1
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Shi J, Xiong Y, Li J, Gao B, Qing G, Sheng Q, Lan M. Utilizing 4-Sulfonylcalix[4]arene as a Selective Mobile Phase Additive for the Capture of Methylated Peptides. Anal Chem 2025; 97:2428-2436. [PMID: 39865840 DOI: 10.1021/acs.analchem.4c06041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Protein methylation has attracted increasing attention due to its significant regulatory roles in various biological processes. However, the diversity of methylation forms, subtle differences between methylated and nonmodified sites, and their ultralow abundances pose substantial challenges for capturing and isolating methylated peptides from biological samples. Herein, we develop a chromatographic method that utilizes 4-sulfonylcalix[4]arene (SC4A) as a mobile phase additive and Click-Maltose as the stationary phase to separate methylated/nonmethylated peptides through the adsorption of the SC4A-K(Me3) complex. By utilization of the interaction between calix[4]arene cavities and trimethylated lysine residues, methylated peptides could be specifically separated from peptide samples. This method significantly improves the signal-to-noise ratio (S/N), even in samples containing a 10-fold excess of bovine serum albumin (BSA) trypsin digests. Additionally, we successfully enriched 12 methylated peptides from histone digests. This study paves the way for the selective enrichment of lysine methylated peptides in post-translational modification proteomics (PTMs), enhancing both the capture efficiency and selectivity of methylated peptides and providing robust technical support for subsequent proteomics research.
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Affiliation(s)
- Jie Shi
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Meilong Road, Shanghai 200237, P. R. China
| | - Yuting Xiong
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Junyan Li
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Meilong Road, Shanghai 200237, P. R. China
| | - Baolei Gao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Meilong Road, Shanghai 200237, P. R. China
| | - Guangyan Qing
- State Key Laboratory of Medical Proteomics, National Chromatographic R. & A. Center, CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Qianying Sheng
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Meilong Road, Shanghai 200237, P. R. China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Meilong Road, Shanghai 200237, P. R. China
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2
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Orlandini M, Bonacini A, Favero A, Secchi A, Lazzarini L, Verucchi R, Dalcanale E, Pedrini A, Sidoli S, Pinalli R. Enrichment of histone tail methylated lysine residues via cavitand-decorated magnetic nanoparticles for ultra-sensitive proteomics. Chem Sci 2024; 15:13102-13110. [PMID: 39148787 PMCID: PMC11322979 DOI: 10.1039/d4sc02076f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/12/2024] [Indexed: 08/17/2024] Open
Abstract
Nearly every protein in the human body is modified with post-translational modifications (PTMs). PTMs affect proteins on many levels, including their function, interaction, half-life, and localization. Specifically, for histone proteins, PTMs such as lysine methylation and acetylation play essential roles in chromatin dynamic regulations. For this reason, methods to accurately detect and quantify PTMs are of paramount importance in cell biology, biochemistry, and disease biology. Most protein modifications are sub-stoichiometric, so, to be analyzed, they need methods of enrichment, which are mostly based on antibodies. Antibodies are produced using animals, resulting in high costs, ecological concerns, significant batch variations, and ethical implications. We propose using ferromagnetic nanoparticles functionalized with synthetic receptors, namely tetraphosphonate cavitands, as a tool for selective enrichment of methylated lysines present on histone tails. Before the enrichment step, histone proteins from calf thymus were digested to facilitate the recognition process and to obtain small peptides suitable for mass analyses. Cavitands were anchored on ferromagnetic nanoparticles to easily separate the PTM-peptides of interest from the rest of the proteolytic peptides. Our approach detects more modified peptides with higher signal intensity, rivaling commercial antibodies. This chemical strategy offers a cost-effective and efficient alternative for PTM detection, potentially advancing proteomic research.
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Affiliation(s)
- Martina Orlandini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, INSTM, UdR Parma Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Alex Bonacini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, INSTM, UdR Parma Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Alessia Favero
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, INSTM, UdR Parma Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Andrea Secchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, INSTM, UdR Parma Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Laura Lazzarini
- IMEM-CNR, Institute of Materials for Electronics and Magnetism, National Research Council Parco Area delle Scienze 37/A 43124 Parma Italy
| | - Roberto Verucchi
- IMEM-CNR, Institute of Materials for Electronics and Magnetism, National Research Council, Trento Unit via alla Cascata 56/C 38123 Trento Italy
| | - Enrico Dalcanale
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, INSTM, UdR Parma Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Alessandro Pedrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, INSTM, UdR Parma Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine Bronx NY 10461 USA
| | - Roberta Pinalli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, INSTM, UdR Parma Parco Area delle Scienze 17/A 43124 Parma Italy
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3
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Maji A, Soutar CP, Zhang J, Lewandowska A, Uno BE, Yan S, Shelke Y, Murhade G, Nimerovsky E, Borcik CG, Arango AS, Lange JD, Marin-Toledo JP, Lyu Y, Bailey KL, Roady PJ, Holler JT, Khandelwal A, SantaMaria AM, Sanchez H, Juvvadi PR, Johns G, Hageman MJ, Krise J, Gebremariam T, Youssef EG, Bartizal K, Marr KA, Steinbach WJ, Ibrahim AS, Patterson TF, Wiederhold NP, Andes DR, Pogorelov TV, Schwieters CD, Fan TM, Rienstra CM, Burke MD. Tuning sterol extraction kinetics yields a renal-sparing polyene antifungal. Nature 2023; 623:1079-1085. [PMID: 37938782 PMCID: PMC10883201 DOI: 10.1038/s41586-023-06710-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 10/04/2023] [Indexed: 11/09/2023]
Abstract
Decades of previous efforts to develop renal-sparing polyene antifungals were misguided by the classic membrane permeabilization model1. Recently, the clinically vital but also highly renal-toxic small-molecule natural product amphotericin B was instead found to kill fungi primarily by forming extramembraneous sponge-like aggregates that extract ergosterol from lipid bilayers2-6. Here we show that rapid and selective extraction of fungal ergosterol can yield potent and renal-sparing polyene antifungals. Cholesterol extraction was found to drive the toxicity of amphotericin B to human renal cells. Our examination of high-resolution structures of amphotericin B sponges in sterol-free and sterol-bound states guided us to a promising structural derivative that does not bind cholesterol and is thus renal sparing. This derivative was also less potent because it extracts ergosterol more slowly. Selective acceleration of ergosterol extraction with a second structural modification yielded a new polyene, AM-2-19, that is renal sparing in mice and primary human renal cells, potent against hundreds of pathogenic fungal strains, resistance evasive following serial passage in vitro and highly efficacious in animal models of invasive fungal infections. Thus, rational tuning of the dynamics of interactions between small molecules may lead to better treatments for fungal infections that still kill millions of people annually7,8 and potentially other resistance-evasive antimicrobials, including those that have recently been shown to operate through supramolecular structures that target specific lipids9.
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Affiliation(s)
- Arun Maji
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Corinne P Soutar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jiabao Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Agnieszka Lewandowska
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Brice E Uno
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Su Yan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Yogesh Shelke
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ganesh Murhade
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Evgeny Nimerovsky
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department for NMR-Based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Collin G Borcik
- Molecule Maker Lab, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA
| | - Andres S Arango
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Justin D Lange
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | | | - Yinghuan Lyu
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Pathology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Keith L Bailey
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Patrick J Roady
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jordan T Holler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anuj Khandelwal
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anna M SantaMaria
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Hiram Sanchez
- Department of Medicine, Section of Infectious Disease, University of Wisconsin-Madison, Madison, WI, USA
| | - Praveen R Juvvadi
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Michael J Hageman
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
| | - Joanna Krise
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
| | | | - Eman G Youssef
- Division of Infectious Diseases, The Lundquist Institute, Torrance, CA, USA
| | | | | | - William J Steinbach
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Ashraf S Ibrahim
- Division of Infectious Diseases, The Lundquist Institute, Torrance, CA, USA
- David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Thomas F Patterson
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Nathan P Wiederhold
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - David R Andes
- Department of Medicine, Section of Infectious Disease, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Taras V Pogorelov
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- School of Chemical Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Charles D Schwieters
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Timothy M Fan
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chad M Rienstra
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, USA.
