1
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Kriebisch CME, Burger L, Zozulia O, Stasi M, Floroni A, Braun D, Gerland U, Boekhoven J. Template-based copying in chemically fuelled dynamic combinatorial libraries. Nat Chem 2024:10.1038/s41557-024-01570-5. [PMID: 39014158 DOI: 10.1038/s41557-024-01570-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 06/06/2024] [Indexed: 07/18/2024]
Abstract
One of science's greatest challenges is determining how life can spontaneously emerge from a mixture of molecules. A complicating factor is that life and its molecules are inherently unstable-RNA and proteins are prone to hydrolysis and denaturation. For the de novo synthesis of life or to better understand its emergence at its origin, selection mechanisms are needed for unstable molecules. Here we present a chemically fuelled dynamic combinatorial library to model RNA oligomerization and deoligomerization and shine new light on selection and purification mechanisms under kinetic control. In the experiments, oligomers can only be sustained by continuous production. Hybridization is a powerful tool for selecting unstable molecules, offering feedback on oligomerization and deoligomerization rates. Moreover, we find that templation can be used to purify libraries of oligomers. In addition, template-assisted formation of oligomers within coacervate-based protocells changes its compartment's physical properties, such as their ability to fuse. Such reciprocal coupling between oligomer production and physical properties is a key step towards synthetic life.
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Affiliation(s)
- Christine M E Kriebisch
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany
| | - Ludwig Burger
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany
| | - Oleksii Zozulia
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany
| | - Michele Stasi
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany
| | - Alexander Floroni
- Systems Biophysics Center for Nano-Science and Origins Cluster Initiative, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dieter Braun
- Systems Biophysics Center for Nano-Science and Origins Cluster Initiative, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ulrich Gerland
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany
| | - Job Boekhoven
- School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching, Germany.
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2
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Yu L, Li D, Ma C, Kauffmann B, Liao S, Gan Q. Redox-Regulated and Guest-Driven Transformations of Aromatic Oligoamide Foldamers in Advanced Structures. J Am Chem Soc 2024; 146:12907-12912. [PMID: 38691420 DOI: 10.1021/jacs.4c03275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
In this study, we demonstrate that an aromatic oligoamide sequence assembles into a trimeric helix-turn-helix architecture with a disulfide linkage, and upon cleavage of this linkage, it reconstructs into an antiparallel double helix. The antiparallel double helix is accessible to encapsulate a diacid guest within its cavity, forming a 2:1 host-guest complex. In contrast, hydrogen-bonding interactions between the trimeric-assembled structure and guests induce a conformational shift in the trimeric helix, resulting in a cross-shaped double-helix complex at a 2:2 host-guest ratio. Interconversions between the trimeric helix and the antiparallel double helix, along with their respective host-guest complexes, can be initiated through thiol/disulfide redox-mediated regulation.
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Affiliation(s)
- Lu Yu
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road No. 1037, 430074, Wuhan, China
| | - Dongyao Li
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, 777 Xingye Avenue East, Panyu District, 511442, Guangzhou, China
| | - Chunmiao Ma
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road No. 1037, 430074, Wuhan, China
| | - Brice Kauffmann
- Université de Bordeaux, CNRS, INSERM, Institut Européen de Chimie Biologie (UMS3033/US001), 2 Rue Escarpit, 33600, Pessac, France
| | - Sibei Liao
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road No. 1037, 430074, Wuhan, China
| | - Quan Gan
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Luoyu Road No. 1037, 430074, Wuhan, China
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3
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Snoj J, Lapenta F, Jerala R. Preorganized cyclic modules facilitate the self-assembly of protein nanostructures. Chem Sci 2024; 15:3673-3686. [PMID: 38455016 PMCID: PMC10915844 DOI: 10.1039/d3sc06658d] [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: 12/12/2023] [Accepted: 01/15/2024] [Indexed: 03/09/2024] Open
Abstract
The rational design of supramolecular assemblies aims to generate complex systems based on the simple information encoded in the chemical structure. Programmable molecules such as nucleic acids and polypeptides are particularly suitable for designing diverse assemblies and shapes not found in nature. Here, we describe a strategy for assembling modular architectures based on structurally and covalently preorganized subunits. Cyclization through spontaneous self-splicing of split intein and coiled-coil dimer-based interactions of polypeptide chains provide structural constraints, facilitating the desired assembly. We demonstrate the implementation of a strategy based on the preorganization of the subunits by designing a two-chain coiled-coil protein origami (CCPO) assembly that adopts a tetrahedral topology only when one or both subunit chains are covalently cyclized. Employing this strategy, we further design a 109 kDa trimeric CCPO assembly comprising 24 CC-forming segments. In this case, intein cyclization was crucial for the assembly of a concave octahedral scaffold, a newly designed protein fold. The study highlights the importance of preorganization of building modules to facilitate the self-assembly of higher-order supramolecular structures.
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Affiliation(s)
- Jaka Snoj
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
- Interdisciplinary Doctoral Program in Biomedicine, University of Ljubljana Kongresni trg 12 SI-1000 Ljubljana Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry Hajdrihova 19 SI-1000 Ljubljana Slovenia
- EN-FIST Centre of Excellence Trg OF 13 SI-1000 Ljubljana Slovenia
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4
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Cougnon FBL, Stefankiewicz AR, Ulrich S. Dynamic covalent synthesis. Chem Sci 2024; 15:879-895. [PMID: 38239698 PMCID: PMC10793650 DOI: 10.1039/d3sc05343a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/10/2023] [Indexed: 01/22/2024] Open
Abstract
Dynamic covalent synthesis aims to precisely control the assembly of simple building blocks linked by reversible covalent bonds to generate a single, structurally complex, product. In recent years, considerable progress in the programmability of dynamic covalent systems has enabled easy access to a broad range of assemblies, including macrocycles, shape-persistent cages, unconventional foldamers and mechanically-interlocked species (catenanes, knots, etc.). The reversibility of the covalent linkages can be either switched off to yield stable, isolable products or activated by specific physico-chemical stimuli, allowing the assemblies to adapt and respond to environmental changes in a controlled manner. This activatable dynamic property makes dynamic covalent assemblies particularly attractive for the design of complex matter, smart chemical systems, out-of-equilibrium systems, and molecular devices.
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Affiliation(s)
- Fabien B L Cougnon
- Department of Chemistry and Nanoscience Centre, University of Jyväskylä Jyväskylä Finland
| | - Artur R Stefankiewicz
- Centre for Advanced Technology and Faculty of Chemistry, Adam Mickiewicz University Poznań Poland
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM), Université de Montpellier, CNRS, ENSCM Montpellier France
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5
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Do CD, Pál D, Belyaev A, Pupier M, Kiesilä A, Kalenius E, Galmés B, Frontera A, Poblador-Bahamonde A, Cougnon FBL. Sulfate-induced large amplitude conformational change in a Solomon link. Chem Commun (Camb) 2023; 59:13010-13013. [PMID: 37830390 DOI: 10.1039/d3cc04555b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
A doubly-interlocked [2]catenane - or Solomon link - undergoes a complex conformational change upon addition of sulfate in methanol. This transformation generates a single pocket where two SO42- anions bind through multiple hydrogen bonds and electrostatic interactions. Despite the close proximity of the two anions, binding is highly cooperative.
