101
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Herrera-España AD, Höpfl H, Morales-Rojas H. Boron-Nitrogen Double Tweezers Comprising Arylboronic Esters and Diamines: Self-Assembly in Solution and Adaptability as Hosts for Aromatic Guests in the Solid State. Chempluschem 2020; 85:548-560. [PMID: 32202393 DOI: 10.1002/cplu.201900717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 12/11/2019] [Indexed: 01/07/2023]
Abstract
The thermodynamic stability of 1 : 1 and 2 : 1 boron-nitrogen (B←N) adducts formed between aromatic boronic esters with mono- and diamines was studied in solution by NMR and UV-vis spectroscopy with association energies (ΔG°) ranging from -11 to -28 kJ mol-1 . The effect of different substituents in the boronic ester, the nature of the diamine linker, and the effect of the solvent was explored. Stable 2 : 1 B←N adducts with diamines such as 1,3-diaminopropane were produced in solutions of hydrogen-bonding acceptor solvents (acetonitrile and ethyl acetate), which can be isolated in the solid state as crystalline solvates, whereas the use of noncoordinating solvents such as 1,2-dichloroethane afforded mainly 1 : 1 B←N adducts. In suitable combinations, aromatic bis-pyridyl diamines produced stable 2 : 1 B←N adducts that were isolated either as solvent-free solids, solvates, or cocrystals. In these crystalline forms, double-tweezer hosts were observed with an exceptional syn/anti conformational guest-adaptability driven by simultaneous donor-acceptor and C-H⋅⋅⋅π interactions in the tweezer cavities, resembling preorganized covalent tweezer hosts. Interestingly, cocrystals with electron-rich guests such as tetrathiafulvalene and pyrene showed non-centrosymmetric crystal lattices with infinite π-stacked donor-acceptor columns.
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Affiliation(s)
- Angel D Herrera-España
- Centro de Investigaciones Químicas Instituto de Investigación en Ciencias Básicas y Aplicadas (IICBA), Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209, Cuernavaca, Morelos, Mexico
| | - Herbert Höpfl
- Centro de Investigaciones Químicas Instituto de Investigación en Ciencias Básicas y Aplicadas (IICBA), Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209, Cuernavaca, Morelos, Mexico
| | - Hugo Morales-Rojas
- Centro de Investigaciones Químicas Instituto de Investigación en Ciencias Básicas y Aplicadas (IICBA), Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, 62209, Cuernavaca, Morelos, Mexico
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102
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Oohora K, Hirayama S, Mashima T, Hayashi T. Supramolecular dimerization of a hexameric hemoprotein via multiple pyrene-pyrene interactions. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s1088424619500949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein assemblies are being investigated as a new-class of biomaterials. A supramolecular assembly of a mutant hexameric tyrosine coordinated hemoprotein (HTHP) modified with a pyrene derivative is described. Cysteine was first introduced as a site-specific reaction point at position V44 which is located at the bottom surface of the cylindrical structure of HTHP. [Formula: see text]-(1-pyrenyl)maleimide was then reacted with the mutant. The modification was confirmed by MALDI-TOF mass spectrometry and UV-vis absorption spectroscopy, indicating that approximately 90% cysteine residues are attached via the pyrene derivative. Size exclusion chromatography (SEC) measurements for pyrene-attached HTHP include a single peak which elutes earlier than the unmodified HTHP. Further investigation by SEC and dynamic light scattering (DLS) measurements indicate the desired size corresponding to the dimer of the hemoprotein hexamers. The multivalent effect of pyrene–pyrene interactions including hydrophobic and [Formula: see text]–[Formula: see text] stacking interactions appears to be responsible for including formation of the stable dimer of the hexamers. Interestingly, the assembly dissociates to the hexamer by removal of heme. In the case of the apo-form of pyrene-attached HTHP, the pyrene moiety appears to be incorporated into the heme pocket because the modification point is located at the adjacent residue of the Tyr45 coordinating to heme in the holo-form of HTHP. Subsequent addition of heme into the apo-form of pyrene-attached HTHP regenerates the dimer of the hexamers. The present study demonstrates a unique heme-dependent system in which HTHP is assembled to form a dimer of hexamers in the presence of heme and disassembled by removal of heme.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
- Frontier Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Shota Hirayama
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Tsuyoshi Mashima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
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103
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Madrigal-Santillán E, Madrigal-Bujaidar E, Reyes-Arellano A, Morales-González JA, Álvarez-González I, Sánchez-Gutiérrez M, Izquierdo-Vega JA, Calzada-Mendoza CC, Anguiano-Robledo L, Morales-González Á. Supramolecular complex formation, a possible antigenotoxic mechanism of glucomannan against aflatoxin B1. TOXICOLOGICAL AND ENVIRONMENTAL CHEMISTRY 2020. [DOI: 10.1080/02772248.2020.1715410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Eduardo Madrigal-Santillán
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Unidad Casco de Santo Tomas, Ciudad de México, México
| | - Eduardo Madrigal-Bujaidar
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Unidad Profesional A. López Mateos, Ciudad de México, México
| | - Alicia Reyes-Arellano
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Unidad Casco de Santo Tomas, Ciudad de México, México
| | | | - Isela Álvarez-González
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Unidad Profesional A. López Mateos, Ciudad de México, México
| | | | | | - Claudia C. Calzada-Mendoza
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Unidad Casco de Santo Tomas, Ciudad de México, México
| | - Liliana Anguiano-Robledo
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Unidad Casco de Santo Tomas, Ciudad de México, México
| | - Ángel Morales-González
- Escuela Superior de Cómputo, Instituto Politécnico Nacional, Unidad Profesional A. López Mateos, Ciudad de México, México
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104
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Hirayama S, Oohora K, Uchihashi T, Hayashi T. Thermoresponsive Micellar Assembly Constructed from a Hexameric Hemoprotein Modified with Poly( N-isopropylacrylamide) toward an Artificial Light-Harvesting System. J Am Chem Soc 2020; 142:1822-1831. [PMID: 31904965 DOI: 10.1021/jacs.9b10080] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Artificial protein assemblies inspired by nature have significant potential in development of emergent functional materials. In order to construct an artificial protein assembly, we employed a mutant of a thermostable hemoprotein, hexameric tyrosine-coordinated heme protein (HTHP), as a building block. The HTHP mutant which has cysteine residues introduced on the bottom surface of its columnar structure was reacted with maleimide-tethering thermoresponsive poly(N-isopropylacrylamide), PNIPAAm, to generate the protein assembly upon heating. The site-specific modification of the cysteine residues with PNIPAAm on the protein surface was confirmed by SDS-PAGE and analytical size exclusion chromatography (SEC). The PNIPAAm-modified HTHP (PNIPAAm-HTHP) is found to provide a 43 nm spherical structure at 60 °C, and the structural changes observed between the assembled and the disassembled forms were duplicated at least five times. High-speed atomic force microscopic measurements of the micellar assembly supported by cross-linkage with glutaraldehyde indicate that the protein matrices are located on the surface of the sphere and cover the inner PNIPAAm core. Furthermore, substitution of heme with a photosensitizer, Zn protoporphyrin IX (ZnPP), in the micellar assembly provides an artificial light-harvesting system. Photochemical measurements of the ZnPP-substituted micellar assembly demonstrate that energy migration among the arrayed ZnPP molecules occurs within the range of several tens of picoseconds. Our present work represents the first example of an artificial light-harvesting system based on an assembled hemoprotein oligomer structure to replicate natural light-harvesting systems.
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Affiliation(s)
| | | | - Takayuki Uchihashi
- Department of Physics , Nagoya University , Nagoya 464-8602 , Japan.,Exploratory Research Center on Life and Living Systems (ExCELLS) , Okazaki 444-8787 , Japan
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105
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Geiselhart CM, Mutlu H, Tzvetkova P, Barner-Kowollik C. Chemiluminescent self-reporting supramolecular transformations on macromolecular scaffolds. Polym Chem 2020. [DOI: 10.1039/d0py00332h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We introduce the synthesis of a self-reporting system with chemiluminescent output, which is regulated via dynamic supramolecular complex formation.
