1
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Ibáñez S, Peris E. Discrete Quadruple Stacks Formed in a Nanosized Metallorectangle. Inorg Chem 2024. [PMID: 39126404 DOI: 10.1021/acs.inorgchem.4c02653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Abstract
An iridium-cornered nanosized metallorectangle was obtained by combining a quinoxalinophenanthrophenazine-connected Janus-di-imidazolylidene ligand and 4,4'-bipyridine. This metallorectangle was used as host for a series of planar molecules, including pyrene, triphenylene, perylene, coronene, and N,N'-dimethyl-naphthalenetetracarboxy-diimide (NTCDI). The binding of coronene and NTCDI followed a strongly positive cooperative 1:2 stoichiometric binding model, as the inclusion of the first guest generates the geometrical requirements for the optimum encapsulation of the second planar molecule. The simultaneous encapsulation of coronene and NTCDI produces a heteroguest inclusion system, whose exchange dynamics was studied by means of variable temperature 1H NMR spectroscopy.
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Affiliation(s)
- Susana Ibáñez
- Institute of Advanced Materials (INAM), Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universitat Jaume I, Av. Vicente Sos Baynat s/n, Castellón E-12006, Spain
| | - Eduardo Peris
- Institute of Advanced Materials (INAM), Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universitat Jaume I, Av. Vicente Sos Baynat s/n, Castellón E-12006, Spain
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2
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Kumar S, Singh D, Rit A. Cooperativity between metal centers in homobimetallic Pd II-NHC complexes: catalytic potential towards hydrodefluorination. Chem Commun (Camb) 2024; 60:7761-7764. [PMID: 38973622 DOI: 10.1039/d4cc02185a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Among the several unsymmetrical bis-NHC derived distinct homo-bimetallic and mono-NHC supported PdII complexes studied here (1-5), the bimetallic complex 1 was noted to be the most effective catalyst for the challenging hydrodefluorination. The electron richness of the metal centers and the synergistic cooperation between the PdII centers (cooperativity index, ɑ = 8.67) have been recognized to be the deciding factor for its better activity.
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Affiliation(s)
- Shashi Kumar
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.
| | - Dushyant Singh
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.
| | - Arnab Rit
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.
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3
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Lee S, Song G, Jeong KS. Stimuli-Responsive Molecular Duplexes Displaying Duplex-to-Duplex Switching. Angew Chem Int Ed Engl 2024:e202410884. [PMID: 38937392 DOI: 10.1002/anie.202410884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 06/27/2024] [Accepted: 06/27/2024] [Indexed: 06/29/2024]
Abstract
Synthetic duplexes with high stabilities have promising potential for mimicking biomolecular functions and developing supramolecular smart materials. Herein, we describe the synthesis and stimuli-responsive properties of molecular duplexes derived from indolocarbazole-pyridine (I-P) oligomers. These duplexes adopt nonclassical helical structures, stabilized by I-P hydrogen-bonding pairs in anhydrous chlorinated solvents. Notably, the longest duplex 62 (11-mer)2 displays remarkable stability, forming twenty hydrogen bonds; its exchange energy barrier was determined to be ΔG≠=22.0 kcal ⋅ mol-1 at 75 °C in anhydrous (CDCl2)2. Upon the addition of water, a hydrated duplex 62 (11-mer)2⊃10H2O was formed, with one water molecule inserted between each I-P hydrogen-bonding pair. The Hill coefficient (n) for this process is 6.1, demonstrating extremely positive cooperativity. Conversely, the hydrated duplex 62 (11-mer)2⊃10H2O was completely converted into the original anhydrous duplex 62 (11-mer)2 when the temperature was increased. Interconversion between these two distinct duplexes can be repeatedly carried out by varying the temperature. Furthermore, reversible switching between hetero-duplexes and homo-duplexes was also demonstrated by controlling the temperature, with concomitant changes in the characteristic emission signals.
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Affiliation(s)
- Seungwon Lee
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Geunmoo Song
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
| | - Kyu-Sung Jeong
- Department of Chemistry, Yonsei University, Seoul, 03722, Republic of Korea
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4
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Becker S. Understanding Cooperativity in Homo- and Heterometallic Complexes: From Basic Concepts to Design. Chempluschem 2024; 89:e202300619. [PMID: 38317458 DOI: 10.1002/cplu.202300619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/12/2023] [Accepted: 02/05/2024] [Indexed: 02/07/2024]
Abstract
Cooperative effects have attracted considerable attention in recent years. These effects are ubiquitous in chemistry and biology and can govern interactions of proteins with other biomolecules, mechanisms of supramolecular recognition and polymerization, catalysis, assembly of compounds on surfaces, and physical properties such as magnetic, electronic or optical properties, e. g. Consequently, the understanding of cooperative effects can lead to a structure-property relation that can pave the way to future applications in various research areas; however, with regard to cooperative effects in homo- and heterometallic complexes, we still are at the beginning of understanding. Nevertheless, concepts to describe cooperativity of metal centers as well as methodologies to investigate and model these effects have emerged over the last years. This concept article gives an overview of these existing concepts, approaches, and strategies to understand cooperative effects in homo- and heterometallic complexes. Special emphasis is put on concepts to define cooperative effects, their quantification, as well as methods to investigate cooperative effects.
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Affiliation(s)
- Sabine Becker
- Fachbereich Chemie, RPTU Kaiserslautern-Landau, Erwin-Schroedinger-Str. 54, 67663, Kaiserslautern, Germany
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5
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Mizuno H, Nakazawa H, Miyagawa A, Yakiyama Y, Sakurai H, Fukuhara G. Amplification sensing manipulated by a sumanene-based supramolecular polymer as a dynamic allosteric effector. Sci Rep 2024; 14:12534. [PMID: 38822045 PMCID: PMC11143208 DOI: 10.1038/s41598-024-63304-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024] Open
Abstract
The synthesis of signal-amplifying chemosensors induced by various triggers is a major challenge for multidisciplinary sciences. In this study, a signal-amplification system that was flexibly manipulated by a dynamic allosteric effector (trigger) was developed. Herein, the focus was on using the behavior of supramolecular polymerization to control the degree of polymerization by changing the concentration of a functional monomer. It was assumed that this control was facilitated by a gradually changing/dynamic allosteric effector. A curved-π buckybowl sumanene and a sumanene-based chemosensor (SC) were employed as the allosteric effector and the molecular binder, respectively. The hetero-supramolecular polymer, (SC·(sumanene)n), facilitated the manipulation of the degree of signal-amplification; this was accomplished by changing the sumanene monomer concentration, which resulted in up to a 62.5-fold amplification of a steroid. The current results and the concept proposed herein provide an alternate method to conventional chemosensors and signal-amplification systems.
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Affiliation(s)
- Hiroaki Mizuno
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8551, Japan
| | - Hironobu Nakazawa
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Akihisa Miyagawa
- Department of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yumi Yakiyama
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
- Division of Applied Chemistry, Graduate School of Engineering and Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives (ICS-OTRI), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Hidehiro Sakurai
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
- Division of Applied Chemistry, Graduate School of Engineering and Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives (ICS-OTRI), Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-Ku, Tokyo, 152-8551, Japan.
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6
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Kimura Y, Matsumura K, Ono K, Tsuchido Y, Kawai H. Recognition of Amino Acid Salts by Temperature-Dependent Allosteric Binding with Stereodynamic Urea Receptors. Chemistry 2024; 30:e202400154. [PMID: 38488291 DOI: 10.1002/chem.202400154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Indexed: 04/11/2024]
Abstract
Positive homotropic artificial allosteric systems are important for the regulation of cooperativity, selectivity and nonlinear amplification. Stereodynamic homotropic allosteric receptors can transmit and amplify induced chirality by the first ligand binding to axial chirality between two chromophores. We herein report stereodynamic allosteric urea receptors consisting of a rotational shaft as the axial chirality unit, terphenyl units as structural transmission sites and four urea units as binding sites. NMR titration experiments revealed that the receptor can bind two carboxylate guests in a positive homotropic allosteric manner attributed to the inactivation by intramolecular hydrogen-bonding between urea units within the receptor. In addition, the VT-CD spectra observed upon binding of the urea receptor with l- or D-amino acid salts in MeCN showed interesting temperature-dependent Cotton effects, based on the differences of the receptor shaft unit and the guest structure. The successful discrimination of hydrocarbon-based side chains of amino acid salts indicated that the input of chiral and steric information for the guest was amplified as outputs of the Cotton effect and the temperature-dependence of VT-CD spectra through cooperativity of positive allosteric binding.
