1
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Ye Y, Ma P, Ma Y, Yang N, Chen X, Yang X, Shen L, Xiao X. Study on the host-guest interactions between tetramethyl cucurbit[6]uril and 2-heterocyclic-substituted benzimidazoles. RSC Adv 2024; 14:2652-2658. [PMID: 38229718 PMCID: PMC10790279 DOI: 10.1039/d3ra07810h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/06/2024] [Indexed: 01/18/2024] Open
Abstract
Cucurbit[n]urils (Q[n]s) are a class of supramolecular host compounds with hydrophilic carbonyl ports and hydrophobic cavities, which can selectively form host-guest inclusion complexes with guest molecules to change the properties of guest molecules. In this paper, tetramethyl cucurbit[6]uril (TMeQ[6]) was used as the host and three 2-heterocyclic substituted benzimidazole derivatives as the guests, and their modes of interaction were investigated using X-ray crystallography, 1H NMR spectrometry, and other analytical techniques. The results showed that TMeQ[6] formed a 1 : 1 host-guest inclusion complex with three guest molecules, and the binding process between them was mainly enthalpy-driven. The X-ray diffraction analysis indicated that the main driving forces for the formation of these three inclusion complexes included hydrogen bonding interactions and ion dipole interactions. There are two modes of interaction between G3 and TMeQ[6] in the liquid phase, indicating that the benzimidazole ring and heterocyclic substituents on the guest molecule compete with the cavity of TMeQ[6]. Besides, the addition of TMeQ[6] significantly enhanced the fluorescence of these guests and slightly improved their solubility.
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Affiliation(s)
- Yanan Ye
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Institute of Applied Chemistry, Guizhou University Guiyang 550025 China
| | - Peihua Ma
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Institute of Applied Chemistry, Guizhou University Guiyang 550025 China
| | - Yue Ma
- Guiyang College of Humanities and Science Guiyang 550025 China
| | - Naqin Yang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Institute of Applied Chemistry, Guizhou University Guiyang 550025 China
| | - Xiaoqian Chen
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Institute of Applied Chemistry, Guizhou University Guiyang 550025 China
| | - Xinan Yang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Institute of Applied Chemistry, Guizhou University Guiyang 550025 China
| | - Lingyi Shen
- School of Basic Medicine, Guizhou Medical University Guiyang 550025 China
| | - Xin Xiao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Institute of Applied Chemistry, Guizhou University Guiyang 550025 China
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2
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Andrianov AK. Noncovalent PEGylation of protein and peptide therapeutics. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2023; 15:e1897. [PMID: 37138514 DOI: 10.1002/wnan.1897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/15/2023] [Accepted: 04/20/2023] [Indexed: 05/05/2023]
Abstract
Clinical applications of protein therapeutics-an advanced generation of drugs characterized by high biological specificity-are rapidly expanding. However, their development is often impeded by unfavorable pharmacokinetic profiles and largely relies on the use of drug delivery systems to prolong their in vivo half-life and suppress undesirable immunogenicity. Although a commercially established PEGylation technology based on protein conjugation with poly(ethylene glycol) (PEG)-protective steric shield resolves some of the challenges, the search for alternatives continues. Noncovalent PEGylation, which mainly relies on multivalent (cooperative) interactions and high affinity (host-guest) complexes formed between protein and PEG offers a number of potential advantages. Among them are dynamic or reversible protection of the protein with minimal loss of biological activity, drastically lower manufacturing costs, "mix-and-match" formulations approaches, and expanded scope of PEGylation targets. While a great number of innovative chemical approaches have been proposed in recent years, the ability to effectively control the stability of noncovalently assembled protein-PEG complexes under physiological conditions presents a serious challenge for the commercial development of the technology. In an attempt to identify critical factors affecting pharmacological behavior of noncovalently linked complexes, this Review follows a hierarchical analysis of various experimental techniques and resulting supramolecular architectures. The importance of in vivo administration routes, degradation patterns of PEGylating agents, and a multitude of potential exchange reactions with constituents of physiological compartments are highlighted. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease.
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Affiliation(s)
- Alexander K Andrianov
- Institute of Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, USA
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3
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Wu Q, Lei Q, Zhong HC, Ren TB, Sun Y, Zhang XB, Yuan L. Fluorophore-based host-guest assembly complexes for imaging and therapy. Chem Commun (Camb) 2023; 59:3024-3039. [PMID: 36785939 DOI: 10.1039/d2cc06286k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Recently, supramolecular chemistry with its unique properties has received considerable attention in many fields. Supramolecular fluorescent systems constructed on the basis of macrocyclic hosts are not only effective in overcoming the limitations of imaging and diagnostic reagents, but also in enhancing their performances. This paper summarizes the recent advances in supramolecular fluorescent systems based on host-guest interactions and their application in bioimaging and therapy as well as the challenges and prospects in developing novel supramolecular fluorescent systems.
