1
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Zhang C, Shi C, Chang P, Bian S, Li B, Li J, Hou P. MRI Directed Magnevist Effective to Study Toxicity of Gd-Doped Mesoporous Carbon Nanoparticles in Mice Model. Int J Nanomedicine 2023; 18:6119-6136. [PMID: 37915747 PMCID: PMC10617538 DOI: 10.2147/ijn.s433213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023] Open
Abstract
Purpose Magnetic resonance imaging (MRI) has been a valuable and widely used examination technique in clinical diagnosis and prognostic efficacy evaluation. The introduction of MRI contrast agent (CA) improves its sensitivity obviously, particularly with the development of nano-CA, which presents higher contrast enhancement ability. However, systematical evaluation of their toxicity is still limited, hampering their further translation in clinics. Methods In this paper, to systematically evaluate the toxicity of nano-CA, Gd-doped mesoporous carbon nanoparticles (Gd-MCNs) prepared by a one-step hard template method were introduced as a model and clinically used MRI CA, Magnevist (Gd-DTPA) as control. Their in vitro blood compatibility, cellular toxicity, DNA damage, oxidative stress, inflammation response as well as in vivo toxicity and MR imaging behaviors were studied and compared. Results The experimental results showed that compared with Gd-DTPA, Gd-MCNs displayed negligible influence on the red blood cell shape, aggregation, BSA structure, macrophage morphology and mitochondrial function. Meanwhile, limited ROS and inflammatory cytokine production also illustrated the cellular compatibility of Gd-MCNs. For in vivo toxicity evaluation, Gd-MCNs presented acceptable in vivo biosafety even under 12 times injection for 12 weeks. More importantly, at the same concentration of Gd, Gd-MCNs displayed better contrast enhancement of tumor than Gd-DTPA, mainly coming from its high MRI relaxation rate which is nearly 9 times that of Gd-DTPA. Conclusion In this paper, we focus on the toxicity evaluation of MRI nano-CA, Gd-MCNs from different angles. With Gd-DTPA as control, Gd-MCNs appeared to be highly biocompatible and safe nanoparticles that possessed promising potentials for the use of MRI nano-CA. In the future, more research on the long-term genotoxicity and the fate of nanoparticles after being swallowed should be performed.
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Affiliation(s)
- Chun Zhang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, People’s Republic of China
- Department of Radiology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, People’s Republic of China
| | - Changzhou Shi
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, People’s Republic of China
| | - Pengzhao Chang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, People’s Republic of China
| | - Shuang Bian
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, People’s Republic of China
- Department of Radiology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, People’s Republic of China
| | - Bangbang Li
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, People’s Republic of China
| | - Jingjing Li
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, 221004, People’s Republic of China
- Department of Radiology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, People’s Republic of China
| | - Pingfu Hou
- Department of Radiology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221006, People’s Republic of China
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People’s Republic of China
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2
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Straßburger D, Herziger S, Huth K, Urschbach M, Haag R, Besenius P. Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders. Beilstein J Org Chem 2021; 17:97-104. [PMID: 33519996 PMCID: PMC7814183 DOI: 10.3762/bjoc.17.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/14/2020] [Indexed: 11/23/2022] Open
Abstract
The synthesis of a sulfate-modified dendritic peptide amphiphile and its self-assembly into one-dimensional rod-like architectures in aqueous medium is reported. The influence of the ionic strength on the supramolecular polymerization was probed via circular dichroism spectroscopy and cryogenic transmission electron microscopy. Physiological salt concentrations efficiently screen the charges of the dendritic building block equipped with eight sulfate groups and trigger the formation of rigid supramolecular polymers. Since multivalent sulfated supramolecular structures mimic naturally occurring L-selectin ligands, the corresponding affinity was evaluated using a competitive SPR binding assay and benchmarked to an ethylene glycol-decorated supramolecular polymer.
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Affiliation(s)
- David Straßburger
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Svenja Herziger
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany.,Research Center of Electron Microscopy, Freie Universität Berlin, Fabeckstr. 34a, 14195 Berlin
| | - Katharina Huth
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Moritz Urschbach
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Rainer Haag
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Pol Besenius
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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3
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Biswas R, Naskar S, Ghosh S, Das M, Banerjee S. A Remarkable Fluorescence Quenching Based Amplification in ATP Detection through Signal Transduction in Self-Assembled Multivalent Aggregates. Chemistry 2020; 26:13595-13600. [PMID: 32776606 DOI: 10.1002/chem.202002648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/22/2020] [Indexed: 01/20/2023]
Abstract
Signal transduction is essential for the survival of living organisms, because it allows them to respond to the changes in external environments. In artificial systems, signal transduction has been exploited for the highly sensitive detection of analytes. Herein, a remarkable signal transduction, upon ATP binding, in the multivalent fibrillar nanoaggregates of anthracene conjugated imidazolium receptors is reported. The aggregates of one particular amphiphilic receptor sensed ATP in high pm concentrations with one ATP molecule essentially quenching the emission of thousands of receptors. A cooperative merging of the multivalent binding and signal transduction led to this superquenching and translated to an outstanding enhancement of more than a millionfold in the sensitivity of ATP detection by the nanoaggregates; in comparison to the "molecular" imidazolium receptors. Furthermore, an exceptional selectivity to ATP over other nucleotides was demonstrated.