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Affiliation(s)
- Cuong Dat Do
- Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Dávid Pál
- Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Andrey Belyaev
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 JYU, Finland.
| | - Marion Pupier
- Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Anniina Kiesilä
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 JYU, Finland.
| | - Elina Kalenius
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 JYU, Finland.
| | - Bartomeu Galmés
- Department de Química, Universitat de les Illes Balears, Carretera de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain
| | - Antonio Frontera
- Department de Química, Universitat de les Illes Balears, Carretera de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain
| | - Amalia Poblador-Bahamonde
- Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Fabien B L Cougnon
- Department of Organic Chemistry, University of Geneva, 30 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 JYU, Finland.
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6
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Kim S, Chae JB, Kim D, Park CW, Sim Y, Lee H, Park G, Lee J, Hong S, Jana B, Kim C, Chung H, Ryu JH. Supramolecular Senolytics via Intracellular Oligomerization of Peptides in Response to Elevated Reactive Oxygen Species Levels in Aging Cells. J Am Chem Soc 2023; 145:21991-22008. [PMID: 37664981 DOI: 10.1021/jacs.3c06898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Senolytics, which eliminate senescent cells from tissues, represent an emerging therapeutic strategy for various age-related diseases. Most senolytics target antiapoptotic proteins, which are overexpressed in senescent cells, limiting specificity and inducing severe side effects. To overcome these limitations, we constructed self-assembling senolytics targeting senescent cells with an intracellular oligomerization system. Intracellular aryl-dithiol-containing peptide oligomerization occurred only inside the mitochondria of senescent cells due to selective localization of the peptides by RGD-mediated cellular uptake into integrin αvβ3-overexpressed senescent cells and elevated levels of reactive oxygen species, which can be used as a chemical fuel for disulfide formation. This oligomerization results in an artificial protein-like nanoassembly with a stable α-helix secondary structure, which can disrupt the mitochondrial membrane via multivalent interactions because the mitochondrial membrane of senescent cells has weaker integrity than that of normal cells. These three specificities (integrin αvβ3, high ROS, and weak mitochondrial membrane integrity) of senescent cells work in combination; therefore, this intramitochondrial oligomerization system can selectively induce apoptosis of senescent cells without side effects on normal cells. Significant reductions in key senescence markers and amelioration of retinal degeneration were observed after elimination of the senescent retinal pigment epithelium by this peptide senolytic in an age-related macular degeneration mouse model and in aged mice, and this effect was accompanied by improved visual function. This system provides a strategy for the treatment of age-related diseases using supramolecular senolytics.
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Affiliation(s)
- Sangpil Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jae-Byoung Chae
- Department of Ophthalmology, Konkuk University School of Medicine, Seoul 05029, Republic of Korea
| | - Dohyun Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Chul-Woo Park
- Department of Ophthalmology, Konkuk University School of Medicine, Seoul 05029, Republic of Korea
| | - Youjung Sim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hyungwoo Lee
- Department of Ophthalmology, Konkuk University School of Medicine, Seoul 05029, Republic of Korea
| | - Gaeun Park
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jaeeun Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Seongho Hong
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Batakrishna Jana
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Chaekyu Kim
- Fusion Biotechnology, Ulsan 44919, Republic of Korea
| | - Hyewon Chung
- Department of Ophthalmology, Konkuk University School of Medicine, Seoul 05029, Republic of Korea
| | - Ja-Hyoung Ryu
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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7
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Chiba Y, Tanabe T, Koizumi K, Toyoda R, Iguchi H, Takaishi S, Sakamoto R. Single-Crystal Structures of Benzenehexathiol and Its Disulfide Forms. Inorg Chem 2023; 62:11731-11736. [PMID: 37436954 DOI: 10.1021/acs.inorgchem.3c01734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Oligothiols are useful as building blocks in the construction of disulfide-based macrocycles and polymers or as ligands for coordination polymers. Above all, benzenehexathiol (BHT) is a particularly important molecule, as it is used to construct conductive two-dimensional MOFs. Despite the desire to clarify its structure and isolate it to high purity, the chemical instability of BHT has hampered single-crystal X-ray structure analysis of intact BHT. In addition, the synthesis of discrete disulfide molecules of BHT has not been reported. Here, we succeed in obtaining the single crystals of intact BHT, which is analyzed by single crystal X-ray structure analysis. Furthermore, the structures of a group of molecules with intermolecular disulfide bonds (BHT·4im and BHT2·2TBA, im = imidazole, TBA = tetrabutylammonium cation) obtained by processing BHT in the presence of bases are determined.
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Affiliation(s)
- Yuta Chiba
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aza-Aoba, Aramaki, Sendai, Miyagi 980-8578, Japan
| | - Tappei Tanabe
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aza-Aoba, Aramaki, Sendai, Miyagi 980-8578, Japan
| | - Kazuma Koizumi
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aza-Aoba, Aramaki, Sendai, Miyagi 980-8578, Japan
| | - Ryojun Toyoda
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aza-Aoba, Aramaki, Sendai, Miyagi 980-8578, Japan
| | - Hiroaki Iguchi
- Department of Materials Chemistry, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Shinya Takaishi
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aza-Aoba, Aramaki, Sendai, Miyagi 980-8578, Japan
| | - Ryota Sakamoto
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aza-Aoba, Aramaki, Sendai, Miyagi 980-8578, Japan
- Division for the Establishment of Frontier Sciences of Organization for Advanced Studies at Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
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8
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Stingley KJ, Carpenter BA, Kean KM, Waters ML. Mismatched covalent and noncovalent templating leads to large coiled coil-templated macrocycles. Chem Sci 2023; 14:4935-4944. [PMID: 37181761 PMCID: PMC10171189 DOI: 10.1039/d3sc00231d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/02/2023] [Indexed: 04/05/2023] Open
Abstract
Herein we describe the use of dynamic combinatorial chemistry to self-assemble complex coiled coil motifs. We amide-coupled a series of peptides designed to form homodimeric coiled coils with 3,5-dithiobenzoic acid (B) at the N-terminus and then allowed each B-peptide to undergo disulfide exchange. In the absence of peptide, monomer B forms cyclic trimers and tetramers, and thus we expected that addition of the peptide to monomer B would shift the equilibrium towards the tetramer to maximize coiled coil formation. Unexpectedly, we found that internal templation of the B-peptide through coiled coil formation shifts the equilibrium towards larger macrocycles up to 13 B-peptide subunits, with a preference for 4, 7, and 10-membered macrocycles. These macrocyclic assemblies display greater helicity and thermal stability relative to intermolecular coiled coil homodimer controls. The preference for large macrocycles is driven by the strength of the coiled coil, as increasing the coiled coil affinity increases the fraction of larger macrocycles. This system represents a new approach towards the development of complex peptide and protein assemblies.
