1
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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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2
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Lazar AN, Perret F, Perez-Lloret M, Michaud M, Coleman AW. Promises of anionic calix[n]arenes in life science: State of the art in 2023. Eur J Med Chem 2024; 264:115994. [PMID: 38070431 DOI: 10.1016/j.ejmech.2023.115994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023]
Abstract
Because they hold together molecules by means of non-covalent interactions - relatively weak and thus, potentially reversible - the anionic calixarenes have become an interesting tool for efficiently binding a large range of ligands - from gases to large organic molecules. Being highly water soluble and conveniently biocompatible, they showed growing interest for many interdisciplinary fields, particularly in biology and medicine. Thanks to their intrinsic conical shape, they provide suitable platforms, from vesicles to bilayers. This is a valuable characteristic, as so they mimic the biologically functional architectures. The anionic calixarenes propose efficient alternatives for overcoming the limitations linked to drug delivery and bioavailability, as well as drug resistance along with limiting the undesirable side effects. Moreover, the dynamic non-covalent binding with the drugs enables predictable and on demand drug release, controlled by the stimuli present in the targeted environment. This particular feature instigated the use of these versatile, stimuli-responsive compounds for sensing biomarkers of diverse pathologies. The present review describes the recent achievements of the anionic calixarenes in the field of life science, from drug carriers to biomedical engineering, with a particular outlook on their applications for the diagnosis and treatment of different pathologies.
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Affiliation(s)
- Adina-N Lazar
- Univ Lyon, INSA-Lyon, CNRS UMR5259, LaMCoS, F-69621, France.
| | - Florent Perret
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR 5246, Univ. Lyon - CNRS - Univ. Claude Bernard Lyon 1 - CPE Lyon, 43 Boulevard du 11 Novembre 1918, Villeurbanne, 69622, Cedex, France.
| | - Marta Perez-Lloret
- School of Biological and Chemical Sciences, University of Galway, Ireland Galway, Ireland
| | - Mickael Michaud
- CIRI, Univ. Lyon1, Inserm, U1111, CNRS, UMR5308, ENS, Lyon, France
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3
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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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4
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Xiong Y, Li M, Cao Y, Li Z, Chang Y, Zhao X, Qing G. Nanofluidic Device for Detection of Lysine Methylpeptides and Sensing of Lysine Methylation. Anal Chem 2023; 95:7761-7769. [PMID: 37140051 DOI: 10.1021/acs.analchem.3c01074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Protein methylation is the smallest possible yet vitally important post-translational modification (PTM). This small and chemically inert addition in proteins makes the analysis of methylation more challenging, thus calling for an efficient tool for the sake of recognition and detection. Herein, we present a nanofluidic electric sensing device based on a functionalized nanochannel that was constructed by introducing monotriazole-containing p-sulfonatocalix[4]arene (TSC) into a single asymmetric polymeric nanochannel via click chemistry. The device can selectively detect lysine methylpeptides with subpicomole sensitivity, distinguish between different lysine methylation states, and monitor the lysine methylation process by methyltransferase at the peptide level in real time. The introduced TSC molecule, with its confined asymmetric configuration, presents the remarkable ability to selectively bind to lysine methylpeptides, which, coupled with the release of the complexed Cu ions, allows the device to transform the molecular-level recognition to the discernible change in ionic current of the nanofluidic electric device, thus enabling detection. This work could serve as a stepping stone to the development of a new methyltransferase assay and the chemical that specifically targets lysine methylation in PTM proteomics.
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Affiliation(s)
- Yuting Xiong
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, College of Chemistry and Materials Science, East China University of Technology, Nanchang 330013, P. R. China
| | - Minmin Li
- Jiangxi Province Key Laboratory of Polymer Micro/Nano Manufacturing and Devices, College of Chemistry and Materials Science, East China University of Technology, Nanchang 330013, P. R. China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yuchen Cao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Zan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Yongxin Chang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Xinjia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
| | - Guangyan Qing
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
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5
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Bartocci A, Pereira G, Cecchini M, Dumont E. Capturing the Recognition Dynamics of para-Sulfonato-calix[4]arenes by Cytochrome c: Toward a Quantitative Free Energy Assessment. J Chem Inf Model 2022; 62:6739-6748. [PMID: 36054284 DOI: 10.1021/acs.jcim.2c00483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Calix[n]arenes' selective recognition of protein surfaces covers a broad range of timely applications, from controlling protein assembly and crystallization to trapping partially disordered proteins. Here, the interaction of para-sulfonated calix-[4]-arenes with cytochrome c is investigated through all-atom, explicit water molecular dynamics simulations which allow characterization of two binding sites in quantitative agreement with experimental evidence. Free energy calculations based on the MM-PBSA and the attach-pull-release (APR) methods highlight key residues implicated in the recognition process and provide binding free energy results in quantitative agreement with isothermal titration calorimetry. Our study emphasizes the role of MD simulations to capture and describe the "walk" of sulfonated calix-[4]-arenes on the cytochrome c surface, with the arginine R13 as a pivotal interacting residue. Our MD investigation allows, through the quasi-harmonic multibasin (QHMB) method, probing an allosteric reinforcement of several per-residue interactions upon calixarene binding, which suggests a more complex mode of action of these supramolecular auxiliaries.
