1
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Suating P, Ewe MB, Kimberly LB, Arman HD, Wherritt DJ, Urbach AR. Peptide recognition by a synthetic receptor at subnanomolar concentrations. Chem Sci 2024; 15:5133-5142. [PMID: 38577360 PMCID: PMC10988627 DOI: 10.1039/d4sc01122h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
This paper describes the discovery and characterization of a dipeptide sequence, Lys-Phe, that binds to the synthetic receptor cucurbit[8]uril (Q8) in neutral aqueous solution with subnanomolar affinity when located at the N-terminus. The thermodynamic and structural basis for the binding of Q8 to a series of four pentapeptides was characterized by isothermal titration calorimetry, NMR spectroscopy, and X-ray crystallography. Submicromolar binding affinity was observed for the peptides Phe-Lys-Gly-Gly-Tyr (FKGGY, 0.3 μM) and Tyr-Leu-Gly-Gly-Gly (YLGGG, 0.2 μM), whereas the corresponding sequence isomers Lys-Phe-Gly-Gly-Tyr (KFGGY, 0.3 nM) and Leu-Tyr-Gly-Gly-Gly (LYGGG, 1.2 nM) bound to Q8 with 1000-fold and 170-fold increases in affinity, respectively. To our knowledge, these are the highest affinities reported between a synthetic receptor and an unmodified peptide. The high-resolution crystal structures of the Q8·Tyr-Leu-Gly-Gly-Gly and Q8·Leu-Tyr-Gly-Gly-Gly complexes have enabled a detailed analysis of the structural determinants for molecular recognition. The high affinity, sequence-selectivity, minimal size of the target binding site, reversibility in the presence of a competitive guest, compatibility with aqueous media, and low toxicity of Q8 should aid in the development of applications involving low concentrations of target polypeptides.
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Affiliation(s)
- Paolo Suating
- Department of Chemistry, Trinity University 1 Trinity Place San Antonio TX 78212 USA
| | - Marc B Ewe
- Department of Chemistry, Trinity University 1 Trinity Place San Antonio TX 78212 USA
| | - Lauren B Kimberly
- Department of Chemistry, Trinity University 1 Trinity Place San Antonio TX 78212 USA
| | - Hadi D Arman
- Department of Chemistry, University of Texas at San Antonio 1 UTSA Circle San Antonio TX 78249 USA
| | - Daniel J Wherritt
- Department of Chemistry, University of Texas at San Antonio 1 UTSA Circle San Antonio TX 78249 USA
| | - Adam R Urbach
- Department of Chemistry, Trinity University 1 Trinity Place San Antonio TX 78212 USA
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2
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Suating P, Kimberly LB, Ewe MB, Chang SL, Fontenot JM, Sultane PR, Bielawski CW, Decato DA, Berryman OB, Taylor AB, Urbach AR. Cucurbit[8]uril Binds Nonterminal Dipeptide Sites with High Affinity and Induces a Type II β-Turn. J Am Chem Soc 2024; 146:7649-7657. [PMID: 38348472 DOI: 10.1021/jacs.3c14045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
In an effort to target polypeptides at nonterminal sites, we screened the binding of the synthetic receptor cucurbit[8]uril (Q8) to a small library of tetrapeptides, each containing a nonterminal dipeptide binding site. The resulting leads were characterized in detail using a combination of isothermal titration calorimetry, 1H NMR spectroscopy, electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS), and X-ray crystallography. The equilibrium dissociation constant values determined for the binding of Q8 to nonterminal dipeptide sites Lys-Phe (KF) and Phe-Lys (FK) were 60 and 86 nm, respectively. These are to the best of our knowledge the highest affinities reported to date for any synthetic receptor targeting a nonterminal site on an unmodified peptide. A 0.79 Å resolution crystal structure was obtained for the complex of Q8 with the peptide Gly-Gly-Leu-Tyr-Gly-Gly-Gly (GGLYGGG) and reveals structural details of the pair-inclusion motif. The molecular basis for recognition is established to be the inclusion of the side chains of Leu and Tyr residues, as well as an extensive network of hydrogen bonds between the peptide backbone, the carbonyl oxygens of Q8, and proximal water molecules. In addition, the crystal structure reveals that Q8 induces a type II β-turn. The sequence-selectivity, high affinity, reversibility, and detailed structural characterization of this system should facilitate the development of applications involving ligand-induced polypeptide folding.
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Affiliation(s)
- Paolo Suating
- Department of Chemistry, Trinity University, 1 Trinity Place, San Antonio, Texas 78212, United States
| | - Lauren B Kimberly
- Department of Chemistry, Trinity University, 1 Trinity Place, San Antonio, Texas 78212, United States
| | - Marc B Ewe
- Department of Chemistry, Trinity University, 1 Trinity Place, San Antonio, Texas 78212, United States
| | - Sarah L Chang
- Department of Chemistry, Trinity University, 1 Trinity Place, San Antonio, Texas 78212, United States
| | - John M Fontenot
- Department of Chemistry, Trinity University, 1 Trinity Place, San Antonio, Texas 78212, United States
| | - Prakash R Sultane
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS) and Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Christopher W Bielawski
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS) and Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Daniel A Decato
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Orion B Berryman
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, United States
| | - Alexander B Taylor
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, 8300 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Adam R Urbach
- Department of Chemistry, Trinity University, 1 Trinity Place, San Antonio, Texas 78212, United States
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3
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Zaorska E, Malinska M. Cucurbit[7]uril-mediated Histidine Dimerization: Exploring the Structure and Binding Mechanism. Chemistry 2024; 30:e202302250. [PMID: 38055216 DOI: 10.1002/chem.202302250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/07/2023]
Abstract
Cucurbit[7,8]urils are known to form inclusion complexes with hydrophobic amino acids such as Trp, Tyr, Phe, and Met, as well as peptides containing these residues at the N-terminus. Despite their widespread use in protein purification, the affinity of histidine (His) for cucurbit[7,8]urils has not been extensively explored. In this study, X-ray diffraction experiments were conducted to investigate the binding of two histidine moieties to the cucurbit[7]uril (CB7) cavity, resulting in a network of π-π and hydrogen bonds. This assembly was found to induce a His pKa shift of ΔpKa=-4. Histidine weakly bound to CB7 or CB8; however, isothermal titration calorimetry revealed micromolar equilibrium dissociation constant values for CB7 and CB8 when bound to dipeptides containing His at the C-terminus. Conversely, dipeptides with His at the N-terminus exhibited millimolar values. Additionally, the His-Gly-Gly tripeptide formed a 2 : 1 complex with CB7. These findings suggest the potential use of histidine and histidine-containing tags in conjunction with CB7 for various biological applications.
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Affiliation(s)
- Ewelina Zaorska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
| | - Maura Malinska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland
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4
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Shuto M, Sumida R, Yuasa M, Sawada T, Yoshizawa M. A Closed Cavity Strategy for Selective Dipeptide Binding by a Polyaromatic Receptor in Water. JACS Au 2023; 3:2905-2911. [PMID: 37885581 PMCID: PMC10598568 DOI: 10.1021/jacsau.3c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 10/28/2023]
Abstract
Precise recognition of peptides is a daunting task owing to the substantial number of available amino acids and their combination into various oligo/polymeric structures in addition to the high hydration of their flexible frameworks. Here, we report the selective recognition of a dipeptide through a closed cavity strategy, in contrast to previous synthetic receptors with open cavities. A polyaromatic receptor with a virtually isolated, hydrophobic cavity exclusively binds one molecule of phenylalanine dipeptide from a mixture with its amino acid and tripeptide in water via multiple CH-π and hydrogen-bonding interactions in the complementary cavity. The binding selectivity persists even in the presence of other dipeptides, such as leucine-leucine, leucine-phenylalanine, tyrosine-phenylalanine, tryptophan-tryptophan, and aspartame, revealed by NMR/MS-based competitive binding experiments. ITC studies reveal that the selective binding of the phenylalanine dipeptide is relatively strong (Ka = 1.1 × 105 M-1) and an enthalpically and entropically favorable process (ΔH = -11.7 kJ mol-1 and TΔS = 17.0 kJ mol-1). In addition, the present receptor can be used for the emission detection of the dipeptide through a combination with a fluorescent dye in water.