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Affiliation(s)
- Yuki Kimura
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Kotaro Matsumura
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Kosuke Ono
- School of Science, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo, 152-8551, Japan
| | - Yoshitaka Tsuchido
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Hidetoshi Kawai
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
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7
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Fagnano A, Frateloreto F, Paoloni R, Sappino C, Lanzalunga O, Costas M, Di Stefano S, Olivo G. Proximity Effects on the Reactivity of a Nonheme Iron (IV) Oxo Complex in C-H Oxidation. Angew Chem Int Ed Engl 2024; 63:e202401694. [PMID: 38478739 DOI: 10.1002/anie.202401694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Indexed: 04/05/2024]
Abstract
Precise control of substrate positioning and orientation (its proximity to the reactive unit) is often invoked to rationalize the superior enzymatic reaction rates and selectivities when compared to synthetic models. Artificial nonheme iron (IV) oxo (Fe(IV)=O) complexes react with C(sp3)-H bonds via a biomimetic Hydrogen Atom Transfer/Hydroxyl Rebound mechanism, but rates, site-selectivity and even hydroxyl rebound efficiency (ligand rebound versus substrate radical diffusion) are smaller than in oxygenases. Herein, we quantitatively analyze how substrate binding modulates nonheme Fe(IV)=O reactivity by comparing rates and outcomes of C-H oxidation by a pair of Fe(IV)=O complexes that share the same first coordination sphere but only one contains a crown ether receptor that recognizes the substrate. Substrate binding makes the reaction intramolecular, exhibiting Michaelis-Menten kinetics and increased reaction rates. In addition, C-H oxidation occurs with high site selectivity for remote sites. Analysis of Effective Molarity reveals that the system operates at its maximal theoretical capability for the oxidation of these remote sites. Remarkably, substrate positioning also affects Hydroxyl Rebound, whose efficiency only increases on the sites placed in proximity by recognition. Overall, these observations provide evidence that supramolecular control of substrate positioning can effectively modulate the reactivity of oxygenases and its models.
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Affiliation(s)
- Alessandro Fagnano
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Federico Frateloreto
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Roberta Paoloni
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Carla Sappino
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Osvaldo Lanzalunga
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Miquel Costas
- QBIS-Cat, Institut de Química Computacional i Catàlisi (IQCC), Departament de Quimica, Universitat de Girona Campus Montilivi, 17071, Girona, Catalonia, Spain
| | - Stefano Di Stefano
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Giorgio Olivo
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
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8
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Rinkovec T, Kalebic D, Dehaen W, Whitelam S, Harvey JN, De Feyter S. On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface. Chem Sci 2024; 15:6076-6087. [PMID: 38665531 PMCID: PMC11041291 DOI: 10.1039/d4sc00284a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/12/2024] [Indexed: 04/28/2024] Open
Abstract
In this work we investigate the behaviour of molecules at the nanoscale using scanning tunnelling microscopy in order to explore the origin of the cooperativity in the formation of self-assembled molecular networks (SAMNs) at the liquid/solid interface. By studying concentration dependence of alkoxylated dimethylbenzene, a molecular analogue to 5-alkoxylated isophthalic derivatives, but without hydrogen bonding moieties, we show that the cooperativity effect can be experimentally evaluated even for low-interacting systems and that the cooperativity in SAMN formation is its fundamental trait. We conclude that cooperativity must be a local effect and use the nearest-neighbor Ising model to reproduce the coverage vs. concentration curves. The Ising model offers a direct link between statistical thermodynamics and experimental parameters, making it a valuable tool for assessing the thermodynamics of SAMN formation.
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Affiliation(s)
- Tamara Rinkovec
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Demian Kalebic
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Wim Dehaen
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory 1 Cyclotron Road Berkeley CA 94720 USA
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
| | - Steven De Feyter
- Department of Chemistry, KU Leuven Celestijnenlaan 200F B-3001 Leuven Belgium
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9
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Zeng YW, He AQ, Yang LM, Ozaki Y, Noda I, Xu YZ. Patterns of Cross-Peaks in Two-Dimensional Correlation Spectra to Probe Intermolecular Interactions Described by Two Reversible Reactions. APPLIED SPECTROSCOPY 2024:37028241245136. [PMID: 38646741 DOI: 10.1177/00037028241245136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Two-dimensional correlation spectroscopy is used to investigate the intermolecular interaction between two substances dissolved in the same solutions, where the intermolecular interaction is described by two reversible reactions producing two supramolecular aggregates. The severe overlappings expected among the characteristic peaks of the original solute and aggregates make conventional one-dimensional spectra difficult to accurately reflect the physiochemical nature of the intermolecular interaction. The double asynchronous orthogonal sample design (DAOSD) approach is utilized to analyze the simulated data for proof-of-principle demonstration. The patterns of cross-peaks are much more complex compared with the intermolecular interaction described by only a single reaction. Four major groups of cross-peaks with characteristic patterns observed in the pair of DAOSD asynchronous spectra are systematically analyzed and classified. Further analysis of the spectral feature of the cross-peaks of the DAOSD asynchronous spectra is helpful to exact additional information concerning the variation of the peak position and peak width of the aggregates compared with those of the original solute. The result is important to reveal the physicochemical nature of intermolecular interaction between the solutes (e.g., changes in conformation, dynamical behavior, etc.). The pattern of cross-peaks in the corresponding 2D asynchronous spectra may become rather complex when the peak position, peak width, and peak intensity of two supramolecular aggregates change simultaneously. Further work using artificial intelligence techniques to interpret the complex cross-peaks is still being carried out.
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Affiliation(s)
- Yi-Wei Zeng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - An-Qi He
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Li-Min Yang
- State Key Laboratory of Nuclear Physics and Technology, Institute of Heavy Ion Physics, School of Physics, Peking University, Beijing, China
| | - Yukihiro Ozaki
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Hyogo, Japan
| | - Isao Noda
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware, USA
| | - Yi-Zhuang Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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10
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Lauzon D, Vallée-Bélisle A. Design and Thermodynamics Principles to Program the Cooperativity of Molecular Assemblies. Angew Chem Int Ed Engl 2024; 63:e202313944. [PMID: 37975629 DOI: 10.1002/anie.202313944] [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: 09/25/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Most functional nanosystems in living organisms are constructed using multimeric assemblies that provide multiple advantages over their monomeric counterparts such as cooperative or anti-cooperative responses, integration of multiple signals and self-regulation. Inspired by these natural nanosystems, chemists have been synthesizing self-assembled supramolecular systems over the last 50 years with increasing complexity with applications ranging from biosensing, drug delivery, synthetic biology, and system chemistry. Although many advances have been made concerning the design principles of novel molecular architectures and chemistries, little is still known, however, about how to program their dynamic of assembly so that they can assemble at the required concentration and with the right sensitivity. Here, we used synthetic DNA assemblies and double-mutant cycle analysis to explore the thermodynamic basis to program the cooperativity of molecular assemblies. The results presented here exemplify how programmable molecular assemblies can be efficiently built by fusing interacting domains and optimizing their compaction. They may also provide the rational basis for understanding the thermodynamic and mechanistic principles driving the evolution of multimeric biological complexes.
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Affiliation(s)
- Dominic Lauzon
- Laboratory of Biosensors & Nanomachines, Department of Chemistry, Université de Montréal, Montréal, H2V 0B3, QC, Canada
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors & Nanomachines, Department of Chemistry, Université de Montréal, Montréal, H2V 0B3, QC, Canada
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11
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Steyn HF, White LJ, Hilton KLF, Hiscock JR, Pohl CH. Supramolecular Self-Associating Amphiphiles Inhibit Biofilm Formation by the Critical Pathogens, Pseudomonas aeruginosa and Candida albicans. ACS OMEGA 2024; 9:1770-1785. [PMID: 38222503 PMCID: PMC10785623 DOI: 10.1021/acsomega.3c08425] [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: 10/25/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 01/16/2024]
Abstract
In 2019, 4.95 million deaths were directly attributed to antimicrobial-resistant bacterial infections globally. In addition, the mortality associated with fungal infections is estimated at 1.7 million annually, with many of these deaths attributed to species that are no longer susceptible to traditional therapeutic regimes. Herein, we demonstrate the use of a novel class of supramolecular self-associating amphiphilic (SSA) salts as antimicrobial agents against the critical pathogens Pseudomonas aeruginosa and Candida albicans. We also identify preliminary structure-activity relationships for this class of compound that will aid the development of next-generation SSAs demonstrating enhanced antibiofilm activity. To gain insight into the possible mode of action for these agents, a series of microscopy studies were performed, taking advantage of the intrinsic fluorescent nature of benzothiazole-substituted SSAs. Analysis of these data showed that the SSAs interact with the cell surface and that a benzothiazole-containing SSA inhibits hyphal formation by C. albicans.