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Affiliation(s)
- Alessio Bartocci
- Laboratoire de Chimie, Ecole Normale Superieure de Lyon, F-69342 Lyon, France.,Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg 67083, France
| | - Gilberto Pereira
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg 67083, France.,Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg 67083, France
| | - Elise Dumont
- Laboratoire de Chimie, Ecole Normale Superieure de Lyon, F-69342 Lyon, France.,Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
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6
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Mining Transcriptomic Data to Uncover the Association between CBX Family Members and Cancer Stemness. Int J Mol Sci 2022; 23:ijms232113083. [PMID: 36361869 PMCID: PMC9656300 DOI: 10.3390/ijms232113083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 12/31/2022] Open
Abstract
Genetic and epigenetic changes might facilitate the acquisition of stem cell-like phenotypes of tumors, resulting in worse patients outcome. Although the role of chromobox (CBX) domain proteins, a family of epigenetic factors that recognize specific histone marks, in the pathogenesis of several tumor types is well documented, little is known about their association with cancer stemness. Here, we have characterized the relationship between the CBX family members' expression and cancer stemness in liver, lung, pancreatic, and uterine tumors using publicly available TCGA and GEO databases and harnessing several bioinformatic tools (i.e., Oncomine, GEPIA2, TISIDB, GSCA, UALCAN, R2 platform, Enrichr, GSEA). We demonstrated that significant upregulation of CBX3 and downregulation of CBX7 are consistently associated with enriched cancer stem-cell-like phenotype across distinct tumor types. High CBX3 expression is observed in higher-grade tumors that exhibit stem cell-like traits, and CBX3-associated gene expression profiles are robustly enriched with stemness markers and targets for c-Myc transcription factor regardless of the tumor type. Similar to high-stemness tumors, CBX3-overexpressing cancers manifest a higher mutation load. On the other hand, higher-grade tumors are characterized by the significant downregulation of CBX7, and CBX7-associated gene expression profiles are significantly depleted with stem cell markers. In contrast to high-stemness tumors, cancer with CBX7 upregulation exhibit a lower mutation burden. Our results clearly demonstrate yet unrecognized association of high CBX3 and low CBX7 expression with cancer stem cell-like phenotype of solid tumors.
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7
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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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8
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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9
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Warmerdam Z, Kamba BE, Le MH, Schrader T, Isaacs L, Bayer P, Hof F. Binding Methylarginines and Methyllysines as Free Amino Acids: A Comparative Study of Multiple Host Classes*. Chembiochem 2021; 23:e202100502. [PMID: 34758178 PMCID: PMC9299052 DOI: 10.1002/cbic.202100502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/09/2021] [Indexed: 01/18/2023]
Abstract
Methylated free amino acids are an important class of targets for host‐guest chemistry that have recognition properties distinct from those of methylated peptides and proteins. We present comparative binding studies for three different host classes that are each studied with multiple methylated arginines and lysines to determine fundamental structure‐function relationships. The hosts studied are all anionic and include three calixarenes, two acyclic cucurbiturils, and two other cleft‐like hosts, a clip and a tweezer. We determined the binding association constants for a panel of methylated amino acids using indicator displacement assays. The acyclic cucurbiturils display stronger binding to the methylated amino acids, and some unique patterns of selectivity. The two other cleft‐like hosts follow two different trends, shallow host (clip) following similar trends to the calixarenes, and the other more closed host (tweezer) binding certain less‐methylated amino acids stronger than their methylated counterparts. Molecular modelling sheds some light on the different preferences of the various hosts. The results identify hosts with new selectivities and with affinities in a range that could be useful for biomedical applications. The overall selectivity patterns are explained by a common framework that considers the geometry, depth of binding pockets, and functional group participation across all host classes.
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Affiliation(s)
- Zoey Warmerdam
- Department of Chemistry and the Centre for, Advanced Materials and Related Technology, University of Victoria, 3800 Finnerty Rd, V8W 3V6, Victoria, BC, Canada
| | - Bianca E Kamba
- Department of Structural and Medicinal Biochemistry, Universität Duisburg Essen, Universitätstrasse 2, 45141, Essen, Germany
| | - My-Hue Le
- Department of Chemistry, Universität Duisburg Essen, Universitätstrasse 7, 45117, Essen, Germany
| | - Thomas Schrader
- Department of Chemistry, Universität Duisburg Essen, Universitätstrasse 7, 45117, Essen, Germany
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, College Park, USA
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Universität Duisburg Essen, Universitätstrasse 2, 45141, Essen, Germany
| | - Fraser Hof
- Department of Chemistry and the Centre for, Advanced Materials and Related Technology, University of Victoria, 3800 Finnerty Rd, V8W 3V6, Victoria, BC, Canada
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10
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Cao W, Qin X, Liu T. When Supramolecular Chemistry Meets Chemical Biology: New Strategies to Target Proteins through Host-Guest Interactions. Chembiochem 2021; 22:2914-2917. [PMID: 34487417 DOI: 10.1002/cbic.202100357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/24/2021] [Indexed: 11/11/2022]
Abstract
Supramolecular chemistry for targeting proteins is of great interest for the development of novel approaches to recognize, isolate and control proteins. Taking advantage of chemical biology approaches, such as genetic-code expansion and enzyme-mediated ligation, guest recognition elements can be built into proteins of interest, allowing supramolecular control of protein function and regulation. In this viewpoint article, we will discuss the methods, applications, limitations, and future perspectives of supramolecular chemistry for targeting proteins in a site-specific manner.
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Affiliation(s)
- Wenbing Cao
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, P. R. China.,College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, P. R. China
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11
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Warmerdam Z, Kamba BE, Shaurya A, Sun X, Maguire MK, Hof F. Calix[4]arene sulfonate hosts selectively modified on the upper rim: a study of nicotine binding strength and geometry. Supramol Chem 2021. [DOI: 10.1080/10610278.2021.1873991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Zoey Warmerdam
- Department of Chemistry, University of Victoria, Victoria, Canada
| | - Bianca E. Kamba
- Department of Structural and Medicinal Biochemistry, Universität Duisburg Essen, Essen, Germany
| | - Alok Shaurya
- Department of Chemistry, University of Victoria, Victoria, Canada
| | - XuXin Sun
- Department of Chemistry, University of Victoria, Victoria, Canada
| | - Mary K. Maguire
- Department of Chemistry, University of Victoria, Victoria, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, Victoria, Canada
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12
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Ramberg KO, Engilberge S, Skorek T, Crowley PB. Facile Fabrication of Protein-Macrocycle Frameworks. J Am Chem Soc 2021; 143:1896-1907. [PMID: 33470808 PMCID: PMC8154523 DOI: 10.1021/jacs.0c10697] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Precisely defined protein aggregates,
as exemplified by crystals,
have applications in functional materials. Consequently, engineered
protein assembly is a rapidly growing field. Anionic calix[n]arenes
are useful scaffolds that can mold to cationic proteins and induce
oligomerization and assembly. Here, we describe protein-calixarene
composites obtained via cocrystallization of commercially available
sulfonato-calix[8]arene (sclx8) with the symmetric and “neutral” protein RSL. Cocrystallization
occurred across a wide range of conditions and protein charge states,
from pH 2.2–9.5, resulting in three crystal forms. Cationization
of the protein surface at pH ∼ 4 drives calixarene complexation
and yielded two types of porous frameworks with pore diameters >3
nm. Both types of framework provide evidence of protein encapsulation
by the calixarene. Calixarene-masked proteins act as nodes within
the frameworks, displaying octahedral-type coordination in one case.