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Affiliation(s)
- Mayu Shuto
- Laboratory for Chemistry
and Life Science, Institute of Innovative
Research, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
| | - Ryuki Sumida
- Laboratory for Chemistry
and Life Science, Institute of Innovative
Research, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
| | - Mana Yuasa
- Laboratory for Chemistry
and Life Science, Institute of Innovative
Research, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
| | - Tomohisa Sawada
- Laboratory for Chemistry
and Life Science, Institute of Innovative
Research, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
| | - Michito Yoshizawa
- Laboratory for Chemistry
and Life Science, Institute of Innovative
Research, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama 226-8503, Japan
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5
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
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6
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Chen X, Yang N, Ma Y, Yang X, Ma P. A fluorescent probe for detection of Hg 2+ ions constructed by tetramethyl cucurbit[6]uril and 1,2-bis(4-pyridyl)ethene. Beilstein J Org Chem 2023; 19:864-872. [PMID: 37346492 PMCID: PMC10280054 DOI: 10.3762/bjoc.19.63] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/02/2023] [Indexed: 06/23/2023] Open
Abstract
In this paper, tetramethyl cucurbit[6]uril (TMeQ[6]) and 1,2-bis(4-pyridyl)ethene (G) were used to construct a supramolecular fluorescent probe G@TMeQ[6]. The host-guest interaction between TMeQ[6] and G was investigated using 1H NMR spectroscopy, single-crystal X-ray diffraction and various experimental techniques. The results show that TMeQ[6] and G form an inclusion complex with a host-guest ratio of 1:1 and the equilibrium association constant (Ka) was 2.494 × 104 M-1. The G@TMeQ[6] fluorescent probe can sensitively recognize Hg2+ ions by fluorescence enhancement. The linear range is 0.33 × 10-5-1.65 × 10-5 mol·L-1, R2 = 0.9926, and the limit of detection is 4.12 × 10-8 mol·L-1. The fluorescent probe can be used to detect the concentration of Hg2+ ions in aqueous solution, and provides a theoretical basis for the development of new fluorescent probes for detecting heavy metal ions.
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Affiliation(s)
- Xiaoqian Chen
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Naqin Yang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Yue Ma
- Guiyang College of Humanities and Science, Guiyang 550025, China
| | - Xinan Yang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
| | - Peihua Ma
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang 550025, China
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7
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Ramberg KO, Crowley PB. Cage versus Sheet: Probing the Determinants of Protein - Cucurbit[7]uril Crystalline Architectures. J Struct Biol 2023; 215:107969. [PMID: 37137399 DOI: 10.1016/j.jsb.2023.107969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/22/2023] [Accepted: 04/25/2023] [Indexed: 05/05/2023]
Abstract
The donut-shaped cucurbit[n]urils (Qn) are a class of rigid macrocyclic receptor with protein recognition capabilities. Qn encapsulation of amino acid side chains can enable protein assembly. Recently, cucurbit[7]uril (Q7) has been applied as a molecular glue for organizing protein building blocks into crystalline architectures. Q7 co-crystallization with dimethylated Ralstonia solanacearum lectin (RSL*) has yielded novel crystalline architectures. Co-crystallization of RSL* and Q7 yields either cage- or sheet-like architectures which may be modulated via protein engineering. However, questions remain as to the factors dictating the formation of one architecture over another (cage versus sheet). Here, we make use of an engineered RSL*-Q7 system which co-crystallizes as the cage or sheet assembly with easily-distinguished crystal morphologies. Using this model system, we probe how the crystallization conditions dictate which crystalline architecture is adopted. Protein-ligand ratios and the sodium concentration were identified as key determinants for the growth of the cage versus sheet assemblies.
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Affiliation(s)
- Kiefer O Ramberg
- School of Biological and Chemical Sciences, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - 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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Zhao Y, Li F, Ma F, Zhi J, Wu G, Zheng X. Theoretical prediction of nanomolar and sequence-selective binding of synthetic supramolecular cucurbit[7]uril to N-terminal Leu-containing tripeptides. Phys Chem Chem Phys 2023; 25:7893-7900. [PMID: 36857719 DOI: 10.1039/d2cp03818h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Molecular recognition towards peptides and proteins with high affinity by synthetic supramolecular hosts is important but challenging. In this work, we investigate the molecular recognition of the synthetic cucurbit[7]uril (CB[7]) to 17 designed N-terminal Leu-containing tripeptides in aqueous medium by molecular dynamics (MD) simulation and screen out tripeptides with high binding affinity. It is found that, compared to LGG, only the third residue is Arg (R), the binding affinity of CB[7] to LGR reaches nanomolar level with binding equilibrium constant (Ka) of 1.1 × 109 M-1. The CB[7] recognition to the N-terminal Leu-containing tripeptides is highly sequence dependent; whether changing the sequence order (from LGR to LRG) or increasing the sequence length (from LGR to LGGR), Ka decreases by about three orders of magnitude. Interestingly, substituting N-terminal Leu for its isomer Ile, the binding of CB[7] to tripeptides weakens significantly with Ka decreasing by 3-8 orders of magnitude. Thus CB[7] can effectively distinguish N-terminal Leu-containing tripeptides from N-terminal Ile-containing tripeptides. Importantly, we predict that when R is as C-terminus, regardless of N-terminal residue being of aromatic type or Leu, the binding strength is always close to the nanomolar level. Therefore, R can be introduced to rationally design novel peptides with high binding affinity to CB[7] in practical applications.
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Affiliation(s)
- Ying Zhao
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
| | - Fei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, China.
| | - Fenfen Ma
- GuSu Laboratory of Materials, Suzhou 215123, Jiangsu, China
| | - Junge Zhi
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
| | - Guanglu Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, China.
| | - Xiaoyan Zheng
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China. .,Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates (South China University of Technology), Guangzhou 510640, China
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9
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Cheng L, Tian P, Duan H, Li Q, Song X, Li A, Cao L. Chiral adaptive recognition with sequence specificity of aromatic dipeptides in aqueous solution by an achiral cage. Chem Sci 2023; 14:833-842. [PMID: 36755713 PMCID: PMC9890615 DOI: 10.1039/d2sc05854e] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Sequence-specific recognition of peptides and proteins by synthetic compounds or systems remains a huge challenge in biocompatible media. Here, we report the chiral adaptive recognition (CAR) with sequence specificity of aromatic dipeptides in a purely aqueous solution using an achiral tetraphenylethene-based octacationic cage (1) as both a molecular receptor and chiroptical sensor. 1 can selectively bind and dimerize aromatic dipeptides to form 1 : 2 host-guest complexes with high binding affinity (>1010 M-2), especially up to ∼1014 M-2 for TrpTrp. Given the dynamic rotational conformation of TPE units, achiral 1 can exhibit chiral adaptive responses with mirror-symmetrical circular dichroism (CD) and circularly polarized luminescence (CPL) spectra to enantiomeric dipeptides via supramolecular chirality transfer in the host-guest complexes. Furthermore, this CAR with sequence specificity of 1 can be applied for molecular recognition of TrpTrp- or PhePhe-containing tetrapeptides, polypeptides (e.g., amyloid β-peptide1-20 and somatostatin), and proteins (e.g., human insulin) with characteristic CD responses.