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Affiliation(s)
- Hendrik
J. F. Steyn
- Department
of Microbiology and Biochemistry, University
of the Free State, Bloemfontein, Free State 9301, South Africa
| | - Lisa J. White
- School
of Chemistry and Forensic Science, University
of Kent, Kent, Canterbury CT2 7NH, United Kingdom
| | - Kira L. F. Hilton
- School
of Chemistry and Forensic Science, University
of Kent, Kent, Canterbury CT2 7NH, United Kingdom
| | - Jennifer R. Hiscock
- School
of Chemistry and Forensic Science, University
of Kent, Kent, Canterbury CT2 7NH, United Kingdom
| | - Carolina H. Pohl
- Department
of Microbiology and Biochemistry, University
of the Free State, Bloemfontein, Free State 9301, South Africa
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12
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de Souza AS, de Souza RF, Guzzo CR. Cooperative and structural relationships of the trimeric Spike with infectivity and antibody escape of the strains Delta (B.1.617.2) and Omicron (BA.2, BA.5, and BQ.1). J Comput Aided Mol Des 2023; 37:585-606. [PMID: 37792106 DOI: 10.1007/s10822-023-00534-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/11/2023] [Indexed: 10/05/2023]
Abstract
Herein, we conducted simulations of trimeric Spike from several SARS-CoV-2 variants of concern (Delta and Omicron sub-variants BA.2, BA.5, and BQ.1) and investigated the mechanisms by which specific mutations confer resistance to neutralizing antibodies. We observed that the mutations primarily affect the cooperation between protein domains within and between protomers. The substitutions K417N and L452R expand hydrogen bonding interactions, reducing their interaction with neutralizing antibodies. By interacting with nearby residues, the K444T and N460K mutations in the SpikeBQ.1 variant potentially reduces solvent exposure, thereby promoting resistance to antibodies. We also examined the impact of D614G, P681R, and P681H substitutions on Spike protein structure that may be related to infectivity. The D614G substitution influences communication between a glycine residue and neighboring domains, affecting the transition between up- and -down RBD states. The P681R mutation, found in the Delta variant, enhances correlations between protein subunits, while the P681H mutation in Omicron sub-variants weakens long-range interactions that may be associated with reduced fusogenicity. Using a multiple linear regression model, we established a connection between inter-protomer communication and loss of sensitivity to neutralizing antibodies. Our findings underscore the importance of structural communication between protein domains and provide insights into potential mechanisms of immune evasion by SARS-CoV-2. Overall, this study deepens our understanding of how specific mutations impact SARS-CoV-2 infectivity and shed light on how the virus evades the immune system.
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Affiliation(s)
- Anacleto Silva de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
| | - Robson Francisco de Souza
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil
| | - Cristiane Rodrigues Guzzo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374, Cidade Universitária, Sao Paulo, SP, 5508-900, Brazil.
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13
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Salvadori K, Onali A, Mathez G, Eigner V, Dendisová M, Matějka P, Mullerová M, Brancale A, Cuřínová P. An Insight into Anion Extraction by Amphiphiles: Hydrophobic Microenvironments as a Requirement for the Extractant Selectivity. ACS OMEGA 2023; 8:44221-44228. [PMID: 38027376 PMCID: PMC10666219 DOI: 10.1021/acsomega.3c06767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023]
Abstract
Coupling of electron-deficient urea units with aliphatic chains gives rise to amphiphilic compounds that bind to phosphate and benzoate anions in the hydrogen bonding competitive solvent (DMSO) with KAss = 6 580 M-1 and KAss = 4 100 M-1, respectively. The anchoring of these receptor moieties to the dendritic support does not result in a loss of anion binding and enables new applications. Due to the formation of a microenvironment in the dendrimer, the high selectivity of the prepared compound toward benzoate is maintained even in the presence of aqueous media during extraction experiments. In the presence of binding sites at 5 mM concentration, the amount of benzoate corresponding to the full binding site occupancy is transferred into the chloroform phase from its 10 mM aqueous solution. A thorough investigation of the extraction behavior of the dendrimer reported here, supported by a series of molecular dynamics simulations, provides new insight into the fundamental principles of extraction of inorganic anions by amphiphiles.
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Affiliation(s)
- Karolína Salvadori
- Department
of Physical Chemistry, University of Chemistry
and Technology Prague, Technická 5, Prague 6 16628, Czech Republic
- Department
of Bioorganic Chemistry and Biomaterials, Institute of Chemical Process Fundamentals of the CAS, v.v.i., Rozvojová 135, Prague 6 16502, Czech Republic
| | - Alessia Onali
- Department
of Organic Chemistry, University of Chemistry
and Technology Prague, Technická 5, Prague 6 16628, Czech Republic
| | - Gregory Mathez
- Department
of Organic Chemistry, University of Chemistry
and Technology Prague, Technická 5, Prague 6 16628, Czech Republic
| | - Václav Eigner
- Department
of Solid-State Chemistry, University of
Chemistry and Technology Prague, Technická 5, Prague 6 16628, Czech Republic
| | - Marcela Dendisová
- Department
of Physical Chemistry, University of Chemistry
and Technology Prague, Technická 5, Prague 6 16628, Czech Republic
| | - Pavel Matějka
- Department
of Physical Chemistry, University of Chemistry
and Technology Prague, Technická 5, Prague 6 16628, Czech Republic
| | - Monika Mullerová
- Department
of Bioorganic Chemistry and Biomaterials, Institute of Chemical Process Fundamentals of the CAS, v.v.i., Rozvojová 135, Prague 6 16502, Czech Republic
| | - Andrea Brancale
- Department
of Organic Chemistry, University of Chemistry
and Technology Prague, Technická 5, Prague 6 16628, Czech Republic
| | - Petra Cuřínová
- Department
of Organic Chemistry, University of Chemistry
and Technology Prague, Technická 5, Prague 6 16628, Czech Republic
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14
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López-Martín I, Veiga-Herrero J, Aparicio F, González-Rodríguez D. A Modular and Convergent Synthetic Route to Supramolecular Cyclic Dimers Based on Amidinium-Carboxylate Interactions. Chemistry 2023; 29:e202302279. [PMID: 37800622 DOI: 10.1002/chem.202302279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Indexed: 10/07/2023]
Abstract
We describe herein the optimized design and modular synthetic approach towards supramolecularly programmed monomers that can form discrete macrocyclic species of controllable size and shape through amidinium-carboxylate interactions in apolar and polar media.
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Affiliation(s)
- Isabel López-Martín
- Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Science Faculty, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Jacobo Veiga-Herrero
- Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Science Faculty, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Fátima Aparicio
- Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Science Faculty, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - David González-Rodríguez
- Nanostructured Molecular Systems and Materials Group, Organic Chemistry Department, Science Faculty, Universidad Autónoma de Madrid, 28049, Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049, Madrid, Spain
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15
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Allam T, Balderston DE, Chahal MK, Hilton KLF, Hind CK, Keers OB, Lilley RJ, Manwani C, Overton A, Popoola PIA, Thompson LR, White LJ, Hiscock JR. Tools to enable the study and translation of supramolecular amphiphiles. Chem Soc Rev 2023; 52:6892-6917. [PMID: 37753825 DOI: 10.1039/d3cs00480e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
This tutorial review focuses on providing a summary of the key techniques used for the characterisation of supramolecular amphiphiles and their self-assembled aggregates; from the understanding of low-level molecular interactions, to materials analysis, use of data to support computer-aided molecular design and finally, the translation of this class of compounds for real world application, specifically within the clinical setting. We highlight the common methodologies used for the study of traditional amphiphiles and build to provide specific examples that enable the study of specialist supramolecular systems. This includes the use of nuclear magnetic resonance spectroscopy, mass spectrometry, X-ray scattering techniques (small- and wide-angle X-ray scattering and single crystal X-ray diffraction), critical aggregation (or micelle) concentration determination methodologies, machine learning, and various microscopy techniques. Furthermore, this review provides guidance for working with supramolecular amphiphiles in in vitro and in vivo settings, as well as the use of accessible software programs, to facilitate screening and selection of druggable molecules. Each section provides: a methodology overview - information that may be derived from the use of the methodology described; a case study - examples for the application of these methodologies; and a summary section - providing methodology specific benefits, limitations and future applications.
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Affiliation(s)
- Thomas Allam
- School of Chemistry, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Dominick E Balderston
- School of Chemistry and Forensic Science, University of Kent, Canterbury, CT2 7NH, UK.
| | - Mandeep K Chahal
- School of Chemistry and Forensic Science, University of Kent, Canterbury, CT2 7NH, UK.
| | - Kira L F Hilton
- School of Chemistry and Forensic Science, University of Kent, Canterbury, CT2 7NH, UK.
| | - Charlotte K Hind
- Research and Evaluation, UKHSA, Porton Down, Salisbury SP4 0JG, UK
| | - Olivia B Keers
- School of Chemistry and Forensic Science, University of Kent, Canterbury, CT2 7NH, UK.
| | - Rebecca J Lilley
- School of Chemistry and Forensic Science, University of Kent, Canterbury, CT2 7NH, UK.
| | - Chandni Manwani
- School of Chemistry and Forensic Science, University of Kent, Canterbury, CT2 7NH, UK.
| | - Alix Overton
- School of Chemistry and Forensic Science, University of Kent, Canterbury, CT2 7NH, UK.
| | - Precious I A Popoola
- School of Chemistry and Forensic Science, University of Kent, Canterbury, CT2 7NH, UK.
| | - Lisa R Thompson
- School of Chemistry and Forensic Science, University of Kent, Canterbury, CT2 7NH, UK.
| | - Lisa J White
- School of Chemistry and Forensic Science, University of Kent, Canterbury, CT2 7NH, UK.
| | - Jennifer R Hiscock
- School of Chemistry and Forensic Science, University of Kent, Canterbury, CT2 7NH, UK.
