveal that cooperativity derives from the extents to which hydrophobic surface area is exposed to the aqueous surroundings.
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Affiliation(s)
- Jianwei Li
- Centre for Systems Chemistry
- Stratingh Institute
- University of Groningen
- 9747 AG Groningen, The Netherlands
| | - Piotr Nowak
- Centre for Systems Chemistry
- Stratingh Institute
- University of Groningen
- 9747 AG Groningen, The Netherlands
| | - Hugo Fanlo-Virgós
- Centre for Systems Chemistry
- Stratingh Institute
- University of Groningen
- 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry
- Stratingh Institute
- University of Groningen
- 9747 AG Groningen, The Netherlands
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36
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Misuraca MC, Moulin E, Ruff Y, Giuseppone N. Experimental and theoretical methods for the analyses of dynamic combinatorial libraries. NEW J CHEM 2014. [DOI: 10.1039/c4nj00304g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Progresses in spatial and temporal analytical tools open new avenues for the study and control of increasingly complex chemical systems.
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Affiliation(s)
- Maria Cristina Misuraca
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
| | - Emilie Moulin
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
| | - Yves Ruff
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
| | - Nicolas Giuseppone
- SAMS research group – University of Strasbourg – Institut Charles Sadron
- CNRS
- 67034 Strasbourg Cedex 2, France
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37
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Ulrich S, Dumy P. Probing secondary interactions in biomolecular recognition by dynamic combinatorial chemistry. Chem Commun (Camb) 2014; 50:5810-25. [DOI: 10.1039/c4cc00263f] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Hamieh S, Saggiomo V, Nowak P, Mattia E, Ludlow RF, Otto S. A “Dial-A-Receptor” Dynamic Combinatorial Library. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305744] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Hamieh S, Saggiomo V, Nowak P, Mattia E, Ludlow RF, Otto S. A “Dial-A-Receptor” Dynamic Combinatorial Library. Angew Chem Int Ed Engl 2013; 52:12368-72. [DOI: 10.1002/anie.201305744] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Indexed: 01/28/2023]
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Li J, Nowak P, Otto S. Dynamic Combinatorial Libraries: From Exploring Molecular Recognition to Systems Chemistry. J Am Chem Soc 2013; 135:9222-39. [DOI: 10.1021/ja402586c] [Citation(s) in RCA: 353] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jianwei Li
- 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
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
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Abstract
Since its inception in the mid-1990s, dynamic combinatorial chemistry (DCC), the chemistry of complex systems under thermodynamic control, has proved valuable in identifying unexpected molecules with remarkable binding properties and in providing effective synthetic routes to complex species. Essentially, in this approach, one designs the experiment rather than the molecule. DCC has also provided us with insights into how some chemical systems respond to external stimuli. Using examples from the work of our laboratory and others, this Account shows how the concept of DCC, inspired by the evolution of living systems, has found an increasing range of applications in diverse areas and has evolved conceptually and experimentally. A dynamic combinatorial library (DCL) is a thermodynamically controlled mixture of interconverting species that can respond to various stimuli. The Cambridge version of dynamic combinatorial chemistry was initially inspired by the mammalian immune system and was conceived as a way to create and identify new unpredictable receptors. For example, an added template can select and stabilize a strongly binding member of the library which is then amplified at the expense of the unsuccessful library members, minimizing the free energy of the system. But researchers have exploited DCC in a variety of other ways: over the past two decades, this technique has contributed to the evolution of chemistry and to applications in the diverse fields of catalysis, fragrance release, and responsive materials. Among these applications, researchers have built intricate and well-defined architectures such as catenanes or hydrogen-bonded nanotubes, using the ability of complex chemical systems to reach a high level of organization. In addition, DCC has proved a powerful tool for the study of complex molecular networks and systems. The use of DCC is improving our understanding of chemical and biological systems. The study of folding or self-replicating macrocycles in DCLs has served as a model for appreciating how complex organisations such as life can emerge from a pool of simple chemicals. Today, DCC is no longer restricted to thermodynamic control, and new systems have recently appeared in which kinetic and thermodynamic control coexist. Expanding the realm of DCC to unexplored and promising new territories, these hybrid systems show that the concept of dynamic combinatorial chemistry continues to evolve.