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Affiliation(s)
- Lin Cheng
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University Xi'an 710069 China
| | - Ping Tian
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University Xi'an 710069 China
| | - Honghong Duan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University Xi'an 710069 China
| | - Qingfang Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University Xi'an 710069 China
| | - Xiaowen Song
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University Xi'an 710069 China
| | - Anyang Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University Xi'an 710069 China
| | - Liping Cao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education, Xi'an Key Laboratory of Functional Supramolecular Structure and Materials, College of Chemistry and Materials Science, Northwest University Xi'an 710069 China
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10
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Anderson HR, Reeves WL, Bockus AT, Suating P, Grice AG, Gallagher M, Urbach AR. Semisynthesis of Aminomethyl-Insulin: An Atom-Economic Strategy to Increase the Affinity and Selectivity of a Protein for Recognition by a Synthetic Receptor. Bioconjug Chem 2023; 34:212-217. [PMID: 36534758 DOI: 10.1021/acs.bioconjchem.2c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Advancements in the molecular recognition of insulin by nonantibody-based means would facilitate the development of methodology for the continuous detection of insulin for the management of diabetes mellitus. Herein, we report a novel insulin derivative that binds to the synthetic receptor cucurbit[7]uril (Q7) at a single site and with high nanomolar affinity. The insulin derivative was prepared by a four-step protein semisynthetic method to present a 4-aminomethyl group on the side chain of the PheB1 position. The resulting aminomethyl insulin binds to Q7 with an equilibrium dissociation constant value of 99 nM in neutral phosphate buffer, as determined by isothermal titration calorimetry. This 6.8-fold enhancement in affinity versus native insulin was gained by an atom-economical modification (-CH2NH2). To the best of our knowledge, this is the highest reported binding affinity for an insulin derivative by a synthetic receptor. This strategy for engineering protein affinity tags induces minimal change to the protein structure while increasing affinity and selectivity for a synthetic receptor.
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Affiliation(s)
- Hayden R Anderson
- Department of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Wei L Reeves
- Department of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Andrew T Bockus
- Department of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Paolo Suating
- Department of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Amy G Grice
- Department of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Madeleine Gallagher
- Department of Chemistry, Trinity University, San Antonio, Texas 78212, United States
| | - Adam R Urbach
- Department of Chemistry, Trinity University, San Antonio, Texas 78212, United States
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11
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Duan Q, Chen R, Deng S, Yang C, Ji X, Qi G, Li H, Li X, Chen S, Lou M, Lu K. Cucurbit[ n]uril-based fluorescent indicator-displacement assays for sensing organic compounds. Front Chem 2023; 11:1124705. [PMID: 36711232 PMCID: PMC9880063 DOI: 10.3389/fchem.2023.1124705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023] Open
Abstract
The widespread conversion of synthetic receptors into luminescent sensors has been achieved via the use of fluorescent-indicator displacement assays (F-IDAs). Due to their rigid structures and efficient binding affinities, cucurbit[n]urils, combined with a variety of fluorescent guests, have gained extensive utilization in fluorescent-indicator displacement assays for sensing non-fluorescent or weakly fluorescent organic compounds (analytes) in a selective and specific manner. This mini-review summarizes recent advances in the design of cucurbit[n]uril-based fluorescent-indicator displacement assays and discusses the current challenges and future prospects in this area.
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Affiliation(s)
- Qunpeng Duan
- School of Chemical and Printing-Dyeing Engineering, Henan University of Engineering, Zhengzhou, China,*Correspondence: Qunpeng Duan, ; Kui Lu,
| | - Ran Chen
- School of Chemical and Printing-Dyeing Engineering, Henan University of Engineering, Zhengzhou, China
| | - Su Deng
- School of Chemical and Printing-Dyeing Engineering, Henan University of Engineering, Zhengzhou, China
| | - Cheng Yang
- School of Chemical and Printing-Dyeing Engineering, Henan University of Engineering, Zhengzhou, China
| | - Xinxin Ji
- School of Chemical and Printing-Dyeing Engineering, Henan University of Engineering, Zhengzhou, China
| | - Gege Qi
- School of Chemical and Printing-Dyeing Engineering, Henan University of Engineering, Zhengzhou, China
| | - Hui Li
- School of Chemical and Printing-Dyeing Engineering, Henan University of Engineering, Zhengzhou, China
| | - Xiaohan Li
- School of Chemical and Printing-Dyeing Engineering, Henan University of Engineering, Zhengzhou, China
| | - Shihao Chen
- School of Chemical and Printing-Dyeing Engineering, Henan University of Engineering, Zhengzhou, China
| | - Mengen Lou
- School of Chemical and Printing-Dyeing Engineering, Henan University of Engineering, Zhengzhou, China
| | - Kui Lu
- School of Chemical and Printing-Dyeing Engineering, Henan University of Engineering, Zhengzhou, China,School of Chemical Engineering and Food Science, Zhengzhou Institute of Technology, Zhengzhou, China,*Correspondence: Qunpeng Duan, ; Kui Lu,
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12
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Abstract
Dimers are probably the simplest model to facilitate the understanding of fundamental physical and chemical processes that take place in much-expanded systems like aggregates, crystals, and other solid states. The molecular interplay within a dimer differentiates it from the corresponding monomeric state and determines its features. Molecular engineering of noncovalent dimerization through applied supramolecular restrictions enables additional control over molecular interplay, particularly over its dynamic aspect. This Perspective introduces the recent effort that has been made in the molecular engineering of noncovalent dimerization, including supramolecular dimers, folda-dimers, and macrocyclic dimers. It showcases how the variation in supramolecular restrictions endows molecular-based materials with improved performance and/or functions like enhanced emission, room-temperature phosphorescence, and effective catalysis. We particularly discuss pseudostatic dimers that can sustain molecular interplay for a long period of time, yet are still flexible enough to adapt to variations. The pseudostatic feature allows for active species to decay along an alternate pathway, thereby spinning off emerging features that are not readily accessible from conventional dynamic systems.
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Affiliation(s)
- Guanglu Wu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Fei Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China
| | - Bohan Tang
- Key Laboratory of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xi Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.,Key Laboratory of Organic Optoelectronics & Molecular Engineering, Department of Chemistry, Tsinghua University, Beijing 100084, China
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13
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Natarajan Sathiyamoorthy V, Suvitha A, Sahara R. Molecular insights into the complex formation between dodecamethylcucurbit[6]uril and phenylenediamine isomers. J INCL PHENOM MACRO 2022; 102:637-51. [DOI: 10.1007/s10847-022-01144-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Das Saha N, Pradhan S, Sasmal R, Sarkar A, Berač CM, Kölsch JC, Pahwa M, Show S, Rozenholc Y, Topçu Z, Alessandrini V, Guibourdenche J, Tsatsaris V, Gagey-Eilstein N, Agasti SS. Cucurbit[7]uril Macrocyclic Sensors for Optical Fingerprinting: Predicting Protein Structural Changes to Identifying Disease-Specific Amyloid Assemblies. J Am Chem Soc 2022; 144:14363-14379. [PMID: 35913703 DOI: 10.1021/jacs.2c05969] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a three-dimensional (3D) representation, each protein molecule displays a specific pattern of chemical and topological features, which are altered during its misfolding and aggregation pathway. Generating a recognizable fingerprint from such features could provide an enticing approach not only to identify these biomolecules but also to gain clues regarding their folding state and the occurrence of pathologically lethal misfolded aggregates. We report here a universal strategy to generate a fluorescent fingerprint from biomolecules by employing the pan-selective molecular recognition feature of a cucurbit[7]uril (CB[7]) macrocyclic receptor. We implemented a direct sensing strategy by covalently tethering CB[7] with a library of fluorescent reporters. When CB[7] recognizes the chemical and geometrical features of a biomolecule, it brings the tethered fluorophore into the vicinity, concomitantly reporting the nature of its binding microenvironment through a change in their optical signature. The photophysical properties of the fluorophores allow a multitude of probing modes, while their structural features provide additional binding diversity, generating a distinct fluorescence fingerprint from the biomolecule. We first used this strategy to rapidly discriminate a diverse range of protein analytes. The macrocyclic sensor was then applied to probe conformational changes in the protein structure and identify the formation of oligomeric and fibrillar species from misfolded proteins. Notably, the sensor system allowed us to differentiate between different self-assembled forms of the disease-specific amyloid-β (Aβ) aggregates and segregated them from other generic amyloid structures with a 100% identification accuracy. Ultimately, this sensor system predicted clinically relevant changes by fingerprinting serum samples from a cohort of pregnant women.