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16
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Rezaie F, Noorizadeh S. Theoretical investigation of tube-like supramolecular structures formed through bifurcated lithium bonds. Sci Rep 2023; 13:15260. [PMID: 37709798 PMCID: PMC10502010 DOI: 10.1038/s41598-023-41979-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023] Open
Abstract
The stability of three supramolecular naostructures, which are formed through the aggregation of identical belts of [12] arene containing p-nitrophenyllithium, 1,4-dilithiatedbenzene and 1,4-dinitrobenzene units, is investigated by density functional theory. The electrostatic potential calculations indicate the ability of these belts in forming bifurcated lithium bonds (BLBs) between the Li atoms of one belt and the oxygen atoms of the NO2 groups in the other belt, which is also confirmed by deformation density maps and quantum theory of atoms in molecules (QTAIM) analysis. Topological analysis and natural bond analysis (NBO) imply to ionic character for these BLBs with binding energies up to approximately - 60 kcal mol-1. The many-body interaction energy analysis shows the strong cooperativity belongs to the configuration with the highest symmetry (C4v) containing p-nitrophenyllithium fragments as the building unit. Therefore, it seems that this configuration could be a good candidate for designing a BLB-based supramolecular nanotube with infinite size in this study.
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Affiliation(s)
- Forough Rezaie
- Chemistry Department, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Siamak Noorizadeh
- Chemistry Department, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
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17
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Yu Y, O'Neill RT, Boulatov R, Widenhoefer RA, Craig SL. Allosteric control of olefin isomerization kinetics via remote metal binding and its mechanochemical analysis. Nat Commun 2023; 14:5074. [PMID: 37604905 PMCID: PMC10442431 DOI: 10.1038/s41467-023-40842-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 08/14/2023] [Indexed: 08/23/2023] Open
Abstract
Allosteric control of reaction thermodynamics is well understood, but the mechanisms by which changes in local geometries of receptor sites lower activation reaction barriers in electronically uncoupled, remote reaction moieties remain relatively unexplored. Here we report a molecular scaffold in which the rate of thermal E-to-Z isomerization of an alkene increases by a factor of as much as 104 in response to fast binding of a metal ion to a remote receptor site. A mechanochemical model of the olefin coupled to a compressive harmonic spring reproduces the observed acceleration quantitatively, adding the studied isomerization to the very few reactions demonstrated to be sensitive to extrinsic compressive force. The work validates experimentally the generalization of mechanochemical kinetics to compressive loads and demonstrates that the formalism of force-coupled reactivity offers a productive framework for the quantitative analysis of the molecular basis of allosteric control of reaction kinetics. Important differences in the effects of compressive vs. tensile force on the kinetic stabilities of molecules are discussed.
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Affiliation(s)
- Yichen Yu
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
| | - Robert T O'Neill
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK
| | - Roman Boulatov
- Department of Chemistry, University of Liverpool, Crown Street, Liverpool, L69 7ZD, UK.
| | | | - Stephen L Craig
- Department of Chemistry, Duke University, Durham, NC, 27708, USA.
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18
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Yin Q, Zhao D, Chang Y, Liu B, Liu Y, Liu M. Functional DNA Superstructures Exhibit Positive Homotropic Allostery in Ligand Binding. Angew Chem Int Ed Engl 2023; 62:e202303838. [PMID: 37071541 DOI: 10.1002/anie.202303838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/18/2023] [Indexed: 04/19/2023]
Abstract
Inspired by intrinsically disordered proteins in nature, DNA aptamers can be engineered to display strongly homotropic allosteric (or cooperative) ligand binding, representing a unique feature that could be of great utility in applications such as biosensing, imaging and drug delivery. The use of an intrinsic disorder mechanism, however, comes with an inherent drawback of significantly reduced overall binding affinity. We hypothesize that it could be addressed via the design of multivalent supramolecular aptamers. We built functional DNA superstructures (denoted as 3D DNA), made of long-chain DNA containing tandem repeating DNA aptamers (or concatemeric aptamers). The 3D DNA systems exhibit highly cooperative binding to both small molecules and proteins, without loss of binding affinities of their parent aptamers. We further produced a highly responsive sensor for fluorescence imaging of glutamate stimulation-evoked adenosine triphosphate (ATP) release in neurons, as well as force stimulus-triggered ATP release in astrocytes.
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Affiliation(s)
- Qingxin Yin
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory, Dalian, 116024, China
| | - Dan Zhao
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory, Dalian, 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory, Dalian, 116024, China
| | - Bo Liu
- School of Biomedical Engineering, Dalian University of Technology, Dalian, 116024, China
| | - Yi Liu
- Department of Neurology, Dalian Municipal Central Hospital Affiliated Hospital of Dalian Medical University, Dalian, 116033, China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory, Dalian, 116024, China
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19
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Lutolli A, Che M, Parks FC, Raghavachari K, Flood AH. Cooperativity in Photofoldamer Chloride Double Helices Turned On with Sequences and Solvents, Around with Guests, and Off with Light. J Org Chem 2023. [PMID: 37130263 DOI: 10.1021/acs.joc.3c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Photofoldamers are sequence-defined receptors capable of switching guest binding on and off. When two foldamer strands wrap around the guest into 2:1 double helical complexes, cooperativity emerges, and with it comes the possibility to switch cooperativity with light and other stimuli. We use lessons from nonswitchable sequence isomers of aryl-triazole foldamers to guide how to vary the sequence location of azobenzenes from the end (FEND) to the interior (FIN) and report their impact on the cooperative formation of 2:1 complexes with Cl-. This sequence change produces a 125-fold increase from anti-cooperative (α = 0.008) for FEND to non-cooperative with FIN (α = 1.0). Density functional theory (DFT) studies show greater H-bonding and a more relaxed double helix for FIN. The solvent and guest complement the synthetic designs. Use of acetonitrile to enhance solvophobicity further enhances cooperativity in FIN (α = 126) but lowers the difference in cooperativity between sequences. Surprisingly, the impact of the sequence on cooperativity is inverted when the guest size is increased from Cl- (3.4 Å) to BF4- (4.1 Å). While photoconversion of interior azobenzenes was poor, the cis-cis isomer forms 1:1 complexes around chloride consistent with switching cooperativity. The effect of the guest, solvent, and light on the double-helix cooperativity depends on the sequence.
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Affiliation(s)
- Alketa Lutolli
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Minwei Che
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Fred C Parks
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Amar H Flood
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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20
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Gou F, Shi D, Kou B, Li Z, Yan X, Wu X, Jiang YB. One-Pot Cyclization to Large Peptidomimetic Macrocycles by In Situ-Generated β-Turn-Enforced Folding. J Am Chem Soc 2023; 145:9530-9539. [PMID: 37037798 DOI: 10.1021/jacs.2c11684] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Macrocycles have been targets of extensive synthetic efforts for decades because of their potent molecular recognition and self-assembly capabilities. Yet, efficient syntheses of macrocyclic molecules via irreversible covalent bonds remain challenging. Here, we report an efficient approach to large peptidomimetic macrocycles by using the in situ-generated β-turn structural motifs afforded in the amidothiourea moieties from the early steps of the reaction of 2 molecules of bilateral amino acid-based acylhydrazine with 2 molecules of diisothiocyanate. Four chiral and achiral peptidomimetic large macrocycles were successfully synthesized in high yields of 45-63% in a feasible one-pot reaction under sub-molar concentration conditions and were purified by simple filtration. X-ray crystallographic characterization of three macrocycles reveals an important feature that their four β-turn structures, each maintained by four 10-membered intramolecular hydrogen bonds, alternatively network the four aromatic arms. This affords an interesting conformation switching mode upon anion binding. Binding of SO42- to 1L or 1D that contains 4 alanine residues (with the lowest steric hinderance among the macrocycles) leads to an inside-out structural change of the host macrocycle, as confirmed by the X-ray crystal structure of 1L-SO42- and 1D-SO42- complexes, accompanied by an inversion of the CD signals. On the basis of the strong sulfate affinity of the macrocycles, we succeeded in the removal of sulfate anions from water via a macrocycle-mediated liquid-liquid extraction method. Our synthetic protocol can be easily extended to other macrocycles of varying arms and/or chiral amino acid residues; thus, a variety of structurally and functionally diverse macrocycles are expected to be readily made.
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Affiliation(s)
- Fei Gou
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
| | - Di Shi
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
| | - Bohan Kou
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
| | - Zhao Li
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
| | - Xiaosheng Yan
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Xin Wu
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yun-Bao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Xiamen University, Xiamen 361005, China
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21
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Szczȩśniak MM, Chałasiński G. Three-body interaction effects in heterolytic hydrogen splitting by frustrated Lewis pairs. Phys Chem Chem Phys 2023; 25:9599-9606. [PMID: 36942673 DOI: 10.1039/d3cp00617d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The reaction of heterolytic dihydrogen splitting by frustrated Lewis pairs P(R)3 and B(C6F5)3 (where R = t-butyl and 1-adamantene) is driven by strong three-body contributions which originate from the induction and charge transfer effects. The three-body effect increases dramatically as a function of inter-hydrogen distance. As predicted by the symmetry adapted perturbation theory, the "frustration" of Lewis pairs originates from the dual role of the exchange effects. First, the exchange manifests itself in the first-order Pauli repulsion by keeping the pairs away. Second, and equally important, the second-order exchange-induction almost completely cancels the effects of the second-order induction. This suppression of induction effects eases up upon the interaction of the frustrated pairs with H2. The activation of induction in this instance constitutes the three-body effect.