- Morgridge Institute for Research, University of Wisconsin-Madison, Madison, WI, USA.
| | - Martin D Burke
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
- Molecule Maker Lab Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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4
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Abuhasan OM, El-Barghouthi MI, Bodoor K, Rawashdeh AMM, Assaf KI. Molecular recognition of tripeptides containing tryptophan by cucurbit[8]uril: A computational study. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
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5
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Liu JL, Zhou XM, Sun M, Jia AQ, Shi HT, Zhang QF. A resorcinarene based chelating agent for selective cloud point extraction of Pb2+ ions in water: Synthesis, structural characterization and analytical applications. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
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6
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Molecular Dynamics and TD‐DFT Study of the Ternary Complexes of Cucurbit[8]uril with Aromatic Amino Acids and Auxiliary Ligands. ChemistrySelect 2022. [DOI: 10.1002/slct.202201988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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King D, Wilson CR, Herron L, Deng CL, Mehdi S, Tiwary P, Hof F, Isaacs L. Molecular recognition of methylated amino acids and peptides by Pillar[6]MaxQ. Org Biomol Chem 2022; 20:7429-7438. [PMID: 36097881 PMCID: PMC9632254 DOI: 10.1039/d2ob01487d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the molecular recognition properties of Pillar[n]MaxQ (P[n]MQ) toward a series of (methylated) amino acids, amino acid amides, and post-translationally modified peptides by a combination of 1H NMR, isothermal titration calorimetry, indicator displacement assays, and molecular dynamics simulations. We find that P6MQ is a potent receptor for N-methylated amino acid side chains. P6MQ recognized the H3K4Me3 peptide with Kd = 16 nM in phosphate buffered saline.
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Affiliation(s)
- David King
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
| | - Chelsea R Wilson
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada.
| | - Lukas Herron
- Biophysics Program, University of Maryland, College Park, MD 20742, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Chun-Lin Deng
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
| | - Shams Mehdi
- Biophysics Program, University of Maryland, College Park, MD 20742, USA
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Pratyush Tiwary
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA.
| | - Fraser Hof
- Department of Chemistry, University of Victoria, Victoria, BC, V8W 3V6, Canada.
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA.
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8
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Montà-González G, Sancenón F, Martínez-Máñez R, Martí-Centelles V. Purely Covalent Molecular Cages and Containers for Guest Encapsulation. Chem Rev 2022; 122:13636-13708. [PMID: 35867555 PMCID: PMC9413269 DOI: 10.1021/acs.chemrev.2c00198] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cage compounds offer unique binding pockets similar to enzyme-binding sites, which can be customized in terms of size, shape, and functional groups to point toward the cavity and many other parameters. Different synthetic strategies have been developed to create a toolkit of methods that allow preparing tailor-made organic cages for a number of distinct applications, such as gas separation, molecular recognition, molecular encapsulation, hosts for catalysis, etc. These examples show the versatility and high selectivity that can be achieved using cages, which is impossible by employing other molecular systems. This review explores the progress made in the field of fully organic molecular cages and containers by focusing on the properties of the cavity and their application to encapsulate guests.
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Affiliation(s)
- Giovanni Montà-González
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM) Universitat
Politècnica de València, Universitat de València. Camino de Vera, s/n 46022, Valencia, Spain
| | - Félix Sancenón
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM) Universitat
Politècnica de València, Universitat de València. Camino de Vera, s/n 46022, Valencia, Spain,CIBER
de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain,Centro
de Investigación Príncipe Felipe, Unidad Mixta UPV-CIPF
de Investigación de Mecanismos de Enfermedades y Nanomedicina,
Valencia, Universitat Politècnica
de València, 46012 Valencia, Spain,Instituto
de Investigación Sanitaria la Fe, Unidad Mixta de Investigación
en Nanomedicina y Sensores, Universitat
Politènica de València, 46026 València, Spain,Departamento
de Química, Universitat Politècnica
de València, 46022 Valencia, Spain
| | - Ramón Martínez-Máñez
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM) Universitat
Politècnica de València, Universitat de València. Camino de Vera, s/n 46022, Valencia, Spain,CIBER
de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain,Centro
de Investigación Príncipe Felipe, Unidad Mixta UPV-CIPF
de Investigación de Mecanismos de Enfermedades y Nanomedicina,
Valencia, Universitat Politècnica
de València, 46012 Valencia, Spain,Instituto
de Investigación Sanitaria la Fe, Unidad Mixta de Investigación
en Nanomedicina y Sensores, Universitat
Politènica de València, 46026 València, Spain,Departamento
de Química, Universitat Politècnica
de València, 46022 Valencia, Spain,R.M.-M.: email,
| | - Vicente Martí-Centelles
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM) Universitat
Politècnica de València, Universitat de València. Camino de Vera, s/n 46022, Valencia, Spain,V.M.-C.:
email,
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9
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Abstract
ConspectusThis Account summarizes the progress in protein-calixarene complexation, tracing the developments from binary recognition to the glue activity of calixarenes and beyond to macrocycle-mediated frameworks. During the past 10 years, we have been tackling the question of protein-calixarene complexation in several ways, mainly by cocrystallization and X-ray structure determination as well as by solution state methods, NMR spectroscopy, isothermal titration calorimetry (ITC), and light scattering. Much of this work benefitted from collaboration, highlighted here. Our first breakthrough was the cocrystallization of cationic cytochrome c with sulfonato-calix[4]arene leading to a crystal structure defining three binding sites. Together with NMR studies, a dynamic complexation was deduced in which the calixarene explores the protein surface. Other cationic proteins were similarly amenable to cocrystallization with sulfonato-calix[4]arene, confirming calixarene-arginine/lysine encapsulation and consequent protein assembly. Calixarenes bearing anionic substituents such as sulfonate or phosphonate, but not carboxylate, have proven useful.Studies with larger calix[n]arenes (n = 6, 8) demonstrated the bigger better binder phenomenon with increased affinities and more interesting assemblies, including solution-state oligomerization and porous frameworks. While the calix[4]arene cavity accommodates a single cationic side chain, the larger macrocycles adopt different conformations, molding to the protein surface and accommodating several residues (hydrophobic, polar, and/or charged) in small cavities. In addition to accommodating protein features, the calixarene can bind exogenous components such as polyethylene glycol (PEG), metal ions, buffer, and additives. Ternary cocrystallization of cytochrome c, sulfonato-calix[8]arene, and spermine resulted in altered framework fabrication due to calixarene encapsulation of the tetraamine. Besides host-guest chemistry with exogenous components, the calixarene can also self-assemble, with numerous instances of macrocycle dimers.Calixarene complexation enables protein encapsulation, not merely side chain encapsulation. Cocrystal structures of sulfonato-calix[8]arene with cytochrome c or Ralstonia solanacearum lectin (RSL) provide evidence of encapsulation, with multiple calixarenes masking the same protein. NMR studies of cytochrome c and sulfonato-calix[8]arene are also consistent with multisite binding. In the case of RSL, a C3 symmetric trimer, up to six calixarenes bind the protein yielding a cubic framework mediated by calixarene dimers. Biomolecular calixarene complexation has evolved from molecular recognition to framework construction. This latter development contributes to the challenge in design and preparation of porous molecular materials. Cytochrome c and sulfonato-calix[8]arene form frameworks with >60% solvent in which the degree of porosity depends on the protein:calixarene ratio and the crystallization conditions. Recent developments with RSL led to three frameworks with varying porosity depending on the crystallization conditions, particularly the pH. NMR studies indicate a pH-triggered assembly in which two acidic residues appear to play key roles. The field of supramolecular protein chemistry is growing, and this Account aims to encourage new developments at the interface between biomolecular and synthetic/supramolecular chemistry.