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Affiliation(s)
- Nilanjana Das Saha
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India.,Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Soumen Pradhan
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Ranjan Sasmal
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Aritra Sarkar
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Christian M Berač
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.,Graduate School of Materials Science in Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Jonas C Kölsch
- Department of Chemistry, Johannes Gutenberg-University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Meenakshi Pahwa
- Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Sushanta Show
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
| | - Yves Rozenholc
- UR 7537 BioSTM, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Zeki Topçu
- UR 7537 BioSTM, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France
| | - Vivien Alessandrini
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | - Jean Guibourdenche
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | - Vassilis Tsatsaris
- INSERM UMR-S 1139, Université Paris Cité, 4 avenue de l'Observatoire, 75006 Paris, France.,Department of Obstetrics, Cochin Hospital, AP-HP, Université Paris Cité, FHU PREMA, 123 Bd Port-Royal, 75014 Paris, France
| | | | - Sarit S Agasti
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India.,Chemistry & Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India
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15
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Grimm LM, Spicher S, Tkachenko B, Schreiner PR, Grimme S, Biedermann F. The Role of Packing, Dispersion, Electrostatics, and Solvation in High-Affinity Complexes of Cucurbit[n]urils with Uncharged Polar Guests. Chemistry 2022; 28:e202200529. [PMID: 35612260 PMCID: PMC9401061 DOI: 10.1002/chem.202200529] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Indexed: 12/21/2022]
Abstract
The rationalization of non‐covalent binding trends is both of fundamental interest and provides new design concepts for biomimetic molecular systems. Cucurbit[n]urils (CBn) are known for a long time as the strongest synthetic binders for a wide range of (bio)organic compounds in water. However, their host‐guest binding mechanism remains ambiguous despite their symmetric and simple macrocyclic structure and the wealth of literature reports. We herein report experimental thermodynamic binding parameters (ΔG, ΔH, TΔS) for CB7 and CB8 with a set of hydroxylated adamantanes, di‐, and triamantanes as uncharged, rigid, and spherical/ellipsoidal guests. Binding geometries and binding energy decomposition were obtained from high‐level theory computations. This study reveals that neither London dispersion interactions, nor electronic energies or entropic factors are decisive, selectivity‐controlling factors for CBn complexes. In contrast, peculiar host‐related solvation effects were identified as the major factor for rationalizing the unique behavior and record‐affinity characteristics of cucurbit[n]urils.
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Affiliation(s)
- Laura M Grimm
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Sebastian Spicher
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Boryslav Tkachenko
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn, Beringstraße 4, 53115, Bonn, Germany
| | - Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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16
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Wang H, Fan Y, Hou Y, Chen B, Lei J, Yu S, Chen X, Hou X. Host-guest liquid gating mechanism with specific recognition interface behavior for universal quantitative chemical detection. Nat Commun 2022; 13:1906. [PMID: 35393415 DOI: 10.1038/s41467-022-29549-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/16/2022] [Indexed: 12/26/2022] Open
Abstract
Universal visual quantitative chemical detection technology has emerged as an increasingly crucial tool for convenient testing with immediate results in the fields of environmental assessment, homeland security, clinical drug testing and health care, particularly in resource-limited settings. Here, we show a host-guest liquid gating mechanism to translate molecular interface recognition behavior into visually quantifiable detection signals. Quantitative chemical detection is achieved, which has obvious advantages for constructing a portable, affordable, on-site sensing platform to enable the visual quantitative testing of target molecules without optical/electrical equipment. Experiments and theoretical calculations confirm the specificity and scalability of the system. This mechanism can also be tailored by the rational design of host-guest complexes to quantitatively and visually detect various molecules. With the advantages of versatility and freedom from additional equipment, this detection mechanism has the potential to revolutionize environmental monitoring, food safety analysis, clinical drug testing, and more. In field, visual, chemical detection is of use for a wide range of possible applications. Here, the authors report on the creation of a host-guest liquid gating mechanism where detection of the target host triggers gate opening allowing for gas through the liquid gate, which can be used for visual detection.
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17
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El-Barghouthi MI, Bodoor K, Abuhasan OM, Assaf KI, Al Hourani BJ, Rawashdeh AMM. Binary and Ternary Complexes of Cucurbit[8]uril with Tryptophan, Phenylalanine, and Tyrosine: A Computational Study. ACS Omega 2022; 7:10729-10737. [PMID: 35382313 PMCID: PMC8973077 DOI: 10.1021/acsomega.2c00511] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
Selective binding of amino acids, peptides, and proteins by synthetic molecules and elucidation of the geometry and dynamics of the resulting complexes and their strengths are active areas of contemporary research. In recent work, we analyzed via molecular dynamics (MD) simulations the complexes formed between cucurbit[7]uril (CB7) and three aromatic amino acids: tryptophan (W), phenylalanine (F), and tyrosine (Y). Herein, we continue this line of research by performing MD simulations lasting 100 ns to investigate the formation, stabilities, binding modes, dynamics, and specific host-guest noncovalent interactions contributing to the formation of the binary (1:1) and ternary (2:1) complexes in aqueous solution between W, F, and Y amino acids and cucurbit[8]uril (CB8). All complexes were found to be stable, with the binding in each complex dominated by one mode (except for the F-CB8 complex, which had two) characterized by encapsulation of the aromatic side chains of the amino acids within the cavity of CB8 and the exclusion of their ammonium and carboxylate groups. Using the molecular mechanics/Poisson-Boltzmann surface area method to estimate the individual contributions to the overall free energies of binding, results revealed that the key role is played by the amino acid side chains in stabilizing the complexes through their favorable van der Waals interactions with the CB8 cavity and the importance of favorable electrostatic interactions between the carbonyl portal of CB8 and the ammonium group of the amino acid. Visual analysis of structures of the ternary complexes indicated the presence of π-π stacking between the aromatic side chains of the included amino acids. The insights provided by this work may be of value for further efforts aiming to employ the recognition properties of CB8 toward amino acids in applications requiring more elaborate recognition of short peptides and proteins.
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Affiliation(s)
- Musa I. El-Barghouthi
- Department
of Chemistry, Faculty of Science, The Hashemite
University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Khaled Bodoor
- Department
of Physics, The University of Jordan, Amman 11942, Jordan
| | - Osama M. Abuhasan
- Department
of Chemistry, Faculty of Science, The Hashemite
University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Khaleel I. Assaf
- Faculty
of Science, Al-Balqa Applied University, Al-Salt 19117, Jordan
| | - Baker Jawabrah Al Hourani
- Department
of Biology and Chemistry, Embry Riddle Aeronautical
University, 3700 Willow
Creek Rd, Prescott, Arizona 86304, USA
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18
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Zheng Z, Ren S, Geng WC, Cui X, Wu B, Wang H. Monitoring Methionine Decarboxylase by Supramolecular Tandem Assay. Chem Asian J 2022; 17:e202200106. [PMID: 35333438 DOI: 10.1002/asia.202200106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/24/2022] [Indexed: 11/12/2022]
Abstract
Methionine is an essential amino acid involved in many physiological and pathological processes. Methionine starvation caused by methionine decarboxylase ( MetDC) degradation becomes a promising strategy for cancer treatment. Multistep colorimetric method, the present approach to monitor the MetDC activity, possesses drawbacks of the complicated process, low accuracy, and poor anti-interference due to indirect detecting. Herein, we report a facile and easy-to-use supramolecular tandem assay (STA) with cucurbit[7]uril and acridine orange reporter pair for the direct and real-time monitoring of MetDC activity. The applicability of this strategy for measuring enzyme-kinetic parameters and screening of inhibitors are also demonstrated. The STA for MetDC activity detection not only provides a feasible method for methionine-related disease diagnosing but also opens a perspective for cancer therapy.