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Affiliation(s)
- Fabien B. L. Cougnon
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Jeremy K. M. Sanders
- University Chemical Laboratory, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
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Stefankiewicz AR, Sambrook MR, Sanders JKM. Template-directed synthesis of multi-component organic cages in water. Chem Sci 2012. [DOI: 10.1039/c2sc20347b] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Berrocal JA, Cacciapaglia R, Stefano SD, Mandolini L. Target-induced amplification in a dynamic library of macrocycles. A quantitative study. NEW J CHEM 2012. [DOI: 10.1039/c1nj20801b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Cougnon FBL, Jenkins NA, Pantoş GD, Sanders JKM. Templated Dynamic Synthesis of a [3]Catenane. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106885] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Cougnon FBL, Jenkins NA, Pantoş GD, Sanders JKM. Templated Dynamic Synthesis of a [3]Catenane. Angew Chem Int Ed Engl 2011; 51:1443-7. [DOI: 10.1002/anie.201106885] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 10/27/2011] [Indexed: 11/09/2022]
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Klein JM, Saggiomo V, Reck L, Lüning U, Sanders JKM. Dynamic combinatorial libraries for the recognition of heavy metal ions. Org Biomol Chem 2011; 10:60-6. [PMID: 22028051 DOI: 10.1039/c1ob05976a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We present the use of hydrazone dynamic combinatorial libraries (DCLs) to identify macrocyclic receptors that are selective for alkaline earth metal ions over alkali metal ions. In particular, the toxic heavy metal ions Sr(2+) and Ba(2+) induce characteristic changes in the DCLs. Four macrocycles were isolated and characterised by LCMS, HRMS, NMR and X-ray crystallography; binding studies by UV-Vis spectroscopy confirm the selectivity observed in the DCLs.
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Affiliation(s)
- Jörg M Klein
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
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Roy N, Lehn JM. Dynamic Covalent Chemistry: A Facile Room-Temperature, Reversible, Diels-Alder Reaction between Anthracene Derivatives and N-Phenyltriazolinedione. Chem Asian J 2011; 6:2419-25. [DOI: 10.1002/asia.201100244] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Indexed: 11/06/2022]
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Beeren SR, Sanders JKM. Discovery of linear receptors for multiple dihydrogen phosphate ions using dynamic combinatorial chemistry. J Am Chem Soc 2011; 133:3804-7. [PMID: 21361379 DOI: 10.1021/ja200130h] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We describe the use of dynamic combinatorial chemistry to discover a new series of linear hydrazone-based receptors that bind multiple dihydrogen phosphate ions. Through the use of a template-driven, selection-based approach to receptor synthesis, dynamic combinatorial chemistry allows for the identification of unexpected host structures and binding motifs. Notably, we observed the unprecedented selection of these linear receptors in preference to competing macrocyclic hosts. Furthermore, linear receptors containing up to nine building blocks and three different building blocks were amplified in the dynamic combinatorial library. The receptors were formed using a dihydrazide building block based on an amino acid-disubstituted ferrocene scaffold. A detailed study of the linear pentamer revealed that it forms a helical ditopic receptor that employs four acylhydrazone hydrogen-bond donor motifs to cooperatively bind two dihydrogen phosphate ions.
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Affiliation(s)
- Sophie R Beeren
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Roy L, Case MA. Recursively Enriched Dynamic Combinatorial Libraries for the Self-Selection of Optimally Stable Proteins. J Phys Chem B 2011; 115:2454-64. [DOI: 10.1021/jp111652n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Liton Roy
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405,
United States
| | - Martin A. Case
- Department of Chemistry, The University of Vermont, Burlington, Vermont 05405,
United States
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Hunt RAR, Otto S. Dynamic combinatorial libraries: new opportunities in systems chemistry. Chem Commun (Camb) 2011; 47:847-58. [PMID: 21116521 DOI: 10.1039/c0cc03759a] [Citation(s) in RCA: 174] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Rosemary A R Hunt
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
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