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Affiliation(s)
- Peter B Crowley
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway H91 TK33, Ireland
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10
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Zhong W, Hooley RJ. Combining Excellent Selectivity with Broad Target Scope: Biosensing with Arrayed Deep Cavitand Hosts. Acc Chem Res 2022; 55:1035-1046. [PMID: 35302733 DOI: 10.1021/acs.accounts.2c00026] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Simple macrocyclic water-soluble hosts such as cucurbiturils, cyclophanes, and calixarenes have long been used for biosensing via indicator displacement assays. Using multiple hosts and dyes in an arrayed format allows pattern recognition-based "chemical nose" sensing, which confers exquisite selectivity, even rivaling the abilities of biological recognition tools such as antibodies. However, a challenge in indicator displacement-based biosensing with macrocyclic hosts is that selectivity and scope are often inversely correlated: strong selectivity for a specific target can limit wide application, and broad scope sensing can suffer from a lack of selectivity between similar targets. This problem can be addressed by using water-soluble, self-folding deep cavitands as hosts. These flexible bowl-shaped receptors can be easily functionalized with different motifs at the upper and lower rim, and the large cavities can bind many different fluorescent dyes, causing either fluorescence enhancement or quenching upon binding.Cavity-based affinity is strongest for NMe3+ groups such as trimethyl-lysine, and we have exploited this for the site-selective recognition of post-translational lysine methylations in oligopeptides. The host recognizes the NMe3+ group, and by applying differently functionalized hosts in an arrayed format, discrimination between identical modifications at different positions on the oligopeptide is possible. Multiple recognition elements can be exploited for selectivity, including a defined, yet "breathable" cavity, and variable upper rim functions oriented toward the target.While the performance of the host/guest sensing system is impressive for lysine methylations, the most important advance is the use of multiple different sensing mechanisms that can target a broad range of different biorelevant species. The amphiphilic deep cavitands can both bind fluorescent dyes and interact with charged biomolecules. These non-cavity-based interactions, when paired with additives such as heavy metal ions, modulate fluorescence response in an indirect manner, and these different mechanisms allow selective recognition of serine phosphorylation, lysine acetylation, and arginine citrullination. Other targets include heavy metals, drugs of abuse, and protein isoforms. Furthermore, the hosts can be applied in supramolecular tandem assays of enzyme function: the broad scope allows analysis of such different enzymes as chromatin writers/erasers, kinases, and phosphatases, all from a single host scaffold. Finally, the indirect sensing concept allows application in sensing different oligonucleotide secondary structures, including G-quadruplexes, hairpins, triplexes, and i-motifs. Discrimination between DNA strands with highly similar structures such as G-quadruplex strands with bulges and vacancies can be achieved. Instead of relying on a single highly specific fluorescent probe, the synthetic hosts tune the fluorophore-DNA interaction, introducing multiple recognition equilibria that modulate the fluorescence signal. By applying machine learning algorithms, a classification model can be established that can accurately predict the folding state of unknown sequences. Overall, the unique recognition profile of self-folded deep cavitands provides a powerful, yet simple sensing platform, one that can be easily tuned for a wide scope of biorelevant targets, in complex biological media, without sacrificing selectivity in the recognition.
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11
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Kubik S. When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water. ChemistryOpen 2022; 11:e202200028. [PMID: 35373466 PMCID: PMC8977507 DOI: 10.1002/open.202200028] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/17/2022] [Indexed: 12/19/2022] Open
Abstract
Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water-mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor-substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.
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Affiliation(s)
- Stefan Kubik
- Technische Universität KaiserslauternFachbereich Chemie – Organische ChemieErwin-Schrödinger-Straße 5467663KaiserslauternGermany
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12
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El-Barghouthi MI, Bodoor K, Abuhasan OM, Assaf KI, Al Hourani BJ, Rawashdeh AMM. Binary and Ternary Complexes of Cucurbit[8]uril with Tryptophan, Phenylalanine, and Tyrosine: A Computational Study. ACS OMEGA 2022; 7:10729-10737. [PMID: 35382313 PMCID: PMC8973077 DOI: 10.1021/acsomega.2c00511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Selective binding of amino acids, peptides, and proteins by synthetic molecules and elucidation of the geometry and dynamics of the resulting complexes and their strengths are active areas of contemporary research. In recent work, we analyzed via molecular dynamics (MD) simulations the complexes formed between cucurbit[7]uril (CB7) and three aromatic amino acids: tryptophan (W), phenylalanine (F), and tyrosine (Y). Herein, we continue this line of research by performing MD simulations lasting 100 ns to investigate the formation, stabilities, binding modes, dynamics, and specific host-guest noncovalent interactions contributing to the formation of the binary (1:1) and ternary (2:1) complexes in aqueous solution between W, F, and Y amino acids and cucurbit[8]uril (CB8). All complexes were found to be stable, with the binding in each complex dominated by one mode (except for the F-CB8 complex, which had two) characterized by encapsulation of the aromatic side chains of the amino acids within the cavity of CB8 and the exclusion of their ammonium and carboxylate groups. Using the molecular mechanics/Poisson-Boltzmann surface area method to estimate the individual contributions to the overall free energies of binding, results revealed that the key role is played by the amino acid side chains in stabilizing the complexes through their favorable van der Waals interactions with the CB8 cavity and the importance of favorable electrostatic interactions between the carbonyl portal of CB8 and the ammonium group of the amino acid. Visual analysis of structures of the ternary complexes indicated the presence of π-π stacking between the aromatic side chains of the included amino acids. The insights provided by this work may be of value for further efforts aiming to employ the recognition properties of CB8 toward amino acids in applications requiring more elaborate recognition of short peptides and proteins.
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Affiliation(s)
- Musa I. El-Barghouthi
- Department
of Chemistry, Faculty of Science, The Hashemite
University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Khaled Bodoor
- Department
of Physics, The University of Jordan, Amman 11942, Jordan
| | - Osama M. Abuhasan
- Department
of Chemistry, Faculty of Science, The Hashemite
University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Khaleel I. Assaf
- Faculty
of Science, Al-Balqa Applied University, Al-Salt 19117, Jordan
| | - Baker Jawabrah Al Hourani
- Department
of Biology and Chemistry, Embry Riddle Aeronautical
University, 3700 Willow
Creek Rd, Prescott, Arizona 86304, USA
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13
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Cesari A, Rosa-Gastaldo D, Pedrini A, Rastrelli F, Dalcanale E, Pinalli R, Mancin F. Selective NMR detection of N-methylated amines using cavitand-decorated silica nanoparticles as receptors. Chem Commun (Camb) 2022; 58:10861-10864. [DOI: 10.1039/d2cc04199e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a strategy for the realization of NMR chemosensors based on the spontaneous self-assembly of lower rim pyridinium-functionalized tetraphopshonate cavitands on commercial silica nanoparticles. These nanohybrids enable the selective...
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14
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Anthrylphosphonate and π-conjugated acid cocrystal as a Mycobacterium tuberculosis inhibitor: Role of P=O…H interactions. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Fujimoto H, Shimoyama D, Katayanagi K, Kawata N, Hirao T, Haino T. Negative Cooperativity in Guest Binding of a Ditopic Self-Folding Biscavitand. Org Lett 2021; 23:6217-6221. [PMID: 34232668 DOI: 10.1021/acs.orglett.1c01837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A brand-new self-folding biscavitand was synthesized from a feet-to-feet-connected bisresorcinarene. The X-ray crystal structure of the biscaivtand showed that the two cavities are tightly connected with four butylene linkages. The conformationally coupled two cavities accommodated two cationic guests, showing a homotropic negative cooperativity in nonpolar solvents (toluene and chloroform). A polar tetrahydrofuran solvent weakened the cyclic hydrogen bonding interactions of the biscavitand, which resulted in noncooperative guest binding.