The other framework formed millimeter-scale crystals within hours,
without the need for precipitants or specialized equipment. NMR experiments
revealed macrocycle-modulated side chain pKa values and suggested a mechanism for pH-triggered assembly.
The same low pH framework was generated at high pH with a permanently
cationic arginine-enriched RSL variant. Finally, in addition to protein
framework fabrication, sclx8 enables de novo structure determination.
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Affiliation(s)
- Kiefer O Ramberg
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Sylvain Engilberge
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland.,Swiss Light Source, Paul Scherrer Institut, Villigen PSI, 5232, Switzerland
| | - Tomasz Skorek
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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13
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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: 123] [Impact Index Per Article: 41.0] [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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14
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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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15
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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: 16] [Impact Index Per Article: 4.0] [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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16
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Pan Y, Barba‐Bon A, Tian H, Ding F, Hennig A, Nau WM, Guo D. An Amphiphilic Sulfonatocalix[5]arene as an Activator for Membrane Transport of Lysine‐rich Peptides and Proteins. Angew Chem Int Ed Engl 2020; 60:1875-1882. [DOI: 10.1002/anie.202011185] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/24/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Yu‐Chen Pan
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andrea Barba‐Bon
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Han‐Wen Tian
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Fei Ding
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andreas Hennig
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
- Institute of Chemistry of New Materials and School of Biology/Chemistry Universität Osnabrück Osnabrück Germany
- Center of Cellular Nanoanalytics (CellNanOs) Universität Osnabrück Osnabrück Germany
| | - Werner M. Nau
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Dong‐Sheng Guo
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
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17
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Pan Y, Barba‐Bon A, Tian H, Ding F, Hennig A, Nau WM, Guo D. An Amphiphilic Sulfonatocalix[5]arene as an Activator for Membrane Transport of Lysine‐rich Peptides and Proteins. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yu‐Chen Pan
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andrea Barba‐Bon
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Han‐Wen Tian
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Fei Ding
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
| | - Andreas Hennig
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
- Institute of Chemistry of New Materials and School of Biology/Chemistry Universität Osnabrück Osnabrück Germany
- Center of Cellular Nanoanalytics (CellNanOs) Universität Osnabrück Osnabrück Germany
| | - Werner M. Nau
- Department of Life Sciences and Chemistry Jacobs University Bremen Campus Ring 1 28759 Bremen Germany
| | - Dong‐Sheng Guo
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) National Demonstration Center for Experimental Chemistry Education Nankai University Tianjin 300071 China
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18
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Pan Y, Hu X, Guo D. Biomedizinische Anwendungen von Calixarenen: Stand der Wissenschaft und Perspektiven. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201916380] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yu‐Chen Pan
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Xin‐Yue Hu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Dong‐Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
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19
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Pan Y, Hu X, Guo D. Biomedical Applications of Calixarenes: State of the Art and Perspectives. Angew Chem Int Ed Engl 2020; 60:2768-2794. [DOI: 10.1002/anie.201916380] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Yu‐Chen Pan
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Xin‐Yue Hu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Dong‐Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education) State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
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20
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Bayer P, Matena A, Beuck C. NMR Spectroscopy of supramolecular chemistry on protein surfaces. Beilstein J Org Chem 2020; 16:2505-2522. [PMID: 33093929 PMCID: PMC7554676 DOI: 10.3762/bjoc.16.203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/18/2020] [Indexed: 01/17/2023] Open
Abstract
As one of the few analytical methods that offer atomic resolution, NMR spectroscopy is a valuable tool to study the interaction of proteins with their interaction partners, both biomolecules and synthetic ligands. In recent years, the focus in chemistry has kept expanding from targeting small binding pockets in proteins to recognizing patches on protein surfaces, mostly via supramolecular chemistry, with the goal to modulate protein-protein interactions. Here we present NMR methods that have been applied to characterize these molecular interactions and discuss the challenges of this endeavor.
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Affiliation(s)
- Peter Bayer
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Anja Matena
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
| | - Christine Beuck
- Structural and Medicinal Biochemistry, University of Duisburg-Essen, Universitätsstr. 1-5, 45141 Essen, Germany
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21
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Baldini L, Casnati A, Sansone F. Multivalent and Multifunctional Calixarenes in Bionanotechnology. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000255] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Laura Baldini
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
| | - Alessandro Casnati
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
| | - Francesco Sansone
- Department of Chemistry Life Sciences and Environmental Sustainability University of Parma Parco Area delle Scienze, 17/a 43124 Parma Italy
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22
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Lee J, Chen J, Sarkar P, Xue M, Hooley RJ, Zhong W. Monitoring the crosstalk between methylation and phosphorylation on histone peptides with host-assisted capillary electrophoresis. Anal Bioanal Chem 2020; 412:6189-6198. [PMID: 32064571 DOI: 10.1007/s00216-020-02486-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/27/2020] [Accepted: 02/03/2020] [Indexed: 11/29/2022]
Abstract
Post-translational modifications (PTMs) greatly increase protein diversity and regulate their functions by changing the structures, properties, and molecular interactions of proteins. In peptide regions with high density of PTMs, PTMs can influence modification on residues in proximity or even at distal positions, adding another layer of regulation. Methods that can monitor the activities of PTM enzymes on peptides carrying multiple modifications are valuable tools for better understanding of PTM crosstalk. Herein, we developed a host-assisted capillary electrophoresis (CE) method to separate histone peptides with methylation and phosphorylation and applied it to monitor the crosstalk between serine phosphorylation and lysine methylation when they were added by Aurora B kinase and G9a lysine methyltransferase, respectively. A synthetic receptor molecule, 4-hexasulfonatocalix[6]arene (CX6), was included in the CE buffer to improve the resolution of the corresponding substrates and products. A linear polyacrylamide-coated capillary was employed to effectively reduce wall adsorption of the cationic histone peptides. The peptide substrates were labeled with fluorescein to enhance their detectability during CE separation. Our method successfully revealed that the activity of G9a methyltransferase was completely inhibited by the adjacent phosphorylation, while 25% reduction in the activity of Aurora B kinase was observed with the presence of dimethylation on the nearby residue. The PTM crosstalk was examined not only using a pure peptide substrate, but also in a competitive reaction environment, in which the modified and unmodified peptides were mixed and the enzyme actions on both peptides were monitored simultaneously. Our work demonstrates that host-assisted CE is an effective method for study of PTM crosstalk, which could offer the advantages of fast separation, high resolution, and low sample consumption. Graphical abstract.