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22
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Twum K, Nadimi S, Osei FB, Puttreddy R, Ojong YB, Hayward JJ, Rissanen K, Trant JF, Beyeh NK. The "Nitrogen Effect": Complexation with Macrocycles Potentiates Fused Heterocycles to Form Halogen Bonds in Competitive Solvents. Chem Asian J 2023; 18:e202201308. [PMID: 36705487 DOI: 10.1002/asia.202201308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/26/2023] [Accepted: 01/27/2023] [Indexed: 01/28/2023]
Abstract
Weak intermolecular forces are typically very difficult to observe in highly competitive polar protic solvents as they are overwhelmed by the quantity of competing solvent. This is even more challenging for three-component ternary assemblies of pure organic compounds. In this work, we overcome these complications by leveraging the binding of fused aromatic N-heterocycles in an open resorcinarene cavity to template the formation of a three-component halogen-bonded ternary assembly in a protic polar solvent system.
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Affiliation(s)
- Kwaku Twum
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309, USA
| | - Sanaz Nadimi
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Frank Boateng Osei
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309, USA
| | - Rakesh Puttreddy
- Department of Chemistry, University of Jyvaskyla, Survontie 9 B, FI-40014, Jyvaskyla, Finland
| | - Yvonne Bessem Ojong
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309, USA
| | - John J Hayward
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Kari Rissanen
- Department of Chemistry, University of Jyvaskyla, Survontie 9 B, FI-40014, Jyvaskyla, Finland
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Ngong Kodiah Beyeh
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan, 48309, USA
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23
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Tang M, Zhong Z, Ke C. Advanced supramolecular design for direct ink writing of soft materials. Chem Soc Rev 2023; 52:1614-1649. [PMID: 36779285 DOI: 10.1039/d2cs01011a] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
The exciting advancements in 3D-printing of soft materials are changing the landscape of materials development and fabrication. Among various 3D-printers that are designed for soft materials fabrication, the direct ink writing (DIW) system is particularly attractive for chemists and materials scientists due to the mild fabrication conditions, compatibility with a wide range of organic and inorganic materials, and the ease of multi-materials 3D-printing. Inks for DIW need to possess suitable viscoelastic properties to allow for smooth extrusion and be self-supportive after printing, but molecularly facilitating 3D printability to functional materials remains nontrivial. While supramolecular binding motifs have been increasingly used for 3D-printing, these inks are largely optimized empirically for DIW. Hence, this review aims to establish a clear connection between the molecular understanding of the supramolecularly bound motifs and their viscoelastic properties at bulk. Herein, extrudable (but not self-supportive) and 3D-printable (self-supportive) polymeric materials that utilize noncovalent interactions, including hydrogen bonding, host-guest inclusion, metal-ligand coordination, micro-crystallization, and van der Waals interaction, have been discussed in detail. In particular, the rheological distinctions between extrudable and 3D-printable inks have been discussed from a supramolecular design perspective. Examples shown in this review also highlight the exciting macroscale functions amplified from the molecular design. Challenges associated with the hierarchical control and characterization of supramolecularly designed DIW inks are also outlined. The perspective of utilizing supramolecular binding motifs in soft materials DIW printing has been discussed. This review serves to connect researchers across disciplines to develop innovative solutions that connect top-down 3D-printing and bottom-up supramolecular design to accelerate the development of 3D-print soft materials for a sustainable future.
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Affiliation(s)
- Miao Tang
- Department of Chemistry, Dartmouth College, 41 College Street, Hanover, 03755 NH, USA.
| | - Zhuoran Zhong
- Department of Chemistry, Dartmouth College, 41 College Street, Hanover, 03755 NH, USA.
| | - Chenfeng Ke
- Department of Chemistry, Dartmouth College, 41 College Street, Hanover, 03755 NH, USA.
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24
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Lisi D, Vezzoni CA, Casnati A, Sansone F, Salvio R. Intra- and Intermolecular Cooperativity in the Catalytic Activity of Phosphodiester Cleavage by Self-Assembled Systems Based on Guanidinylated Calix[4]arenes. Chemistry 2023; 29:e202203213. [PMID: 36382737 DOI: 10.1002/chem.202203213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022]
Abstract
The calix[4]arene scaffold, blocked in the cone conformation through alkylation with long alkyl chains, and decorated at the upper rim with four guanidine or arginine units, effectively catalyzes the cleavage of the phosphodiester bond of DNA and RNA model compounds in water. An exhaustive kinetic investigation unequivocally points to the existence of spontaneous aggregation phenomena, driven by hydrophobic effect, occurring at different critical concentrations that depend on the identity of the compound. A pronounced superiority of the assembled structures compared with the monomers in solution was observed. Moreover, the catalytically active units, clustered on the macrocyclic tetrafunctional scaffold, were proved to efficiently cooperate in the catalytic mechanism and result in improved reaction rates compared to those of the monofunctional model compounds. The kinetic analysis is also integrated and corroborated with further experiments based on fluorescence spectroscopy and light scattering. The advantage of the supramolecular assemblies based on tetrafunctional calixarenes leads to believe that the active units can cooperate not only intramolecularly but also intermolecularly. The molecules in the aggregates can probably mold, flex and rearrange but, at the same time, keep an ordered structure that favors phosphodiester bond cleavage. This dynamic preorganization can allow the catalytic units to reach a better fitting with the substrates and perform a superior catalytic activity.
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Affiliation(s)
- Daniele Lisi
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Roma, Italy
| | - Carlo Alberto Vezzoni
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze, 17/A, 43124, Parma, Italy
| | - Alessandro Casnati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze, 17/A, 43124, Parma, Italy
| | - Francesco Sansone
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze, 17/A, 43124, Parma, Italy
| | - Riccardo Salvio
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Roma, Italy.,ISB - CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185, Roma, Italy
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25
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Deiana M, Chand K, Chorell E, Sabouri N. Parallel G-Quadruplex DNA Structures from Nuclear and Mitochondrial Genomes Trigger Emission Enhancement in a Nonfluorescent Nano-aggregated Fluorine-Boron-Based Dye. J Phys Chem Lett 2023; 14:1862-1869. [PMID: 36779779 PMCID: PMC9940295 DOI: 10.1021/acs.jpclett.2c03301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/02/2023] [Indexed: 05/28/2023]
Abstract
Molecular self-assembly is a powerful tool for the development of functional nanostructures with adaptive optical properties. However, in aqueous solution, the hydrophobic effects in the monomeric units often afford supramolecular architectures with typical side-by-side π-stacking arrangement with compromised emissive properties. Here, we report on the role of parallel DNA guanine quadruplexes (G4s) as supramolecular disaggregating-capture systems capable of coordinating a zwitterionic fluorine-boron-based dye and promoting activation of its fluorescence signal. The dye's high binding affinity for parallel G4s compared to nonparallel topologies leads to a selective disassembly of the dye's supramolecular state upon contact with parallel G4s. This results in a strong and selective disaggregation-induced emission that signals the presence of parallel G4s observable by the naked eye and inside cells. The molecular recognition strategy reported here will be useful for a multitude of affinity-based applications with potential in sensing and imaging systems.
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Affiliation(s)
- Marco Deiana
- Department
of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Karam Chand
- Department
of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Erik Chorell
- Department
of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Nasim Sabouri
- Department
of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
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26
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Sobiech TA, Zhong Y, Miller DP, McGrath JK, Scalzo CT, Redington MC, Zurek E, Gong B. Ultra-Tight Host-Guest Binding with Exceptionally Strong Positive Cooperativity. Angew Chem Int Ed Engl 2022; 61:e202213467. [PMID: 36259360 DOI: 10.1002/anie.202213467] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Indexed: 11/16/2022]
Abstract
Cooperativity plays a critical role in self-assembly and molecular recognition. A rigid aromatic oligoamide macrocycle with a cyclodirectional backbone binds with DABCO-based cationic guests in a 2 : 1 ratio in high affinities (Ktotal ≈1013 M-2 ) in the highly polar DMF. The host-guest binding also exhibits exceptionally strong positive cooperativity quantified by interaction factors α that are among the largest for synthetic host-guest systems. The unusually strong positive cooperativity, revealed by isothermal titration calorimetry (ITC) and fully corroborated by mass spectrometry, NMR and computational studies, is driven by guest-induced stacking of the macrocycles and stabilization from the alkyl end chains of the guests, interactions that appear upon binding the second macrocycle. With its tight binding driven by extraordinary positive cooperativity, this host-guest system provides a tunable platform for studying molecular interactions and for constructing stable supramolecular assemblies.