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Affiliation(s)
- Christina M. Geiselhart
- Soft Matter Synthesis Laboratory
- Institut für Biologische Grenzflächen 3
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - Hatice Mutlu
- Soft Matter Synthesis Laboratory
- Institut für Biologische Grenzflächen 3
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - Pavleta Tzvetkova
- Institute for Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance
- Karlsruhe Institute of Technology (KIT)
- 76344 Eggenstein-Leopoldshafen
- Germany
| | - Christopher Barner-Kowollik
- Macromolecular Architectures
- Institut für Technische Chemie und Polymerchemie
- Karlsruhe Institute of Technology (KIT)
- 76128 Karlsruhe
- Germany
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106
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Rizvi MA, Hussain Z, Ali F, Amin A, Mir SH, Rydzek G, Jagtap RM, Pardeshi SK, Qadri RA, Ariga K. Bioactive supra decorated thiazolidine-4-carboxylic acid derivatives attenuate cellular oxidative stress by enhancing catalase activity. Phys Chem Chem Phys 2020; 22:7942-7951. [DOI: 10.1039/d0cp00253d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioactive (2S,4R)-3-(tert-butoxycarbonyl)-2-(2-hydroxyphenyl)thiazolidine-4-carboxylic acid molecules restructure enzymes through complexation, allowing enhancing their activity to protect cells from oxidative stress.
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Affiliation(s)
| | - Zakir Hussain
- Department of Chemistry
- University of Kashmir
- Srinagar
- India
| | - Fasil Ali
- Department of Studies and Research in Biochemistry
- Mangalore University
- India
| | - Asif Amin
- Department of Biotechnology
- University of Kashmir
- Srinagar 190006
- India
| | - Sajjad Husain Mir
- Advanced Materials and Bio Engineering Research Centre (AMBER)
- Ireland
- Department of Chemistry
- Trinity College Dublin
- The University of Dublin
| | - Gaulthier Rydzek
- Institut Charles Gerhardt Montpellier
- UMR 5253
- CNRS
- ENSCM
- Univ. Montpellier
| | - Rohidas M. Jagtap
- Department of Chemistry
- Savitribai Phule Pune University
- Pune 411007
- India
| | | | - Raies A. Qadri
- Department of Biotechnology
- University of Kashmir
- Srinagar 190006
- India
| | - Katsuhiko Ariga
- World Premier International Center for Materials Nanoarchitectonics (MANA)
- National Institute for Materials Science (NIMS)
- Tsukuba 305-0044
- Japan
- Graduate School of Frontier Sciences
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107
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Gill AD, Hickey BL, Zhong W, Hooley RJ. Selective sensing of THC and related metabolites in biofluids by host:guest arrays. Chem Commun (Camb) 2020; 56:4352-4355. [DOI: 10.1039/d0cc01489c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A host–guest fluorescence sensor array can selectively detect THC and its metabolites in biofluids such as urine and saliva.
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Affiliation(s)
- Adam D. Gill
- Department of Biochemistry and Molecular Biology
- University of California-Riverside
- Riverside
- USA
| | - Briana L. Hickey
- Department of Chemistry
- University of California-Riverside
- Riverside
- USA
| | - Wenwan Zhong
- Department of Chemistry
- University of California-Riverside
- Riverside
- USA
- Environmental Toxicology Program
| | - Richard J. Hooley
- Department of Biochemistry and Molecular Biology
- University of California-Riverside
- Riverside
- USA
- Department of Chemistry
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108
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Beltrán A, Burguete MI, Galindo F, Luis SV. Synthesis of new fluorescent pyrylium dyes and study of their interaction with N-protected amino acids. NEW J CHEM 2020. [DOI: 10.1039/d0nj02033h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Six new fluorescent styrylpyrylium dyes have been synthesized and the collisional quenching taking place upon their interaction with Z-protected amino acids has been studied.
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Affiliation(s)
- Alicia Beltrán
- Universitat Jaume I
- Departamento de Química Inorgánica y Orgánica
- Avda. Vicente Sos Baynat s/n
- Castellón
- Spain
| | - M. Isabel Burguete
- Universitat Jaume I
- Departamento de Química Inorgánica y Orgánica
- Avda. Vicente Sos Baynat s/n
- Castellón
- Spain
| | - Francisco Galindo
- Universitat Jaume I
- Departamento de Química Inorgánica y Orgánica
- Avda. Vicente Sos Baynat s/n
- Castellón
- Spain
| | - Santiago V. Luis
- Universitat Jaume I
- Departamento de Química Inorgánica y Orgánica
- Avda. Vicente Sos Baynat s/n
- Castellón
- Spain
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109
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Magdalena Estirado E, Aleman Garcia MA, Schill J, Brunsveld L. Multivalent Ultrasensitive Interfacing of Supramolecular 1D Nanoplatforms. J Am Chem Soc 2019; 141:18030-18037. [PMID: 31622094 PMCID: PMC6856958 DOI: 10.1021/jacs.9b05629] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Multivalent display on linear platforms is used by many biomolecular systems to effectively interact with their corresponding binding partners in a dose-responsive and ultrasensitive manner appropriate to the biological system at hand. Synthetic supramolecular multivalent displays offer a matching approach for the modular and bottom-up construction and systematic study of dynamic 1D materials. Fundamental studies into multivalent interactions between such linear, 1D materials have been lacking because of the absence of appropriate modular nanoplatforms. In this work we interfaced two synthetic multivalent linear nanoplatforms based on a dynamic supramolecular polymer, formed by hybrid discotic-oligonucleotide monomers, and a series of complementary DNA-duplex-based multivalent ligands, also with appended short oligonucleotides. The combination of these two multivalent nanoplatforms provides for the first time entry to study multivalent effects in dynamic 1D systems, of relevance for the conceptual understanding of multivalency in biology and for the generation of novel multivalent biomaterials. Together the two nanoscaffolds provide easy access to libraries of multivalent ligands with tunable affinities. The DNA scaffold allows for exact control over valency and spatial ligand distribution, and the discotic supramolecular polymer allows for dynamic adaptation and control over receptor density. The interaction between the two nanoplatforms was studied as a function of ligand interaction strength, valency, and density. Usage of the enhancement parameter β allowed quantification of the effects of ligand valency and affinity. The results reveal a generalized principle of additive binding increments. Receptor density is shown to be crucially and nonlinearly correlated to complex formation, leading to ultrasensitive responses. The results reveal that, not unlike biomolecular signaling, high density multivalent display of receptors is crucial for functionally increased affinities.
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Affiliation(s)
- Eva Magdalena Estirado
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands
| | - Miguel Angel Aleman Garcia
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands
| | - Jurgen Schill
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands
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110
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Gill AD, Hickey BL, Wang S, Xue M, Zhong W, Hooley RJ. Sensing of citrulline modifications in histone peptides by deep cavitand hosts. Chem Commun (Camb) 2019; 55:13259-13262. [PMID: 31621759 PMCID: PMC6872487 DOI: 10.1039/c9cc07002h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Arrayed cavitand:fluorophore sensor complexes can selectively sense small citrulline modifications at arginine residues on post-translationally modified peptides. The sensor can differentiate between different numbers of citrulline modifications, and a simple two-fluorophore, 6-component array can effect cross-reactive discrimination between single modifications in aqueous solution.
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Affiliation(s)
- Adam D Gill
- Department of Biochemistry and Molecular Biology, University of California-Riverside, Riverside, CA 92521, USA.
| | - Briana L Hickey
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA
| | - Siwen Wang
- Environmental Toxicology Program, University of California-Riverside, Riverside, CA 92521, USA
| | - Min Xue
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA and Environmental Toxicology Program, University of California-Riverside, Riverside, CA 92521, USA
| | - Wenwan Zhong
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA and Environmental Toxicology Program, University of California-Riverside, Riverside, CA 92521, USA
| | - Richard J Hooley
- Department of Chemistry, University of California-Riverside, Riverside, CA 92521, USA and Department of Biochemistry and Molecular Biology, University of California-Riverside, Riverside, CA 92521, USA.