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Affiliation(s)
- Jiwon Lee
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA
| | - Junyi Chen
- Department of Environmental Toxicology Program, University of California-Riverside, 00 University Ave., Riverside, CA, 92521, USA
| | - Priyanka Sarkar
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA
| | - Min Xue
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA.,Department of Environmental Toxicology Program, University of California-Riverside, 00 University Ave., Riverside, CA, 92521, USA
| | - Richard J Hooley
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA.,Department of Biochemistry and Molecular Biology, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA
| | - Wenwan Zhong
- Department of Chemistry, University of California-Riverside, 900 University Ave., Riverside, CA, 92521, USA. .,Department of Environmental Toxicology Program, University of California-Riverside, 00 University Ave., Riverside, CA, 92521, USA.
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23
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Alex JM, McArdle P, Crowley PB. Supramolecular stacking in a high Z′ calix[8]arene–porphyrin assembly. CrystEngComm 2020. [DOI: 10.1039/c9ce01646e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A co-crystal structure of sulfonato-calix[8]arene (sclx8) and trimethylanilinium-porphyrin (tmap) at 1.0 Å resolution is reported.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
| | - Patrick McArdle
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
| | - Peter B. Crowley
- School of Chemistry
- National University of Ireland Galway
- Galway
- Ireland
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24
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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: 0.8] [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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25
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Screening of inhibitors against histone demethylation jumonji domain-containing protein 3 by capillary electrophoresis. J Chromatogr A 2019; 1613:460625. [PMID: 31668999 DOI: 10.1016/j.chroma.2019.460625] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 11/21/2022]
Abstract
Jumonji domain-containing proteins (JMJDs) play an important role in the epigenetic regulation of gene expression. Aberrant regulation of histone modification has been observed in the progression of a variety of diseases, such as neurological disorders and cancer. Therefore, discovery of selective modulators of JMJDs is very attractive in new drug discovery. Herein, a simple capillary electrophoresis (CE) method was developed for screening of inhibitors against JMJD3. A known JMJD3 inhibitor GSK-J1, 5-carboxyfluorescein labeled substrate peptide with an amino acid sequence of KAPRKQLATKAARK(me3)SAPATGG (truncated from histone H3), as well as a small chemical library composed of 37 purified natural compounds and 30 natural extracts were used for method development and validation. The separation of substrate from its demethylated product was achieved by addition of polycation hexadimethrine bromide (HDB) in the running buffer. The enzyme activity was thus assayed accurately through separating the demethylated product from the substrate and then measuring the peak area of the product. The enzyme inhibition can be read out by comparing the peak area of the demethylated product obtained in the present of inhibitors and that of the negative control in the absence of any inhibitor. The merit of the method is proved by discovering two new JMJD3 inhibitors: salvianic acid A and puerarin 6''-O-xyloside.
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26
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Jangal M, Lebeau B, Witcher M. Beyond EZH2: is the polycomb protein CBX2 an emerging target for anti-cancer therapy? Expert Opin Ther Targets 2019; 23:565-578. [PMID: 31177918 DOI: 10.1080/14728222.2019.1627329] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Epigenetic modifications are important regulators of transcription and appropriate gene expression answering an environmental stimulus. In cancer, these epigenetic modifications are altered, which impact the transcriptome, promoting initiation and cancer progression. Thus, targeting epigenetic machinery has proven to be an efficient cancer therapy. Areas covered: We review CBX2 as a therapeutic target. CBX2 is a polycomb protein, responsible for polycomb-repressive complex 1 (PRC1) targeting to chromatin via recognition of the repressive mark H3K27me3. Mechanistically, CBX2 overexpression may be implicated in poor survival by maintaining cancer stem cells in an undifferentiated state and via repression of tumor suppressors. We discuss strategies used to target CBX proteins and provide insights into biomarker considerations that may be important when targeting CBX family members for anti-cancer therapy. Expert opinion: CBX2 inhibition is a promising approach for the targeting of polycomb complexes in the cancer stem cell niche. However, extensive optimization of the current field of small molecules targeting CBX family proteins will be critical to reach in vivo, or clinical, utility.
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Affiliation(s)
- Maïka Jangal
- a The Lady Davis Institute of the Jewish General Hospital, Department of Oncology , McGill University , Montreal , Canada
| | - Benjamin Lebeau
- a The Lady Davis Institute of the Jewish General Hospital, Department of Oncology , McGill University , Montreal , Canada
| | - Michael Witcher
- a The Lady Davis Institute of the Jewish General Hospital, Department of Oncology , McGill University , Montreal , Canada
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27
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Abstract
Cation and anion recognition have both played central roles in the development of supramolecular chemistry. Much of the associated research has focused on the development of receptors for individual cations or anions, as well as their applications in different areas. Rarely is complexation of the counterions considered. In contrast, ion pair recognition chemistry, emerging from cation and anion coordination chemistry, is a specific research field where co-complexation of both anions and cations, so-called ion pairs, is the center of focus. Systems used for the purpose, known as ion pair receptors, are typically di- or polytopic hosts that contain recognition sites for both cations and anions and which permit the concurrent binding of multiple ions. The field of ion pair recognition has blossomed during the past decades. Several smaller reviews on the topic were published roughly 5 years ago. They provided a summary of synthetic progress and detailed the various limiting ion recognition modes displayed by both acyclic and macrocyclic ion pair receptors known at the time. The present review is designed to provide a comprehensive and up-to-date overview of the chemistry of macrocycle-based ion pair receptors. We specifically focus on the relationship between structure and ion pair recognition, as well as applications of ion pair receptors in sensor development, cation and anion extraction, ion transport, and logic gate construction.