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Affiliation(s)
- Haruna Fujimoto
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Daisuke Shimoyama
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Katsuo Katayanagi
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Naomi Kawata
- Natural Science Center for Basic Research and Development (N-BARD), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Takehiro Hirao
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Takeharu Haino
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
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16
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Vušak D, Smrečki N, Muratović S, Žilić D, Prugovečki B, Matković-Čalogović D. Structural diversity in the coordination compounds of cobalt, nickel and copper with N-alkylglycinates: crystallographic and ESR study in the solid state. RSC Adv 2021; 11:23779-23790. [PMID: 35479809 PMCID: PMC9036651 DOI: 10.1039/d1ra04219j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/01/2021] [Indexed: 12/26/2022] Open
Abstract
Reactions of N-methylglycine (HMeGly), N-ethylglycine-hydrochloride (H2EtGlyCl) and N-propylglycine-hydrochloride (H2PrGlyCl) with cobalt(ii), nickel(ii) and copper(ii) ions in aqueous solutions resulted in ten new coordination compounds [Co(MeGly)2(H2O)2] (1), [{Co(MeGly)2}2(μ-OH)2]·2H2O (1d), [Cu(MeGly)2(H2O)2] (2α), [Co(EtGly)2(H2O)2] (3), [Ni(EtGly)2(H2O)2] (4), [Cu(μ-EtGly)2] n (5p), [Co(PrGly)2(H2O)2] (6), [Ni(PrGly)2(H2O)2] (7), and two polymorphs of [Cu(PrGly)2(H2O)2] (8α and 8β). Compounds were characterized by single-crystal and powder X-ray diffraction, infrared spectroscopy, thermal analysis and X-band electron spin resonance (ESR) spectroscopy. These studies revealed a wide range of structural types including monomeric, dimeric and polymeric architectures, as well as different polymorphs. In all monomeric compounds, except 2α, and in the coordination polymer 5p hydrogen bonds interconnect the molecules into 2D layers with the alkyl chain pointing outward of the layer. In 2α and in the dimeric compound 1d hydrogen bonds link the molecules into 3D structures. 1d with cobalt(iii), and 4 and 7 with nickel(ii) are ESR silent. The ESR spectra of 1, 3 and 6 are characteristic for paramagnetic high-spin cobalt(ii). The ESR spectra of all copper(ii) coordination compounds show that the unpaired copper electron is located in the d x 2-y 2 orbital, being in agreement with the elongated octahedral geometry.
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Affiliation(s)
- Darko Vušak
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102a HR-10000 Zagreb Croatia
| | - Neven Smrečki
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102a HR-10000 Zagreb Croatia
| | - Senada Muratović
- Laboratory for Magnetic Resonances, Division of Physical Chemistry, Ruđer Bošković Institute Bijenička 54 HR-10000 Zagreb Croatia
| | - Dijana Žilić
- Laboratory for Magnetic Resonances, Division of Physical Chemistry, Ruđer Bošković Institute Bijenička 54 HR-10000 Zagreb Croatia
| | - Biserka Prugovečki
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102a HR-10000 Zagreb Croatia
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17
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Chen LJ, Humphrey SJ, Zhu JL, Zhu FF, Wang XQ, Wang X, Wen J, Yang HB, Gale PA. A Two-Dimensional Metallacycle Cross-Linked Switchable Polymer for Fast and Highly Efficient Phosphorylated Peptide Enrichment. J Am Chem Soc 2021; 143:8295-8304. [PMID: 34042430 PMCID: PMC8193630 DOI: 10.1021/jacs.0c12904] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The selective and
efficient capture of phosphopeptides is critical
for comprehensive and in-depth phosphoproteome analysis. Here we report
a new switchable two-dimensional (2D) supramolecular polymer that
serves as an ideal platform for the enrichment of phosphopeptides.
A well-defined, positively charged metallacycle incorporated into
the polymer endows the resultant polymer with a high affinity for
phosphopeptides. Importantly, the stimuli-responsive nature of the
polymer facilitates switchable binding affinity of phosphopeptides,
thus resulting in an excellent performance in phosphopeptide enrichment
and separation from model proteins. The polymer has a high enrichment
capacity (165 mg/g) and detection sensitivity (2 fmol), high enrichment
recovery (88%), excellent specificity, and rapid enrichment and separation
properties. Additionally, we have demonstrated the capture of phosphopeptides
from the tryptic digest of real biosamples, thus illustrating the
potential of this polymeric material in phosphoproteomic studies.
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Affiliation(s)
- Li-Jun Chen
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia
| | - Sean J Humphrey
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Jun-Long Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Fan-Fan Zhu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xu-Qing Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Xiang Wang
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials & College of Materials Science and Engineering, Donghua University, Shanghai 201620, China
| | - Jin Wen
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials & College of Materials Science and Engineering, Donghua University, Shanghai 201620, China.,Institute of Theoretical Chemistry, Faculty of Vienna, University of Vienna, Währinger Straße 17, A-1090 Vienna, Austria
| | - Hai-Bo Yang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Chang-Kung Chuang Institute, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Philip A Gale
- School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.,The University of Sydney Nano Institute (Sydney Nano), The University of Sydney, Sydney, NSW 2006, Australia
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18
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Selective discrimination and classification of G-quadruplex structures with a host-guest sensing array. Nat Chem 2021; 13:488-495. [PMID: 33795843 DOI: 10.1038/s41557-021-00647-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 01/27/2021] [Indexed: 02/01/2023]
Abstract
The secondary structures of nucleic acids have an important influence on their cellular functions but can be difficult to identify and classify quickly. Here, we show that an arrayed suite of synthetic hosts and dyes is capable of fluorescence detection of oligonucleotide secondary structures. Multivariate analysis of different fluorescence enhancements-generated using cationic dyes that show affinity for both DNA G-quadruplexes and the synthetic hosts-enables discrimination between G-quadruplex structures of identical length and highly similar topological types. Different G-quadruplexes that display the same folding topology can also be easily differentiated by the number of G-quartets and sequence differences at the 3' or 5' ends. The array is capable of both differentiation and classification of the G-quadruplex structures at the same time. This simple non-invasive sensing method does not require the discovery and synthesis of specific G-quadruplex binding ligands, but employs a simple multicomponent approach to ensure wide applicability.
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19
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Wan YH, Zhu YJ, Rebek J, Yu Y. Recognition of Hydrophilic Cyclic Compounds by a Water-Soluble Cavitand. Molecules 2021; 26:molecules26071922. [PMID: 33808102 PMCID: PMC8037811 DOI: 10.3390/molecules26071922] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
A water-soluble deep cavitand bearing amides on the upper rim and trimethyl ammonium groups on the feet was synthesized. The open-ended cavity is stabilized by the intramolecular hydrogen bonds formed between the adjacent amides, and the introduction of trimethylammonium imparts to the cavitand good solubility in water. The cavitand exhibits high binding affinity and selectivity to hydrophilic molecules in water. With certain guests, such as cyclohexyl alcohols, amines and acids, the recognition involves the synergistic action of hydrogen bonding with hydrophobic effects. The binding phenomena are interpreted in terms of a fixed solvent cage presented by the host to the guest.
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Affiliation(s)
- Yun-Hui Wan
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China; (Y.-H.W.); (Y.-J.Z.)
| | - Yu-Jie Zhu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China; (Y.-H.W.); (Y.-J.Z.)
| | - Julius Rebek
- Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA;
| | - Yang Yu
- Center for Supramolecular Chemistry & Catalysis and Department of Chemistry, College of Science, Shanghai University, 99 Shang-Da Road, Shanghai 200444, China; (Y.-H.W.); (Y.-J.Z.)