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Affiliation(s)
- Kyla J Stingley
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Benjamin A Carpenter
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Kelsey M Kean
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill CB 3290 Chapel Hill NC 27599 USA
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9
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Marić I, Yang L, Li X, Santiago GM, Pappas CG, Qiu X, Dijksman JA, Mikhailov K, van Rijn P, Otto S. Tailorable and Biocompatible Supramolecular-Based Hydrogels Featuring two Dynamic Covalent Chemistries. Angew Chem Int Ed Engl 2023; 62:e202216475. [PMID: 36744522 DOI: 10.1002/anie.202216475] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/17/2023] [Accepted: 02/01/2023] [Indexed: 02/07/2023]
Abstract
Dynamic covalent chemistry (DCC) has proven to be a valuable tool in creating fascinating molecules, structures, and emergent properties in fully synthetic systems. Here we report a system that uses two dynamic covalent bonds in tandem, namely disulfides and hydrazones, for the formation of hydrogels containing biologically relevant ligands. The reversibility of disulfide bonds allows fiber formation upon oxidation of dithiol-peptide building block, while the reaction between NH-NH2 functionalized C-terminus and aldehyde cross-linkers results in a gel. The same bond-forming reaction was exploited for the "decoration" of the supramolecular assemblies by cell-adhesion-promoting sequences (RGD and LDV). Fast triggered gelation, cytocompatibility and ability to "on-demand" chemically customize fibrillar scaffold offer potential for applying these systems as a bioactive platform for cell culture and tissue engineering.
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Affiliation(s)
- Ivana Marić
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen (The, Netherlands
- Dutch Polymer Institute, P. O. Box 902, 5600 AX, Eindhoven (The, Netherlands
| | - Liangliang Yang
- University Medical Center Groningen, Department of Biomedical Engineering-FB40 and W. J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen (The, Netherlands
| | - Xiufeng Li
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE, Wageningen (The, Netherlands
| | - Guillermo Monreal Santiago
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen (The, Netherlands
| | - Charalampos G Pappas
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen (The, Netherlands
| | - Xinkai Qiu
- Stratingh Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Joshua A Dijksman
- Physical Chemistry and Soft Matter, Wageningen University, Stippeneng 4, 6708 WE, Wageningen (The, Netherlands
| | - Kirill Mikhailov
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen (The, Netherlands
| | - Patrick van Rijn
- University Medical Center Groningen, Department of Biomedical Engineering-FB40 and W. J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen (The, Netherlands
| | - Sijbren Otto
- Stratingh Institute, Centre for Systems Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen (The, Netherlands
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10
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Erichsen A, Peters GHJ, Beeren SR. Templated Enzymatic Synthesis of δ-Cyclodextrin. J Am Chem Soc 2023; 145:4882-4891. [PMID: 36802551 DOI: 10.1021/jacs.3c00341] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
While α-, β-, and γ-cyclodextrin (CD) are ubiquitous hosts employed by supramolecular chemists, δ-CD (formed from nine α-1,4-linked glucopyranose units) has received very little attention. α-, β-, and γ-CD are the major products of the enzymatic breakdown of starch by cyclodextrin glucanotransferase (CGTase), but δ-CD forms only transiently in this reaction, as a minor component of a complex mixture of linear and cyclic glucans. In this work, we show how δ-CD can be synthesized in unprecedented yields by employing a bolaamphiphile template in an enzyme-mediated dynamic combinatorial library of cyclodextrins. NMR spectroscopy studies revealed that δ-CD can thread up to three bolaamphiphiles forming [2]-, [3]-, or [4]-pseudorotaxanes, depending on the size of the hydrophilic headgroup and the length of the alkyl chain axle. Threading of the first bolaamphiphile occurs in fast exchange on the NMR chemical shift time scale, while subsequent threading occurs in slow exchange. To extract quantitative information for 1:2 and 1:3 binding events occurring in mixed exchange regimes, we derived equations for nonlinear curve fitting that take into consideration both the chemical shift changes for species in fast exchange and the integrals for species in slow exchange to determine Ka1, Ka2, and Ka3. Template T1 could be used to direct the enzymatic synthesis of δ-CD due to the cooperative formation of a 1:2 complex─the [3]-pseudorotaxane δ-CD·T12. Importantly, T1 is recyclable. It can be readily recovered from the enzymatic reaction by precipitation and reused in subsequent syntheses enabling preparative-scale synthesis of δ-CD.
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Affiliation(s)
- Andreas Erichsen
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sophie R Beeren
- Department of Chemistry, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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11
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Jin Y, Mandal PK, Wu J, Böcher N, Huc I, Otto S. (Re-)Directing Oligomerization of a Single Building Block into Two Specific Dynamic Covalent Foldamers through pH. J Am Chem Soc 2023; 145:2822-2829. [PMID: 36705469 PMCID: PMC9912251 DOI: 10.1021/jacs.2c09325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Dynamic foldamers are synthetic folded molecules which can change their conformation in response to an external stimulus and are currently at the forefront of foldamer chemistry. However, constitutionally dynamic foldamers, which can change not only their conformation but also their molecular constitution in response to their environment, are without precedent. We now report a size- and shape-switching small dynamic covalent foldamer network which responds to changes in pH. Specifically, acidic conditions direct the oligomerization of a dipeptide-based building block into a 16-subunit macrocycle with well-defined conformation and with high selectivity. At higher pH the same building block yields another cyclic foldamer with a smaller ring size (9mer). The two foldamers readily and repeatedly interconvert upon adjustment of the pH of the solution. We have previously shown that addition of a template can direct oligomerization of the same building block to yet other rings sizes (including a 12mer and a 13mer, accompanied by a minor amount of 14mer). This brings the total number of discrete foldamers that can be accessed from a single building block to five. For a single building block system to exhibit such highly diverse structure space is unique and sets this system of foldamers apart from proteins. Furthermore, the emergence of constitutional dynamicity opens up new avenues to foldamers with adaptive behavior.