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Affiliation(s)
- Qian Wu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Qian Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Hai-Chen Zhong
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Tian-Bing Ren
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Yao Sun
- Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, China.
| | - Xiao-Bing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
| | - Lin Yuan
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
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4
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Barravecchia L, Neira I, Pazos E, Peinador C, García MD. Amino Acid-Viologen Hybrids: Synthesis, Cucurbituril Host-Guest Chemistry, and Implementation on the Production of Peptides. J Org Chem 2021; 87:760-764. [PMID: 34889610 PMCID: PMC8749954 DOI: 10.1021/acs.joc.1c02040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We present herein
the development of a series of viologen–amino
acid hybrids, obtained in good yields either by successive alkylations
of 4,4′-bipyridine, or by Zincke reactions followed by a second
alkylation step. The potential of the obtained amino acids has been
exemplified, either as typical guests of the curcubituril family of
hosts (particularly CB[7]/[8]) or as suitable building blocks for
the solution/solid-phase synthesis of two model tripeptides with the
viologen core inserted within their sequences.
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Affiliation(s)
- Liliana Barravecchia
- Universidade da Coruña, Centro de Investigacións Científicas Avanzadas (CICA), Elviña, 15071 A Coruña, Spain.,Universidade da Coruña, Departamento de Química, Facultade de Ciencias, Zapateira, 15071 A Coruña, Spain
| | - Iago Neira
- Universidade da Coruña, Centro de Investigacións Científicas Avanzadas (CICA), Elviña, 15071 A Coruña, Spain.,Universidade da Coruña, Departamento de Química, Facultade de Ciencias, Zapateira, 15071 A Coruña, Spain
| | - Elena Pazos
- Universidade da Coruña, Centro de Investigacións Científicas Avanzadas (CICA), Elviña, 15071 A Coruña, Spain.,Universidade da Coruña, Departamento de Química, Facultade de Ciencias, Zapateira, 15071 A Coruña, Spain
| | - Carlos Peinador
- Universidade da Coruña, Centro de Investigacións Científicas Avanzadas (CICA), Elviña, 15071 A Coruña, Spain.,Universidade da Coruña, Departamento de Química, Facultade de Ciencias, Zapateira, 15071 A Coruña, Spain
| | - Marcos D García
- Universidade da Coruña, Centro de Investigacións Científicas Avanzadas (CICA), Elviña, 15071 A Coruña, Spain.,Universidade da Coruña, Departamento de Química, Facultade de Ciencias, Zapateira, 15071 A Coruña, Spain
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5
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Zhu H, Mao Z, Chen J, Hu J, Hu X, Koh K, Chen H. Cucurbit[7]urils induced bimetallic nanoparticles network for ultra-sensitive detection of Caspase-3 based on surface plasmon resonance. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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7
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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] [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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8
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Koshti B, Kshtriya V, Nardin C, Gour N. Chemical Perspective of the Mechanism of Action of Antiamyloidogenic Compounds Using a Minimalistic Peptide as a Reductionist Model. ACS Chem Neurosci 2021; 12:2851-2864. [PMID: 34264635 DOI: 10.1021/acschemneuro.1c00221] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The diphenylalanine (FF) residue which is present at the 19 and 20 positions of the amyloid beta (1-42) (Aβ42) peptide sequence is considered as a reductionist model for studying Aβ42 aggregation. FF self-assembles into well-ordered tubular structures via aromatic π-π stacking. Herein the manuscript, we have presented a chemical perspective on the mechanism of action of antiamyloid compounds by assessing their interaction with FF. Therefore, we first coincubated FF fibers with single amino acids, since they are constituted of different R side chains yet have a common structural unit. This study revealed a crucial role of aromatic rings and functional groups like thiol (-SH) in causing destabilization of FF assembly via their interaction with π-electrons participating in π-π stacking present in FF. We further studied the interaction of different nonsteroidal anti-inflammatory drugs (NSAIDs), other known antiamyloidogenic compounds, and host-guest inclusion compounds like cyclodextrin (CD) to assess their mechanism of action and to decipher the functional moiety present in these compounds which could cause destabilization of π-π stacking. From the coincubation experiments, we could surmise a crucial role of aromatic rings present in these compounds for causing interference in aromatic stacking. We further consolidated our observations through microscopy analysis by various spectroscopic methods such as aggregation-induced emission enhancement (AIEE), fluorescence spectroscopy, solution-state 1H NMR, FTIR, and circular dichroism. The studies presented in the manuscript thus provide significant insights into the role of functional groups in imparting antiamyloid action and open new avenues for an efficient design of antiamyloid drugs in the future.
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Affiliation(s)
- Bharti Koshti
- Department of Chemistry, School of Science, Indrashil University, Kadi, Mehsana, Gujarat 382740, India
| | - Vivekshinh Kshtriya
- Department of Chemistry, School of Science, Indrashil University, Kadi, Mehsana, Gujarat 382740, India
| | - Corinne Nardin
- Universite de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Nidhi Gour
- Department of Chemistry, School of Science, Indrashil University, Kadi, Mehsana, Gujarat 382740, India
- Department of Medicinal Chemistry, Indian Institute of Advanced Research, Gandhinagar, Gujarat 382426, India
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9
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Fernandes RJ, Remón P, Moro AJ, Seco A, Ferreira ASD, Pischel U, Basílio N. Toward Light-Controlled Supramolecular Peptide Dimerization. J Org Chem 2021; 86:8472-8478. [PMID: 34060851 PMCID: PMC9161448 DOI: 10.1021/acs.joc.1c00464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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10
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Novo P, García MD, Peinador C, Pazos E. Reversible Control of DNA Binding with Cucurbit[8]uril-Induced Supramolecular 4,4'-Bipyridinium-Peptide Dimers. Bioconjug Chem 2021; 32:507-511. [PMID: 33683100 DOI: 10.1021/acs.bioconjchem.1c00063] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Many cellular processes in living organisms are regulated by complex regulatory networks, built from noncovalent interactions between relatively few proteins that perform their functions by switching between homo- and heterooligomeric assemblies or mono- and bivalent states. Herein, we demonstrate that the conjugation of a 4,4'-bipyridinium scaffold to the basic region of the GCN4 bZip transcription factor can be exploited to control the dimerization of the conjugate by formation of a supramolecular complex with cucurbit[8]uril. Importantly, this supramolecular complex is able to specifically recognize its target dsDNA, and this binding can be reversibly switched by the application of external stimuli.