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Affiliation(s)
- Thomas A Sobiech
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Yulong Zhong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Daniel P Miller
- Department of Chemistry, Hofstra University, Hempstead, NY 11549, USA
| | - Jillian K McGrath
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Christina T Scalzo
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Morgan C Redington
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Eva Zurek
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
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27
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Hübler C. Analysing binding stoichiometries in NMR titration experiments using Monte Carlo simulation and resampling techniques. PEERJ ANALYTICAL CHEMISTRY 2022. [DOI: 10.7717/peerj-achem.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The application of Monte Carlo simulation and resampling techniques to analyse possible binding stoichiometries in NMR titration experiments is presented. Four simulated NMR titration experiments having complex species with 1:1, 2:1 and 1:2 stoichiometries were each analysed using a 1:1, 2:1/1:1, 1:1/1:2 and a 2:1/1:1/1:2 model as implemented in SupraFit. Each best-fit model was inspected using Monte Carlo simulation (MC), Cross Validation (CV) and a new protocol termed Reduction Analysis (RA). The results of the statistical post-processes were used to calculate characteristic descriptors that are the base of the judgment for both, the models and individual stability constants. The results indicate promising approaches to correctly identify 1:1, 2:1/1:1 and 1:1/1:2 models, however with some limitations in case of the 2:1/1:1/1:2 model. All simulations and post-processing protocols were performed with the newly presented SupraFit.
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Affiliation(s)
- Conrad Hübler
- Institut für Organische Chemie, Technische Universität Bergakademie Freiberg, Freiberg, Saxony, Germany
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28
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Kundu S, Mondal D, Elramadi E, Valiyev I, Schmittel M. Parallel Allosteric Inhibition of Shuttling Motion and Catalysis in a Silver(I)-loaded [2]Rotaxane. Org Lett 2022; 24:6609-6613. [PMID: 36053156 DOI: 10.1021/acs.orglett.2c02609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A dynamic silver(I)-loaded [2]rotaxane shuttle (k298 = 135 kHz) was converted allosterically into a conformationally restricted [2]rotaxane due to the creation of a bulky imine in the center of the axle component. Only the dynamic silver(I)-loaded [2]rotaxane was able to catalyze a 6-endo-cyclization reaction, whereas the static one was catalytically quiet. The mechanism of catalyst deactivation was elucidated.
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Affiliation(s)
- Sohom Kundu
- Center of Micro- and Nanochemistry and (Bio)Technology, Universität Siegen, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Debabrata Mondal
- Center of Micro- and Nanochemistry and (Bio)Technology, Universität Siegen, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Emad Elramadi
- Center of Micro- and Nanochemistry and (Bio)Technology, Universität Siegen, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Isa Valiyev
- Center of Micro- and Nanochemistry and (Bio)Technology, Universität Siegen, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Michael Schmittel
- Center of Micro- and Nanochemistry and (Bio)Technology, Universität Siegen, Organische Chemie I, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
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29
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Suzuki S, Homma A, Nishi R, Mizuno H, Kawauchi S, Fukuhara G. A Dynamically Responsive Chemosensor That Can be Modulated by an Effector: Amplification Sensing by Positive Heterotropic Allosterism. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2022. [DOI: 10.1246/bcsj.20220088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sho Suzuki
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Amane Homma
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Reiya Nishi
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hiroaki Mizuno
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Susumu Kawauchi
- Tokyo Tech Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6-23, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Gaku Fukuhara
- Department of Chemistry, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8551, Japan
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30
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Miyake R. Cooperative systems constructed using crystalline metal complexes of short flexible peptides. J INCL PHENOM MACRO 2022. [DOI: 10.1007/s10847-022-01145-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Tuning the viscoelastic response of hydrogel scaffolds with covalent and dynamic bonds. J Mech Behav Biomed Mater 2022; 130:105179. [DOI: 10.1016/j.jmbbm.2022.105179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/09/2021] [Accepted: 03/12/2022] [Indexed: 02/07/2023]
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32
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Larsen ES, Ahumada G, Sultane PR, Bielawski CW. Stereoelectronically-induced allosteric binding: shape complementarity promotes positive cooperativity in fullerene/buckybowl complexes. Chem Commun (Camb) 2022; 58:6498-6501. [PMID: 35575168 DOI: 10.1039/d2cc01908f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel 2 : 1 host-guest complex forms between 8-tert-butyl-6b2-azapenta-benzo[bc,ef,hi,kl,no]corannulene (1) and C60 with positive cooperativity (α = 2.56) and high affinity (K1 × K2 = 2.8 × 106 M-2) at 25 °C. The C60 undergoes increasing shape complementarity toward 1 throughout the binding process.
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Affiliation(s)
- Eric S Larsen
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea. .,Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Guillermo Ahumada
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
| | - Prakash R Sultane
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea.
| | - Christopher W Bielawski
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea. .,Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
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33
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Kubik S. When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water. Chemistry 2022; 11:e202200028. [PMID: 35373466 PMCID: PMC8977507 DOI: 10.1002/open.202200028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/17/2022] [Indexed: 12/19/2022]
Abstract
Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water‐mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor‐substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.
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Affiliation(s)
- Stefan Kubik
- Technische Universität Kaiserslautern, Fachbereich Chemie - Organische Chemie, Erwin-Schrödinger-Straße 54, 67663, Kaiserslautern, Germany
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34
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35
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Encapsulation within a coordination cage modulates the reactivity of redox-active dyes. Commun Chem 2022; 5:44. [PMID: 36697669 PMCID: PMC9814915 DOI: 10.1038/s42004-022-00658-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 02/18/2022] [Indexed: 02/08/2023] Open
Abstract
Confining molecules within well-defined nanosized spaces can profoundly alter their physicochemical characteristics. For example, the controlled aggregation of chromophores into discrete oligomers has been shown to tune their optical properties whereas encapsulation of reactive species within molecular hosts can increase their stability. The resazurin/resorufin pair has been widely used for detecting redox processes in biological settings; yet, how tight confinement affects the properties of these two dyes remains to be explored. Here, we show that a flexible PdII6L4 coordination cage can efficiently encapsulate both resorufin and resazurin in the form of dimers, dramatically modulating their optical properties. Furthermore, binding within the cage significantly decreases the reduction rate of resazurin to resorufin, and the rate of the subsequent reduction of resorufin to dihydroresorufin. During our studies, we also found that upon dilution, the PdII6L4 cage disassembles to afford PdII2L2 species, which lacks the ability to form inclusion complexes - a process that can be reversed upon the addition of the strongly binding resorufin/resazurin guests. We expect that the herein disclosed ability of a water-soluble cage to reversibly modulate the optical and chemical properties of a molecular redox probe will expand the versatility of synthetic fluorescent probes in biologically relevant environments.
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36
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Serrano-Molina D, Montoro-García C, Mayoral MJ, de Juan A, González-Rodríguez D. Self-Sorting Governed by Chelate Cooperativity. J Am Chem Soc 2022; 144:5450-5460. [PMID: 35311263 PMCID: PMC8972263 DOI: 10.1021/jacs.1c13295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Self-sorting
phenomena are the basis of manifold relevant (bio)chemical
processes where a set of molecules is able to interact with no interference
from other sets and are ruled by a number of codes that are programmed
in molecular structures. In this work, we study, the relevance of
chelate cooperativity as a code for achieving high self-sorting fidelities.
In particular, we establish qualitative and quantitative relationships
between the cooperativity of a cyclic system and the self-sorting
fidelity when combined with other molecules that share identical geometry
and/or binding interactions. We demonstrate that only systems displaying
sufficiently strong chelate cooperativity can achieve quantitative
narcissistic self-sorting fidelities either by dictating the distribution
of cyclic species in complex mixtures or by ruling the competition
between the intra- and intermolecular versions of a noncovalent interaction.
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Affiliation(s)
- David Serrano-Molina
- Nanostructured Molecular Systems and Materials Group, Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Carlos Montoro-García
- Nanostructured Molecular Systems and Materials Group, Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - María J. Mayoral
- Nanostructured Molecular Systems and Materials Group, Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Alberto de Juan
- Nanostructured Molecular Systems and Materials Group, Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - David González-Rodríguez
- Nanostructured Molecular Systems and Materials Group, Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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37
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Matsuno T, Takahashi K, Ikemoto K, Isobe H. Activation of positive cooperativity by size-mismatch assembly via inclination of guests in a single-site receptor. Chem Asian J 2022; 17:e202200076. [PMID: 35156775 DOI: 10.1002/asia.202200076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/09/2022] [Indexed: 11/11/2022]
Abstract
A halogenated bowl-shaped guest, corannulene, was encapsulated in a cylindrical host, [4]cyclochrysenylene, to form a bowl-in-tube complex, which mimicked supramolecular complexes between bowl guests and carbon nanotubes. As was the case with carbon nanotubes, the cylindrical space of [4]cyclochrysenylene trapped multiple corannulene molecules in an array, and 1:2 complexes were commonly obtained with the corannulene guests with various halogen substituents (F, Cl, Br and I). Careful statistical analyses of isothermal titration calorimetry titration data succeeded in revealing the stoichiometry, and the molecular structures of the 1:2 complexes were further clarified by X-ray crystallographic analyses. Two fluorinated corannulene guests were stacked perpendicular to the cylinder axis, while two chlorinated guests were stacked with inclined orientations. The structural difference resulted in a large difference in the cooperativity of the two-stage association in solution: fluorinated corannulene guests showed negative cooperativity for the 1:2 complexation, and the other, larger halogenated corannulene guests showed positive cooperativity.