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Affiliation(s)
- Zhe Zheng
- China University of Mining and Technology - Xuzhou Campus: China University of Mining and Technology, School of Chemical Engineering & Technology, No. 1, Daxue Road, 221116, XuZhou, CHINA
| | - Siying Ren
- China University of Mining and Technology - Xuzhou Campus: China University of Mining and Technology, School of Chemical Engineering & Technology, CHINA
| | - Wen-Chao Geng
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, Key Laboratory of Systems Microbial Biotechnology, CHINA
| | - Xuexian Cui
- Institute of Microbiology Chinese Academy of Sciences, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, CHINA
| | - Bian Wu
- Institute of Microbiology Chinese Academy of Sciences, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, CHINA
| | - Hong Wang
- China University of Mining and Technology, School of Chemical Engineering & Technology, No1,Daxue Road, 221116, Xuzhou, CHINA
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19
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Jiang C, Song Z, Fizir M, Yang P, Liu M, Dramou P, He H. Host-guest interaction between cucurbit[6]uril and chain amino acids. Chem Phys Lett 2021; 783:139039. [DOI: 10.1016/j.cplett.2021.139039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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20
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Ramberg KO, Guagnini F, Engilberge S, Wrońska MA, Rennie ML, Pérez J, Crowley PB. Segregated Protein-Cucurbit[7]uril Crystalline Architectures via Modulatory Peptide Tectons. Chemistry 2021; 27:14619-14627. [PMID: 34432924 PMCID: PMC8596587 DOI: 10.1002/chem.202103025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Indexed: 12/30/2022]
Abstract
One approach to protein assembly involves water-soluble supramolecular receptors that act like glues. Bionanoarchitectures directed by these scaffolds are often system-specific, with few studies investigating their customization. Herein, the modulation of cucurbituril-mediated protein assemblies through the inclusion of peptide tectons is described. Three peptides of varying length and structural order were N-terminally appended to RSL, a β-propeller building block. Each fusion protein was incorporated into crystalline architectures mediated by cucurbit[7]uril (Q7). A trimeric coiled-coil served as a spacer within a Q7-directed sheet assembly of RSL, giving rise to a layered material of varying porosity. Within the spacer layers, the coiled-coils were dynamic. This result prompted consideration of intrinsically disordered peptides (IDPs) as modulatory tectons. Similar to the coiled-coil, a mussel adhesion peptide (Mefp) also acted as a spacer between protein-Q7 sheets. In contrast, the fusion of a nucleoporin peptide (Nup) to RSL did not recapitulate the sheet assembly. Instead, a Q7-directed cage was adopted, within which disordered Nup peptides were partially "captured" by Q7 receptors. IDP capture occurred by macrocycle recognition of an intrapeptide Phe-Gly motif in which the benzyl group was encapsulated by Q7. The modularity of these protein-cucurbituril architectures adds a new dimension to macrocycle-mediated protein assembly. Segregated protein crystals, with alternating layers of high and low porosity, could provide a basis for new types of materials.
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Affiliation(s)
- Kiefer O Ramberg
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Francesca Guagnini
- 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
| | - Małgorzata A Wrońska
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Martin L Rennie
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
| | - Javier Pérez
- Synchrotron SOLEIL, L'Orme des Merisiers, Saint-Aubin BP 48, 91192, Gif-sur-Yvette Cedex, France
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, H91 TK33, Ireland
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21
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Abstract
Overcoming the synthetic burden related to covalently connected receptors with appropriate indicators for sensing various analytes via an indicator spacer receptor (ISR) approach, the indicator displacement assay (IDA) seems to be a very sophisticated and versatile supramolecular sensing paradigm, and it has taken the phenomenon of molecular recognition to the next level in the realm of host-guest chemistry. Due to the unavailability of a comprehensive report on what has been done in the last decade in relation to IDAs, we decided to set down this account illustrating diverse indicator displacement assays (IDAs) in detail from the concept stage to recent developments relating to the detection of cationic, anionic, and neutral analytes. The authors conclude this account with future perspectives and highlight the limitations and challenges relating to IDAs which need to be overcome in order to realize the full potential of this popular sensing phenomenon. While we were finalizing our account for publication, a tutorial review by the research groups of Anslyn, Sessler, and Sun was published, which focuses mainly on diverse aspects of the chemistry related to IDAs. As can be seen, our review, besides discussing various basic IDA concepts, has a vast collection of information published in the past decade and hence, hopefully, will be very informative for the supramolecular community. We believe that this work will offer new insights for the construction of novel sensors operating through the IDA approach.
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Affiliation(s)
- Ishfaq Ahmad Rather
- Organic and Supramolecular Functional Materials Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi 110025, India.
| | - Rashid Ali
- Organic and Supramolecular Functional Materials Research Laboratory, Department of Chemistry, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi 110025, India.
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22
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Tapia L, Solozabal N, Solà J, Pérez Y, Miller WT, Alfonso I. Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages. Chemistry 2021; 27:9542-9549. [PMID: 33904620 PMCID: PMC8362067 DOI: 10.1002/chem.202100990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Indexed: 12/15/2022]
Abstract
The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.
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Affiliation(s)
- Lucía Tapia
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Naiara Solozabal
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Jordi Solà
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - Yolanda Pérez
- NMR FacilityInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
| | - W. Todd Miller
- Department of Physiology and BiophysicsStony Brook University and Department of Veterans Affairs Medical CenterStony BrookNY, 11794USA
| | - Ignacio Alfonso
- Department of Biological ChemistryInstitute for Advanced Chemistry of Catalonia, IQAC-CSICJordi Girona 18–2608034BarcelonaSpain
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23
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Ma F, Zheng X, Li Z. Sequence-selective recognition of cationic amphipathic tripeptides with similar structures in aqueous solutions by cucurbit[7]uril. Phys Chem Chem Phys 2021; 23:13724-13733. [PMID: 34128514 DOI: 10.1039/d1cp01326b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sequence-selective recognition of cationic amphipathic peptides by synthetic receptors is significant to biological applications, but it is still a great challenging task. Here we first study the binding characteristics of receptor cucurbit[7]uril (CB[7]) to the smallest aromatic tripeptides X1GG (X1 = tryptophan (W), phenylalanine (F), and tyrosine (Y)) and basic tripeptides X2GG (X2 = arginine (R), lysine (K), and histidine (H)) by molecular dynamics simulations. The study indicates that the sidechains of aromatic X1 residues can be encapsulated into the CB[7] cavity, while the sidechains of basic X2 residues prefer to locate at the CB[7] portal. Based on that, we consider hydrophobic aromatic residues as the N-terminus, the smallest glycine (G) as the 2nd-residue and basic residues as the C-terminus, and design nine tripeptides X1GX2 (X1 = F, Y, W and X2 = H, K, R). We found that there is a great influence of the C-terminal basic residue of X1GX2 on binding with CB[7] due to the introduction of a new binding site between CB[7] and the sidechain of the C-terminal residue. Interestingly, CB[7] can differentiate WGR and WGK with similar structures efficiently because of their eight orders of magnitude difference in the association constant (Ka). Besides, for WGR, YGR, and YGK with a nanomolar binding affinity (Ka > 109 M-1), on reversing the sequence order of the 2nd-residue and 3rd-residue, their Ka reduces by about at least 1000-fold, implying the sequence dependence of CB[7] on recognizing these tripeptides. These results predict the potential applications of CB[7] in recognizing cationic amphipathic peptides.
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Affiliation(s)
- Fenfen Ma
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
| | - Xiaoyan Zheng
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
| | - Zesheng Li
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electro-photonic Conversion Materials, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China.