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Affiliation(s)
- Yulong Jin
- Beijing
National Laboratory for Molecular Sciences, CAS Key Laboratory of
Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, 100190 Beijing, China,Centre
for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Pradeep K. Mandal
- Department
of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians Universität, 81377 Munich, Germany
| | - Juntian Wu
- Centre
for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Niklas Böcher
- Department
of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians Universität, 81377 Munich, Germany
| | - Ivan Huc
- Department
of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians Universität, 81377 Munich, Germany,
| | - Sijbren Otto
- Centre
for Systems Chemistry, Stratingh Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands,
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12
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Roy S, Chatterjee A, Bal S, Das D. Cross β Amyloid Nanotubes Demonstrate Promiscuous Catalysis in a Chemical Reaction Network via Co‐option. Angew Chem Int Ed Engl 2022; 61:e202210972. [DOI: 10.1002/anie.202210972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Soumili Roy
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Ayan Chatterjee
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Subhajit Bal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur West Bengal 741246 India
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13
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Wootten MM, Tshepelevitsh S, Leito I, Clayden J. A Chemically Fuelled Molecular Automaton Displaying Programmed Migration of Zn 2+ Between Alternative Binding Sites. Chemistry 2022; 28:e202202247. [PMID: 35880579 PMCID: PMC9804598 DOI: 10.1002/chem.202202247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Indexed: 01/05/2023]
Abstract
A molecular system comprising a cationic zinc complex and an amino acid-derived ambident ligand having phosphate and carboxylate binding sites undergoes a series of rearrangements in which the metal cation migrates autonomously from one site to another. The location of the metal is identified by the circular dichroism spectrum of a ligated bis(2-quinolylmethyl)-(2-pyridylmethyl)amine (BQPA) chromophore, which takes a characteristic shape at each binding site. Migration is fuelled by the decomposition of trichloroacetic acid to CO2 and CHCl3 , which progressively neutralises the acidity of the system as a function of time, revealing in sequence binding sites of increasing basicity. The migration rate responds to control by variation of the temperature, water content and triethylamine concentration, while an excess of fuel controls the duration of an induction period before the migration event.
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Affiliation(s)
- Matthew M Wootten
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Sofja Tshepelevitsh
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu, 50411, Estonia
| | - Ivo Leito
- Institute of Chemistry, University of Tartu, Ravila 14a, Tartu, 50411, Estonia
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
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14
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Chatterjee A, Ghosh S, Ghosh C, Das D. Fluorescent Microswimmers Based on Cross-β Amyloid Nanotubes and Divergent Cascade Networks. Angew Chem Int Ed Engl 2022; 61:e202201547. [PMID: 35578748 DOI: 10.1002/anie.202201547] [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: 01/28/2022] [Indexed: 12/21/2022]
Abstract
Shaped through millions of years of evolution, the spatial localization of multiple enzymes in living cells employs extensive cascade reactions to enable highly coordinated multimodal functions. Herein, by utilizing a complex divergent cascade, we exploit the catalytic potential as well as templating abilities of streamlined cross-β amyloid nanotubes to yield two orthogonal roles simultaneously. The short peptide based paracrystalline nanotube surfaces demonstrated the generation of fluorescence signals within entangled networks loaded with alcohol dehydrogenase (ADH). The nanotubular morphologies were further used to generate cascade-driven microscopic motility through surface entrapment of sarcosine oxidase (SOX) and catalase (Cat). Moreover, a divergent cascade network was initiated by upstream catalysis of the substrate molecules through the surface mutation of catalytic moieties. Notably, the resultant downstream products led to the generation of motile fluorescent microswimmers by utilizing the two sets of orthogonal properties and, thus, mimicked the complex cascade-mediated functionalities of extant biology.
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Affiliation(s)
- Ayan Chatterjee
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
| | - Souvik Ghosh
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
| | - Chandranath Ghosh
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER), Kolkata, Mohanpur, West Bengal, 741246, India
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15
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Orrillo AG, Furlan RLE. Sulfur in Dynamic Covalent Chemistry. Angew Chem Int Ed Engl 2022; 61:e202201168. [PMID: 35447003 DOI: 10.1002/anie.202201168] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Indexed: 12/21/2022]
Abstract
Sulfur has been important in dynamic covalent chemistry (DCC) since the beginning of the field. Mainly as part of disulfides and thioesters, dynamic sulfur-based bonds (DSBs) have a leading role in several remarkable reactions. Part of this success is due to the almost ideal properties of DSBs for the preparation of dynamic covalent systems, including high reactivity and good reversibility under mild aqueous conditions, the possibility of exploiting supramolecular interactions, access to isolable structures, and easy experimental control to turn the reaction on/off. DCC is currently witnessing an increase in the importance of DSBs. The chemical flexibility offered by DSBs opens the door to multiple applications. This Review presents an overview of all the DSBs used in DCC, their applications, and remarks on the interesting properties that they confer on dynamic chemical systems, especially those containing several DSBs.
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Affiliation(s)
- A Gastón Orrillo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, Rosario, S2002LRK, Argentina
| | - Ricardo L E Furlan
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, CONICET, Suipacha 531, Rosario, S2002LRK, Argentina
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16
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Sudan S, Fadaei‐Tirani F, Scopelliti R, Ebbert KE, Clever GH, Severin K. LiBF
4
‐Induced Rearrangement and Desymmetrization of a Palladium‐Ligand Assembly. Angew Chem Int Ed Engl 2022; 61:e202201823. [PMID: 35348279 PMCID: PMC9320841 DOI: 10.1002/anie.202201823] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Indexed: 02/02/2023]
Affiliation(s)
- Sylvain Sudan
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Farzaneh Fadaei‐Tirani
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Rosario Scopelliti
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Kristina E. Ebbert
- Fakultät für Chemie und Chemische Biologie Technische Universität Dortmund 44227 Dortmund Germany
| | - Guido H. Clever
- Fakultät für Chemie und Chemische Biologie Technische Universität Dortmund 44227 Dortmund Germany
| | - Kay Severin
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
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17
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Fluorescent Microswimmers Based on Cross‐β Amyloid Nanotubes and Divergent Cascade Networks. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Yao C, Kauffmann B, Huc I, Ferrand Y. Self-assembling figure-of-eight and pseudoplectoneme aromatic oligoamide ribbons. Chem Commun (Camb) 2022; 58:5789-5792. [PMID: 35466334 DOI: 10.1039/d2cc01696f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two oligoamide macrocycles composed of eight and twelve 7-amino-8-fluoro-2-quinolinecarboxylic acid monomers were synthesised despite the propensity of their acyclic precursors to fold and self-assemble into double helices. Macrocyclisations were made possible through the transient use of helicity disruptors. The resulting macrocyclic ribbons were found to adopt figure-of-eight and pseudoplectoneme shapes that maintain an ability to self-assemble.
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Affiliation(s)
- Chenhao Yao
- Univ. Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN UMR 5248, 2 rue Escarpit, 33600 Pessac, France.
| | - Brice Kauffmann
- Univ. Bordeaux, CNRS, INSERM, Institut Européen de Chimie Biologie (UMS3033/US001), 2 rue Escarpit, 33600 Pessac, France
| | - Ivan Huc
- Department Pharmazie, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377 München, Germany.,Cluster of Excellence e-conversion, 85748 Garching, Germany.
| | - Yann Ferrand
- Univ. Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN UMR 5248, 2 rue Escarpit, 33600 Pessac, France.