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Affiliation(s)
- Paula Novo
- Departamento de Química, Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain
| | - Marcos D García
- Departamento de Química, Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain
| | - Carlos Peinador
- Departamento de Química, Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain
| | - Elena Pazos
- Departamento de Química, Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña, 15071 A Coruña, Spain
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11
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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] [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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12
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Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors. Molecules 2020; 26:molecules26010106. [PMID: 33379401 PMCID: PMC7796322 DOI: 10.3390/molecules26010106] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/14/2020] [Accepted: 12/22/2020] [Indexed: 12/30/2022] Open
Abstract
To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.
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13
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Liu Y, Zhang Y, Yu H, Liu Y. Cucurbituril‐Based Biomacromolecular Assemblies. Angew Chem Int Ed Engl 2020; 60:3870-3880. [DOI: 10.1002/anie.202009797] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Indexed: 12/29/2022]
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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14
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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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15
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Chernikova EY, Berdnikova DV. Cucurbiturils in nucleic acids research. Chem Commun (Camb) 2020; 56:15360-15376. [PMID: 33206072 DOI: 10.1039/d0cc06583h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
During the past ten years, the importance of cucurbiturils (CB[n]) as macrocyclic hosts in supramolecular assemblies with various types of natural and synthetic nucleic acids (NAs) has increased explosively. As a component of such systems, CB[n] macrocycles can play a wide spectrum of roles from drug and gene delivery vehicles to catalysts/inhibitors of biochemical reactions and even building blocks for NA-based materials. The aim of this highlight article is to describe the development of the CB[n] applications in nucleic acids research and to outline the current situation and perspectives of this fascinating synergistic combination of supramolecular chemistry of CB[n] and NAs.
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Affiliation(s)
- Ekaterina Y Chernikova
- Laboratory of Photoactive Supramolecular Systems, A. N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, Russia.
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16
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Oohora K, Hirayama S, Mashima T, Hayashi T. Supramolecular dimerization of a hexameric hemoprotein via multiple pyrene-pyrene interactions. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s1088424619500949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein assemblies are being investigated as a new-class of biomaterials. A supramolecular assembly of a mutant hexameric tyrosine coordinated hemoprotein (HTHP) modified with a pyrene derivative is described. Cysteine was first introduced as a site-specific reaction point at position V44 which is located at the bottom surface of the cylindrical structure of HTHP. [Formula: see text]-(1-pyrenyl)maleimide was then reacted with the mutant. The modification was confirmed by MALDI-TOF mass spectrometry and UV-vis absorption spectroscopy, indicating that approximately 90% cysteine residues are attached via the pyrene derivative. Size exclusion chromatography (SEC) measurements for pyrene-attached HTHP include a single peak which elutes earlier than the unmodified HTHP. Further investigation by SEC and dynamic light scattering (DLS) measurements indicate the desired size corresponding to the dimer of the hemoprotein hexamers. The multivalent effect of pyrene–pyrene interactions including hydrophobic and [Formula: see text]–[Formula: see text] stacking interactions appears to be responsible for including formation of the stable dimer of the hexamers. Interestingly, the assembly dissociates to the hexamer by removal of heme. In the case of the apo-form of pyrene-attached HTHP, the pyrene moiety appears to be incorporated into the heme pocket because the modification point is located at the adjacent residue of the Tyr45 coordinating to heme in the holo-form of HTHP. Subsequent addition of heme into the apo-form of pyrene-attached HTHP regenerates the dimer of the hexamers. The present study demonstrates a unique heme-dependent system in which HTHP is assembled to form a dimer of hexamers in the presence of heme and disassembled by removal of heme.
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Affiliation(s)
- Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
- Frontier Research Base for Global Young Researchers, Graduate School of Engineering, Osaka University, Suita 565-0871, Japan
| | - Shota Hirayama
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Tsuyoshi Mashima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
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17
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Chernikova EY, Ruleva AY, Tsvetkov VB, Fedorov YV, Novikov VV, Aliyeu TM, Pavlov AA, Shepel NE, Fedorova OA. Cucurbit[7]uril-driven modulation of ligand-DNA interactions by ternary assembly. Org Biomol Chem 2020; 18:755-766. [PMID: 31912862 DOI: 10.1039/c9ob02543j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design of small organic molecules with a predictable and desirable DNA-binding mechanism is a topical research task for biomedicine application. Herein, we demonstrate an attractive supramolecular strategy for controlling the non-covalent ligand-DNA interaction by binding with cucurbituril as a synthetic receptor. With a combination of UV/vis, CD and NMR experiments, we demonstrate that the bis-styryl dye with two suitable binding sites can involve double stranded DNA and cucurbituril in the formation of the supramolecular triad. The ternary assembly is formed as a result of the interaction of macrocyclic cucurbituril with one pyridinium fragment of the bis-styryl dye, while the second pyridinium fragment of the dye is effectively associated with DNA backbones, which leads to a change in the ligand-DNA binding mode from aggregation to a minor groove. This exciting outcome was supported by molecular docking studies that help to understand the molecular orientation of the supramolecular triad and elucidate the destruction of dye aggregates caused by cucurbituril. These studies provide valuable information on the mechanisms of DNA binding to small molecules and recognition processes in bioorganic supramolecular assemblies constructed from multiple non-covalent interactions.