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24
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Abstract
The selective photodeprotection of the NVoc-modified FGG tripeptide yields the transformation of its 1:1 receptor-ligand complex with cucurbit[8]uril into a homoternary FGG2@CB8 assembly. The resulting light-induced dimerization of the model peptide provides a tool for the implementation of stimuli-responsive supramolecular chemistry in biologically relevant contexts.
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Affiliation(s)
- Rita J Fernandes
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Patricia Remón
- CIQSO - Centre for Research in Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, E-21071 Huelva, Spain
| | - Artur J Moro
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - André Seco
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Ana S D Ferreira
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Uwe Pischel
- CIQSO - Centre for Research in Sustainable Chemistry and Department of Chemistry, University of Huelva, Campus de El Carmen s/n, E-21071 Huelva, Spain
| | - Nuno Basílio
- Laboratorio Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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25
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Barbero H, Masson E. Design and recognition of cucurbituril-secured platinum-bound oligopeptides. Chem Sci 2021; 12:9962-9968. [PMID: 34349966 PMCID: PMC8317623 DOI: 10.1039/d1sc02637b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/16/2021] [Indexed: 11/21/2022] Open
Abstract
Platinum terpyridyl complexes, stacked on top of one another and secured as dimers with cucurbit[8]uril (CB[8]) in aqueous medium, were functionalized quantitatively and in situ with a pair of pentapeptides Phe-(Gly)3-Cys by grafting their cysteine residues to the Pt centers. The resulting CB[8]·(Pt·peptide)2 assemblies were used to target secondary hosts CB[7] and CB[8] via their pair of phenylalanine residues, again in situ. A series of well-defined architectures, including a supramolecular “pendant necklace” with hybrid head-to-head and head-to-tail arrangements inside CB[8], were obtained during the self-sorting process after combining only 3 or 4 simple building units. A platinum terpyridyl complex, pentapeptide Phe-(Gly)3-Cys and cucurbit[8]uril assemble into a “pendant necklace” with hybrid head-to-head and head-to-tail arrangements in aqueous medium.![]()
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Affiliation(s)
- Héctor Barbero
- Department of Chemistry and Biochemistry, Ohio University Athens Ohio 45701 USA
| | - Eric Masson
- Department of Chemistry and Biochemistry, Ohio University Athens Ohio 45701 USA
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26
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Falconer RJ, Schuur B, Mittermaier AK. Applications of isothermal titration calorimetry in pure and applied research from 2016 to 2020. J Mol Recognit 2021; 34:e2901. [PMID: 33975380 DOI: 10.1002/jmr.2901] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/02/2021] [Accepted: 04/26/2021] [Indexed: 02/06/2023]
Abstract
The last 5 years have seen a series of advances in the application of isothermal titration microcalorimetry (ITC) and interpretation of ITC data. ITC has played an invaluable role in understanding multiprotein complex formation including proteolysis-targeting chimeras (PROTACS), and mitochondrial autophagy receptor Nix interaction with LC3 and GABARAP. It has also helped elucidate complex allosteric communication in protein complexes like trp RNA-binding attenuation protein (TRAP) complex. Advances in kinetics analysis have enabled the calculation of kinetic rate constants from pre-existing ITC data sets. Diverse strategies have also been developed to study enzyme kinetics and enzyme-inhibitor interactions. ITC has also been applied to study small molecule solvent and solute interactions involved in extraction, separation, and purification applications including liquid-liquid separation and extractive distillation. Diverse applications of ITC have been developed from the analysis of protein instability at different temperatures, determination of enzyme kinetics in suspensions of living cells to the adsorption of uremic toxins from aqueous streams.
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Affiliation(s)
- Robert J Falconer
- School of Chemical Engineering & Advanced Materials, University of Adelaide, Adelaide, South Australia, Australia
| | - Boelo Schuur
- Faculty of Science and Technology, University of Twente, Enschede, Netherlands
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27
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Cao W, Qin X, Wang Y, Dai Z, Dai X, Wang H, Xuan W, Zhang Y, Liu Y, Liu T. A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Wenbing Cao
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yong Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Zhen Dai
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xianyin Dai
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Haoyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Weimin Xuan
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Yingming Zhang
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Yu Liu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University 94 Weijin Road, Nankai District Tianjin 300071 P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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28
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Cao W, Qin X, Wang Y, Dai Z, Dai X, Wang H, Xuan W, Zhang Y, Liu Y, Liu T. A General Supramolecular Approach to Regulate Protein Functions by Cucurbit[7]uril and Unnatural Amino Acid Recognition. Angew Chem Int Ed Engl 2021; 60:11196-11200. [PMID: 33580548 DOI: 10.1002/anie.202100916] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/10/2021] [Indexed: 01/24/2023]
Abstract
Regulation of specific protein function is of great importance for both research and therapeutic development. Many small or large molecules have been developed to control specific protein function, but there is a lack of a universal approach to regulate the function of any given protein. We report a general host-guest molecular recognition approach involving modification of the protein functional surfaces with genetically encoded unnatural amino acids bearing guest side chains that can be specifically recognized by cucurbit[7]uril. Using two enzymes and a cytokine as models, we showed that the activity of proteins bearing unnatural amino acid could be turned off by host molecule binding, which blocked its functional binding surface. Protein activity can be switched back by treatment with a competitive guest molecule. Our approach provides a general tool for reversibly regulating protein function through molecular recognition and can be expected to be valuable for studying protein functions.
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Affiliation(s)
- Wenbing Cao
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xuewen Qin
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Yong Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Zhen Dai
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China.,State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Xianyin Dai
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Haoyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
| | - Weimin Xuan
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yingming Zhang
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yu Liu
- College of Chemistry, State Key Laboratory of Elemento-Organic Chemistry, Nankai University, 94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Molecular and Cellular Pharmacology, Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China
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29
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Abstract
Controlling the spatial and temporal behavior of peptide segments is essential in the fabrication of functional peptide-based materials and nanostructures. To achieve a desired structure, complex sequence design is often required, coupled with the inclusion of unnatural amino acids or synthetic modifications. Herein, we investigate the structural properties of 1:1 inclusion complexes between specific oligopeptides and cucurbit[8]uril (CB[8]), inducing the formation of turns, and by alteration of the peptide sequence, tunable structural chirality. We also explore extended peptide sequence binding with CB[8], demonstrating a simple approach to construct a peptide hairpin.
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Affiliation(s)
- David E Clarke
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Guanglu Wu
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Ce Wu
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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30
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Ma F, Zheng X, Xie L, Li Z. Sequence-dependent nanomolar binding of tripeptides containing N-terminal phenylalanine by Cucurbit[7]uril: A theoretical study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115479] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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31
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Ferguson Johns HP, Harrison EE, Stingley KJ, Waters ML. Mimicking Biological Recognition: Lessons in Binding Hydrophilic Guests in Water. Chemistry 2021; 27:6620-6644. [PMID: 33048395 DOI: 10.1002/chem.202003759] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Indexed: 01/25/2023]
Abstract
Selective molecular recognition of hydrophilic guests in water plays a fundamental role in a vast number of biological processes, but synthetic mimicry of biomolecular recognition in water still proves challenging both in terms of achieving comparable affinities and selectivities. This Review highlights strategies that have been developed in the field of supramolecular chemistry to selectively and non-covalently bind three classes of biologically relevant molecules: nucleotides, carbohydrates, and amino acids. As several groups have systematically modified receptors for a specific guest, an evolutionary perspective is also provided in some cases. Trends in the most effective binding forces for each class are described, providing insight into selectivity and potential directions for future work.