- Correspondence:
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20
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Ferguson Johns HP, Harrison EE, Stingley KJ, Waters ML. Mimicking Biological Recognition: Lessons in Binding Hydrophilic Guests in Water. Chemistry 2021; 27:6620-6644. [PMID: 33048395 DOI: 10.1002/chem.202003759] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Indexed: 01/25/2023]
Abstract
Selective molecular recognition of hydrophilic guests in water plays a fundamental role in a vast number of biological processes, but synthetic mimicry of biomolecular recognition in water still proves challenging both in terms of achieving comparable affinities and selectivities. This Review highlights strategies that have been developed in the field of supramolecular chemistry to selectively and non-covalently bind three classes of biologically relevant molecules: nucleotides, carbohydrates, and amino acids. As several groups have systematically modified receptors for a specific guest, an evolutionary perspective is also provided in some cases. Trends in the most effective binding forces for each class are described, providing insight into selectivity and potential directions for future work.
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Affiliation(s)
- Hannah P Ferguson Johns
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Emily E Harrison
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kyla J Stingley
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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21
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Escobar L, Ballester P. Molecular Recognition in Water Using Macrocyclic Synthetic Receptors. Chem Rev 2021; 121:2445-2514. [PMID: 33472000 DOI: 10.1021/acs.chemrev.0c00522] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Molecular recognition in water using macrocyclic synthetic receptors constitutes a vibrant and timely research area of supramolecular chemistry. Pioneering examples on the topic date back to the 1980s. The investigated model systems and the results derived from them are key for furthering our understanding of the remarkable properties exhibited by proteins: high binding affinity, superior binding selectivity, and extreme catalytic performance. Dissecting the different effects contributing to the proteins' properties is severely limited owing to its complex nature. Molecular recognition in water is also involved in other appreciated areas such as self-assembly, drug discovery, and supramolecular catalysis. The development of all these research areas entails a deep understanding of the molecular recognition events occurring in aqueous media. In this review, we cover the past three decades of molecular recognition studies of neutral and charged, polar and nonpolar organic substrates and ions using selected artificial receptors soluble in water. We briefly discuss the intermolecular forces involved in the reversible binding of the substrates, as well as the hydrophobic and Hofmeister effects operating in aqueous solution. We examine, from an interdisciplinary perspective, the design and development of effective water-soluble synthetic receptors based on cyclic, oligo-cyclic, and concave-shaped architectures. We also include selected examples of self-assembled water-soluble synthetic receptors. The catalytic performance of some of the presented receptors is also described. The latter process also deals with molecular recognition and energetic stabilization, but instead of binding ground-state species, the targets become elusive counterparts: transition states and other high-energy intermediates.
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Affiliation(s)
- Luis Escobar
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Av. Països Catalans 16, 43007 Tarragona, Spain.,Departament de Química Analítica i Química Orgánica, Universitat Rovira i Virgili, c/Marcel·lí Domingo 1, 43007 Tarragona, Spain
| | - Pablo Ballester
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology (BIST), Av. Països Catalans 16, 43007 Tarragona, Spain.,ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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22
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Shaurya A, Garnett GAE, Starke MJ, Grasdal MC, Dewar CC, Kliuchynskyi AY, Hof F. An easily accessible, lower rim substituted calix[4]arene selectively binds N, N-dimethyllysine. Org Biomol Chem 2021; 19:4691-4696. [PMID: 33978657 DOI: 10.1039/d1ob00524c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Post-translational modifications (PTMs) are critical controllers of protein functions. One set of important PTMs are N-methylated side chains of lysine and arginine, which exist in several functionally distinct forms. Multiple groups have demonstrated the selective binding of the most hydrophobic family member, trimethyllysine (Kme3), using various macrocyclic hosts, but the selective binding of lower methylation states remains challenging. Herein we report that the installation of a sulfonate ester on the lower rim phenol of p-sulfonatocalix[4]arene efficiently generates a potent, N,N-dimethyllysine (Kme2)-selective host in one step from commercially available starting materials. We characterize its binding behaviors in solution, and examine the relationship between its unusual conformational dynamics and its guest-binding properties.
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Affiliation(s)
- Alok Shaurya
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Graham A E Garnett
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Melissa J Starke
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Mark C Grasdal
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Charlotte C Dewar
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Anton Y Kliuchynskyi
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
| | - Fraser Hof
- Department of Chemistry and Centre for Advanced Materials and Related Technologies (CAMTEC), University of Victoria, 3800 Finnerty Rd, Victoria, BC V8P 5C2, Canada.
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23
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Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors. Molecules 2020; 26:molecules26010106. [PMID: 33379401 PMCID: PMC7796322 DOI: 10.3390/molecules26010106] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 12/30/2022] Open
Abstract
To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.
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24
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Castillo-Aguirre A, Esteso MA, Maldonado M. Resorcin[4]arenes: Generalities and Their Role in the Modification and Detection of Amino Acids. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999200510232141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The characteristics and properties that enable resorcin[4]arenes to self-assemble
in order to form derivatives with amino acids with a high potential for application in various
fields are reviewed. In particular, resorcin[4]arene synthesis, their characteristics, the
variety in the size of cavity, their functional groups, and their applications associated with
molecular interactions are described in this study. Also, the types of amino acids that can
be recognized by resorcin[4]arenes, their interactions, the techniques that allow the determination
of the association constants, and the evaluation of the stoichiometry of the complex
formed, are reviewed.
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Affiliation(s)
- Alver Castillo-Aguirre
- Department of Chemistry, Faculty of Science, National University of Colombia-Bogota Headquarters, 30 No. 45-03 Carrera, Colombia
| | - Miguel Angel Esteso
- Universidad Catolica Santa Teresa de Jesus de Avila. Calle los Canteros s/n. 05005 Avila, Spain
| | - Mauricio Maldonado
- Department of Chemistry, Faculty of Science, National University of Colombia-Bogota Headquarters, 30 No. 45-03 Carrera, Colombia
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25
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Jiao J, Sun B, Ding Y, Zheng H, Zhao Y, Jiang J, Lin C, Wang L. A CTV Analogue: Arene-Persubstituted Cyclotrixylohydroquinoylene and Its Derivatives. Org Lett 2020; 22:8984-8988. [PMID: 33112620 DOI: 10.1021/acs.orglett.0c03385] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A crown-shaped cyclotriveratrylene (CTV) analogue with persubstituted arene units-namely, cyclotrixylohydroquinoylene (CTX)-was synthesized from tetrasubstituted o-xylohydroquinone. Importantly, a series of CTX derivatives were prepared by introducing second bridged methylene, phenylphosphine oxide, and dimethylsilyl at the middle rim, referred to as CTX[CH2], CTX[P(O)Ph], and CTX[SiMe2], respectively, with the completely locked crown conformation, leading to the formation of unique C3-symmetric Chinese censer-shaped pocket structures. In addition, the water-soluble CTX[CH2] derivative (WCTX[CH2]) was synthesized from CTX[CH2] by simple oxidation reaction with the modification at the upper rim, and its host-guest interaction with methyl viologen in water was investigated.