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19
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Orrillo AG, Furlan RLE. Sulfur in Dynamic Covalent Chemistry. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201168] [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)
- Alfredo Gastón Orrillo
- Universidad Nacional de Rosario Facultad de Ciencias Bioquimicas y Farmaceuticas Organic Chemistry Suipacha 530 2000 Rosario ARGENTINA
| | - Ricardo L. E. Furlan
- Universidad Nacional de Rosario Facultad de Ciencias Bioquimicas y Farmaceuticas Organic Chemistry Suipacha 530 2000 Rosario ARGENTINA
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20
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Sudan S, Fadaei‐Tirani F, Scopelliti R, Ebbert KE, Clever GH, Severin K. LiBF
4
‐Induced Rearrangement and Desymmetrization of a Palladium‐Ligand Assembly. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sylvain Sudan
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Farzaneh Fadaei‐Tirani
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Rosario Scopelliti
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Kristina E. Ebbert
- Fakultät für Chemie und Chemische Biologie Technische Universität Dortmund 44227 Dortmund Germany
| | - Guido H. Clever
- Fakultät für Chemie und Chemische Biologie Technische Universität Dortmund 44227 Dortmund Germany
| | - Kay Severin
- Institut des Sciences et Ingénierie Chimiques Ecole Polytechnique Fédérale de Lausanne (EPFL) 1015 Lausanne Switzerland
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21
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Zhou Y, Dong J, Zhou C, Wang Q. Finite Assembly of Three-Dimensional DNA Hierarchical Nanoarchitectures through Orthogonal and Directional Bonding. Angew Chem Int Ed Engl 2022; 61:e202116416. [PMID: 35147275 DOI: 10.1002/anie.202116416] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Indexed: 01/01/2023]
Abstract
Reliable orthogonal bonding with precise and flexible orientation control would be ideal for building finite complex nanostructures via self-assembly. Employing a three-dimensional (3D) DNA origami, hexagonal prism DNA origami (HDO), as building block, we demonstrate it is practical to construct finite hierarchical nanoarchitectures with complicated conformations through orthogonal and directional bonding. The as-designed HDO building block has twelve prescribed directional valences in 3D space and each of them supports two opposite orientations, yielding the capability to generate abundant directional bonding. Meanwhile, we minimize the thorny non-specific interactions among HDOs and enable the orthogonal bonding between any two valences based on self-similar designing. Consequently, various hierarchical nanostructures are prepared at will simply by the combination of HDOs with appropriate valences. We believe this route towards hierarchically assembly is inspiring and hope it will facilitate the fabrication of functional superstructures.
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Affiliation(s)
- Yihao Zhou
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, China.,School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, China
| | - Jinyi Dong
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, China
| | - Chao Zhou
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, China.,School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, China
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Key Laboratory of Functional Molecular Imaging Technology, Division of Nanobiomedicine and i-Lab, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, China.,School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, China.,College of Materials Sciences and Opto-Electronic Technology, University of Chinese Academy of Sciences, China
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22
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Dual-responsive drug release and fluorescence imaging based on disulfide-pillar[4]arene aggregate in cancer cells. Bioorg Med Chem 2022; 57:116649. [DOI: 10.1016/j.bmc.2022.116649] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/12/2022] [Accepted: 01/26/2022] [Indexed: 12/17/2022]
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23
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Zhou Y, Dong J, Zhou C, Wang Q. Finite Assembly of Three‐Dimensional DNA Hierarchical Nanoarchitectures through Orthogonal and Directional Bonding. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yihao Zhou
- CAS Key Laboratory of Nano-Bio Interface Suzhou Key Laboratory of Functional Molecular Imaging Technology Division of Nanobiomedicine and i-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences China
- School of Nano-Tech and Nano-Bionics University of Science and Technology of China China
| | - Jinyi Dong
- CAS Key Laboratory of Nano-Bio Interface Suzhou Key Laboratory of Functional Molecular Imaging Technology Division of Nanobiomedicine and i-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences China
| | - Chao Zhou
- CAS Key Laboratory of Nano-Bio Interface Suzhou Key Laboratory of Functional Molecular Imaging Technology Division of Nanobiomedicine and i-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences China
- School of Nano-Tech and Nano-Bionics University of Science and Technology of China China
| | - Qiangbin Wang
- CAS Key Laboratory of Nano-Bio Interface Suzhou Key Laboratory of Functional Molecular Imaging Technology Division of Nanobiomedicine and i-Lab Suzhou Institute of Nano-Tech and Nano-Bionics Chinese Academy of Sciences China
- School of Nano-Tech and Nano-Bionics University of Science and Technology of China China
- College of Materials Sciences and Opto-Electronic Technology University of Chinese Academy of Sciences China
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24
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Computational Design of Single-Peptide Nanocages with Nanoparticle Templating. Molecules 2022; 27:molecules27041237. [PMID: 35209027 PMCID: PMC8874777 DOI: 10.3390/molecules27041237] [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: 12/24/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 01/25/2023] Open
Abstract
Protein complexes perform a diversity of functions in natural biological systems. While computational protein design has enabled the development of symmetric protein complexes with spherical shapes and hollow interiors, the individual subunits often comprise large proteins. Peptides have also been applied to self-assembly, and it is of interest to explore such short sequences as building blocks of large, designed complexes. Coiled-coil peptides are promising subunits as they have a symmetric structure that can undergo further assembly. Here, an α-helical 29-residue peptide that forms a tetrameric coiled coil was computationally designed to assemble into a spherical cage that is approximately 9 nm in diameter and presents an interior cavity. The assembly comprises 48 copies of the designed peptide sequence. The design strategy allowed breaking the side chain conformational symmetry within the peptide dimer that formed the building block (asymmetric unit) of the cage. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) techniques showed that one of the seven designed peptide candidates assembled into individual nanocages of the size and shape. The stability of assembled nanocages was found to be sensitive to the assembly pathway and final solution conditions (pH and ionic strength). The nanocages templated the growth of size-specific Au nanoparticles. The computational design serves to illustrate the possibility of designing target assemblies with pre-determined specific dimensions using short, modular coiled-coil forming peptide sequences.