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Affiliation(s)
- Hannah P Ferguson Johns
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Emily E Harrison
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Kyla J Stingley
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Marcey L Waters
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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32
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Ramberg KO, Engilberge S, Guagnini F, Crowley PB. Protein recognition by cucurbit[6]uril: high affinity N-terminal complexation. Org Biomol Chem 2021; 19:837-844. [PMID: 33406171 DOI: 10.1039/d0ob02356f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The donut-shaped cucurbit[n]urils (Qn, n = 6-8) are rigid macrocyclic receptors with widespread use in protein recognition. To date, most applications have centred on the encapsulation of N-terminal aromatic residues by Q7 or Q8. Less attention has been placed on Q6, which can recognize lysine side chains due to its high affinity for alkylamines. In this work, we investigated protein-Q6 complexation by using NMR spectroscopy. Attempts to crystallize protein-Q6 complexes were thwarted by the crystallization of Q6. We studied four proteins that vary in size, net charge, and lysine content. In addition to Q6 interactions with specific Lys or dimethylated Lys residues, we report striking evidence for N-terminal recognition. High affinity (micromolar) binding occurred with the N-terminal Met-Lys motif present in one of the four model proteins. Engineering this feature into another model protein yielded a similar high affinity site. We also present evidence for Q8 binding at this N-terminal feature. These data expand the cucurbituril toolkit for protein sensing.
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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.
| | - Francesca Guagnini
- 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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33
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Li XX, Xu WT, Deng XY, Tian LF, Huang Y, Tao Z. Selective Identification of Phenylalanine Using Cucurbit[7,8]uril-Based Fluorescent Probes. Aust J Chem 2021. [DOI: 10.1071/ch20029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The interactions of two host–guest inclusion complexes comprised of cucurbit[7]uril (Q[7]) and cucurbit[8]uril (Q[8]) with a derivative of toluidine blue O (TB) have been investigated using 1H NMR and fluorescence spectroscopy. The experimental results revealed that the Q[7] host interacts with a TB molecule to form a 1:1 inclusion complex and the Q[8] host interacts with two TB guest molecules to form a 1:2 inclusion complex. The inclusion of the TB guest molecule within the Q[7] host gave rise to significant fluorescence enhancement, whereas the inclusion of the TB guest molecule within the Q[8] host resulted in significant fluorescence quenching. Further recognition experiments involving a series of l-α-amino acids revealed that the TB@Q[7] inclusion fluorescence probe exhibits high selectivity for the recognition of phenylalanine via significant fluorescence quenching in an aqueous solution, whereas the TB@Q[8] inclusion fluorescence probe also exhibited high selectivity for phenylalanine recognition via fluorescence enhancement in an aqueous solution.
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34
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Martins JN, Lima JC, Basílio N. Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors. Molecules 2020; 26:E106. [PMID: 33379401 DOI: 10.3390/molecules26010106] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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35
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Affiliation(s)
- Yao‐Hua Liu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Ying‐Ming Zhang
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Hua‐Jiang Yu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Yu Liu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
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36
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Affiliation(s)
- Yao‐Hua Liu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Ying‐Ming Zhang
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Hua‐Jiang Yu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
| | - Yu Liu
- College of Chemistry State Key Laboratory of Elemento-Organic Chemistry Nankai University Tianjin 300071 China
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37
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Shusterman-Krush R, Grimm L, Avram L, Biedermann F, Bar-Shir A. Elucidating dissociation activation energies in host-guest assemblies featuring fast exchange dynamics. Chem Sci 2020; 12:865-871. [PMID: 34163853 PMCID: PMC8179218 DOI: 10.1039/d0sc05666a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The ability to mediate the kinetic properties and dissociation activation energies (E a) of bound guests by controlling the characteristics of "supramolecular lids" in host-guest molecular systems is essential for both their design and performance. While the synthesis of such systems is well advanced, the experimental quantification of their kinetic parameters, particularly in systems experiencing fast association and dissociation dynamics, has been very difficult or impossible with the established methods at hand. Here, we demonstrate the utility of the NMR-based guest exchange saturation transfer (GEST) approach for quantifying the dissociation exchange rates (k out) and activation energy (E a,out) in host-guest systems featuring fast dissociation dynamics. Our assessment of the effect of different monovalent cations on the extracted E a,out in cucurbit[7]uril:guest systems with very fast k out highlights their role as "supramolecular lids" in mediating a guest's dissociation E a. We envision that GEST could be further extended to study kinetic parameters in other supramolecular systems characterized by fast kinetic properties and to design novel switchable host-guest assemblies.
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Affiliation(s)
| | - Laura Grimm
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen Germany
| | - Liat Avram
- Department of Chemical Research Support, Weizmann Institute of Science Rehovot 7610001 Israel
| | - Frank Biedermann
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen Germany
| | - Amnon Bar-Shir
- Department of Organic Chemistry, Weizmann Institute of Science Rehovot 7610001 Israel
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38
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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39
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Hennig A, Nau WM. Interaction of Cucurbit[7]uril With Protease Substrates: Application to Nanosecond Time-Resolved Fluorescence Assays. Front Chem 2020; 8:806. [PMID: 33134264 PMCID: PMC7511663 DOI: 10.3389/fchem.2020.00806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023] Open
Abstract
We report the use of the macrocyclic host cucurbit[7]uril (CB7) as a supramolecular additive in nanosecond time-resolved fluorescence (Nano-TRF) assays for proteases to enhance the discrimination of substrates and products and, thereby, the sensitivity. A peptide substrate was labeled with 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a long-lived (>300 ns) fluorescent probe and 3-nitrotyrosine was established as a non-fluorescent fluorescence resonance energy transfer (FRET) acceptor that acts as a “dark quencher.” The substrate was cleaved by the model proteases trypsin and chymotrypsin and the effects of the addition of CB7 to the enzyme assay mixture were investigated in detail using UV/VIS absorption as well as steady-state and time-resolved fluorescence spectroscopy. This also allowed us to identify the DBO and nitrotyrosine residues as preferential binding sites for CB7 and suggested a hairpin conformation of the peptide, in which the guanidinium side chain of an arginine residue is additionally bound to a vacant ureido rim of one of the CB7 hosts.
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Affiliation(s)
- Andreas Hennig
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Bremen, Germany.,Institute of Chemistry of New Materials, 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 gGmbH, Bremen, Germany
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40
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Li L, Liu M, Yue L, Wang R, Zhang N, Liang Y, Zhang L, Cheng L, Xia J, Wang R. Host-Guest Protein Assembly for Affinity Purification of Methyllysine Proteomes. Anal Chem 2020; 92:9322-9329. [PMID: 32510198 DOI: 10.1021/acs.analchem.0c01643] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein-protein interactions drive self-assembly of biomacromolecules and thus enable important physiological functions at a cellular level. Supramolecular chemists have developed artificial host-guest interactions that are similar with, yet distinct from and orthogonal to, the natural protein-protein interactions. For instance, cucurbit[n]urils are synthetic receptors that can specifically recognize proteins with N-terminal aromatic residues with high affinities, yet this interaction can be reversed by the competition of small molecules such as amantadine. Herein, we develop a site-specific, oriented protein-display method by combining the host-guest interaction based on cucurbit[7]uril and a covalent protein-peptide reaction. A methyllysine-binding protein HP1β chromodomain (CD) is immobilized via host-guest interactions and used as the "bait" to capture methyllysine proteomes from cancer cells. The captured "fish"-methyllysine-containing proteins-can be released via competitive displacement by amantadine in a nondenaturing and traceless manner. This affinity purification method found 73 novel methyllysine sites from 101 identified sites among 66 methylated proteins from 255 HP1β CD-binding proteins in cancer cells via subsequent mass spectrometric analysis. This work thereby presents a new strategy of artificial host-guest protein assembly in affinity purification of methyllysine proteins in coupling to mass spectrometry.