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Affiliation(s)
- Ekaterina Y Chernikova
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Anna Y Ruleva
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Vladimir B Tsvetkov
- Computational Oncology Group, I.M. Sechenov First Moscow State Medical University, Trubetskaya str, 8/2, Moscow, 119146 Russia and Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia and Polyelectrolytes and Biomedical Polymers Laboratory, A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky prospect str. 29, Moscow, 119991, Russia
| | - Yuri V Fedorov
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Valentin V Novikov
- Laboratory of Nuclear Magnetic Resonances, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia
| | - Tseimur M Aliyeu
- Center for Molecule Composition Studies, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia
| | - Alexander A Pavlov
- Laboratory of Nuclear Magnetic Resonances, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia
| | - Nikolay E Shepel
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Olga A Fedorova
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
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18
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Andrýs R, Klusoňová A, Lísa M, Žd'árová Karasová J. Encapsulation of oxime acetylcholinesterase reactivators: influence of physiological conditions on the stability of oxime-cucurbit[7]uril complexes. NEW J CHEM 2020. [DOI: 10.1039/d0nj03102j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The influence of physiological conditions on the host–guest chemistry of oxime acetylcholinesterase reactivators with cucurbit[7]urile was investigated to increase their effectiveness for the treatment of organophosphate intoxication.
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Affiliation(s)
- Rudolf Andrýs
- Department of Chemistry
- Faculty of Science
- University of Hradec Králové
- 50003 Hradec Králové
- Czech Republic
| | - Aneta Klusoňová
- Department of Chemistry
- Faculty of Science
- University of Hradec Králové
- 50003 Hradec Králové
- Czech Republic
| | - Miroslav Lísa
- Department of Chemistry
- Faculty of Science
- University of Hradec Králové
- 50003 Hradec Králové
- Czech Republic
| | - Jana Žd'árová Karasová
- Department of Toxicology and Military Pharmacy
- Faculty of Military Health Sciences Hradec Králové
- University of Defence
- Praha
- Czech Republic
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19
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Yin H, Cheng Q, Rosas R, Viel S, Monnier V, Charles L, Siri D, Gigmes D, Ouari O, Wang R, Kermagoret A, Bardelang D. A Cucurbit[8]uril 2:2 Complex with a Negative pK a Shift. Chemistry 2019; 25:12552-12559. [PMID: 31286592 DOI: 10.1002/chem.201902057] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/13/2019] [Indexed: 12/22/2022]
Abstract
A viologen derivative carrying a benzimidazole group (V-P-I 2+ ; viologen-phenylene-imidazole V-P-I) can be dimerized in water using cucurbit[8]uril (CB[8]) in the form of a 2:2 complex resulting in a negative shift of the guest pKa , by more than 1 pH unit, contrasting with the positive pKa shift usually observed for CB-based complexes. Whereas 2:2 complex protonation is unclear by NMR, silver cations have been used for probing the accessibility of the imidazole groups of the 2:2 complexes. The protonation capacity of the buried imidazole groups is reduced, suggesting that CB[8] could trigger proton release upon 2:2 complex formation. The addition of CB[8] to a solution containing V-P- I3+ indeed released protons as monitored by pH-metry and visualized by a coloured indicator. This property was used to induce a host/guest swapping, accompanied by a proton transfer, between V-P-I 3+ ⋅CB[7] and a CB[8] complex of 1-methyl-4-(4-pyridyl)pyridinium. The origin of this negative pKa shift is proposed to stand in an ideal charge state, and in the position of the two pH-responsive fragments inside the two CB[8] which, alike residues engulfed in proteins, favour the deprotonated form of the guest molecules. Such proton release triggered by a recognition event is reminiscent of several biological processes and may open new avenues toward bioinspired enzyme mimics catalyzing proton transfer or chemical reactions.