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25
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Harders P, Griebenow T, Businski A, Kaus AJ, Pietsch L, Näther C, McConnell A. The Dynamic Covalent Chemistry of Amidoboronates: Tuning the rac5/rac6 Ratio via the B‑N and B‐O Dynamic Covalent Bonds. Chempluschem 2022; 87:e202200022. [DOI: 10.1002/cplu.202200022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/07/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Patrick Harders
- Christian-Albrechts-Universitat zu Kiel Otto Diels Institute of Organic Chemistry GERMANY
| | - Thomas Griebenow
- Christian Albrechts Universität zu Kiel: Christian-Albrechts-Universitat zu Kiel Otto Diels Institute of Organic Chemistry GERMANY
| | - Artjom Businski
- Christian-Albrechts-Universitat zu Kiel Otto Diels Institute of Organic Chemistry GERMANY
| | - Anton J. Kaus
- Christian-Albrechts-Universitat zu Kiel Otto Diels Institute of Organic Chemistry GERMANY
| | - Lorenz Pietsch
- Christian-Albrechts-Universitat zu Kiel Otto Diels Institute of Organic Chemistry GERMANY
| | - Christian Näther
- Christian-Albrechts-Universitat zu Kiel Institute of Inorganic Chemistry GERMANY
| | - Anna McConnell
- Kiel University Institute of Organic Chemistry Otto-Hahn-Platz 4 24098 Kiel GERMANY
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26
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Coste M, Suárez-Picado E, Ulrich S. Hierarchical self-assembly of aromatic peptide conjugates into supramolecular polymers: it takes two to tango. Chem Sci 2022; 13:909-933. [PMID: 35211257 PMCID: PMC8790784 DOI: 10.1039/d1sc05589e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/10/2021] [Indexed: 12/26/2022] Open
Abstract
Supramolecular polymers are self-assembled materials displaying adaptive and responsive "life-like" behaviour which are often made of aromatic compounds capable of engaging in π-π interactions to form larger assemblies. Major advances have been made recently in controlling their mode of self-assembly, from thermodynamically-controlled isodesmic to kinetically-controlled living polymerization. Dynamic covalent chemistry has been recently implemented to generate dynamic covalent polymers which can be seen as dynamic analogues of biomacromolecules. On the other hand, peptides are readily-available and structurally-rich building blocks that can lead to secondary structures or specific functions. In this context, the past decade has seen intense research activity in studying the behaviour of aromatic-peptide conjugates through supramolecular and/or dynamic covalent chemistries. Herein, we review those impressive key achievements showcasing how aromatic- and peptide-based self-assemblies can be combined using dynamic covalent and/or supramolecular chemistry, and what it brings in terms of the structure, self-assembly pathways, and function of supramolecular and dynamic covalent polymers.
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Affiliation(s)
- Maëva Coste
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Esteban Suárez-Picado
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM Montpellier France
| | - Sébastien Ulrich
- IBMM, Institut des Biomolécules Max Mousseron, CNRS, Université de Montpellier, ENSCM Montpellier France
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27
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Afrose SP, Mahato C, Sharma P, Roy L, Das D. Nonequilibrium Catalytic Supramolecular Assemblies of Melamine- and Imidazole-Based Dynamic Building Blocks. J Am Chem Soc 2022; 144:673-678. [PMID: 34990140 DOI: 10.1021/jacs.1c11457] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The development of synthetic nonequilibrium systems has gathered increasing attention due to their potential to illustrate the dynamic, complex, and emergent traits of biological systems. Simple building blocks capable of interacting via dynamic covalent chemistry and physical assembly in a reaction network under nonequilibrium conditions can contribute to our understanding of complex systems of life and its origin. Herein, we have demonstrated the nonequilibrium generation of catalytic supramolecular assemblies from simple heterocycle melamine driven by a thermodynamically activated ester. Utilizing a reversible covalent linkage, an imidazole moiety was recruited by the assemblies to access a catalytic transient state that dissipated energy via accelerated hydrolysis of the activated ester. The nonequilibrium assemblies were further capable of temporally binding to a hydrophobic guest to modulate its photophysical properties. Notably, the presence of an exogenous aromatic base augmented the lifetime of the catalytic microphases, reflecting their higher kinetic stability.
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Affiliation(s)
- Syed Pavel Afrose
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Chiranjit Mahato
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Pooja Sharma
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
| | - Lisa Roy
- Institute of Chemical Technology Mumbai-IOC Odisha Campus Bhubaneswar, IIT Kharagpur Extension Centre, Bhubaneswar 751013, India
| | - Dibyendu Das
- Department of Chemical Sciences and Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246, India
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28
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Abstract
As the remit of chemistry expands beyond molecules to systems, new synthetic targets appear on the horizon. Among these, life represents perhaps the ultimate synthetic challenge. Building on an increasingly detailed understanding of the inner workings of living systems and advances in organic synthesis and supramolecular chemistry, the de novo synthesis of life (i.e., the construction of a new form of life based on completely synthetic components) is coming within reach. This Account presents our first steps in the journey toward this long-term goal. The synthesis of life requires the functional integration of different subsystems that harbor the different characteristics that are deemed essential to life. The most important of these are self-replication, metabolism, and compartmentalization. Integrating these features into a single system, maintaining this system out of equilibrium, and allowing it to undergo Darwinian evolution should ideally result in the emergence of life. Our journey toward de novo life started with the serendipitous discovery of a new mechanism of self-replication. We found that self-assembly in a mixture of interconverting oligomers is a general way of achieving self-replication, where the assembly process drives the synthesis of the very molecules that assemble. Mechanically induced breakage of the growing replicating assemblies resulted in their exponential growth, which is an important enabler for achieving Darwinian evolution. Through this mechanism, the self-replication of compounds containing peptides, nucleobases, and fully synthetic molecules was achieved. Several examples of evolutionary dynamics have been observed in these systems, including the spontaneous diversification of replicators allowing them to specialize on different food sets, history dependence of replicator composition, and the spontaneous emergence of parasitic behavior. Peptide-based replicator assemblies were found to organize their peptide units in space in a manner that, inadvertently, gives rise to microenvironments that are capable of catalysis of chemical reactions or binding-induced activation of cofactors. Among the reactions that can be catalyzed by the replicators are ones that produce the precursors from which these replicators grow, amounting to the first examples of the assimilation of a proto-metabolism. Operating these replicators in a chemically fueled out-of-equilibrium replication-destruction regime was found to promote an increase in their molecular complexity. Fueling counteracts the inherent tendency of replicators to evolve toward lower complexity (caused by the fact that smaller replicators tend to replicate faster). Among the remaining steps on the road to de novo life are now to assimilate compartmentalization and achieve open-ended evolution of the resulting system. Success in the synthesis of de novo life, once obtained, will have far-reaching implications for our understanding of what life is, for the search for extraterrestrial life, for how life may have originated on earth, and for every-day life by opening up new vistas in the form living technology and materials.
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Affiliation(s)
- Sijbren Otto
- Centre for Systems Chemistry, Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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29
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Vial L, Perret F, Leclaire J. Dyn[
n
]arenes: Versatile Platforms To Study the Interplay between Covalent and Noncovalent Bonds. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Laurent Vial
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires UMR 5246 CNRS Univ. Lyon Université Lyon 1 CPE INSA 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne France
| | - Florent Perret
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires UMR 5246 CNRS Univ. Lyon Université Lyon 1 CPE INSA 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne France
| | - Julien Leclaire
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires UMR 5246 CNRS Univ. Lyon Université Lyon 1 CPE INSA 43 Boulevard du 11 Novembre 1918 69622 Villeurbanne France
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30
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Pal S, Reja A, Bal S, Tikader B, Das D. Emergence of a Promiscuous Peroxidase Under Non-Equilibrium Conditions. Angew Chem Int Ed Engl 2022; 61:e202111857. [PMID: 34767668 DOI: 10.1002/anie.202111857] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Indexed: 11/07/2022]
Abstract
Herein, we report the substrate induced generation of a transient catalytic microenvironment from a single amino acid functionalized fatty acid in presence of a cofactor hemin. The catalytic state accessed under non-equilibrium conditions showed acceleration of peroxidase activity resulting in degradation of the substrate and subsequently led to disassembly. Equilibrated systems could not access the three-dimensional microphases and showed substantially lower catalytic activity. Further, the assembled state showed latent catalytic function (promiscuity) to hydrolyze a precursor to yield the same substrate. Consequently, the assembly demonstrated protometabolism by exploiting the peroxidase-hydrolase cascade to augment the lifetime and the mechanical properties of the catalytic state.