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Affiliation(s)
- Jianmin Jiao
- Key Laboratory of Mesoscopic Chemistry of MOE, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Baobao Sun
- Key Laboratory of Mesoscopic Chemistry of MOE, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yihan Ding
- Key Laboratory of Mesoscopic Chemistry of MOE, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hao Zheng
- Key Laboratory of Mesoscopic Chemistry of MOE, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yue Zhao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Juli Jiang
- Key Laboratory of Mesoscopic Chemistry of MOE, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Chen Lin
- Key Laboratory of Mesoscopic Chemistry of MOE, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Leyong Wang
- Key Laboratory of Mesoscopic Chemistry of MOE, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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26
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Li L, Zhang Y, Du P, Qian Y, Zhang P, Guo Q. Polymeric Membrane Electrodes Using Calix[4]pyrrole Bis/Tetra-Phosphonate Cavitands as Ionophores for Potentiometric Acetylcholine Sensing with High Selectivity. Anal Chem 2020; 92:14740-14746. [PMID: 33064457 DOI: 10.1021/acs.analchem.0c03319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A handful of bis/tetra-phosphonate calix[4]pyrroles with recognition sites embedding in hydrophobic cavitands were evaluated for the first time as ionophores for polymeric membrane Ach+-selective electrodes. Highly selective potentiometric Ach+ could be achieved over its analogues, especially for Ch+, which differs only by an acetate tail from Ach+. The superior performance of the proposed ISEs might be ascribed to a dual-site binding mode, in which the trimethylammonium head and acetate tail were accommodated by the phosphonate group-bridged aryl walls and the bowl-shaped aromatic cavity, through cation-π/charge-dipole interaction and the convergent four N-H···O hydrogen bonds, respectively. To gain more insight into the performance of the proposed ISEs, the cation-ionophore complex constants in the membrane phase were determined, and the binding affinity trend correlates well with the selectivity pattern. These results suggest that conformational preorganization of the ionophores and complementary weak interactions do change the selectivity of the ionophores. Studies on the influence of the sample solution pH demonstrated that the developed ISEs can be employed in a wide pH range of 4.0-9.6 with a fast response (<60 s), good reversibility, and long lifetime. Optimizing the membrane components, such as ionophores, lipophilic additives, and plasticizers, yielded ISEs, showing Nernstian responses to Ach+ with improved linear ranges and detection limits (a slope of -59.5 mV/dec in the linear range of 1 × 10-6-1 × 10-2 M with a detection limit of 3 × 10-7 M), which led to the success of the determination of Ach+ in spiked urine and milk samples.
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Affiliation(s)
- Long Li
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Yihao Zhang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Pengcheng Du
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Yi Qian
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Peidong Zhang
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Qingjie Guo
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, Ningxia University, Yinchuan 750021, P. R. China
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27
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Di Costanzo L, Geremia S. Atomic Details of Carbon-Based Nanomolecules Interacting with Proteins. Molecules 2020; 25:E3555. [PMID: 32759758 PMCID: PMC7435792 DOI: 10.3390/molecules25153555] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/21/2022] Open
Abstract
Since the discovery of fullerene, carbon-based nanomolecules sparked a wealth of research across biological, medical and material sciences. Understanding the interactions of these materials with biological samples at the atomic level is crucial for improving the applications of nanomolecules and address safety aspects concerning their use in medicine. Protein crystallography provides the interface view between proteins and carbon-based nanomolecules. We review forefront structural studies of nanomolecules interacting with proteins and the mechanism underlying these interactions. We provide a systematic analysis of approaches used to select proteins interacting with carbon-based nanomolecules explored from the worldwide Protein Data Bank (wwPDB) and scientific literature. The analysis of van der Waals interactions from available data provides important aspects of interactions between proteins and nanomolecules with implications on functional consequences. Carbon-based nanomolecules modulate protein surface electrostatic and, by forming ordered clusters, could modify protein quaternary structures. Lessons learned from structural studies are exemplary and will guide new projects for bioimaging tools, tuning of intrinsically disordered proteins, and design assembly of precise hybrid materials.
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Affiliation(s)
- Luigi Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico II, 100, 80055 Portici, Italy
| | - Silvano Geremia
- Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, 34127 Trieste, Italy;
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28
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Che Y, Gaitzsch J, Liubimtsev N, Zschoche S, Bauer T, Appelhans D, Voit B. Double cross-linked supramolecular hydrogels with tunable properties based on host-guest interactions. SOFT MATTER 2020; 16:6733-6742. [PMID: 32588870 DOI: 10.1039/d0sm00833h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
We report a novel double cross-linked hydrogel system based on polyacrylamide and poly(2-methyl-2-oxazoline) (PMOXA) network chains, as well as on supramolecular host-guest interactions with on-demand tailored mechanical properties. Well-defined vinyl-bearing PMOXA macromonomers, functionalized with either β-cyclodextrin units (β-CD-PMOXA) or adamantane units (Ada-PMOXA), were synthesized and confirmed using 1H NMR, MALDI-TOF-MS and GPC measurements. The complexation between adamantane and β-CD modified macromonomers in solution towards bismacromonomers was confirmed by 2D NOESY NMR and DLS. After introducing these bismacromonomers into the polyacrylamide hydrogel, the supramolecular non-covalent Ada/β-CD bond was responsible for the presence of PMOXA network chains to form a dense network. Once the interactions broke, the PMOXA chains no longer contributed to the network, but became dangling graft side chains in a predominated polyacrylamide network. Their dissociative nature influenced the physical properties, including the swelling behavior and mechanics of the final hydrogel. Rheological experiments proved that the E-modulus of the network was significantly increased by the supramolecular host-guest interactions. Tuning the lengths of PMOXA network chains even allowed the modification of the changes in mechanical strength, also through the addition of free β-CD. The tunable properties of the double cross-linked supramolecular hydrogel proved their unique strength for future applications.
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Affiliation(s)
- Yunjiao Che
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany. and Technische Universität Dresden, Faculty of Chemistry and Food Chemistry, Organic Chemistry of Polymers, 01069 Dresden, Germany
| | - Jens Gaitzsch
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany.
| | - Nikolai Liubimtsev
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany. and Technische Universität Dresden, Faculty of Chemistry and Food Chemistry, Organic Chemistry of Polymers, 01069 Dresden, Germany
| | - Stefan Zschoche
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany.
| | - Tim Bauer
- Technische Universität Dresden, Faculty of Chemistry and Food Chemistry, Chair of Macromolecular Chemistry, 01069 Dresden, Germany
| | - Dietmar Appelhans
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany.
| | - Brigitte Voit
- Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Straße 6, 01069 Dresden, Germany. and Technische Universität Dresden, Faculty of Chemistry and Food Chemistry, Organic Chemistry of Polymers, 01069 Dresden, Germany
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29
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Shimoyama D, Haino T. Entropy‐Driven Cooperativity in the Guest Binding of an Octaphosphonate Bis‐cavitand. Chemistry 2020; 26:3074-3079. [DOI: 10.1002/chem.201905036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Daisuke Shimoyama
- Department of ChemistryGraduate School of ScienceHiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima 739-8526 Japan
| | - Takeharu Haino
- Department of ChemistryGraduate School of ScienceHiroshima University 1-3-1 Kagamiyama Higashi-Hiroshima 739-8526 Japan
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30
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Mullins AG, St. Louis LE, Waters ML. Using changes in speciation in a dynamic combinatorial library as a fingerprint to differentiate the methylation states of arginine. Chem Commun (Camb) 2020; 56:3947-3950. [DOI: 10.1039/d0cc00415d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A dynamic combinatorial library was shown to provide a direct method of sensing methylated arginine and lysine due to differences in speciation. This provides the first sensor array for all the methylation states of arginine.