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Affiliation(s)
- Hang Yin
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, P. R. China
| | - Qian Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, P. R. China
| | - Roselyne Rosas
- Aix Marseille Univ, CNRS, Spectropole, FR 1739, Marseille, France
| | - Stéphane Viel
- Aix Marseille Univ, CNRS, ICR, Marseille, France.,Institut Universitaire de France, Paris, France
| | - Valérie Monnier
- Aix Marseille Univ, CNRS, Spectropole, FR 1739, Marseille, France
| | | | - Didier Siri
- Aix Marseille Univ, CNRS, ICR, Marseille, France
| | | | | | - Ruibing Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, Macau, P. R. China
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20
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Zhang Y, Liu J, Yu Q, Wen X, Liu Y. Targeted Polypeptide–Microtubule Aggregation with Cucurbit[8]uril for Enhanced Cell Apoptosis. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ying‐Ming Zhang
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Jiang‐Hua Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Qilin Yu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Xin Wen
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
- Department of Chemical BiologyNational Pesticide Engineering Research CenterNankai University Tianjin 300071 China
| | - Yu Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
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21
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Zhang Y, Liu J, Yu Q, Wen X, Liu Y. Targeted Polypeptide–Microtubule Aggregation with Cucurbit[8]uril for Enhanced Cell Apoptosis. Angew Chem Int Ed Engl 2019; 58:10553-10557. [DOI: 10.1002/anie.201903243] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/04/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Ying‐Ming Zhang
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Jiang‐Hua Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Qilin Yu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
| | - Xin Wen
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
- Department of Chemical BiologyNational Pesticide Engineering Research CenterNankai University Tianjin 300071 China
| | - Yu Liu
- College of ChemistryState Key Laboratory of Elemento-Organic ChemistryNankai University Tianjin 300071 China
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22
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Abstract
Molecular conjugation refers to methods used in biomedicine, advanced materials and nanotechnology to link two partners - from small molecules to large and sometimes functionally complex biopolymers. The methods ideally have a broad structural scope, proceed under very mild conditions (including in H2O), occur at a rapid rate and in quantitative yield with no by-products, enable bioorthogonal reactivity and have zero toxicity. Over the past two decades, the field of click chemistry has emerged to afford us new and efficient methods of molecular conjugation. These methods are based on chemical reactions that produce permanently linked conjugates, and we refer to this field here as covalent click chemistry. Alternatively, if molecular conjugation is undertaken using a pair of complementary molecular recognition partners that associate strongly and selectively to form a thermodynamically stable non-covalent complex, then we refer to this strategy as non-covalent click chemistry. This Perspective is concerned with this latter approach and highlights two distinct applications of non-covalent click chemistry in molecular conjugation: the pre-assembly of molecular conjugates or surface-coated nanoparticles and the in situ capture of tagged biomolecular targets for imaging or analysis.
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Affiliation(s)
- Cynthia L Schreiber
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
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23
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Ferreira P, Ventura B, Barbieri A, Da Silva JP, Laia CAT, Parola AJ, Basílio N. A Visible–Near‐Infrared Light‐Responsive Host–Guest Pair with Nanomolar Affinity in Water. Chemistry 2019; 25:3477-3482. [DOI: 10.1002/chem.201806105] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 01/09/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Pedro Ferreira
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE)Departmento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Barbara Ventura
- Istituto per la Sintesi Organica e la Fotoreattivitá (ISOF)Consiglio Nazionale delle Ricerche (CNR) Via P. Gobetti 101 40129 Bologna Italy
| | - Andrea Barbieri
- Istituto per la Sintesi Organica e la Fotoreattivitá (ISOF)Consiglio Nazionale delle Ricerche (CNR) Via P. Gobetti 101 40129 Bologna Italy
| | - José P. Da Silva
- CCMAR–Centre of Marine SciencesUniversity of Algarve Campus de Gambelas 8005-139 Faro Portugal
| | - César A. T. Laia
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE)Departmento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - A. Jorge Parola
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE)Departmento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Nuno Basílio
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE)Departmento de QuímicaFaculdade de Ciências e TecnologiaUniversidade NOVA de Lisboa 2829-516 Caparica Portugal
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24
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Strebl MG, Yang J, Isaacs L, Hooker JM. Adamantane/Cucurbituril: A Potential Pretargeted Imaging Strategy in Immuno-PET. Mol Imaging 2019; 17:1536012118799838. [PMID: 30354934 PMCID: PMC6204619 DOI: 10.1177/1536012118799838] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Positron emission tomography (PET) imaging with biological macromolecules greatly expands the possibilities of molecular imaging. There are, however, practical aspects limiting the potential of the approach, including the dosimetric consequences of the slow kinetics of radiolabeled biomacromolecules. Pretargeting strategies have led to impactful improvements in the field but are themselves limited by shortcomings of available bioconjugation methodology. We report our initial findings concerning the suitability of the adamantane/cucurbit[7]uril system for pretargeted immuno-PET imaging and provide proof-of-concept PET/computed tomography imaging experiments to establish the stability and rapid formation of host–guest complexes in vivo. The adamantane/cucurbit[7]uril system itself without antibody conjugation has shown remarkably fast association kinetics and clearance in vivo. We further demonstrate the modulation of biodistribution achievable by cucurbituril complexation with relevance for pharmaceutical formulation as well as the radiosynthetic access to relevant reporter molecules labeled with 11C or 18F. This work, an early proof-of-concept, supports the notion that the adamantane/cucurbit[7]uril system warrants further exploration in pretargeted PET imaging applications.