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111
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Heilmann M, Tiefenbacher K. A Modular Phosphorylated Glycoluril-Derived Molecular Tweezer for Potent Binding of Aliphatic Diamines. Chemistry 2019; 25:12900-12904. [PMID: 31348566 DOI: 10.1002/chem.201902556] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/15/2019] [Indexed: 12/16/2022]
Abstract
A molecular tweezer based on a glycoluril-derived framework bearing four phosphate groups was synthesized and shown to be capable of binding organic amines in aqueous solution. This work reports the Ka values for 30 complexes of this molecular tweezer and amine guests, determined by means of 1 H NMR titrations. Both the hydrophobic cavity and the phosphate groups contribute to the binding. Bulkier molecules and molecules bearing negatively charged groups like carboxylates in amino acids bind less tightly due to a steric clash and coulombic repulsion. The narrow cavity and the strong ionic interactions of the phosphate groups with ammonium guests favor binding of aliphatic diamines. These binding properties clearly distinguish this system from structurally related molecular clips and tweezers.
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Affiliation(s)
- Michael Heilmann
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058, Basel, Switzerland
| | - Konrad Tiefenbacher
- Department of Chemistry, University of Basel, Mattenstrasse 24a, 4058, Basel, Switzerland.,Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland
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112
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Engilberge S, Rennie ML, Dumont E, Crowley PB. Tuning Protein Frameworks via Auxiliary Supramolecular Interactions. ACS NANO 2019; 13:10343-10350. [PMID: 31490058 DOI: 10.1021/acsnano.9b04115] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Protein crystals with their precise, periodic array of functional building blocks have potential applications in biomaterials, sensing, and catalysis. This paper describes how a highly porous crystalline framework of a cationic redox protein and an anionic macrocycle can be modulated by a small cationic effector. Ternary composites of protein (∼13 kDa), calix[8]arene (∼1.5 kDa), and effector (∼0.2 kDa) formed distinct crystalline architectures, dependent on the effector concentration and the crystallization technique. A combination of X-ray crystallography and density functional theory (DFT) calculations was used to decipher the framework variations, which appear to be dependent on a calixarene conformation change mediated by the effector. This "switch" calixarene was observed in three states, each of which is associated with a different interaction network. Two structures obtained by co-crystallization with the effector contained an additional protein "pillar", resulting in framework duplication and decreased porosity. These results suggest how protein assembly can be engineered by supramolecular host-guest interactions.
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Affiliation(s)
- Sylvain Engilberge
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
| | - Martin L Rennie
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
| | - Elise Dumont
- Université de Lyon, ENS de Lyon, CNRS UMR 5182 , Université Claude Bernard Lyon 1, Laboratoire de Chimie , 69342 Lyon , France
| | - Peter B Crowley
- School of Chemistry , National University of Ireland Galway , University Road , Galway H91 TK33 , Ireland
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113
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Liu B, Ianosi-Irimie M, Thayumanavan S. Reversible Click Chemistry for Ultrafast and Quantitative Formation of Protein-Polymer Nanoassembly and Intracellular Protein Delivery. ACS NANO 2019; 13:9408-9420. [PMID: 31335116 PMCID: PMC6713578 DOI: 10.1021/acsnano.9b04198] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Construction of polymer-protein nanoassemblies is a challenge as reactions between macromolecules, especially those involving proteins, are inherently inefficient due to the sparse reactive functional groups and low concentration requirements. We address this challenge using an ultrafast and reversible click reaction, which forms the basis for a covalent self-assembly strategy between side-chain functionalized polymers and surface-modified proteins. The linkers in the assembly have been programmed to release the incarcerated proteins in its native form, only when subjected to the presence of a specific trigger. The generality and the versatility of the approach have been demonstrated by showing that this strategy can be used for proteins of different sizes and isoelectric points. Moreover, simple modifications in the linker chemistry offers the ability to trigger these assemblies with various chemical inputs. Efficient formation of nanoassemblies based on polymer-protein conjugates has implications in a variety of areas at the interface of chemistry with materials and biology, such as in the generation of active surfaces and in delivery of biologics. As a demonstration of utility in the latter, we have shown that these conjugates can be used to transport functional proteins across cellular membranes.
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Affiliation(s)
- Bin Liu
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | | | - S. Thayumanavan
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Center for Bioactive Delivery, Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, Massachusetts 01003, USA
- Corresponding Author:
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114
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Kovalska V, Vakarov S, Losytskyy M, Kuperman M, Chornenka N, Toporivska Y, Gumienna-Kontecka E, Voloshin Y, Varzatskii O, Mokhir A. Dicarboxyl-terminated iron(ii) clathrochelates as ICD-reporters for globular proteins. RSC Adv 2019; 9:24218-24230. [PMID: 35527894 PMCID: PMC9069836 DOI: 10.1039/c9ra04102h] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/26/2019] [Indexed: 01/07/2023] Open
Abstract
Cage metal complexes iron(ii) clathrochelates, which are inherently CD silent, were discovered to demonstrate intensive output in induced circular dichroism (ICD) spectra upon their assembly to albumins. With the aim to design clathrochelates as protein-sensitive CD reporters, the approach for the functionalization of one chelate α-dioximate fragment of the clathrochelate framework with two non-equivalent substituents was developed, and constitutional isomers of clathrochelate with two non-equivalent carboxyphenylsulfide groups were synthesized. The interaction of designed iron(ii) clathrochelates and their symmetric homologues with globular proteins (serum albumins, lysozyme, β-lactoglobulin (BLG), trypsin, insulin) was studied by protein fluorescence quenching and CD techniques. A highly-intensive ICD output of the clathrochelates was observed upon their association with albumins and BLG. It was shown that in the presence of BLG, different clathrochelate isomers gave spectra of inverted signs, indicating the stabilization of opposite configurations (Λ or Δ) of the clathrochelate framework in the assembly with this protein. So, we suggest that the isomerism of the terminal carboxy group determined preferable configurations of the clathrochelate framework for the fixation in the protein binding site. MALDI TOF results show the formation of BLG-clathrochelate complex with ratio 1 : 1. Based on the docking simulations, the binding of the clathrochelate molecule (all isomers) to the main BLG binding site (calyx) in its open conformation is suggested. The above results point that the variation of the ribbed substituents at the clathrochelate framework is an effective tool to achieve the specificity of clathrochelate ICD reporting properties to the target protein.
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Affiliation(s)
- Vladyslava Kovalska
- Institute of Molecular Biology and Genetics, NASU 150 Zabolotnogo St. 03143 Kyiv Ukraine
| | - Serhii Vakarov
- Princeton Biomolecular Research Labs 26A Saperne Pole St. 01042 Kyiv Ukraine
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU 32/34 Palladin Av. 03142 Kyiv Ukraine
| | - Mykhaylo Losytskyy
- Institute of Molecular Biology and Genetics, NASU 150 Zabolotnogo St. 03143 Kyiv Ukraine
| | - Marina Kuperman
- Institute of Molecular Biology and Genetics, NASU 150 Zabolotnogo St. 03143 Kyiv Ukraine
| | - Nina Chornenka
- Princeton Biomolecular Research Labs 26A Saperne Pole St. 01042 Kyiv Ukraine
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU 32/34 Palladin Av. 03142 Kyiv Ukraine
| | - Yuliya Toporivska
- Faculty of Chemistry, University of Wroclaw 14 F. Joliot-Curie St. 50-383 Wroclaw Poland
| | | | - Yan Voloshin
- Nesmeyanov Institute of Organoelement Compounds RAS 28 Vavilova St. 119991 Moscow Russia
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences 31 Leninsky Prosp. 119991 Moscow Russia
| | - Oleg Varzatskii
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU 32/34 Palladin Av. 03142 Kyiv Ukraine
| | - Andriy Mokhir
- Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg Henkestr. 42 91054 Erlangen Germany
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115
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Fa S, Zhao Y. General Method for Peptide Recognition in Water through Bioinspired Complementarity. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2019; 31:4889-4896. [PMID: 32921904 PMCID: PMC7486028 DOI: 10.1021/acs.chemmater.9b01613] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A general method for peptide recognition has been elusive despite decades of research. Strong binding and selectivity among closely related peptides are necessary for biological applications but have been difficult to achieve with synthetic receptors. With inspiration from highly specific protein-protein and protein-ligand interactions, protein-sized, water-soluble imprinted nanoparticles were prepared via templated polymerization of peptides within cross-linked micelles. Combination of hydrophobic and polar interactions afforded micromolar to submicromolar binding affinities for selected tripeptides. A "golden pair" of functional monomers was identified to enhance both the affinity and selectivity of binding, and enabled differentiation of subtly different sequences including single-point variation of lysine by arginine and insertion of a single glycine at the N- or C-terminus. Biological peptides (β-amyloid peptides) afforded even stronger binding (tens of nanomolar) due to a larger number of complementary interactions between the host and the guest, opening doors to a wide range of biological applications.