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Affiliation(s)
- Alexandria G. Mullins
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Lauren E. St. Louis
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
| | - Marcey L. Waters
- Department of Chemistry
- CB 3290
- University of North Carolina at Chapel Hill
- Chapel Hill
- USA
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31
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La Manna P, Soriente A, De Rosa M, Buonerba A, Talotta C, Gaeta C, Neri P. Green, Mild, and Efficient Friedel-Crafts Benzylation of Scarcely Reactive Arenes and Heteroarenes under On-Water Conditions. CHEMSUSCHEM 2019; 12:1673-1683. [PMID: 30775871 DOI: 10.1002/cssc.201900137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/17/2019] [Indexed: 06/09/2023]
Abstract
Metal-free Friedel-Crafts benzylation (FCB) of scarcely reactive arenes and heteroarenes was performed under on-water conditions by an environmentally sustainable procedure. The catalytic strategy exploits the hydrophobicity of the resorcinarene macrocycle 1 a. The proposed mechanism is based on the activation of benzyl chloride by H-bonding interactions with catalyst 1 a. In fact, under on-water conditions the hydrophobic amplification of the strength of the H-bonding interactions between the OH groups of the resorcinarene catalyst and the chlorine atom of benzyl chloride leads to polarization of the C-Cl bond, which consequently promotes electrophilic attack of the π nucleophile. Thus, many arenes and heteroarenes were efficiently benzylated under mild on-water conditions by using resorcinarene 1 a as catalyst. The FCB of benzene is industrially relevant for the synthesis of diphenylmethane, and hence the on-water procedure was extended to the gram-scale synthesis of diphenylmethane, starting from benzene and benzyl chloride in the presence of resorcinarene catalyst 1 a.
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Affiliation(s)
- Pellegrino La Manna
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano (SALERNO), 84084, Italy
| | - Annunziata Soriente
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano (SALERNO), 84084, Italy
| | - Margherita De Rosa
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano (SALERNO), 84084, Italy
| | - Antonio Buonerba
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano (SALERNO), 84084, Italy
| | - Carmen Talotta
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano (SALERNO), 84084, Italy
| | - Carmine Gaeta
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano (SALERNO), 84084, Italy
| | - Placido Neri
- Dipartimento di Chimica e Biologia "A. Zambelli", Università di Salerno, Via Giovanni Paolo II, Fisciano (SALERNO), 84084, Italy
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32
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Velcrand Functionalized Polyethylene. Molecules 2019; 24:molecules24050902. [PMID: 30841484 PMCID: PMC6429461 DOI: 10.3390/molecules24050902] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 02/27/2019] [Accepted: 03/01/2019] [Indexed: 11/16/2022] Open
Abstract
Velcrands are a specific class of cavitands whose complementary surfaces induce self-dimerization. The insertion of a velcrand as physical cross-linking unit into a polymer is reported. To this purpose, the velcrand was functionalized at the lower rim with an isocyanate group. The functional velcrand was reacted with poly (ethylene-co-(2-hydroxethylmethacrylate)) (PE-HEMA), a polymer equipped with free hydroxyl groups suitable for reaction with the isocyanate group. The obtained functionalized polymer was characterized by nuclear magnetic resonance (NMR), differential scanning calorimetry (DSC), and Fourier transform infrared spectroscopy (FTIR), proving the introduction of velcraplexes in the polymer. Films with varying amounts of velcrands were obtained by solution casting and slow evaporation, testifying the processability of the functionalized polymers. The obtained films were used to measure the oxygen barrier properties of the functionalized material.
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33
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Peñuelas-Haro G, Ballester P. Efficient hydrogen bonding recognition in water using aryl-extended calix[4]pyrrole receptors. Chem Sci 2019; 10:2413-2423. [PMID: 30931096 PMCID: PMC6399678 DOI: 10.1039/c8sc05034a] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/19/2018] [Indexed: 12/25/2022] Open
Abstract
We describe the synthesis of four water-soluble aryl-extended calix[4]pyrrole receptors and report their binding properties with multiple neutral polar guests in water. The prepared receptors present different functionalization at their upper rims and have in common the placement of water solubilizing pyridinium groups at their lower rims. We investigate the interaction of the receptors with a guest series in water solution using 1H NMR titrations and ITC experiments. Despite the known competitive nature of water for hydrogen-bonding interactions, we demonstrate the formation of thermodynamically highly stable 1 : 1 inclusion complexes stabilized by hydrogen-bonding interactions. We show that increasing the hydrogen-bond acceptor character of the guest has a positive impact on binding affinity. This result suggests that the receptor's cavity is indeed a better hydrogen-bond donor to interact with the guests than water molecules. We also assess the important contribution of the hydrophobic effect to binding by comparing the binding affinities of analogous inclusion complexes in water and chloroform solutions. The more polar guests are bound with similar affinities in the two solvents. We compare the binding properties of the different complexes in order to derive general trends.
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Affiliation(s)
- G Peñuelas-Haro
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology (BIST) , Av. Països Catalans, 16 , 43007-Tarragona , Spain .
- Universitat Rovira i Virgili , Departament de Química Analítica i Química Orgànica , c/Marcel·li Domingo, 1 , 43007-Tarragona , Spain
| | - P Ballester
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology (BIST) , Av. Països Catalans, 16 , 43007-Tarragona , Spain .
- ICREA , Pg. Lluís Companys, 23 , 08018-Barcelona , Spain
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34
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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: 1.0] [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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35
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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: 2.9] [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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36
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Fluorinated Tetraphosphonate Cavitands. Molecules 2018; 23:molecules23102670. [PMID: 30336589 PMCID: PMC6222714 DOI: 10.3390/molecules23102670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/12/2018] [Accepted: 10/14/2018] [Indexed: 11/17/2022] Open
Abstract
Two synthetic protocols for the introduction of fluorine atoms into resorcinarene-based cavitands, at the lower and upper rim, respectively, are reported. Cavitand 1, bearing four fluorocarbon tails, and cavitand 2, which presents a fluorine atom on the para position of a diester phosphonate phenyl substituent, were synthesized and their complexation abilities toward the model guest sarcosine methyl ester hydrochloride were evaluated via NMR titration experiments. The effect of complexation on the 19F NMR resonance of the probe is evident only in the case of cavitand 2, where the inset of the cation-dipole and H-bonding interactions between the P=O bridges and the guest is reflected in a sizable downfield shift of the fluorine probe.
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37
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Gruber T. Synthetic Receptors for the Recognition and Discrimination of Post-Translationally Methylated Lysines. Chembiochem 2018; 19:2324-2340. [DOI: 10.1002/cbic.201800398] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Tobias Gruber
- School of Pharmacy; University of Lincoln; Joseph Banks Laboratories; Green Lane Lincoln LN6 7DL UK
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38
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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: 116] [Impact Index Per Article: 16.6] [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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39
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Shibaeva KS, Mostovaya OA, Nazarova AA, Shurpik DN, Shiabiev IE, Kuznetsova DI, Stoykov II. The Kabachnik–Fields Reaction in the Synthesis of Polyaminophosphonate Derivatives of p-tert-Butylthiacalix[4]arene. RUSS J GEN CHEM+ 2018. [DOI: 10.1134/s1070363218090086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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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: 2.1] [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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41
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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: 6.7] [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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42
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Metal ion complexation by tetraphosphonate cavitands: The influence of the ionic radius. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.05.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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43
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Liu G, Yuan Q, Hollett G, Zhao W, Kang Y, Wu J. Cyclodextrin-based host–guest supramolecular hydrogel and its application in biomedical fields. Polym Chem 2018. [DOI: 10.1039/c8py00730f] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
CD-based host–guest supramolecular hydrogels and their potential biomedical application.
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Affiliation(s)
- Guiting Liu
- School of Biomedical Engineering
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Qijuan Yuan
- School of Biomedical Engineering
- Sun Yat-sen University
- Guangzhou
- P. R. China
| | - Geoffrey Hollett
- Materials Science and Engineering Program
- University of California San Diego
- La Jolla
- USA
| | - Wei Zhao
- Laboratory for Stem Cells and Tissue Engineering
- Ministry of Education
- Sun Yat-sen University
- Guangzhou 510080
- China
| | - Yang Kang
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization
- Chengdu Institute of Biology
- Chinese Academy of Sciences
- Chengdu
- China
| | - Jun Wu
- School of Biomedical Engineering
- Sun Yat-sen University
- Guangzhou
- P. R. China
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44
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Pisagatti I, Gattuso G, Notti A, Parisi MF, Brancatelli G, Geremia S, Greco F, Millesi S, Pappalardo A, Spitaleri L, Gulino A. Recognition and optical sensing of amines by a quartz-bound 7-chloro-4-quinolylazopillar[5]arene monolayer. RSC Adv 2018; 8:33269-33275. [PMID: 35548123 PMCID: PMC9086462 DOI: 10.1039/c8ra06792a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/19/2018] [Indexed: 11/21/2022] Open
Abstract
Pillar[5]arene-decorated quartz slides for the direct detection of linear amines and diamines are now available.