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Affiliation(s)
- Martin G Strebl
- 1 Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Jane Yang
- 1 Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
| | - Lyle Isaacs
- 2 Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
| | - Jacob M Hooker
- 1 Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA
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25
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Yang Q, Fang C, Zhao N, Jiang Y, Xu B, Chai S, Zhou Y. Enhancing electron-hole utilization of CdS Based on cucurbiturils vis electrostatic interaction in visible light. J SOLID STATE CHEM 2019. [DOI: 10.1016/j.jssc.2018.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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26
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Kuan SL, Bergamini FRG, Weil T. Functional protein nanostructures: a chemical toolbox. Chem Soc Rev 2018; 47:9069-9105. [PMID: 30452046 PMCID: PMC6289173 DOI: 10.1039/c8cs00590g] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Indexed: 01/08/2023]
Abstract
Nature has evolved an optimal synthetic factory in the form of translational and posttranslational processes by which millions of proteins with defined primary sequences and 3D structures can be built. Nature's toolkit gives rise to protein building blocks, which dictates their spatial arrangement to form functional protein nanostructures that serve a myriad of functions in cells, ranging from biocatalysis, formation of structural networks, and regulation of biochemical processes, to sensing. With the advent of chemical tools for site-selective protein modifications and recombinant engineering, there is a rapid development to develop and apply synthetic methods for creating structurally defined, functional protein nanostructures for a broad range of applications in the fields of catalysis, materials and biomedical sciences. In this review, design principles and structural features for achieving and characterizing functional protein nanostructures by synthetic approaches are summarized. The synthetic customization of protein building blocks, the design and introduction of recognition units and linkers and subsequent assembly into structurally defined protein architectures are discussed herein. Key examples of these supramolecular protein nanostructures, their unique functions and resultant impact for biomedical applications are highlighted.
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Affiliation(s)
- Seah Ling Kuan
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
| | - Fernando R. G. Bergamini
- Institute of Chemistry
, Federal University of Uberlândia – UFU
,
38400-902 Uberlândia
, MG
, Brazil
| | - Tanja Weil
- Max-Planck Institute for Polymer Research
,
Ackermannweg 10
, 55128 Mainz
, Germany
.
;
- Institute of Inorganic Chemistry I – Ulm University
,
Albert-Einstein-Allee 11
, 89081 Ulm
, Germany
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27
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Dang DT, van Onzen AHAM, Dorland YL, Brunsveld L. Cucurbit[8]uril Reactivation of an Inactivated Caspase-8 Mutant Reveals Differentiated Enzymatic Substrate Processing. Chembiochem 2018; 19:2490-2494. [PMID: 30300966 PMCID: PMC6391946 DOI: 10.1002/cbic.201800521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Indexed: 01/26/2023]
Abstract
Caspase-8 constructs featuring an N-terminal FGG sequence allow for selective twofold recognition by cucurbit[8]uril, which leads to an increase of the enzymatic activity in a cucurbit[8]uril dose-dependent manner. This supramolecular switching has enabled for the first time the study of the same caspase-8 in its two extreme states; as full monomer and as cucurbit[8]uril induced dimer. A mutated, fully monomeric caspase-8 (D384A), which is enzymatically inactive towards its natural substrate caspase-3, could be fully reactivated upon addition of cucurbit[8]uril. In its monomeric state caspase-8 (D384A) still processes a small synthetic substrate, but not the natural caspase-3 substrate, highlighting the close interplay between protein dimerization and active site rearrangement for substrate selectivity. The ability to switch the caspase-8 activity by a supramolecular system thus provides a flexible approach to studying the activity of a protein at different oligomerization states.
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Affiliation(s)
- Dung T. Dang
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering, andInstitute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
| | - Arthur H. A. M. van Onzen
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering, andInstitute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
| | - Yvonne L. Dorland
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering, andInstitute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering, andInstitute for Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZEindhovenThe Netherlands
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28
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Zou H, Liu J, Li Y, Li X, Wang X. Cucurbit[8]uril-Based Polymers and Polymer Materials. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802234. [PMID: 30168673 DOI: 10.1002/smll.201802234] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Cucurbit[8]uril (CB[8]) is unique and notable in the cucurbit[n]uril family, since it has a relatively large cavity and thus is able to simultaneously accommodate two guest molecules. Typically, an electron-deficient first guest and an electron-rich second guest can be bound by CB[8] to form a stable 1:1:1 heteroternary supramolecular complex. Additionally, two homo guests can also be strongly dimerized inside the cavity of CB[8] to form a 2:1 homoternary supramolecular complex. During the past decade, by combining polymer science and CB[8] host-guest chemistry, a variety of systems have been established to construct supramolecular polymers with polymer chains typically at the nanoscale/sub-microscale, and CB[8]-based micro/nanostructured polymer materials in the form of polymer networks and hydrogels, microcapsules, micelles, vesicles, and colloidal particles, normally in solution and occasionally on surfaces. This Review summarizes the noncovalent interactions and strategies used for the preparation of CB[8]-based polymers and polymer materials with a focus on the representative and latest developments, followed by a brief discussion of their characterization, properties, and applications.