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Affiliation(s)
| | | | | | - Hiroyuki Isobe
- The University of Tokyo, Department of Chemistry, Hongo 7-3-1, 113-0033, Bunkyo-ku, JAPAN
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38
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Aristov VV, Buchelnikov AS, Nechipurenko YD. The Use of the Statistical Entropy in Some New Approaches for the Description of Biosystems. ENTROPY (BASEL, SWITZERLAND) 2022; 24:172. [PMID: 35205467 PMCID: PMC8871276 DOI: 10.3390/e24020172] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 01/13/2023]
Abstract
Some problems of describing biological systems with the use of entropy as a measure of the complexity of these systems are considered. Entropy is studied both for the organism as a whole and for its parts down to the molecular level. Correlation of actions of various parts of the whole organism, intercellular interactions and control, as well as cooperativity on the microlevel lead to a more complex structure and lower statistical entropy. For a multicellular organism, entropy is much lower than entropy for the same mass of a colony of unicellular organisms. Cooperativity always reduces the entropy of the system; a simple example of ligand binding to a macromolecule carrying two reaction centers shows how entropy is consistent with the ambiguity of the result in the Bernoulli test scheme. Particular attention is paid to the qualitative and quantitative relationship between the entropy of the system and the cooperativity of ligand binding to macromolecules. A kinetic model of metabolism. corresponding to Schrödinger's concept of the maintenance biosystems by "negentropy feeding", is proposed. This model allows calculating the nonequilibrium local entropy and comparing it with the local equilibrium entropy inherent in non-living matter.
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Affiliation(s)
- Vladimir V. Aristov
- Dorodnicyn Computing Centre, Federal Research Center “Computer Science and Control” of Russian Academy of Sciences, Vavilova Str. 40, 119333 Moscow, Russia
| | - Anatoly S. Buchelnikov
- Laboratory of Molecular and Cellular Biophysics, Sevastopol State University, Universitetskaya Str. 33, 299053 Sevastopol, Russia;
| | - Yury D. Nechipurenko
- Laboratory of DNA–Protein Recognition, Engelhardt Institute of Molecular Biology of Russian Academy of Sciences, Vavilova Str. 32, 119991 Moscow, Russia;
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39
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Niklas J, Hiti E, Wilkinson G, Mayhugh J, Gorden J, Gorden A. Steric control of mesocate and helicate formation: Bulky pyrrol-2-yl Schiff base complexes of Zn2+. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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40
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de Vink PJ, Koops AA, D'Arrigo G, Cruciani G, Spyrakis F, Brunsveld L. Cooperativity as quantification and optimization paradigm for nuclear receptor modulators. Chem Sci 2022; 13:2744-2752. [PMID: 35340861 PMCID: PMC8890100 DOI: 10.1039/d1sc06426f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 01/19/2022] [Indexed: 01/01/2023] Open
Abstract
A cooperativity framework describes the formation of nuclear receptor ternary complexes and deconvolutes ligand and cofactor binding into intrinsic affinities and a cooperativity factor, providing a conceptually new understanding of NR modulation.
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Affiliation(s)
- Pim J. de Vink
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Auke A. Koops
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Giulia D'Arrigo
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 5600MB Eindhoven, The Netherlands
- Department of Drug Science and Technology, University of Turin, via Giuria 9, 10125 Turin, Italy
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123, Perugia, Italy
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, via Giuria 9, 10125 Turin, Italy
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P. O. Box 513, 5600MB Eindhoven, The Netherlands
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41
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Liang Y, Xiang D, Hou Y, Li G, Feng S, Yang M. Size-encoded hierarchical self-assembly of nanoparticles into chains and tubules. J Colloid Interface Sci 2021; 604:866-875. [PMID: 34303886 DOI: 10.1016/j.jcis.2021.07.047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/18/2021] [Accepted: 07/12/2021] [Indexed: 11/24/2022]
Abstract
Hierarchical structures with sophisticated patterns allow the emergence of challenging properties. However, the highly cooperative and specific interactions needed for assembly spanning different length scales are typically lacking in inorganic nanoparticles (NPs). Here we show that size can be a common structural driving force for controlling hierarchical assembly of inorganic NPs into anisotropic superstructures. It involves first the self-limiting assembly of small CdS NPs into large supraparticles and their subsequent spontaneous organization into chains and tubules hundreds of nanometers long. Our quantitative calculations based on DLVO theory reveals an intrinsic size effect relating to the dimension change of assembly units in accordance with a negative cooperativity. It is shown that the size increase in building blocks creates an effective kinetic barrier contrast at different attachment sites due to the increase of interparticle electrostatic repulsion, switching the assembly from thermodynamically preferred 3D to kinetically favored 1D pathway. The size-encoded hierarchical assembly is accompanied by the ligand-controlled Oswald ripening process, which is responsible for the variation of hierarchical patterns from chains to tubules. The general principle in governing multistage inorganic NP ordering represents an important guideline toward the complex mesoscale structures that may surpass traditional materials in both design and functionality.
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Affiliation(s)
- Yuting Liang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China; Key Laboratory of Microsystems and Micronanostructures Manufacturing, Harbin Institute of Technology 2 Yikuang Street, Harbin 150080, PR China
| | - Di Xiang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China; Key Laboratory of Microsystems and Micronanostructures Manufacturing, Harbin Institute of Technology 2 Yikuang Street, Harbin 150080, PR China
| | - Ying Hou
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China
| | - Guangshe Li
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
| | - Shouhua Feng
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
| | - Ming Yang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun 130012, PR China.
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42
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Lacham-Hartman S, Shmidov Y, Radisky ES, Bitton R, Lukatsky DB, Papo N. Avidity observed between a bivalent inhibitor and an enzyme monomer with a single active site. PLoS One 2021; 16:e0249616. [PMID: 34847142 PMCID: PMC8631645 DOI: 10.1371/journal.pone.0249616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 11/13/2021] [Indexed: 12/16/2022] Open
Abstract
Although myriad protein–protein interactions in nature use polyvalent binding, in which multiple ligands on one entity bind to multiple receptors on another, to date an affinity advantage of polyvalent binding has been demonstrated experimentally only in cases where the target receptor molecules are clustered prior to complex formation. Here, we demonstrate cooperativity in binding affinity (i.e., avidity) for a protein complex in which an engineered dimer of the amyloid precursor protein inhibitor (APPI), possessing two fully functional inhibitory loops, interacts with mesotrypsin, a soluble monomeric protein that does not self-associate or cluster spontaneously. We found that each inhibitory loop of the purified APPI homodimer was over three-fold more potent than the corresponding loop in the monovalent APPI inhibitor. This observation is consistent with a suggested mechanism whereby the two APPI loops in the homodimer simultaneously and reversibly bind two corresponding mesotrypsin monomers to mediate mesotrypsin dimerization. We propose a simple model for such dimerization that quantitatively explains the observed cooperativity in binding affinity. Binding cooperativity in this system reveals that the valency of ligands may affect avidity in protein–protein interactions including those of targets that are not surface-anchored and do not self-associate spontaneously. In this scenario, avidity may be explained by the enhanced concentration of ligand binding sites in proximity to the monomeric target, which may favor rebinding of the multiple ligand binding sites with the receptor molecules upon dissociation of the protein complex.
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Affiliation(s)
- Shiran Lacham-Hartman
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yulia Shmidov
- Deprtment of Chemical Engineering and the Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Evette S. Radisky
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America
| | - Ronit Bitton
- Deprtment of Chemical Engineering and the Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - David B. Lukatsky
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail: (NP); (DBL)
| | - Niv Papo
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail: (NP); (DBL)
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43
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Chen X, Mao H, Feng Y, Cai K, Shen D, Wu H, Zhang L, Zhao X, Chen H, Song B, Jiao Y, Wu Y, Stern CL, Wasielewski MR, Stoddart JF. Radically Enhanced Dual Recognition. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiao‐Yang Chen
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Haochuan Mao
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
- Institute for Sustainability and Energy at Northwestern Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Yuanning Feng
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Kang Cai
- Department of Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 China
| | - Dengke Shen
- Institutes of Physical Science and Information Technology Anhui University Hefei 230601 China
| | - Huang Wu
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Long Zhang
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Xingang Zhao
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Hongliang Chen
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Bo Song
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Yang Jiao
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Yong Wu
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Charlotte L. Stern
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Michael R. Wasielewski
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
- Institute for Sustainability and Energy at Northwestern Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - J. Fraser Stoddart
- Department of Chemistry Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
- School of Chemistry University of New South Wales Sydney NSW 2052 Australia
- Stoddart Institute of Molecular Science Department of Chemistry Zhejiang University Hangzhou 310027 China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center Hangzhou 311215 China
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44
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McNaughton DA, Macreadie LK, Gale PA. Acridinone-based anion transporters. Org Biomol Chem 2021; 19:9659-9674. [PMID: 34515286 DOI: 10.1039/d1ob01545a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The arrangement of hydrogen bond donors around a central lipophilic scaffold has proven to be a successful strategy in the development of potent chloride transporters. In this work, we revisit an acridinone 1,9-bis(thio)urea motif which had previously shown promise as an anion sensor and expand the series of compounds by appending a variety of electron-withdrawing groups to the peripheral phenyl moieties. High levels of activity were achieved by the most effective compounds in the series, which facilitated strictly electroneutral transport.