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45
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Maffei F, Brancatelli G, Barboza T, Dalcanale E, Geremia S, Pinalli R. Inherently chiral phosphonate cavitands as enantioselective receptors for mono-methylated L-amino acids. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1417991] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Francesca Maffei
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma and INSTM UdR Parma, Parma, Italy
| | - Giovanna Brancatelli
- CEB Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Tahnie Barboza
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma and INSTM UdR Parma, Parma, Italy
| | - Enrico Dalcanale
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma and INSTM UdR Parma, Parma, Italy
| | - Silvano Geremia
- CEB Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Roberta Pinalli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma and INSTM UdR Parma, Parma, Italy
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46
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Pinalli R, Massera C. Nitro-sonium complexation by the tetra-phospho-nate cavitand 5,11,17,23-tetra-methyl-6,10:12,16:18,22:24,4-tetra-kis-(phenyl-phospho-nato-κ 2O, O)resorcin(4)arene. Acta Crystallogr E Crystallogr Commun 2017; 73:1801-1805. [PMID: 29250390 PMCID: PMC5730227 DOI: 10.1107/s2056989017015857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 11/24/2022]
Abstract
The crystal structure of a new supra-molecular complex between the tetra-phos-pho-nate cavitand 5,11,17,23-tetra-methyl-6,10:12,16:18,22:24,4-tetra-kis(phenyl-phospho-nato-κ2O,O')resorcin(4)arene and the nitrosyl cation NO+, as the BF4- salt, is reported. The complex, of general formula [(C56H44P4O12)(NO)]BF4·CH2Cl2 or NO@Tiiii[H, CH3, C6H5] BF4·CH2Cl2, crystallizes in the space group P-1. The nitrosyl cation is disordered over two equivalent positions, with occupancies of 0.503 (2) and 0.497 (2), and inter-acts with two adjacent P=O groups at the upper rim of the cavitand through dipole-charge inter-actions. In the lattice, the cavitands are connected through a series of C-H⋯π inter-actions involving the methyl and methyl-enic H atoms and the aromatic rings of the macrocycle. The structure is further stabilized by the presence of C-H⋯F inter-actions between the hydrogen atoms of the cavitands and the F atoms of the tetra-fluorido-borate anion. As a result of the disorder, the lattice di-chloro-methane mol-ecules could not be modelled in terms of atomic sites, and were treated using the PLATON SQUEEZE procedure [Spek (2015 ▸). Acta Cryst. C71, 9-18]. The complexation process has also been studied in solution through NMR titrations.
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Affiliation(s)
- Roberta Pinalli
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Chiara Massera
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università di Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
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47
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van Dun S, Ottmann C, Milroy LG, Brunsveld L. Supramolecular Chemistry Targeting Proteins. J Am Chem Soc 2017; 139:13960-13968. [PMID: 28926241 PMCID: PMC5639466 DOI: 10.1021/jacs.7b01979] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Indexed: 12/19/2022]
Abstract
The specific recognition of protein surface elements is a fundamental challenge in the life sciences. New developments in this field will form the basis of advanced therapeutic approaches and lead to applications such as sensors, affinity tags, immobilization techniques, and protein-based materials. Synthetic supramolecular molecules and materials are creating new opportunities for protein recognition that are orthogonal to classical small molecule and protein-based approaches. As outlined here, their unique molecular features enable the recognition of amino acids, peptides, and even whole protein surfaces, which can be applied to the modulation and assembly of proteins. We believe that structural insights into these processes are of great value for the further development of this field and have therefore focused this Perspective on contributions that provide such structural data.
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Affiliation(s)
- Sam van Dun
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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48
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Li X, Wang K, Ma N, Jia X. Poly(Ionic Liquid) Based Chemosensors for Detection of Basic Amino Acids in Aqueous Medium. Front Chem 2017; 5:69. [PMID: 29018795 PMCID: PMC5622980 DOI: 10.3389/fchem.2017.00069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/11/2017] [Indexed: 11/30/2022] Open
Abstract
Naked-eye detection of amino acids (AA) in water is of great significance in the field of bioanalytical applications. Herein, polymerized ionic liquids (PILs) with controlled chain length structures were synthesized via reversible addition–fragmentation chain-transfer (RAFT) polymerization and post-quaternization approach. The AA recognition performance of PILs with different alkyl chain lengths and molecular weights was evaluated by naked-eye color change and ultraviolet-visible (UV–vis) spectral studies. These PILs were successfully used for highly sensitive and selective detection of Arg, Lys, and His in water. The recognition performance was improved effectively with increased molecular weight of PILs. The biosensitivity of the PILs in water was strongly dependent on their aggregation effect and polarization effect. Highly sensitive and selective detection of AA was successfully accomplished by introducing positively charged pyridinium moieties and controlled RAFT radical polymerization.
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Affiliation(s)
- Xinjuan Li
- Key Laboratory of Green Chemical Media and Reactions, School of Chemistry and Chemical Engineering, State Education Ministry of China, Henan Normal University, Xinxiang, China
| | - Kai Wang
- Key Laboratory of Green Chemical Media and Reactions, School of Chemistry and Chemical Engineering, State Education Ministry of China, Henan Normal University, Xinxiang, China
| | - Nana Ma
- Key Laboratory of Green Chemical Media and Reactions, School of Chemistry and Chemical Engineering, State Education Ministry of China, Henan Normal University, Xinxiang, China
| | - Xianbin Jia
- Key Laboratory of Green Chemical Media and Reactions, School of Chemistry and Chemical Engineering, State Education Ministry of China, Henan Normal University, Xinxiang, China
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49
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Mundlapati VR, Gautam S, Sahoo DK, Ghosh A, Biswal HS. Thioamide, a Hydrogen Bond Acceptor in Proteins and Nucleic Acids. J Phys Chem Lett 2017; 8:4573-4579. [PMID: 28876948 DOI: 10.1021/acs.jpclett.7b01810] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thioamides are used as potential surrogates of amides to study the structure and dynamics of proteins and nucleic acids. However, incorporation of thioamides in biomolecules leads to changes in their structures and conformations mostly attributed to the strength of the amide-N-H···S═C hydrogen bond. In most cases, it is considered weak owing to the small electronegativity of sulfur, and in some cases, it is as strong as conventional H-bonds. Herein, adopting PDB structure analysis, NMR spectroscopy, and quantum chemistry calculations, we have shown that thioamides in a geometrical and structural constraint-free environment are capable of forming strong H-bonds like their amide counterparts. These studies also enabled us to determine the amide-N-H···S═C H-bond enthalpy (ΔH) very precisely. The estimated ΔH for the amide-N-H···S═C H-bond is ∼-30 kJ/mol, which suggests that the amide-N-H···S═C H-bond is a strong H-bond and merits its inclusion in computational force fields for biomolecular structure simulations to explore the role of amide-N-H···S═C H-bonds in nucleobase pairing and protein folding.
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Affiliation(s)
- V Rao Mundlapati
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Sanjeev Gautam
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Arindam Ghosh
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
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50
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Synthesis, structure and binding properties of a series of dissymmetric resorcin[4]arene-based cavitands. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.06.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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