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Affiliation(s)
- Hua Zou
- School of Materials Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Jing Liu
- School of Materials Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Ying Li
- School of Materials Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Xiaoyan Li
- School of Materials Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
| | - Xia Wang
- School of Materials Science and Engineering, University of Shanghai for Science and Technology, 516 Jungong Road, Shanghai, 200093, China
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29
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Correia HD, Chowdhury S, Ramos AP, Guy L, Demets GJ, Bucher C. Dynamic supramolecular polymers built from cucurbit[n]urils and viologens. POLYM INT 2018. [DOI: 10.1002/pi.5709] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Henrique Dias Correia
- Escola Técnica Escola técnica estadual Ângelo Cavalheiro, Rua José Correia Filho 750 Serrana Brazil
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, CEP 14040‐901 Ribeirão Preto Brazil
| | - Shagor Chowdhury
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie Lyon France
| | - Ana Paula Ramos
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, CEP 14040‐901 Ribeirão Preto Brazil
| | - Laure Guy
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie Lyon France
| | - Grégoire Jean‐François Demets
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, CEP 14040‐901 Ribeirão Preto Brazil
| | - Christophe Bucher
- Univ Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie Lyon France
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30
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Finbloom JA, Francis MB. Supramolecular strategies for protein immobilization and modification. Curr Opin Chem Biol 2018; 46:91-98. [DOI: 10.1016/j.cbpa.2018.05.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/19/2018] [Accepted: 05/29/2018] [Indexed: 02/03/2023]
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31
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Yang B, Yu SB, Wang H, Zhang DW, Li ZT. 2:2 Complexes from Diphenylpyridiniums and Cucurbit[8]uril: Encapsulation-Promoted Dimerization of Electrostatically Repulsing Pyridiniums. Chem Asian J 2018; 13:1312-1317. [PMID: 29480650 DOI: 10.1002/asia.201701816] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/29/2018] [Indexed: 01/07/2023]
Abstract
Rigid linear compounds G1 and G2, which contained two 4-phenylpyridinium (PhPy+ ) units, have been prepared to investigate their binding with cucurbit[8]uril (CB[8]). X-ray crystallographic structures revealed that in the solid state both compounds were included by CB[8], through antiparallel stacking, to form 2:2 quaternary complexes (G1)2 @(CB[8])2 and (G2)2 @(CB[8])2 . For the former complex, CB[8] entrapped G1 by holding two heterodimers of its Py+ and benzyl units, which were at opposite ends of the backbone. In contrast, for the first time, the second complex disclosed parallel stacking of two cationic Py+ units of G2 in the cavity of CB[8] in the solid state, despite the generation of important electrostatic repulsion. Isothermal titrations in water afforded high apparent association constants of 4.36×106 and 6.43×106 m-1 for 1:1 complexes G1@CB[8] and G2@CB[8], respectively, and 1 H NMR spectroscopy experiments in D2 O confirmed a similar stacking pattern to that observed in the solid state. A previous study and crystal structures of the 2:1 complexes formed between three new controls, G3-5, and CB[8] did not display such unusual stacking of the cationic Py+ unit; this may be attributed to the multivalency of the two CB[8] encapsulation interactions.
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Affiliation(s)
- Bo Yang
- Department of Chemistry, Collaborative Innovation Centre of, Chemistry for Energy Materials (iChEM), Shanghai Key, Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, 220 Handan Road, Shanghai, 200433, P.R. China
| | - Shang-Bo Yu
- Department of Chemistry, Collaborative Innovation Centre of, Chemistry for Energy Materials (iChEM), Shanghai Key, Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, 220 Handan Road, Shanghai, 200433, P.R. China
| | - Hui Wang
- Department of Chemistry, Collaborative Innovation Centre of, Chemistry for Energy Materials (iChEM), Shanghai Key, Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, 220 Handan Road, Shanghai, 200433, P.R. China
| | - Dan-Wei Zhang
- Department of Chemistry, Collaborative Innovation Centre of, Chemistry for Energy Materials (iChEM), Shanghai Key, Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, 220 Handan Road, Shanghai, 200433, P.R. China
| | - Zhan-Ting Li
- Department of Chemistry, Collaborative Innovation Centre of, Chemistry for Energy Materials (iChEM), Shanghai Key, Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, 220 Handan Road, Shanghai, 200433, P.R. China
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32
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Yang X, Cong H, Yan S, Wang ZC, Li JX, Tao Z. Supramolecular Interactions of Bambus[6]urils with Quinoline and 6-Hydroxyisoquinoline Hydrochloride Salts. ChemistrySelect 2018. [DOI: 10.1002/slct.201800179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Xi Yang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province; Guizhou University; Guiyang 550025, P. R. China
| | - Hang Cong
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province; Guizhou University; Guiyang 550025, P. R. China
| | - Shan Yan
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province; Guizhou University; Guiyang 550025, P. R. China
| | - Zhong-Cai Wang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province; Guizhou University; Guiyang 550025, P. R. China
| | - Jia-Xing Li
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province; Guizhou University; Guiyang 550025, P. R. China
| | - Zhu Tao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province; Guizhou University; Guiyang 550025, P. R. China
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Affiliation(s)
- Ofer Reany
- Department of Natural Sciences; The Open University of Israel; 1 University Rd Ra'anana 43537 Israel
| | - Amar Mohite
- Department of Natural Sciences; The Open University of Israel; 1 University Rd Ra'anana 43537 Israel
| | - Ehud Keinan
- Schulich Faculty of Chemistry; Technion - Israel Institute of Technology; Technion City Haifa 32000 Israel
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34
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Okesola BO, Mata A. Multicomponent self-assembly as a tool to harness new properties from peptides and proteins in material design. Chem Soc Rev 2018; 47:3721-3736. [DOI: 10.1039/c8cs00121a] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nature is enriched with a wide variety of complex, synergistic and highly functional protein-based multicomponent assemblies.