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Affiliation(s)
- Sumit Pal
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Antara Reja
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Subhajit Bal
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
| | - Baishakhi Tikader
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Dibyendu Das
- Department of Chemical Sciences &, Centre for Advanced Functional Materials, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, West Bengal, 741246, India
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31
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Pal S, Reja A, Bal S, Tikader B, Das D. Emergence of a Promiscuous Peroxidase Under Non‐Equilibrium Conditions**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sumit Pal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Antara Reja
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Subhajit Bal
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
| | - Baishakhi Tikader
- Department of Chemistry Indian Institute of Technology Bombay Powai Mumbai 400076 India
| | - Dibyendu Das
- Department of Chemical Sciences & Centre for Advanced Functional Materials Indian Institute of Science Education and Research (IISER) Kolkata Mohanpur West Bengal 741246 India
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32
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McTiernan TJ, Diaz DB, Saunders GJ, Sprang F, Yudin AK. Navigating complex peptide structures using macrocycle conformational maps. RSC Chem Biol 2022; 3:739-747. [PMID: 35755184 PMCID: PMC9175111 DOI: 10.1039/d2cb00016d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/14/2022] [Indexed: 11/21/2022] Open
Abstract
Identification of turn motifs that are stabilized by intramolecular hydrogen bonds can be useful in describing the conformation of peptide systems. However, this approach is somewhat insufficient for cyclic peptides because peptide regions that are not positioned within a hydrogen bond can be left with no description. Furthermore, non-regular secondary structures and other rarely-observed conformations can be left without detailed evaluation. Herein, we describe “higher-order” ϕ/ψ plots termed macrocycle conformational maps (MCMs) as a tool for evaluating and comparing the conformations of a series of structurally related macrocyclic peptides. Identification of turn motifs that are stabilized by hydrogen bonds can be useful in describing the conformation of peptides. Herein, we describe “higher-order” ϕ/ψ plots termed macrocycle conformational maps (MCMs) as a tool to evaluate and compare the conformations of related macrocycles.![]()
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Affiliation(s)
- Timothy J McTiernan
- Davenport Research Laboratories, Department of Chemistry, University of Toronto Toronto ON M5S 3H6 Canada
| | - Diego B Diaz
- Davenport Research Laboratories, Department of Chemistry, University of Toronto Toronto ON M5S 3H6 Canada
| | - George J Saunders
- Davenport Research Laboratories, Department of Chemistry, University of Toronto Toronto ON M5S 3H6 Canada
| | - Fiona Sprang
- Davenport Research Laboratories, Department of Chemistry, University of Toronto Toronto ON M5S 3H6 Canada
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto Toronto ON M5S 3H6 Canada
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33
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Sheehan F, Sementa D, Jain A, Kumar M, Tayarani-Najjaran M, Kroiss D, Ulijn RV. Peptide-Based Supramolecular Systems Chemistry. Chem Rev 2021; 121:13869-13914. [PMID: 34519481 DOI: 10.1021/acs.chemrev.1c00089] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide-based supramolecular systems chemistry seeks to mimic the ability of life forms to use conserved sets of building blocks and chemical reactions to achieve a bewildering array of functions. Building on the design principles for short peptide-based nanomaterials with properties, such as self-assembly, recognition, catalysis, and actuation, are increasingly available. Peptide-based supramolecular systems chemistry is starting to address the far greater challenge of systems-level design to access complex functions that emerge when multiple reactions and interactions are coordinated and integrated. We discuss key features relevant to systems-level design, including regulating supramolecular order and disorder, development of active and adaptive systems by considering kinetic and thermodynamic design aspects and combinatorial dynamic covalent and noncovalent interactions. Finally, we discuss how structural and dynamic design concepts, including preorganization and induced fit, are critical to the ability to develop adaptive materials with adaptive and tunable photonic, electronic, and catalytic properties. Finally, we highlight examples where multiple features are combined, resulting in chemical systems and materials that display adaptive properties that cannot be achieved without this level of integration.
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Affiliation(s)
- Fahmeed Sheehan
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States
| | - Deborah Sementa
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States
| | - Ankit Jain
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States
| | - Mohit Kumar
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, Barcelona 08028, Spain
| | - Mona Tayarani-Najjaran
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States
| | - Daniela Kroiss
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Biochemistry The Graduate Center of the City University of New York 365 5th Avenue, New York, New York 10016, United States
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center City University of New York 85 St. Nicholas Terrace New York, New York 10031, United States.,Department of Chemistry, Hunter College City University of New York 695 Park Avenue, New York, New York 10065, United States.,Ph.D. Program in Chemistry The Graduate Center of the City University of New York 365 fifth Avenue, New York, New York 10016, United States.,Ph.D. Program in Biochemistry The Graduate Center of the City University of New York 365 5th Avenue, New York, New York 10016, United States
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34
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Li D, Ma C, Xiang J, Zhang K, Yang L, Gan Q. A Disulfide Switch Providing Absolute Handedness Control in Double Helices via Conversion from the Antiparallel to Parallel Helical Pattern. Chemistry 2021; 27:11663-11669. [PMID: 34014575 DOI: 10.1002/chem.202101221] [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: 04/06/2021] [Indexed: 11/09/2022]
Abstract
A strategy to reversibly switch the parallel/antiparallel helical conformation of aromatic double helices through the formation/breakage of a disulfide bond is presented. Single-crystal X-ray structures, NMR, and circular dichroism spectroscopy demonstrate that the double helices with terminal thiol groups favor an antiparallel helical arrangement both in the solid state and in solution, while the P/M bias of helicity induced by chiral segments from another extremity of the sequence is weak in this structural motif. The antiparallel helices can be rearranged to parallel helices through the disulfide connection of the sequences. This change enhances the bias of helical handedness and results in absolute chirality control of the double helices. The handedness-mediated process can be governed by the oxidation-reduction cycle, thereby switching the structural arrangement and the enhancement of chiral bias. In addition, we find that the sequences can dimerize into an intermolecular double helix with the disulfide connection. And the helical handedness is also fully controlled due to the head-to-head structural motif.