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Affiliation(s)
- Qing He
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States.,State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering , Hunan University , Changsha 410082 , P. R. China
| | - Gabriela I Vargas-Zúñiga
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Seung Hyun Kim
- Department of Chemistry and Research Institute of Natural Science , Gyeongsang National University , Jinju , 660-701 , Korea
| | - Sung Kuk Kim
- Department of Chemistry and Research Institute of Natural Science , Gyeongsang National University , Jinju , 660-701 , Korea
| | - Jonathan L Sessler
- Institute for Supramolecular Chemistry and Catalysis , Shanghai University , Shanghai 200444 , P.R. China.,Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
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28
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Tauran Y, Kumemura M, Tarhan MC, Perret G, Perret F, Jalabert L, Collard D, Fujita H, Coleman AW. Direct measurement of the mechanical properties of a chromatin analog and the epigenetic effects of para-sulphonato-calix[4]arene. Sci Rep 2019; 9:5816. [PMID: 30967623 PMCID: PMC6456576 DOI: 10.1038/s41598-019-42267-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 03/25/2019] [Indexed: 02/06/2023] Open
Abstract
By means of Silicon Nano Tweezers (SNTs) the effects on the mechanical properties of λ-phage DNA during interaction with calf thymus nucleosome to form an artificial chromatin analog were measured. At a concentration of 100 nM, a nucleosome solution induced a strong stiffening effect on DNA (1.1 N m-1). This can be compared to the effects of the histone proteins, H1, H2A, H3 where no changes in the mechanical properties of DNA were observed and the complex of the H3/H4 proteins where a smaller increase in the stiffness is observed (0.2 N m-1). Para-sulphonato-calix[4]arene, SC4, known for epigenetic activity by interacting specifically with the lysine groups of histone proteins, was studied for its effect on an artificial chromatin. Using a microfluidic SNT device, SC4 was titrated against the artificial chromatin, at a concentration of 1 mM in SC4 a considerable increase in stiffness, 15 N m-1, was observed. Simultaneously optical microscopy showed a physical change in the DNA structure between the tips of the SNT device. Electronic and Atomic Force microscopy confirmed this structural re-arrangement. Negative control experiments confirmed that these mechanical and physical effects were induced neither by the acidity of SC4 nor through nonspecific interactions of SC4 on DNA.
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Affiliation(s)
- Yannick Tauran
- LMI CNRS UMR 5615, Université Lyon 1, Villeurbanne, 69622, France.
- LIMMS/CNRS-IIS UMI 2820, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan.
| | - Momoko Kumemura
- LIMMS/CNRS-IIS UMI 2820, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
- CIRMM, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Fukuoka, 808-0196, Japan
| | - Mehmet C Tarhan
- Univ. Lille, CNRS, Centrale Lille, ISEN, Univ. Valenciennes, UMR 8520-IEMN, Lille, F59000, France
- CNRS/IIS/COL/Lille 1 SMMiL-E project, 59046, Lille Cedex, France
| | - Grégoire Perret
- LIMMS/CNRS-IIS UMI 2820, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
- CNRS/IIS/COL/Lille 1 SMMiL-E project, 59046, Lille Cedex, France
| | - Florent Perret
- ICBMS, CNRS UMR 5246, Université Lyon 1, Villeurbanne, 69622, France
| | - Laurent Jalabert
- LIMMS/CNRS-IIS UMI 2820, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
- CIRMM, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
| | - Dominique Collard
- LIMMS/CNRS-IIS UMI 2820, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
- CNRS/IIS/COL/Lille 1 SMMiL-E project, 59046, Lille Cedex, France
| | - Hiroyuki Fujita
- LIMMS/CNRS-IIS UMI 2820, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
- CIRMM, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
| | - Anthony W Coleman
- CIRMM, Institute of Industrial Science, The University of Tokyo, Tokyo, 153-8505, Japan
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29
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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: 2.7] [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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30
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Guagnini F, Antonik PM, Rennie ML, O'Byrne P, Khan AR, Pinalli R, Dalcanale E, Crowley PB. Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803232] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Francesca Guagnini
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Paweł M. Antonik
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Peter O'Byrne
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Roberta Pinalli
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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31
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Guagnini F, Antonik PM, Rennie ML, O'Byrne P, Khan AR, Pinalli R, Dalcanale E, Crowley PB. Cucurbit[7]uril-Dimethyllysine Recognition in a Model Protein. Angew Chem Int Ed Engl 2018; 57:7126-7130. [DOI: 10.1002/anie.201803232] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Francesca Guagnini
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Paweł M. Antonik
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Peter O'Byrne
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Amir R. Khan
- School of Biochemistry and Immunology; Trinity College Dublin; Dublin 2 Ireland
| | - Roberta Pinalli
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Enrico Dalcanale
- Dipartimento di Scienze Chimiche della Vita e della Sostenibilità Ambientale; Università di Parma and INSTM UdR Parma; Parco Area delle Scienze 17/A 43124 Parma Italy
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
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32
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Beatty MA, Borges-González J, Sinclair NJ, Pye AT, Hof F. Analyte-Driven Disassembly and Turn-On Fluorescent Sensing in Competitive Biological Media. J Am Chem Soc 2018; 140:3500-3504. [DOI: 10.1021/jacs.7b13298] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Meagan A. Beatty
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3V6, Canada
| | - Jorge Borges-González
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3V6, Canada
| | - Nicholas J. Sinclair
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3V6, Canada
| | - Aidan T. Pye
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3V6, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, PO Box 3065, STN CSC, Victoria, British Columbia V8W 3V6, Canada
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33
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Lee J, Perez L, Liu Y, Wang H, Hooley RJ, Zhong W. Separation of Methylated Histone Peptides via Host-Assisted Capillary Electrophoresis. Anal Chem 2018; 90:1881-1888. [PMID: 29286640 DOI: 10.1021/acs.analchem.7b03969] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Lysine methylation in protein is one important epigenetic mechanism that regulates diverse biological processes but is challenging to study due to the large variability in methylation levels and sites. Here, we show that supramolecular hosts such as calixarenes and cucurbiturils can be applied in the background electrolyte (BGE) of capillary electrophoresis (CE) for highly effective separation of post-translationally methylated histone peptides. The molecular recognition event causes a shift in the electrophoretic mobility of the peptide, allowing affinity measurement for binding between the synthetic receptor and various methylated lysine species. Successful separation of the H3 peptides carrying different methylation levels at the K9 position can be achieved using CX4 and CX6 as the BGE additives in CE, enabling monitoring of the activity of the histone lysine demethylase JMJD2E. This reveals the power of combining high resolution CE with synthetic hosts for study of protein methylation, and the method should be capable of analyzing complex biological samples for better understanding of the functions of histone methylation.