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Affiliation(s)
- Babatunde O. Okesola
- School of Engineering and Materials Science
- Institute of Bioengineering
- Queen Mary University of London
- UK
| | - Alvaro Mata
- School of Engineering and Materials Science
- Institute of Bioengineering
- Queen Mary University of London
- UK
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35
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Hou C, Zeng X, Gao Y, Qiao S, Zhang X, Xu J, Liu J. Cucurbituril As A Versatile Tool to Tune the Functions of Proteins. Isr J Chem 2017. [DOI: 10.1002/ijch.201700105] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Chunxi Hou
- State Key laboratory of Supramolecular Structure and Materials; College of Chemistry, and
| | - Xiangzhi Zeng
- College of Life Science; Jilin University; 2699 Qianjin Road Changchun 130012 China
| | - Yuzhou Gao
- Suzhou Institute of Biomedical Engineering and Technology; Chinese Academy of Sciences; No.88, Keling Road Suzhou New District, Suzhou 215163 China
| | - Shanpeng Qiao
- State Key laboratory of Supramolecular Structure and Materials; College of Chemistry, and
| | - Xin Zhang
- State Key laboratory of Supramolecular Structure and Materials; College of Chemistry, and
| | - Jiayun Xu
- State Key laboratory of Supramolecular Structure and Materials; College of Chemistry, and
| | - Junqiu Liu
- State Key laboratory of Supramolecular Structure and Materials; College of Chemistry, and
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Barooah N, Khurana R, Bhasikuttan AC, Mohanty J. Stimuli-responsive Supra-biomolecular Nanoassemblies of Cucurbit[7]uril with Bovine Serum Albumin: Drug Delivery and Sensor Applications. Isr J Chem 2017. [DOI: 10.1002/ijch.201700104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nilotpal Barooah
- Radiation & Photochemistry Division; Bhabha Atomic Research Centre; Mumbai 400 085 India
| | - Raman Khurana
- Radiation & Photochemistry Division; Bhabha Atomic Research Centre; Mumbai 400 085 India
- Homi Bhabha National Institute; Training School Complex, Anushaktinagar; Mumbai 400 094 India
| | - Achikanath C. Bhasikuttan
- Radiation & Photochemistry Division; Bhabha Atomic Research Centre; Mumbai 400 085 India
- Homi Bhabha National Institute; Training School Complex, Anushaktinagar; Mumbai 400 094 India
| | - Jyotirmayee Mohanty
- Radiation & Photochemistry Division; Bhabha Atomic Research Centre; Mumbai 400 085 India
- Homi Bhabha National Institute; Training School Complex, Anushaktinagar; Mumbai 400 094 India
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37
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van Dun S, Ottmann C, Milroy LG, Brunsveld L. Supramolecular Chemistry Targeting Proteins. J Am Chem Soc 2017; 139:13960-13968. [PMID: 28926241 PMCID: PMC5639466 DOI: 10.1021/jacs.7b01979] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Indexed: 12/19/2022]
Abstract
The specific recognition of protein surface elements is a fundamental challenge in the life sciences. New developments in this field will form the basis of advanced therapeutic approaches and lead to applications such as sensors, affinity tags, immobilization techniques, and protein-based materials. Synthetic supramolecular molecules and materials are creating new opportunities for protein recognition that are orthogonal to classical small molecule and protein-based approaches. As outlined here, their unique molecular features enable the recognition of amino acids, peptides, and even whole protein surfaces, which can be applied to the modulation and assembly of proteins. We believe that structural insights into these processes are of great value for the further development of this field and have therefore focused this Perspective on contributions that provide such structural data.
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Affiliation(s)
- Sam van Dun
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology
and Institute for Complex Molecular Systems, Department of Biomedical
Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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38
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Hou C, Guan S, Wang R, Zhang W, Meng F, Zhao L, Xu J, Liu J. Supramolecular Protein Assemblies Based on DNA Templates. J Phys Chem Lett 2017; 8:3970-3979. [PMID: 28792224 DOI: 10.1021/acs.jpclett.7b01564] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA plays an important role in the process of protein assembly. DNA viruses such as the M13 virus are typical examples in which single DNA genomes behave as templates to induce the assembly of multiple major coat protein (PVIII) monomers. Thus, the design of protein assemblies based on DNA templates attracts much interest in the construction of supramolecular structures and materials. With the development of DNA nanotechnology, precise 1D and 3D protein nanostructures have been designed and constructed by using DNA templates through DNA-protein interactions, protein-ligand interactions, and protein-adapter interactions. These DNA-templated protein assemblies show great potential in catalysis, medicine, light-responsive systems, drug delivery, and signal transduction. Herein, we review the progress on DNA-based protein nanostructures that possess sophisticated nanometer-sized structures with programmable shapes and stimuli-responsive parameters, and we present their great potential in the design of biomaterials and biodevices in the future.
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Affiliation(s)
| | | | - Ruidi Wang
- Department of Chemistry, University of British Columbia , Vancouver, British Columbia V6T 1Z1, Canada
| | - Wei Zhang
- Zhuhai United Laboratories Co., Ltd. , Nation High & New Technology Industry Development Zone, Zhuhai 519040, China
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39
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Danylyuk O. Exploring cucurbit[6]uril–peptide interactions in the solid state: crystal structure of cucurbit[6]uril complexes with glycyl-containing dipeptides. CrystEngComm 2017. [DOI: 10.1039/c7ce00881c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Macrocyclic host cucurbit[6]uril forms supramolecular complexes with dipeptides sequenced as Gly-X, where X is either an aromatic amino acid residue Phe, Tyr, and Trp or Gly in the solid state.
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Affiliation(s)
- Oksana Danylyuk
- Institute of Physical Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
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