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Affiliation(s)
- Shixin Fa
- Department of Chemistry, Iowa State University, Ames, IA 50011-3111
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, IA 50011-3111
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116
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Zhang Y, Liu J, Yu Q, Wen X, Liu Y. Targeted Polypeptide–Microtubule Aggregation with Cucurbit[8]uril for Enhanced Cell Apoptosis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ying‐Ming Zhang
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Jiang‐Hua Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Qilin Yu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Xin Wen
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
- Department of Chemical BiologyNational Pesticide Engineering Research CenterNankai University Tianjin 300071 China
| | - Yu Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
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117
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Zhang Y, Liu J, Yu Q, Wen X, Liu Y. Targeted Polypeptide–Microtubule Aggregation with Cucurbit[8]uril for Enhanced Cell Apoptosis. Angew Chem Int Ed Engl 2019; 58:10553-10557. [DOI: 10.1002/anie.201903243] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/04/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Ying‐Ming Zhang
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Jiang‐Hua Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Qilin Yu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Xin Wen
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
- Department of Chemical BiologyNational Pesticide Engineering Research CenterNankai University Tianjin 300071 China
| | - Yu Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
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118
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Zebaze Ndendjio SA, Isaacs L. Molecular recognition properties of acyclic cucurbiturils toward amino acids, peptides, and a protein. Supramol Chem 2019. [DOI: 10.1080/10610278.2019.1619737] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
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119
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Abstract
Molecular conjugation refers to methods used in biomedicine, advanced materials and nanotechnology to link two partners - from small molecules to large and sometimes functionally complex biopolymers. The methods ideally have a broad structural scope, proceed under very mild conditions (including in H2O), occur at a rapid rate and in quantitative yield with no by-products, enable bioorthogonal reactivity and have zero toxicity. Over the past two decades, the field of click chemistry has emerged to afford us new and efficient methods of molecular conjugation. These methods are based on chemical reactions that produce permanently linked conjugates, and we refer to this field here as covalent click chemistry. Alternatively, if molecular conjugation is undertaken using a pair of complementary molecular recognition partners that associate strongly and selectively to form a thermodynamically stable non-covalent complex, then we refer to this strategy as non-covalent click chemistry. This Perspective is concerned with this latter approach and highlights two distinct applications of non-covalent click chemistry in molecular conjugation: the pre-assembly of molecular conjugates or surface-coated nanoparticles and the in situ capture of tagged biomolecular targets for imaging or analysis.
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Affiliation(s)
- Cynthia L Schreiber
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
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120
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Oohora K, Kajihara R, Jiromaru M, Kitagishi H, Hayashi T. Arginine Residues Provide a Multivalent Effect for Cellular Uptake of a Hemoprotein Assembly. CHEM LETT 2019. [DOI: 10.1246/cl.180897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Ryota Kajihara
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Misa Jiromaru
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Hiroaki Kitagishi
- Department of Molecular Chemistry and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
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121
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Alex JM, Rennie ML, Engilberge S, Lehoczki G, Dorottya H, Fizil Á, Batta G, Crowley PB. Calixarene-mediated assembly of a small antifungal protein. IUCRJ 2019; 6:238-247. [PMID: 30867921 PMCID: PMC6400181 DOI: 10.1107/s2052252519000411] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/08/2019] [Indexed: 05/24/2023]
Abstract
Synthetic macrocycles such as calixarenes and cucurbiturils are increasingly applied as mediators of protein assembly and crystallization. The macrocycle can facilitate assembly by providing a surface on which two or more proteins bind simultaneously. This work explores the capacity of the sulfonato-calix[n]arene (sclx n ) series to effect crystallization of PAF, a small, cationic antifungal protein. Co-crystallization with sclx4, sclx6 or sclx8 led to high-resolution crystal structures. In the absence of sclx n , diffraction-quality crystals of PAF were not obtained. Interestingly, all three sclx n were bound to a similar patch on PAF. The largest and most flexible variant, sclx8, yielded a dimer of PAF. Complex formation was evident in solution via NMR and ITC experiments, showing more pronounced effects with increasing macrocycle size. In agreement with the crystal structure, the ITC data suggested that sclx8 acts as a bidentate ligand. The contributions of calixarene size/conformation to protein recognition and assembly are discussed. Finally, it is suggested that the conserved binding site for anionic calixarenes implicates this region of PAF in membrane binding, which is a prerequisite for antifungal activity.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Martin L. Rennie
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
| | - Gábor Lehoczki
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Hajdu Dorottya
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Ádám Fizil
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Gyula Batta
- Institute of Chemistry, Centre of Arts, Humanities and Sciences, University of Debrecen, Hungary
| | - Peter B. Crowley
- School of Chemistry, National University of Ireland, University Road, Galway, Ireland
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122
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Oohora K, Kajihara R, Fujimaki N, Uchihashi T, Hayashi T. A ring-shaped hemoprotein trimer thermodynamically controlled by the supramolecular heme-heme pocket interaction. Chem Commun (Camb) 2019; 55:1544-1547. [PMID: 30565588 DOI: 10.1039/c8cc09314h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Engineered cytochrome b562, a small hemoprotein, with an externally-attached heme moiety via a moderately long linker at a suitable position predominantly forms a thermodynamically stable ring-shaped trimer in dilute solution. In an equilibrium between supramolecular polymerization and depolymerization, the ring-shaped trimer is kinetically trapped even in a concentrated solution.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan.
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123
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Gill AD, Perez L, Salinas INQ, Byers SR, Liu Y, Hickey BL, Zhong W, Hooley RJ. Selective Array‐Based Sensing of Anabolic Steroids in Aqueous Solution by Host–Guest Reporter Complexes. Chemistry 2019; 25:1740-1745. [DOI: 10.1002/chem.201804854] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Adam D. Gill
- Department of Biochemistry and Molecular Biology University of California-Riverside Riverside CA 92521 USA
| | - Lizeth Perez
- Department of Chemistry University of California-Riverside Riverside CA 92521 USA
| | - Isaac N. Q. Salinas
- Department of Statistics University of California-Riverside Riverside CA 92521 USA
| | - Samantha R. Byers
- Department of Biochemistry and Molecular Biology University of California-Riverside Riverside CA 92521 USA
| | - Yang Liu
- Environmental Toxicology Program University of California-Riverside Riverside CA 92521 USA
| | - Briana L. Hickey
- Department of Chemistry University of California-Riverside Riverside CA 92521 USA
| | - Wenwan Zhong
- Department of Chemistry University of California-Riverside Riverside CA 92521 USA
- Environmental Toxicology Program University of California-Riverside Riverside CA 92521 USA
| | - Richard J. Hooley
- Department of Chemistry University of California-Riverside Riverside CA 92521 USA
- Department of Biochemistry and Molecular Biology University of California-Riverside Riverside CA 92521 USA
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124
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Miskolczy Z, Megyesi M, Toke O, Biczók L. Change of the kinetics of inclusion in cucurbit[7]uril upon hydrogenation and methylation of palmatine. Phys Chem Chem Phys 2019; 21:4912-4919. [DOI: 10.1039/c8cp07231k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The negative activation entropy of tetrahydropalmatine inclusion makes the entry into cucurbit[7]uril significantly slower than in the case of dehydrocorydaline.