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Affiliation(s)
| | | | | | - Hua Wang
- Instrument Analysis Center, Yancheng Teachers University , Yancheng, Jiangsu 224007, China
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34
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Doolan AM, Rennie ML, Crowley PB. Protein Recognition by Functionalized Sulfonatocalix[4]arenes. Chemistry 2017; 24:984-991. [PMID: 29125201 DOI: 10.1002/chem.201704931] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Indexed: 12/31/2022]
Abstract
The interactions of two mono-functionalized sulfonatocalix[4]arenes with cytochrome c were investigated by structural and thermodynamic methods. The replacement of a single sulfonate with either a bromo or a phenyl substituent resulted in altered recognition of cytochrome c as evidenced by X-ray crystallography. The bromo-substituted ligand yielded a new binding mode in which a self-encapsulated calixarene dimer contributed to crystal packing. This ligand also formed a weak halogen bond with the protein. The phenyl-substituted ligand was bound to Lys4 of cytochrome c, in a 1.7 Å resolution crystal structure. A dimeric packing arrangement mediated by ligand-ligand contacts in the crystal suggested a possible assembly mechanism. The different protein recognition properties of these calixarenes are discussed.
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Affiliation(s)
- Aishling M Doolan
- 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 B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
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35
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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: 153] [Impact Index Per Article: 21.9] [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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36
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Bontempi N, Biavardi E, Bordiga D, Candiani G, Alessandri I, Bergese P, Dalcanale E. Probing lysine mono-methylation in histone H3 tail peptides with an abiotic receptor coupled to a non-plasmonic resonator. NANOSCALE 2017; 9:8639-8646. [PMID: 28608884 DOI: 10.1039/c7nr02491f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Binder and effector molecules that allow studying and manipulating epigenetic processes are of biological relevance and pose severe technical challenges. We report the first example of a synthetic receptor able to recognize mono-methylated lysines in a histone H3 tail peptide, which has relevant functions in epigenetic regulation. Recognition is robust and specific regardless of the position and the number of mono-methylated lysines along the polypeptide chain. The peptide is first captured in solution by a tetraphosphonate cavitand (Tiiii) that selectively binds its Lys-NMe+ moieties. Separation from solution and detection of the peptide-Tiiii complexes is then enabled in one single step by an all dielectric SiO2-TiO2 core-shell resonator (T-rex), which captures the complex and operates fully reproducible signal transduction by non-plasmonic surface enhanced Raman scattering (SERS) without degrading the complex. The realized abiotic probe is able to distinguish multiple mono-methylated peptides from the single mono-methylated ones.
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Affiliation(s)
- N Bontempi
- Department of Mechanical and Industrial Engineering, Chemistry for Technologies Laboratory, University of Brescia and INSTM UdR Brescia, Via Branze 38, 25123 Brescia, Italy.
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37
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Hanauer T, Hopkinson RJ, Patel K, Li Y, Correddu D, Kawamura A, Sarojini V, Leung IKH, Gruber T. Selective recognition of the di/trimethylammonium motif by an artificial carboxycalixarene receptor. Org Biomol Chem 2017; 15:1100-1105. [PMID: 28091667 DOI: 10.1039/c6ob02616h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2024]
Abstract
Chemical tools that recognise post-translational modifications have promising applications in biochemistry and in therapy. We report a simple carboxycalixarene that selectively binds molecules containing di/trimethylammonium moieties in isolation, in cell lysates and when incorporated in histone peptides. Our findings reveal the potential of using carboxycalixarene-based receptors to study epigenetic regulation.
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Affiliation(s)
- Thomas Hanauer
- Institute of Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, Freiberg, Sachsen, Germany.
| | - Richard J Hopkinson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Kamal Patel
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Yu Li
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Danilo Correddu
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Ivanhoe K H Leung
- School of Chemical Sciences and Centre for Green Chemical Science, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
| | - Tobias Gruber
- Institute of Organic Chemistry, Technische Universität Bergakademie Freiberg, Leipziger Strasse 29, Freiberg, Sachsen, Germany.
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38
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Peacor BC, Ramsay CM, Waters ML. Fluorogenic sensor platform for the histone code using receptors from dynamic combinatorial libraries. Chem Sci 2016; 8:1422-1428. [PMID: 28451282 PMCID: PMC5390788 DOI: 10.1039/c6sc03003c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/20/2016] [Indexed: 12/13/2022] Open
Abstract
A sensor array has been developed that can differentiate multiple post-translational modifications in the same peptide and their relative positions in the sequence, including multiple methylations, providing a promising new tool for deciphering the histone code.
Post-translational modifications (PTMs) on histone tails act in diverse combinations in the ‘histone code’ to control gene expression, with dysregulation observed in a variety of diseases. However, detection and sensing methods are limited, expensive, and/or low-throughput, including MS and antibody based detection. We found that by combining four synthetic receptors developed by dynamic combinatorial chemistry (DCC) in an indicator displacement system, we are able to create a pattern-based sensor platform that can discriminate single PTMs such as methylation and acetylation on a representative histone peptide with 100% accuracy as well as peptides bearing both dimethyl and trimethyl lysine in the presence of arginine methylation, which has not previously been demonstrated, and can even correctly distinguish the position of lysine methylation individually or in the presence of other PTMs. To extend this approach, a full panel of thirteen analytes containing different combinations of PTMs were classified with 96 ± 1% overall accuracy in a 50% left-out analysis, demonstrating the robustness and versatility of the sensor array. Finally, the sensor platform was also used to demonstrate proof of concept for enzymatic assays by analysing the mock reaction of a threonine kinase, successfully identifying analytes representative of substrate conversion both with and without neighboring PTMs. This work provides a rapid platform for the analysis of peptides bearing complex modifications and highlights the utility of receptors discovered though DCC that display variations in binding affinity and selectivity.
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Affiliation(s)
- Brendan C Peacor
- Department of Chemistry , University of North Carolina at Chapel Hill , CB 3290 , Chapel Hill , NC 27599 , USA .
| | - Christopher M Ramsay
- Department of Chemistry , University of North Carolina at Chapel Hill , CB 3290 , Chapel Hill , NC 27599 , USA .
| | - Marcey L Waters
- Department of Chemistry , University of North Carolina at Chapel Hill , CB 3290 , Chapel Hill , NC 27599 , USA .