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Affiliation(s)
- Linting Li
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Min Liu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Ludan Yue
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518000, P. R. China
| | - Ning Zhang
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen 518000, P. R. China
| | - Yujie Liang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, P. R. China
| | - Lixin Cheng
- Department of Critical Care Medicine, Shenzhen People's Hospital, The Second Clinical Medicine College of Jinan University, Shenzhen 518000, P. R. China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong, P. R. China
| | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau SAR 999078, P. R. China
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41
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Smith AAA, Maikawa CL, Roth GA, Appel EA. Site-selective modification of proteins using cucurbit[7]uril as supramolecular protection for N-terminal aromatic amino acids. Org Biomol Chem 2020; 18:4371-4375. [PMID: 32459261 DOI: 10.1039/d0ob01004a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Cucurbit[7,8]urils are known to form inclusion complexes with aromatic amino acids, hosting the hydrohobic side chains within the cavity and adjacent cations within the portal of the macrocyclic host. Here we show that cucurbit[7]uril binding with N-terminal phenylalanine significantly reduces the nucleophilicity of the amine, likely due to an increase in stability of the ammonium ion, rendering it unreactive at neutral pH. Using insulin as a model protein, we show that this supramolecular protection strategy can drive selectivity of N-terminal amine conjugation away from the preferred B chain N-terminal phenylalanine towards the A chain N-terminal glycine. Cucurbit[7]uril can therefore be used as a supramolecular protecting group for site-selective protein modification.
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Affiliation(s)
- Anton A A Smith
- Department of Materials Science & Engineering, Stanford University, Stanford, CA 94305, USA. and Department of Chemistry, Aarhus University, 8000, Denmark
| | - Caitlin L Maikawa
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Gillie A Roth
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Eric A Appel
- Department of Materials Science & Engineering, Stanford University, Stanford, CA 94305, USA. and Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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42
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Abstract
Phenyl-perfluorophenyl polar-π interactions have been revisited for the design and fabrication of functional supramolecular systems. The relatively weak associative interactions (ΔG ≈ -1.0 kcal/mol) have limited their use in aqueous self-assembly to date. Herein, we propose a strategy to strengthen phenyl-perfluorophenyl polar-π interactions by encapsulation within a synthetic host, thus increasing the binding affinity to ΔG= -15.5 kcal/mol upon formation of heteroternary complexes through social self-sorting. These heteroternary complexes were used as dynamic, yet strong, cross-linkers in the fabrication of supramolecular gels, which exhibited excellent viscoelasticity, stretchability, self-recovery, self-healing, and energy dissipation. This work unveils a general approach to exploit host-enhanced polar-π interactions in the design of robust aqueous supramolecular systems.
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Affiliation(s)
- Zehuan Huang
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Xiaoyi Chen
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Guanglu Wu
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pierangelo Metrangolo
- Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Via L. Mancinelli 7, 20131 Milano, Italy
| | - Daniel Whitaker
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Jade A McCune
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Oren A Scherman
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
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Abstract
Gold nanoclusters (AuNCs) with well-defined atomically precise structures present promising emissive prospects for excellent biocompatibility and optical properties. However, the relatively low luminescence efficiency in solutions for most AuNCs is still a perplexing issue to be resolved. In this study, a facile supramolecular strategy was developed to rigidify the surface of FGGC-AuNCs by modifying transition rates in excited states via host-guest self-assembly between cucurbiturils (CBs) and FGGC (Phe-Gly-Gly-Cys peptide). In aqueous solutions, CB/FGGC-AuNCs presented an extremely enhanced red phosphorescence emission with a quantum yield (QY) of 51% for CB[7] and 39% for CB[8], while simple FGGC-AuNCs only showed a weak emission with a QY of 7.5%. Furthermore, CB[7]/FGGC-AuNCs showed excellent results in live cell luminescence imaging for A549 cancer cells. Our study demonstrates that host-guest self-assembly assisted by macrocycles is a facile and effective tool to non-covalently modify and adjust optical properties of nanostructures on ultra-small scales.
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Affiliation(s)
- Tao Jiang
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130 Meilong Road Shanghai 200237 China
| | - Guojuan Qu
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130 Meilong Road Shanghai 200237 China
| | - Jie Wang
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130 Meilong Road Shanghai 200237 China
| | - Xiang Ma
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130 Meilong Road Shanghai 200237 China
| | - He Tian
- Key Laboratory for Advanced Materials, Feringa Nobel Prize Scientist Joint Research Center, Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science & Technology 130 Meilong Road Shanghai 200237 China
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44
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Abstract
Host-guest complexes exhibiting a 1 : 1 binding stoichiometry need not consist of a single host and guest. A series of oligopeptides, which were previously reported to have abnormally high binding enthalpies were investigated to deduce whether they exist as a 2 : 2 quaternary or a 1 : 1 binary complex with cucurbit[8]uril (CB[8]). Through a systematic study of the sequence-specific binding pathways of peptide-CB[8] association, a phenylalanine-leucine dipeptide was found to be capable of switching from a 1 : 1 stoichiometric complex to a 2 : 1 complex. By studying the differences in size-based diffusion properties of these two binding modes, the presence of a 1 : 1 pairwise inclusion complex was verified for the regime where CB[8] is in excess. Findings in this study can be utilised to 'customise' the precise CB[8]-oligopeptide self-assembly pathway, acting as a useful toolbox in the design of supramolecular systems.
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Affiliation(s)
- Guanglu Wu
- Melville Laboratory for Polymer Synthesis, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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45
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Sasmal R, Das Saha N, Schueder F, Joshi D, Sheeba V, Jungmann R, Agasti SS. Dynamic host-guest interaction enables autonomous single molecule blinking and super-resolution imaging. Chem Commun (Camb) 2019; 55:14430-14433. [PMID: 31737873 DOI: 10.1039/c9cc07153a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Synthetic host-guest complexes are inherently dynamic as they employ weak and reversible noncovalent interactions for their recognition processes. We strategically exploited dynamic supramolecular recognition between fluorescently labeled guest molecules to complementary cucurbit[7]uril hosts to obtain stochastic switching between fluorescence ON- and OFF-states, enabling PAINT-based nanoscopic imaging in cells and tissues.
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Affiliation(s)
- Ranjan Sasmal
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore, Karnataka 560064, India.
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46
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Jia J, Wen H, Zhao S, Wang L, Qiao H, Shen H, Yu Z, Di B, Xu L, Hu C. Displacement Induced Off–On Fluorescent Biosensor Targeting IDO1 Activity in Live Cells. Anal Chem 2019; 91:14943-14950. [DOI: 10.1021/acs.analchem.9b03387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jing Jia
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing 210009, PR China
| | - Huilin Wen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, PR China
| | - Sibo Zhao
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 211198, PR China
| | - Lancheng Wang
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 211198, PR China
| | - Haishi Qiao
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 211198, PR China
| | - Haowen Shen
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing 210009, PR China
| | - Ziyi Yu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing 211816, PR China
| | - Bin Di
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing 210009, PR China
| | - Lili Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Ministry of Education, Nanjing 210009, PR China
| | - Chi Hu
- Department of Pharmaceutical Engineering, School of Engineering, China Pharmaceutical University, Nanjing 211198, PR China
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47
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Abstract
The supramolecular chemistry of cucurbit[n]urils (CBn) has been rapidly developing to encompass diverse medicinal applications, including drug formulation and delivery, controlled drug release, and sensing for bioanalytical purposes. This is made possible by their unique recognition properties and very low cytotoxicity. In this review, we summarize the host-guest complexation of biologically important molecules with CBn, and highlight their implementation in medicinal chemistry and chemical biology.
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Affiliation(s)
- Debapratim Das
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, India
| | - Khaleel I. Assaf
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
- Department of Chemistry, Faculty of Science, Al-Balqa Applied University, Al-Salt, Jordan
| | - Werner M. Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen, Germany
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48
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Affiliation(s)
| | - Lyle Isaacs
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
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49
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Affiliation(s)
- Xiaoni Fang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yongzan Zheng
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yaokai Duan
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yang Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California, Riverside, California 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
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50
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Venkataramanan NS, Suvitha A, Sahara R. Structure, stability, and nature of bonding between high energy water clusters confined inside cucurbituril: A computational study. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2018.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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