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Affiliation(s)
- Zsombor Miskolczy
- Institute of Materials and Environmental Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1519 Budapest
- Hungary
| | - Mónika Megyesi
- Institute of Materials and Environmental Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1519 Budapest
- Hungary
| | - Orsolya Toke
- Laboratory for NMR Spectroscopy
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1519 Budapest
- Hungary
| | - László Biczók
- Institute of Materials and Environmental Chemistry
- Research Centre for Natural Sciences
- Hungarian Academy of Sciences
- 1519 Budapest
- Hungary
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125
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Ertürk G, Akhoundian M, Lueg-Althoff K, Shinde S, Yeung SY, Hedström M, Schrader T, Mattiasson B, Sellergren B. Bisphosphonate ligand mediated ultrasensitive capacitive protein sensor: complementary match of supramolecular and dynamic chemistry. NEW J CHEM 2019. [DOI: 10.1039/c8nj05238g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A powerful polymeric protein sensor was constructed by microcontact imprinting taking advantage of the specific interaction between a bisphosphonate binding monomer and lysine/arginine residues on the surface of trypsin.
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Affiliation(s)
- Gizem Ertürk
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE-20506 Malmö
- Sweden
| | - Maedeh Akhoundian
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE-20506 Malmö
- Sweden
| | | | - Sudhirkumar Shinde
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE-20506 Malmö
- Sweden
| | - Sing Yee Yeung
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE-20506 Malmö
- Sweden
| | - Martin Hedström
- CapSenze Biosystems AB
- Lund
- Sweden
- Department of Biotechnology
- Lund University
| | - Thomas Schrader
- Department of Chemistry
- University of Duisburg-Essen
- Essen
- Germany
| | - Bo Mattiasson
- CapSenze Biosystems AB
- Lund
- Sweden
- Department of Biotechnology
- Lund University
| | - Börje Sellergren
- Department of Biomedical Sciences
- Faculty of Health and Society
- Malmö University
- SE-20506 Malmö
- Sweden
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126
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Alex JM, Corvaglia V, Hu X, Engilberge S, Huc I, Crowley PB. Crystal structure of a protein–aromatic foldamer composite: macromolecular chiral resolution. Chem Commun (Camb) 2019; 55:11087-11090. [DOI: 10.1039/c9cc05330a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A protein–foldamer crystal structure illustrates protein assembly by a sulfonated aromatic oligoamide, and chiral resolution of the foldamer helix handedness.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland
- Galway
- Ireland
| | - Valentina Corvaglia
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
| | - Xiaobo Hu
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
| | | | - Ivan Huc
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
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127
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Brancatelli G, Dalcanale E, Pinalli R, Geremia S. Probing the Structural Determinants of Amino Acid Recognition: X-Ray Studies of Crystalline Ditopic Host-Guest Complexes of the Positively Charged Amino Acids, Arg, Lys, and His with a Cavitand Molecule. Molecules 2018; 23:molecules23123368. [PMID: 30572602 PMCID: PMC6321202 DOI: 10.3390/molecules23123368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/13/2018] [Accepted: 12/18/2018] [Indexed: 11/16/2022] Open
Abstract
Crystallization of tetraphosphonate cavitand Tiiii[H, CH3, CH3] in the presence of positively charged amino acids, namely arginine, lysine, or histidine, afforded host-guest complex structures. The X-ray structure determination revealed that in all three structures, the fully protonated form of the amino acid is ditopically complexed by two tetraphosphonate cavitand molecules. Guanidinium, ammonium, and imidazolium cationic groups of the amino acid side chain are hosted in the cavity of a phosphonate receptor, and are held in place by specific hydrogen bonding interactions with the P=O groups of the cavitand molecule. In all three structures, the positively charged α-ammonium groups form H-bonds with the P=O groups, and with a water molecule hosted in the cavity of a second tetraphosphonate molecule. Furthermore, water-assisted dimerization was observed for the cavitand/histidine ditopic complex. In this 4:2 supramolecular complex, a bridged water molecule is held by two carboxylic acid groups of the dimerized amino acid. The structural information obtained on the geometrical constrains necessary for the possible encapsulation of the amino acids are important for the rational design of devices for analytical and medical applications.
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Affiliation(s)
- Giovanna Brancatelli
- Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy.
| | - Enrico Dalcanale
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Roberta Pinalli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, and INSTM, UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy.
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128
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Dang DT, van Onzen AHAM, Dorland YL, Brunsveld L. Cucurbit[8]uril Reactivation of an Inactivated Caspase-8 Mutant Reveals Differentiated Enzymatic Substrate Processing. Chembiochem 2018; 19:2490-2494. [PMID: 30300966 PMCID: PMC6391946 DOI: 10.1002/cbic.201800521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Indexed: 01/26/2023]
Abstract
Caspase-8 constructs featuring an N-terminal FGG sequence allow for selective twofold recognition by cucurbit[8]uril, which leads to an increase of the enzymatic activity in a cucurbit[8]uril dose-dependent manner. This supramolecular switching has enabled for the first time the study of the same caspase-8 in its two extreme states; as full monomer and as cucurbit[8]uril induced dimer. A mutated, fully monomeric caspase-8 (D384A), which is enzymatically inactive towards its natural substrate caspase-3, could be fully reactivated upon addition of cucurbit[8]uril. In its monomeric state caspase-8 (D384A) still processes a small synthetic substrate, but not the natural caspase-3 substrate, highlighting the close interplay between protein dimerization and active site rearrangement for substrate selectivity. The ability to switch the caspase-8 activity by a supramolecular system thus provides a flexible approach to studying the activity of a protein at different oligomerization states.
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Affiliation(s)
- Dung T. Dang
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering, andInstitute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
| | - Arthur H. A. M. van Onzen
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering, andInstitute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
| | - Yvonne L. Dorland
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering, andInstitute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering, andInstitute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
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129
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Zhang J, Chen H, Cao Y, Feng C, Zhu X, Li G. Design Nanoprobe Based on Its Binding with Amino Acid Residues on Cell Surface and Its Application to Electrochemical Analysis of Cells. Anal Chem 2018; 91:1005-1010. [DOI: 10.1021/acs.analchem.8b04247] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Juan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Hong Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Ya Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Chang Feng
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Genxi Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
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130
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Feng Z, Wang H, Xu B. Instructed Assembly of Peptides for Intracellular Enzyme Sequestration. J Am Chem Soc 2018; 140:16433-16437. [PMID: 30452246 DOI: 10.1021/jacs.8b10542] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Liquid-like droplets of biomacromolecules are emerging as a fundamental mechanism of cellular signaling, but designing synthetic mimics to form such membraneless organelles remains unexplored. Here we report the use of supramolecular assemblies of small peptides, as a mimic of biomacromolecular condensates, for intracellular sequestration of enzymes on endoplasmic reticulum (ER). Specifically, integrating a short peptide with naproxen (a nonsteroidal anti-inflammatory drug (NSAID) and a ligand of cyclooxygenase-2 (COX-2)) generates an enzymatic substrate that acts as a precursor for instructed assembly. Slowly dephosphorylating the precursors by phosphatases forms the corresponding hydrogelators in a cellular environment, which results in the supramolecular assemblies on ER. Consisting of the precursor and the hydrogelator molecules, the assemblies enable the sequestration of COX-2 and protein-tyrosine phosphatase 1B (PTP1B) on ER. Further structure-activity investigation reveals that the colocalization of COX-2 and PTP1B relies on the NSAID motif, the phosphotyrosine, and the enzymatic dephosphorylation of the precursor. This work, for the first time, illustrates the use of supramolecular processes for associating enzymes in cells and may provide insights for understanding intracellular liquid condensates and a new strategy for modulating protein-protein interactions.