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Affiliation(s)
- Dongyao Li
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Chunmiao Ma
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Junfeng Xiang
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Kai Zhang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Ling Yang
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Quan Gan
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
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35
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Urushibara K, Ferrand Y, Liu Z, Katagiri K, Kawahata M, Morvan E, D'Elia R, Pophristic V, Tanatani A, Huc I. Accessing Improbable Foldamer Shapes with Strained Macrocycles. Chemistry 2021; 27:11205-11215. [PMID: 33905165 PMCID: PMC8453500 DOI: 10.1002/chem.202101201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Indexed: 11/07/2022]
Abstract
The alkylation of some secondary amide functions with a dimethoxybenzyl (DMB) group in oligomers of 8-amino-2-quinolinecarboxylic acid destabilizes the otherwise favored helical conformations, and allows for cyclization to take place. A cyclic hexamer and a cyclic heptamer were produced in this manner. After DMB removal, X-ray crystallography and NMR show that the macrocycles adopt strained conformations that would be improbable in noncyclic species. The high helix folding propensity of the main chain is partly expressed in these conformations, but it remains frustrated by macrocyclization. Despite being homomeric, the macrocycles possess inequivalent monomer units. Experimental and computational studies highlight specific fluxional pathways within these structures. Extensive simulated annealing molecular dynamics allow for the prediction of the conformations for larger macrocycles with up to sixteen monomers.
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Affiliation(s)
- Ko Urushibara
- Department of ChemistryFaculty of ScienceOchanomizu University2-1-1 Otsuka, Bunkyo-kuTokyo112-8610Japan
- CBMN (UMR 5248)Université de BordeauxCNRSBordeaux Institut National Polytechnique2 rue Robert Escarpit33600PessacFrance
| | - Yann Ferrand
- CBMN (UMR 5248)Université de BordeauxCNRSBordeaux Institut National Polytechnique2 rue Robert Escarpit33600PessacFrance
| | - Zhiwei Liu
- Department of Chemistry & BiochemistryUniversity of the Sciences600 South 43rd StreetPhiladelphiaPA19104USA
| | - Kosuke Katagiri
- Department of ChemistryFaculty of Science and EngineeringKonan University8-9-1 Okamoto, Higashinada-kuKobe658-8501Japan
| | - Masatoshi Kawahata
- Faculty of Pharmaceutical SciencesShowa Pharmaceutical University3-3165 Higashi-TamagawagakuenMachidaTokyo194-8543Japan
| | - Estelle Morvan
- IECB (UMS3033/US001)Université de Bordeaux, CNRS, INSERM2 rue Robert Escarpit33600PessacFrance
| | - Ryan D'Elia
- Department of Chemistry & BiochemistryUniversity of the Sciences600 South 43rd StreetPhiladelphiaPA19104USA
| | - Vojislava Pophristic
- Department of Chemistry & BiochemistryUniversity of the Sciences600 South 43rd StreetPhiladelphiaPA19104USA
| | - Aya Tanatani
- Department of ChemistryFaculty of ScienceOchanomizu University2-1-1 Otsuka, Bunkyo-kuTokyo112-8610Japan
| | - Ivan Huc
- CBMN (UMR 5248)Université de BordeauxCNRSBordeaux Institut National Polytechnique2 rue Robert Escarpit33600PessacFrance
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
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36
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Liu B, Beatty MA, Pappas CG, Liu K, Ottelé J, Otto S. Self‐Sorting in Dynamic Combinatorial Libraries Leads to the Co‐Existence of Foldamers and Self‐Replicators. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Meagan A. Beatty
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Charalampos G. Pappas
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Kai Liu
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry Stratingh Institute University of Groningen Nijenborgh 4 9747 AG Groningen Netherlands
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37
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Liu B, Beatty MA, Pappas CG, Liu K, Ottelé J, Otto S. Self-Sorting in Dynamic Combinatorial Libraries Leads to the Co-Existence of Foldamers and Self-Replicators. Angew Chem Int Ed Engl 2021; 60:13569-13573. [PMID: 33949062 PMCID: PMC8252005 DOI: 10.1002/anie.202101052] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 12/27/2022]
Abstract
Nature segregates fundamental tasks such as information storage/transmission and catalysis between two different compound classes (e.g. polynucleotides for replication and folded polyamides for catalysis). This division of labor is likely a product of evolution, raising the question of how simpler systems in which replicators and folded macromolecules co-exist may emerge in the transition from chemistry to biology. In synthetic systems, achieving co-existence of replicators and foldamers in a single molecular network remains an unsolved problem. Previous work on dynamic molecular networks has given rise to either self-replicating fibers or well-defined foldamer structures (or completely un-sorted complex systems). We report a system in which two cross-reactive dithiol (nucleobase- and peptide-based) building blocks self-sort into a replicator fiber and foldamer that both emerge spontaneously and co-exist. The self-sorting behavior remains prevalent across different building block ratios as two phases of emergence occur: replicator growth followed by foldamer formation. This is attributed to the autocatalytic formation of the replicator fiber, followed by enrichment of the system in the remaining building block, which is subsequently incorporated into a foldamer.
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Affiliation(s)
- Bin Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Meagan A Beatty
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Charalampos G Pappas
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Kai Liu
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Jim Ottelé
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
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38
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Abstract
N,N'-linked oligoureas are a class of enantiopure, sequence-defined peptidomimetic oligomers without amino acids that form well-defined and predictable helical structures akin to the peptide α-helix. Oligourea-based foldamers combine a number of features-such as synthetic accessibility, sequence modularity, and folding fidelity-that bode well for their use in a range of applications from medicinal chemistry to catalysis. Moreover, it was recently recognized that this synthetic helical backbone can be combined with regular peptides to generate helically folded peptide-oligourea hybrids that display additional features in terms of helix mimicry and protein-surface recognition properties. Here we provide detailed protocols for the preparation of requested monomers and for the synthesis and purification of homo-oligoureas and peptide-oligourea hybrids.
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39
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Pappas CG, Liu B, Marić I, Ottelé J, Kiani A, van der Klok ML, Onck PR, Otto S. Two Sides of the Same Coin: Emergence of Foldamers and Self-Replicators from Dynamic Combinatorial Libraries. J Am Chem Soc 2021; 143:7388-7393. [PMID: 33955219 PMCID: PMC8154527 DOI: 10.1021/jacs.1c00788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The ability of molecules
and systems to make copies of themselves
and the ability of molecules to fold into stable, well-defined three-dimensional
conformations are of considerable importance in the formation and
persistence of life. The question of how, during the emergence of
life, oligomerization reactions become selective and channel these
reactions toward a small number of specific products remains largely
unanswered. Herein, we demonstrate a fully synthetic chemical system
where structurally complex foldamers and self-replicating assemblies
emerge spontaneously and with high selectivity from pools of oligomers
as a result of forming noncovalent interactions. Whether foldamers
or replicators form depends on remarkably small differences in building
block structures and composition and experimental conditions. We also
observed the dynamic transformation of a foldamer into a replicator.
These results show that the structural requirements/design criteria
for building blocks that lead to foldamers are similar to those that
lead to replicators. What determines whether folding or replication
takes place is not necessarily the type of noncovalent interaction,
but only whether they occur intra- or intermolecularly. This work
brings together, for the first time, the fields of replicator and
foldamer chemistry.
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Affiliation(s)
- Charalampos G Pappas
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Bin Liu
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ivana Marić
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jim Ottelé
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Armin Kiani
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marcus L van der Klok
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Sijbren Otto
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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