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39
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Gober IN, Waters ML. Supramolecular Affinity Labeling of Histone Peptides Containing Trimethyllysine and Its Application to Histone Deacetylase Assays. J Am Chem Soc 2016; 138:9452-9. [DOI: 10.1021/jacs.6b02836] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Isaiah N. Gober
- Department
of Chemistry,
CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Marcey L. Waters
- Department
of Chemistry,
CB 3290, UNC Chapel Hill, Chapel Hill, North Carolina 27599, United States
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40
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Pinalli R, Brancatelli G, Pedrini A, Menozzi D, Hernández D, Ballester P, Geremia S, Dalcanale E. The Origin of Selectivity in the Complexation of N-Methyl Amino Acids by Tetraphosphonate Cavitands. J Am Chem Soc 2016; 138:8569-80. [PMID: 27310660 DOI: 10.1021/jacs.6b04372] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report on the eligibility of tetraphosphonate resorcinarene cavitands for the molecular recognition of amino acids. We determined the crystal structure of 13 complexes of the tetraphosphonate cavitand Tiiii[H, CH3, CH3] with amino acids. (1)H NMR and (31)P NMR experiments and ITC analysis were performed to probe the binding between cavitand Tiiii[C3H7, CH3, C2H5] or the water-soluble counterpart Tiiii[C3H6Py(+)Cl(-), CH3, C2H5] and a selection of representative amino acids. The reported studies and results allowed us (i) to highlight the noncovalent interactions involved in the binding event in each case; (ii) to investigate the ability of tetraphosphonate cavitand receptors to discriminate between the different amino acids; (iii) to calculate the Ka values of the different complexes formed and evaluate the thermodynamic parameters of the complexation process, dissecting the entropic and enthalpic contributions; and (iv) to determine the solvent influence on the complexation selectivity. By moving from methanol to water, the complexation changed from entropy driven to entropy opposed, leading to a drop of almost three orders in the magnitude of the Ka. However, this reduction in binding affinity is associated with a dramatic increase in selectivity, since in aqueous solutions only N-methylated amino acids are effectively recognized. The thermodynamic profile of the binding does not change in PBS solution. The pivotal role played by cation-π interactions is demonstrated by the linear correlation found between the log Ka in methanol solution and the depth of (+)N-CH3 cavity inclusion in the molecular structures. These findings are relevant for the potential use of phosphonate cavitands as synthetic receptors for the detection of epigenetic modifications of histones in physiological media.
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Affiliation(s)
- Roberta Pinalli
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Giovanna Brancatelli
- CEB Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste , Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Alessandro Pedrini
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Daniela Menozzi
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
| | - Daniel Hernández
- Catalan Institution for Research and Advanced Studies (ICREA) , Passeig Lluís Companys, 23, 08018 Barcelona, Spain
| | - Pablo Ballester
- Catalan Institution for Research and Advanced Studies (ICREA) , Passeig Lluís Companys, 23, 08018 Barcelona, Spain.,Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology , Avgda. Països Catalans 16, 43007 Tarragona, Spain
| | - Silvano Geremia
- CEB Centre of Excellence in Biocrystallography, Department of Chemical and Pharmaceutical Sciences, University of Trieste , Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Enrico Dalcanale
- Department of Chemistry, University of Parma, and INSTM , UdR Parma, Parco Area delle Scienze 17/A, 43124 Parma, Italy
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41
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Garnett GA, Starke MJ, Shaurya A, Li J, Hof F. Supramolecular Affinity Chromatography for Methylation-Targeted Proteomics. Anal Chem 2016; 88:3697-703. [DOI: 10.1021/acs.analchem.5b04508] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Graham A.E. Garnett
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W3 V6, Canada
| | - Melissa J. Starke
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W3 V6, Canada
| | - Alok Shaurya
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W3 V6, Canada
| | - Janessa Li
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W3 V6, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W3 V6, Canada
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42
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Abstract
A network of reader proteins and enzymes precisely controls gene transcription through the dynamic addition, removal, and recognition of post-translational modifications (PTMs) of histone tails. Histone PTMs work in concert with this network to regulate gene transcription through the histone code, and the dysregulation of PTM maintenance is linked to a large number of diseases, including many types of cancer. A wealth of research aims to elucidate the functions of this code, but our understanding of the effects of PTMs, specifically the methylation of lysine (Lys) and arginine (Arg), is lacking. The development of new tools to study PTMs relies on a sophisticated understanding of the mechanisms that drive protein and small molecule recognition in water. In this review, we outline the physical organic concepts that drive the molecular recognition of Lys and Arg methylation by reader proteins and draw comparisons to the binding mechanisms of small molecule receptors for methylated Lys and Arg that have been developed recently.
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Affiliation(s)
- Joshua E. Beaver
- Department of Chemistry, University of North Carolina, CB 3290, Chapel Hill, North Carolina 27599, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina, CB 3290, Chapel Hill, North Carolina 27599, United States
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43
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Peacock H, Thinnes CC, Kawamura A, Hamilton AD. Tetracyanoresorcin[4]arene selectively recognises trimethyllysine and inhibits its enzyme-catalysed demethylation. Supramol Chem 2016. [DOI: 10.1080/10610278.2016.1140898] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Hayden Peacock
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Cyrille C. Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Andrew D. Hamilton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
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44
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Hof F. Host–guest chemistry that directly targets lysine methylation: synthetic host molecules as alternatives to bio-reagents. Chem Commun (Camb) 2016; 52:10093-108. [DOI: 10.1039/c6cc04771h] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Post-translational methylation regulates the function of hundreds of proteins in profound ways, and is the target of many efforts to use host–guest chemistry to solve biochemical and biological problems.