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Affiliation(s)
- Zhaoqianqi Feng
- Department of Chemistry , Brandeis University , 415 South Street , Waltham , Massachusetts 02454 , United States
| | - Huaimin Wang
- Department of Chemistry , Brandeis University , 415 South Street , Waltham , Massachusetts 02454 , United States
| | - Bing Xu
- Department of Chemistry , Brandeis University , 415 South Street , Waltham , Massachusetts 02454 , United States
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131
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Pradeepkiran JA, Reddy AP, Reddy PH. Pharmacophore-based models for therapeutic drugs against phosphorylated tau in Alzheimer's disease. Drug Discov Today 2018; 24:616-623. [PMID: 30453058 DOI: 10.1016/j.drudis.2018.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 09/22/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
Abstract
Phosphorylated tau (P-tau) has received much attention in the field of Alzheimer's disease (AD), as a potential therapeutic target owing to its involvement with synaptic damage and neuronal dysfunction. The continuous failure of amyloid β (Aβ)-targeted therapeutics highlights the urgency to consider alternative therapeutic strategies for AD. The present review describes the latest developments in tau biology and function. It also explains abnormal interactions between P-tau with Aβ and the mitochondrial fission protein Drp1, leading to excessive mitochondrial fragmentation and synaptic damage in AD neurons. This article also addresses 3D pharmacophore-based drug models designed to treat patients with AD and other tauopathies.
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Affiliation(s)
- Jangampalli Adi Pradeepkiran
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA
| | - Arubala P Reddy
- Pharmacology & Neuroscience Department, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA
| | - P Hemachandra Reddy
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA; Cell Biology & Biochemistry Department, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA; Pharmacology & Neuroscience Department, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA; Neurology Department, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA; Speech, Language and Hearing Sciences Departments, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA; Garrison Institute on Aging, South West Campus, Texas Tech University Health Sciences Center, 6630 S. Quaker Suite E, MS 7495, Lubbock, TX 79413, USA.
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132
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Zou H, Liu J, Li Y, Li X, Wang X. Cucurbit[8]uril-Based Polymers and Polymer Materials. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802234. [PMID: 30168673 DOI: 10.1002/smll.201802234] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Cucurbit[8]uril (CB[8]) is unique and notable in the cucurbit[n]uril family, since it has a relatively large cavity and thus is able to simultaneously accommodate two guest molecules. Typically, an electron-deficient first guest and an electron-rich second guest can be bound by CB[8] to form a stable 1:1:1 heteroternary supramolecular complex. Additionally, two homo guests can also be strongly dimerized inside the cavity of CB[8] to form a 2:1 homoternary supramolecular complex. During the past decade, by combining polymer science and CB[8] host-guest chemistry, a variety of systems have been established to construct supramolecular polymers with polymer chains typically at the nanoscale/sub-microscale, and CB[8]-based micro/nanostructured polymer materials in the form of polymer networks and hydrogels, microcapsules, micelles, vesicles, and colloidal particles, normally in solution and occasionally on surfaces. This Review summarizes the noncovalent interactions and strategies used for the preparation of CB[8]-based polymers and polymer materials with a focus on the representative and latest developments, followed by a brief discussion of their characterization, properties, and applications.
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Affiliation(s)
- Hua Zou
- School of Materials Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Jing Liu
- School of Materials Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Ying Li
- School of Materials Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Xiaoyan Li
- School of Materials Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Xia Wang
- School of Materials Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
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133
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Mariottini D, Idili A, Nijenhuis MAD, de Greef TFA, Ricci F. DNA-Based Nanodevices Controlled by Purely Entropic Linker Domains. J Am Chem Soc 2018; 140:14725-14734. [PMID: 30351025 DOI: 10.1021/jacs.8b07640] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We demonstrate here the rational design of purely entropic domains as a versatile approach to achieve control of the input/output response of synthetic molecular receptors. To do so and to highlight the versatility and generality of this approach, we have rationally re-engineered two model DNA-based receptors: a clamp-like DNA-based switch that recognizes a specific DNA sequence and an ATP-binding aptamer. We show that, by varying the length of the linker domain that connects the two recognition portions of these receptors, it is possible to finely control their affinity for their specific ligand. Through mathematical modeling and thermodynamic characterization, we also demonstrate for both systems that entropy changes associated with changes in linker length are responsible for affinity modulation and that the linker we have designed behaves as a disordered random-coil polymer. The approach also allows us to regulate the ligand concentration range at which the receptors respond and show optimal specificity. Given these attributes, the use of purely entropic domains appears as a versatile and general approach to finely control the activity of synthetic receptors in a highly predictable and controlled fashion.
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Affiliation(s)
- Davide Mariottini
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , 00133 Rome , Italy
| | - Andrea Idili
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , 00133 Rome , Italy
| | - Minke A D Nijenhuis
- Institute for Complex Molecular Systems , Eindhoven University of Technology , 5600 MB Eindhoven , The Netherlands
| | - Tom F A de Greef
- Institute for Complex Molecular Systems , Eindhoven University of Technology , 5600 MB Eindhoven , The Netherlands
| | - Francesco Ricci
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , 00133 Rome , Italy
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134
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Rennie ML, Fox GC, Pérez J, Crowley PB. Auto‐regulated Protein Assembly on a Supramolecular Scaffold. Angew Chem Int Ed Engl 2018; 57:13764-13769. [DOI: 10.1002/anie.201807490] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/26/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Martin L. Rennie
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
| | - Gavin C. Fox
- Synchrotron SOLEILL'Orme des Merisiers Saint-Aubin BP48 91192 Gif-sur-Yvette Cedex France
| | - Javier Pérez
- Synchrotron SOLEILL'Orme des Merisiers Saint-Aubin BP48 91192 Gif-sur-Yvette Cedex France
| | - Peter B. Crowley
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
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135
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Hisamatsu Y, Umezawa N, Yagi H, Kato K, Higuchi T. Design and synthesis of a 4-aminoquinoline-based molecular tweezer that recognizes protoporphyrin IX and iron(iii) protoporphyrin IX and its application as a supramolecular photosensitizer. Chem Sci 2018; 9:7455-7467. [PMID: 30319746 PMCID: PMC6180317 DOI: 10.1039/c8sc02133c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/14/2018] [Indexed: 01/08/2023] Open
Abstract
We report on the design and synthesis of a new type of 4-aminoquinoline-based molecular tweezer 1 which forms a stable host-guest complex with protoporphyrin IX (PPIX) via multiple interactions in a DMSO and HEPES buffer (pH 7.4) mixed solvent system. The binding constant for the 1 : 1 complex (K 11) between 1 and PPIX is determined to be 4 × 106 M-1. Furthermore, 1 also forms a more stable complex with iron(iii) protoporphyrin IX (Fe(iii)PPIX), the K 11 value for which is one order of magnitude greater than that for PPIX, indicating that 1 could be used as a recognition unit of a synthetic heme sensor. On the other hand, the formation of the stable PPIX·1 complex (supramolecular photosensitizer) prompted us to apply it to photodynamic therapy (PDT). Cell staining experiments using the supramolecular photosensitizer and evaluations of its photocytotoxicity indicate that the PDT activity of PPIX is improved as the result of the formation of a complex with 1.