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Affiliation(s)
| | - Lauren K Macreadie
- School of Chemistry (F11), The University of Sydney, NSW 2006, Australia.
| | - Philip A Gale
- School of Chemistry (F11), The University of Sydney, NSW 2006, Australia. .,The University of Sydney Nano Institute (SydneyNano), The University of Sydney, NSW 2006, Australia
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45
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Utilizing an Amino Acid Scaffold to Construct Heteroditopic Receptors Capable of Interacting with Salts under Interfacial Conditions. Int J Mol Sci 2021; 22:ijms221910754. [PMID: 34639095 PMCID: PMC8509731 DOI: 10.3390/ijms221910754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 11/17/2022] Open
Abstract
A 4-nitro-L-phenylalanine scaffold was used to construct effective ion pair receptors capable of binding anions in an enhanced manner with the assistance of alkali metal cations. A benzocrown ether was linked to a receptor platform via the amide function so as to support the squaramide function in anion binding and to allow all three NHs to act simultaneously. The binding properties of the receptors were determined using UV-vis, 1H NMR, 2D NMR, and DOSY spectroscopy in MeCN and in the solid state by X-ray measurements. Ion pair receptor 2 was found to interact with the most strongly with salts, and the removal of its key structural elements was shown to hinder the receptor action. The amide proton was recognized to switch from having involvement in an intramolecular hydrogen bond to interacting with anions upon complexation. Apart from carboxylates, which promote deprotonation, and other monovalent salts creating 1:1 complexes with the receptor, more complex equilibria were established upon the complexation of 2 with sulfates. Receptor 2 was shown to be capable of the extraction of ion pairs from the aqueous to organic phase and of the cation-enhanced transport chloride and sulfate anions across a bulk chloroform membrane. These features may open the door for its use in regulating ion concertation under interfacial conditions and acting as a potential drug to treat channelopathies.
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46
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Matsumura K, Tateno K, Tsuchido Y, Kawai H. Spacer-Dependent Cooperativity of Helicity in Fluorescent Bishelical Foldamers Based on L-Shaped Dibenzopyrrolo[1,2-a][1,8]naphthyridine. Chempluschem 2021; 86:1421-1425. [PMID: 34636489 DOI: 10.1002/cplu.202100407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 09/21/2021] [Indexed: 12/21/2022]
Abstract
For the construction of helical foldamers composed of π-frameworks, the choice of appropriate π-π stacking units and π-spacers connecting them is important. The transfer of helicity between the minimal helix structural units is also an essential factor in the construction of homochiral helical foldamers. Tetramers 4 a-4 d, which have four L-shaped dibenzopyrrolo[1,2-a]naphthyridine units, were synthesized to investigate the interplay and cooperativity of the helical structures. Tetramer 4 a bridged with a biphenyl unit formed a homochiral bishelical structure with π-π stacking between the L-shaped units (3.3 Å), consisting only of (P,P)- and (M,M)-enantiomers without the (P,M)-diastereomer, owing to interplay through the axial chirality of biphenyl unit in the solid state. Similarly, in solution, thermodynamic stabilization of the two helix formations worked cooperatively to favor the bishelical form of 4 a. Furthermore, bishelical foldamer 4 a emitted intense fluorescence (Φ=0.86).
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Affiliation(s)
- Kotaro Matsumura
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Kotaro Tateno
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Yoshitaka Tsuchido
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
| | - Hidetoshi Kawai
- Department of Chemistry, Faculty of Science, Tokyo University of Science, 1-3 Kagurazaka, Shinjuku-ku, Tokyo, 162-8601, Japan
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47
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Ghosh A, Paul I, Schmittel M. Cooperative Effects in Switchable Catalysis: Enhancing Double-Click Reaction Yield of Symmetrical Rotaxanes. Angew Chem Int Ed Engl 2021; 60:20558-20562. [PMID: 34289211 PMCID: PMC8457069 DOI: 10.1002/anie.202108269] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 01/30/2023]
Abstract
Reversible switching between the closed cyclic dimeric assembly [Cu2 (1)2 ]2+ (OFF state) and the extended dimeric homoleptic complex [FeCu2 (1)2 ]4+ (ON State) by addition/removal of Fe2+ triggered catalysis of a double-click reaction and high yield preparation of [2]rotaxanes. Mechanistic and computational studies provide valuable general insight for double-click strategies by revealing cooperative effects in the second cycloaddition step due to a distance-tolerant preorganization of the first-click product by the two copper(I)-loaded phenanthroline subunits of [FeCu2 (1)2 ]4+ .
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Affiliation(s)
- Amit Ghosh
- Center of Micro and Nanochemistry and EngineeringOrganische Chemie IUniversity of SiegenAdolf-Reichwein Strasse 257068SiegenGermany
| | - Indrajit Paul
- Center of Micro and Nanochemistry and EngineeringOrganische Chemie IUniversity of SiegenAdolf-Reichwein Strasse 257068SiegenGermany
| | - Michael Schmittel
- Center of Micro and Nanochemistry and EngineeringOrganische Chemie IUniversity of SiegenAdolf-Reichwein Strasse 257068SiegenGermany
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48
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Ghosh A, Paul I, Schmittel M. Kooperative Effekte in schaltbarer Katalyse: Verbesserung der Doppel‐Click‐Reaktionsausbeuten von symmetrischen Rotaxanen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Amit Ghosh
- Center of Micro and Nanochemistry and Engineering Organische Chemie I University of Siegen Adolf-Reichwein Straße 2 57068 Siegen Deutschland
| | - Indrajit Paul
- Center of Micro and Nanochemistry and Engineering Organische Chemie I University of Siegen Adolf-Reichwein Straße 2 57068 Siegen Deutschland
| | - Michael Schmittel
- Center of Micro and Nanochemistry and Engineering Organische Chemie I University of Siegen Adolf-Reichwein Straße 2 57068 Siegen Deutschland
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49
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Deiana M, Mosser M, Le Bahers T, Dumont E, Dudek M, Denis-Quanquin S, Sabouri N, Andraud C, Matczyszyn K, Monnereau C, Guy L. Light-induced in situ chemical activation of a fluorescent probe for monitoring intracellular G-quadruplex structures. NANOSCALE 2021; 13:13795-13808. [PMID: 34477654 DOI: 10.1039/d1nr02855c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Light-activated functional materials capable of remote control over duplex and G-quadruplex (G4) nucleic acids formation at the cellular level are still very rare. Herein, we report on the photoinduced macrocyclisation of a helicenoid quinoline derivative of binaphthol that selectively provides easy access to an unprecedented class of extended heteroaromatic structures with remarkable photophysical and DNA/RNA binding properties. Thus, while the native bisquinoline precursor shows no DNA binding activity, the new in situ photochemically generated probe features high association constants to DNA and RNA G4s. The latter inhibits DNA synthesis by selectively stabilizing G4 structures associated with oncogenic promoters and telomere repeat units. Finally, the light sensitive compound is capable of in cellulo photoconversion, localizes primarily in the G4-rich sites of cancer cells, competes with a well-known G4 binder and shows a clear nuclear co-localization with the quadruplex specific antibody BG4. This work provides a benchmark for the future design and development of a brand-new generation of light-activated target-selective G4-binders.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
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50
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Deiana M, Obi I, Andreasson M, Tamilselvi S, Chand K, Chorell E, Sabouri N. A Minimalistic Coumarin Turn-On Probe for Selective Recognition of Parallel G-Quadruplex DNA Structures. ACS Chem Biol 2021; 16:1365-1376. [PMID: 34328300 PMCID: PMC8397291 DOI: 10.1021/acschembio.1c00134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
G-quadruplex (G4)
DNA structures are widespread in the human genome
and are implicated in biologically important processes such as telomere
maintenance, gene regulation, and DNA replication. Guanine-rich sequences
with potential to form G4 structures are prevalent in the promoter
regions of oncogenes, and G4 sites are now considered as attractive
targets for anticancer therapies. However, there are very few reports
of small “druglike” optical G4 reporters that are easily
accessible through one-step synthesis and that are capable of discriminating
between different G4 topologies. Here, we present a small water-soluble
light-up fluorescent probe that features a minimalistic amidinocoumarin-based
molecular scaffold that selectively targets parallel G4 structures
over antiparallel and non-G4 structures. We showed that this biocompatible
ligand is able to selectively stabilize the G4 template resulting
in slower DNA synthesis. By tracking individual DNA molecules, we
demonstrated that the G4-stabilizing ligand perturbs DNA replication
in cancer cells, resulting in decreased cell viability. Moreover,
the fast-cellular entry of the probe enabled detection of nucleolar
G4 structures in living cells. Finally, insights gained from the structure–activity
relationships of the probe suggest the basis for the recognition of
parallel G4s, opening up new avenues for the design of new biocompatible
G4-specific small molecules for G4-driven theranostic applications.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Måns Andreasson
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Shanmugam Tamilselvi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Karam Chand
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
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