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Affiliation(s)
- Fraser Hof
- Department of Chemistry
- University of Victoria
- V8W3V6 Canada
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45
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Pinkin NK, N Power A, Waters ML. Late stage modification of receptors identified from dynamic combinatorial libraries. Org Biomol Chem 2015; 13:10939-45. [PMID: 26384269 PMCID: PMC5523513 DOI: 10.1039/c5ob01649e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Small molecule receptors are attractive potential sensors of post-translational modifications, including methylated lysine and methylated arginine. Using dynamic combinatorial chemistry (DCC), our lab previously identified a suite of receptors that bind to Kme3 with a range of affinities ranging from low micromolar to high nanomolar, each with a unique selectivity for Kme3 over the lower methylation states. To enable these receptors to have broad application as Kme3 sensors, we have developed a method for their late-stage modification, which we used to synthesize biotinylated derivatives of A2B, A2D, and A2G in a single step. For our most attractive receptor for applications, A2N, we needed to develop an alternative method for its selective functionalization, which we achieved by "activating" the carboxylic acids on the constituent monomer A or N by pre-functionalizing them with glycine (Gly). Using the resulting Gly-A and Gly-N monomers, we synthesized the novel A2N variants A2Gly-N, Gly-A2N, and Gly-A2Gly-N, which enabled the late stage biotinylation of A2N wherever Gly was incorporated. Finally, we performed ITC and NMR binding experiments to study the effect that carboxylate spacing has on the affinity and selectivity of A2Gly-N and Gly-A2N for KmeX guests compared to A2N. These studies revealed the proximity of the carboxylates to play a complex role in the molecular recognition event, despite their positioning on the outside of the receptor.
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Affiliation(s)
- Nicholas K Pinkin
- Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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46
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Kimura Y, Saito N, Hanada K, Liu J, Okabe T, Kawashima SA, Yamatsugu K, Kanai M. Supramolecular Ligands for Histone Tails by Employing a Multivalent Display of Trisulfonated Calix[4]arenes. Chembiochem 2015; 16:2599-604. [DOI: 10.1002/cbic.201500448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Yasuaki Kimura
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Japan Science and Technology Agency (JST); ERATO; Kanai Life Science Catalysis Project; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Nae Saito
- Drug Discovery Initiative; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kayo Hanada
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Jiaan Liu
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Okabe
- Drug Discovery Initiative; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Shigehiro A. Kawashima
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Japan Science and Technology Agency (JST); ERATO; Kanai Life Science Catalysis Project; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Kenzo Yamatsugu
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Japan Science and Technology Agency (JST); ERATO; Kanai Life Science Catalysis Project; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Japan Science and Technology Agency (JST); ERATO; Kanai Life Science Catalysis Project; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
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Conway JH, Fiedler D. An Affinity Reagent for the Recognition of Pyrophosphorylated Peptides. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201411232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Conway JH, Fiedler D. An affinity reagent for the recognition of pyrophosphorylated peptides. Angew Chem Int Ed Engl 2015; 54:3941-5. [PMID: 25651128 DOI: 10.1002/anie.201411232] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Indexed: 11/05/2022]
Abstract
A resin-bound dinuclear zinc(II) complex for the selective capture of pyrophosphopeptides is reported. The metal complex binds diphosphate esters over other anionic groups, such as monophosphate esters, sulfate esters, and carboxylic acids, with high specificity. Immobilization of the compound provided a reagent capable of binding and retaining nanomolar quantities of pyrophosphopeptide in the presence of cell lysate. The high affinity and specificity of the reagent makes it an attractive tool for the study of in vivo pyrophosphorylation.
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Affiliation(s)
- John H Conway
- Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544 (USA)
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McGovern RE, Snarr BD, Lyons JA, McFarlane J, Whiting AL, Paci I, Hof F, Crowley PB. Structural study of a small molecule receptor bound to dimethyllysine in lysozyme. Chem Sci 2015; 6:442-449. [PMID: 25530835 PMCID: PMC4266562 DOI: 10.1039/c4sc02383h] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Lysine is a ubiquitous residue on protein surfaces. Post translational modifications of lysine, including methylation to the mono-, di- or trimethylated amine result in chemical and structural alterations that have major consequences for protein interactions and signalling pathways. Small molecules that bind to methylated lysines are potential tools to modify such pathways. To make progress in this direction, detailed structural data of ligands in complex with methylated lysine is required. Here, we report a crystal structure of p-sulfonatocalix[4]arene (sclx4) bound to methylated lysozyme in which the lysine residues were chemically modified from Lys-NH3+ to Lys-NH(Me2)+. Of the six possible dimethyllysine sites, sclx4 selected Lys116-Me2 and the dimethylamino substituent was deeply buried in the calixarene cavity. This complex confirms the tendency for Lys-Me2 residues to form cation-π interactions, which have been shown to be important in protein recognition of histone tails bearing methylated lysines. Supporting data from NMR spectroscopy and MD simulations confirm the selectivity for Lys116-Me2 in solution. The structure presented here may serve as a stepping stone to the development of new biochemical reagents that target methylated lysines.
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Affiliation(s)
- Róise E McGovern
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Brendan D Snarr
- Department of Chemistry, University of Victoria, British Columbia, V8W 3V6, Canada
| | - Joseph A Lyons
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - James McFarlane
- Department of Chemistry, University of Victoria, British Columbia, V8W 3V6, Canada
| | - Amanda L Whiting
- Department of Chemistry, University of Victoria, British Columbia, V8W 3V6, Canada
| | - Irina Paci
- Department of Chemistry, University of Victoria, British Columbia, V8W 3V6, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, British Columbia, V8W 3V6, Canada
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
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Abstract
The tandem PHD (plant homeodomain) fingers of the CHD4 (chromodomain helicase DNA-binding protein 4) ATPase are epigenetic readers that bind either unmodified histone H3 tails or H3K9me3 (histone H3 trimethylated at Lys⁹). This dual function is necessary for the transcriptional and chromatin remodelling activities of the NuRD (nucleosome remodelling and deacetylase) complex. In the present paper, we show that calixarene-based supramolecular hosts disrupt binding of the CHD4 PHD2 finger to H3K9me3, but do not affect the interaction of this protein with the H3K9me0 (unmodified histone H3) tail. A similar inhibitory effect, observed for the association of chromodomain of HP1γ (heterochromatin protein 1γ) with H3K9me3, points to a general mechanism of methyl-lysine caging by calixarenes and suggests a high potential for these compounds in biochemical applications. Immunofluorescence analysis reveals that the supramolecular agents induce changes in chromatin organization that are consistent with their binding to and disruption of H3K9me3 sites in living cells. The results of the present study suggest that the aromatic macrocyclic hosts can be used as a powerful new tool for characterizing methylation-driven epigenetic mechanisms.
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