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Affiliation(s)
- Yosuke Hisamatsu
- Graduate School of Pharmaceutical Sciences , Nagoya City University , 3-1 Tanabe-dori, Mizuho-ku , Nagoya 467-8603 , Japan . ;
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences , Nagoya City University , 3-1 Tanabe-dori, Mizuho-ku , Nagoya 467-8603 , Japan . ;
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences , Nagoya City University , 3-1 Tanabe-dori, Mizuho-ku , Nagoya 467-8603 , Japan . ;
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences , Nagoya City University , 3-1 Tanabe-dori, Mizuho-ku , Nagoya 467-8603 , Japan . ;
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS) , National Institutes of Natural Sciences , 5-1 Higashiyama, Myodaiji , Okazaki 444-8787 , Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences , Nagoya City University , 3-1 Tanabe-dori, Mizuho-ku , Nagoya 467-8603 , Japan . ;
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136
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Sasmal R, Das Saha N, Pahwa M, Rao S, Joshi D, Inamdar MS, Sheeba V, Agasti SS. Synthetic Host-Guest Assembly in Cells and Tissues: Fast, Stable, and Selective Bioorthogonal Imaging via Molecular Recognition. Anal Chem 2018; 90:11305-11314. [PMID: 30148612 PMCID: PMC6569623 DOI: 10.1021/acs.analchem.8b01851] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/27/2018] [Indexed: 12/16/2022]
Abstract
Bioorthogonal strategies are continuing to pave the way for new analytical tools in biology. Although a significant amount of progress has been made in developing covalent reaction based bioorthogonal strategies, balanced reactivity, and stability are often difficult to achieve from these systems. Alternatively, despite being kinetically beneficial, the development of noncovalent approaches that utilize fully synthetic and stable components remains challenging due to the lack of selectivity in conventional noncovalent interactions in the living cellular environment. Herein, we introduce a bioorthogonal assembly strategy based on a synthetic host-guest system featuring Cucurbit[7]uril (CB[7]) and adamantylamine (ADA). We demonstrate that highly selective and ultrastable host-guest interaction between CB[7] and ADA provides a noncovalent mechanism for assembling labeling agents, such as fluorophores and DNA, in cells and tissues for bioorthogonal imaging of molecular targets. Additionally, by combining with covalent reaction, we show that this CB[7]-ADA based noncovalent interaction enables simultaneous bioorthogonal labeling and multiplexed imaging in cells as well as tissue sections. Finally, we show that interaction between CB[7] and ADA fulfills the demands of specificity and stability that is required for assembling molecules in the complexities of a living cell. We demonstrate this by sensitive detection of metastatic cancer-associated cell surface protein marker as well as by showing the distribution and dynamics of F-actin in living cells.
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Affiliation(s)
- Ranjan Sasmal
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
(JNCASR), Bangalore, Karnataka 560064, India
| | - Nilanjana Das Saha
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
(JNCASR), Bangalore, Karnataka 560064, India
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
(JNCASR), Bangalore, Karnataka 560064, India
| | - Meenakshi Pahwa
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
(JNCASR), Bangalore, Karnataka 560064, India
| | - Sushma Rao
- Neuroscience
Unit, Jawaharlal Nehru Centre for Advanced
Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Divyesh Joshi
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Maneesha S. Inamdar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Vasu Sheeba
- Neuroscience
Unit, Jawaharlal Nehru Centre for Advanced
Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Sarit S. Agasti
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
(JNCASR), Bangalore, Karnataka 560064, India
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research
(JNCASR), Bangalore, Karnataka 560064, India
- School of Advanced Materials” (SAMat), Jawaharlal Nehru Centre for Advanced Scientific Research
(JNCASR), Bangalore, Karnataka 560064, India
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137
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Finbloom JA, Francis MB. Supramolecular strategies for protein immobilization and modification. Curr Opin Chem Biol 2018; 46:91-98. [DOI: 10.1016/j.cbpa.2018.05.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/19/2018] [Accepted: 05/29/2018] [Indexed: 02/03/2023]
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138
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Pinalli R, Pedrini A, Dalcanale E. Biochemical sensing with macrocyclic receptors. Chem Soc Rev 2018; 47:7006-7026. [PMID: 30175351 DOI: 10.1039/c8cs00271a] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Preventive healthcare asks for the development of cheap, precise and non-invasive sensor devices for the early detection of diseases and continuous population screening. The actual techniques used for diagnosis, e.g. MRI and PET, or for biochemical marker sensing, e.g. immunoassays, are not suitable for continuous monitoring since they are expensive and prone to false positive responses. Synthetic supramolecular receptors offer new opportunities for the creation of specific, selective and cheap sensor devices for biological sensing of specific target molecules in complex mixtures of organic substances. The fundamental challenges faced in developing such devices are the precise transfer of the molecular recognition events at the solid-liquid interface and its transduction into a readable signal. In this review we present the progress made so far in turning synthetic macrocyclic hosts, namely cyclodextrins, calixarenes, cucurbiturils and cavitands, into effective biochemical sensors and the strategies utilized to solve the above mentioned issues. The performances of the developed sensing devices based on these receptors in detecting specific biological molecules, drugs and proteins are critically discussed.
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Affiliation(s)
- Roberta Pinalli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy.
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139
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Zhao Y. Sequence-Selective Recognition of Peptides in Aqueous Solution: A Supramolecular Approach through Micellar Imprinting. Chemistry 2018; 24:14001-14009. [PMID: 29694679 PMCID: PMC6150789 DOI: 10.1002/chem.201801401] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 04/20/2018] [Indexed: 11/09/2022]
Abstract
Sequence-selective recognition of peptides in water has been one of the most important and yet unsolved problems in bioorganic and supramolecular chemistry. The motivation comes from not only the importance of these molecules in biology but also the fundamental challenges involved in the research. Molecular imprinting in doubly cross-linked surfactant micelles offers a unique solution to this problem by creating a "supramolecular code" on the micelle surface that matches the structural features of the peptide chain. Hydrophobic "dimples" are constructed on imprinted micelles that match the hydrophobic side chains of the peptide precisely in size and shape. Polar binding functionalities are installed at correct positions to interact with specific acidic and basic groups on the peptide. Secondary hydrogen-bonding and electrostatic interactions are introduced through imprinting to enhance the binding affinity and specificity further. Binding affinities of tens of nanomolar are readily achieved in water for biological peptides with over a dozen residues. Excellent binding selectivity is observed even for subtly different peptides. The synthesis of these protein-sized nanoparticles involves a one-pot reaction complete within 2 days; purification requires nothing but precipitation and solvent washing. These features make the molecularly imprinted nanoparticles (MINPs) highly promising peptide-binding "artificial antibodies" for chemical and biological applications.
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Affiliation(s)
- Yan Zhao
- Department of Chemistry, Iowa State University, Ames, IA 50011-3111, U.S.A., Fax: (+1) 515-294-0105,
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140
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Rennie ML, Fox GC, Pérez J, Crowley PB. Auto‐regulated Protein Assembly on a Supramolecular Scaffold. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807490] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Martin L. Rennie
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
| | - Gavin C. Fox
- Synchrotron SOLEILL'Orme des Merisiers Saint-Aubin BP48 91192 Gif-sur-Yvette Cedex France
| | - Javier Pérez
- Synchrotron SOLEILL'Orme des Merisiers Saint-Aubin BP48 91192 Gif-sur-Yvette Cedex France
| | - Peter B. Crowley
- School of ChemistryNational University of Ireland Galway University Road Galway Ireland
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141
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Oohora K, Fujimaki N, Kajihara R, Watanabe H, Uchihashi T, Hayashi T. Supramolecular Hemoprotein Assembly with a Periodic Structure Showing Heme-Heme Exciton Coupling. J Am Chem Soc 2018; 140:10145-10148. [PMID: 30067348 DOI: 10.1021/jacs.8b06690] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A supramolecular assembly of units of cytochrome b562 with externally attached heme having intermolecular linkages formed via the heme-heme pocket interaction was investigated in an effort to construct a well-defined structure. The engineered site for surface attachment of heme at Cys80 in an N80C mutant of cytochrome b562 provides the primary basis for the formation of the periodic assembly structure, which is characterized herein by circular dichroism (CD) spectroscopy and high-speed atomic force microscopy (AFM). This assembly represents the first example of the observation of a split-type Cotton effect by heme-heme exciton coupling in an artificial hemoprotein assembly system. Molecular dynamics simulations validated by simulated CD spectra, AFM images, and mutation experiments reveal that the assembly has a periodic helical structure with 3 nm pitches, suggesting the formation of the assembled structure is driven not only by the heme-heme pocket interaction but also by additional secondary hydrogen bonding and/or electrostatic interactions at the protein interfaces of the assembly.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering , Osaka University , Suita 565-0871 , Japan.,Frontier Research Base for Global Young Researchers, Graduate School of Engineering , Osaka University , Suita 565-0871 , Japan.,PRESTO, Japan Science and Technology Agency (JST) , Kawaguchi 332-0012 , Japan
| | - Nishiki Fujimaki
- Department of Applied Chemistry, Graduate School of Engineering , Osaka University , Suita 565-0871 , Japan
| | - Ryota Kajihara
- Department of Applied Chemistry, Graduate School of Engineering , Osaka University , Suita 565-0871 , Japan
| | - Hiroki Watanabe
- Department of Physics , Nagoya University , Nagoya 464-8602 , Japan
| | | | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering , Osaka University , Suita 565-0871 , Japan
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142
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Zhang Y, Zhang N, Xiao K, Yu Q, Liu Y. Photo‐Controlled Reversible Microtubule Assembly Mediated by Paclitaxel‐Modified Cyclodextrin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804620] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ying‐Ming Zhang
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Ni‐Yuan Zhang
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Kui Xiao
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Qilin Yu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Yu Liu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
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143
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Zhang Y, Zhang N, Xiao K, Yu Q, Liu Y. Photo‐Controlled Reversible Microtubule Assembly Mediated by Paclitaxel‐Modified Cyclodextrin. Angew Chem Int Ed Engl 2018; 57:8649-8653. [DOI: 10.1002/anie.201804620] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Ying‐Ming Zhang
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Ni‐Yuan Zhang
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Kui Xiao
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Qilin Yu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Yu Liu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China
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144
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Guagnini F, Antonik PM, Rennie ML, O'Byrne P, Khan AR, Pinalli R, Dalcanale E, Crowley PB. Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803232] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Francesca Guagnini
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Paweł M. Antonik
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Peter O'Byrne
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Roberta Pinalli
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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145
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Guagnini F, Antonik PM, Rennie ML, O'Byrne P, Khan AR, Pinalli R, Dalcanale E, Crowley PB. Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Angew Chem Int Ed Engl 2018; 57:7126-7130. [DOI: 10.1002/anie.201803232] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Francesca Guagnini
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Paweł M. Antonik
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Peter O'Byrne
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Roberta Pinalli
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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146
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Huang Y, Liu Y, Liu S, Wu R, Wu Z. One-Pot formation of novel [3+3] NH-CH2 bridged cyclophanes. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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147
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Hewitt SH, Wilson AJ. Generation of Dynamic Combinatorial Libraries Using Hydrazone-Functionalized Surface Mimetics. European J Org Chem 2018; 2018:1872-1879. [PMID: 29780280 PMCID: PMC5947633 DOI: 10.1002/ejoc.201800022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Indexed: 01/01/2023]
Abstract
Dynamic combinatorial chemistry (DCC) represents an approach, whereby traditional supramolecular scaffolds used for protein surface recognition might be exploited to achieve selective high affinity target recognition. Synthesis, in situ screening and amplification under selection pressure allows the generation of ligands, which bear different moieties capable of making multivalent non‐covalent interactions with target proteins. Generic tetracarboxyphenyl porphyrin scaffolds bearing four hydrazide moieties have been used to form dynamic combinatorial libraries (DCLs) using aniline‐catalyzed reversible hydrazone exchange reactions, in 10 % DMSO, 5 mm NH4OAc, at pH 6.75. High resolution mass spectrometry (HRMS) was used to monitor library composition and establish conditions under which equilibria were established.
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Affiliation(s)
- Sarah H Hewitt
- School of Chemistry University of Leeds Woodhouse Lane 9JT Leeds LS2 UK.,Astbury Centre for Structural Molecular Biology University of Leeds Woodhouse Lane 9JT Leeds LS2 UK
| | - Andrew J Wilson
- School of Chemistry University of Leeds Woodhouse Lane 9JT Leeds LS2 UK.,Astbury Centre for Structural Molecular Biology University of Leeds Woodhouse Lane 9JT Leeds LS2 UK
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148
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Alemán García MÁ, Magdalena Estirado E, Milroy LG, Brunsveld L. Dual-Input Regulation and Positional Control in Hybrid Oligonucleotide/Discotic Supramolecular Wires. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201800148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Miguel Ángel Alemán García
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; PO Box 513 5600MB Eindhoven The Netherlands
| | - Eva Magdalena Estirado
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; PO Box 513 5600MB Eindhoven The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; PO Box 513 5600MB Eindhoven The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems; Department of Biomedical Engineering; Eindhoven University of Technology; PO Box 513 5600MB Eindhoven The Netherlands
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149
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Alemán García MÁ, Magdalena Estirado E, Milroy L, Brunsveld L. Dual-Input Regulation and Positional Control in Hybrid Oligonucleotide/Discotic Supramolecular Wires. Angew Chem Int Ed Engl 2018; 57:4976-4980. [PMID: 29457856 PMCID: PMC5969285 DOI: 10.1002/anie.201800148] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/14/2018] [Indexed: 12/27/2022]
Abstract
The combination of oligonucleotides and synthetic supramolecular systems allows for novel and long‐needed modes of regulation of the self‐assembly of both molecular elements. Discotic molecules were conjugated with short oligonucleotides and their assembly into responsive supramolecular wires studied. The self‐assembly of the discotic molecules provides additional stability for DNA‐duplex formation owing to a cooperative effect. The appended oligonucleotides allow for positional control of the discotic elements within the supramolecular wire. The programmed assembly of these hybrid architectures can be modulated through the DNA, for example, by changing the number of base pairs or salt concentration, and through the discotic platform by the addition of discotic elements without oligonucleotide handles. These hybrid supramolecular‐DNA structures allow for advanced levels of control over 1D dynamic platforms with responsive regulatory elements at the interface with biological systems.
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Affiliation(s)
- Miguel Ángel Alemán García
- Laboratory of Chemical Biology and Institute for Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyPO Box 5135600MBEindhovenThe Netherlands
| | - Eva Magdalena Estirado
- Laboratory of Chemical Biology and Institute for Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyPO Box 5135600MBEindhovenThe Netherlands
| | - Lech‐Gustav Milroy
- Laboratory of Chemical Biology and Institute for Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyPO Box 5135600MBEindhovenThe Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute for Complex Molecular SystemsDepartment of Biomedical EngineeringEindhoven University of TechnologyPO Box 5135600MBEindhovenThe Netherlands
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Iskierko Z, Noworyta K, Sharma PS. Molecular recognition by synthetic receptors: Application in field-effect transistor based chemosensing. Biosens Bioelectron 2018. [PMID: 29525669 DOI: 10.1016/j.bios.2018.02.058] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Molecular recognition, i.e., ability of one molecule to recognize another through weak bonding interactions, is one of the bases of life. It is often implemented to sensing systems of high merits. Preferential recognition of the analyte (guest) by the receptor (host) induces changes in physicochemical properties of the sensing system. These changes are measured by using suitable signal transducers. Because of possibility of miniaturization, fast response, and high sensitivity, field-effect transistors (FETs) are more frequently being used for that purpose. A FET combined with a biological material offers the potential to overcome many challenges approached in sensing. However, low stability of biological materials under measurement conditions is a serious problem. To circumvent this problem, synthetic receptors were integrated with the gate surface of FETs to provide robust performance. In the present critical review, the approach utilized to devise chemosensors integrating synthetic receptors and FET transduction is discussed in detail. The progress in this field was summarized and important outcome was provided.
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Affiliation(s)
- Zofia Iskierko
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Krzysztof Noworyta
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
| | - Piyush Sindhu Sharma
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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