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Affiliation(s)
- Rakesh Biswas
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Sumit Naskar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Surya Ghosh
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Mousumi Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Supratim Banerjee
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
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4
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Bhaumik SK, Patra YS, Banerjee S. High affinity heparin detection by multivalent supramolecular polymers through aggregation induced emission. Chem Commun (Camb) 2020; 56:9541-9544. [DOI: 10.1039/d0cc03644g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Supramolecular polymers based on aggregation induced emission active cationic cyanostilbenes provide a highly sensitive “light-up” platform for heparin detection.
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Affiliation(s)
- Shubhra Kanti Bhaumik
- The Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Nadia
- India
| | - Yoti Shankar Patra
- The Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Nadia
- India
| | - Supratim Banerjee
- The Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Nadia
- India
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5
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Kovalska V, Vakarov S, Losytskyy M, Kuperman M, Chornenka N, Toporivska Y, Gumienna-Kontecka E, Voloshin Y, Varzatskii O, Mokhir A. Dicarboxyl-terminated iron(ii) clathrochelates as ICD-reporters for globular proteins. RSC Adv 2019; 9:24218-24230. [PMID: 35527894 PMCID: PMC9069836 DOI: 10.1039/c9ra04102h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/26/2019] [Indexed: 01/07/2023] Open
Abstract
Cage metal complexes iron(ii) clathrochelates, which are inherently CD silent, were discovered to demonstrate intensive output in induced circular dichroism (ICD) spectra upon their assembly to albumins. With the aim to design clathrochelates as protein-sensitive CD reporters, the approach for the functionalization of one chelate α-dioximate fragment of the clathrochelate framework with two non-equivalent substituents was developed, and constitutional isomers of clathrochelate with two non-equivalent carboxyphenylsulfide groups were synthesized. The interaction of designed iron(ii) clathrochelates and their symmetric homologues with globular proteins (serum albumins, lysozyme, β-lactoglobulin (BLG), trypsin, insulin) was studied by protein fluorescence quenching and CD techniques. A highly-intensive ICD output of the clathrochelates was observed upon their association with albumins and BLG. It was shown that in the presence of BLG, different clathrochelate isomers gave spectra of inverted signs, indicating the stabilization of opposite configurations (Λ or Δ) of the clathrochelate framework in the assembly with this protein. So, we suggest that the isomerism of the terminal carboxy group determined preferable configurations of the clathrochelate framework for the fixation in the protein binding site. MALDI TOF results show the formation of BLG-clathrochelate complex with ratio 1 : 1. Based on the docking simulations, the binding of the clathrochelate molecule (all isomers) to the main BLG binding site (calyx) in its open conformation is suggested. The above results point that the variation of the ribbed substituents at the clathrochelate framework is an effective tool to achieve the specificity of clathrochelate ICD reporting properties to the target protein.
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Affiliation(s)
- Vladyslava Kovalska
- Institute of Molecular Biology and Genetics, NASU 150 Zabolotnogo St. 03143 Kyiv Ukraine
| | - Serhii Vakarov
- Princeton Biomolecular Research Labs 26A Saperne Pole St. 01042 Kyiv Ukraine
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU 32/34 Palladin Av. 03142 Kyiv Ukraine
| | - Mykhaylo Losytskyy
- Institute of Molecular Biology and Genetics, NASU 150 Zabolotnogo St. 03143 Kyiv Ukraine
| | - Marina Kuperman
- Institute of Molecular Biology and Genetics, NASU 150 Zabolotnogo St. 03143 Kyiv Ukraine
| | - Nina Chornenka
- Princeton Biomolecular Research Labs 26A Saperne Pole St. 01042 Kyiv Ukraine
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU 32/34 Palladin Av. 03142 Kyiv Ukraine
| | - Yuliya Toporivska
- Faculty of Chemistry, University of Wroclaw 14 F. Joliot-Curie St. 50-383 Wroclaw Poland
| | | | - Yan Voloshin
- Nesmeyanov Institute of Organoelement Compounds RAS 28 Vavilova St. 119991 Moscow Russia
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences 31 Leninsky Prosp. 119991 Moscow Russia
| | - Oleg Varzatskii
- V.I. Vernadsky Institute of General and Inorganic Chemistry, NASU 32/34 Palladin Av. 03142 Kyiv Ukraine
| | - Andriy Mokhir
- Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg Henkestr. 42 91054 Erlangen Germany
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Hatai J, Schmuck C. Diverse Properties of Guanidiniocarbonyl Pyrrole-Based Molecules: Artificial Analogues of Arginine. Acc Chem Res 2019; 52:1709-1720. [PMID: 31150198 DOI: 10.1021/acs.accounts.9b00142] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The guanidinium moiety, which is present in active sites of many enzymes, plays an important role in the binding of anionic substrates. In addition, it was also found to be an excellent binding motif for supramolecular chemistry. Inspired by Nature, scientists have developed artificial receptors containing guanidinium scaffolds that bind to a variety of oxoanions through hydrogen bonding and charge pairing interactions. However, the majority of binding studies is restricted to organic solvents. Polyguanidinium based molecules can form efficient complexes in aqueous solvents due to strong electrostatic interactions. However, they only have moderate association constants, which are significantly decreased in the presence of competing anions and salts. Hence, to improve the binding affinity of the guanidinium moiety, our group developed the cationic guanidiniocarbonyl pyrrole (GCP) moiety. This rigid planar analogue binds efficiently to oxoanions, like carboxylates even in aqueous solvents. The lower p Ka value (7-8) of GCP compared to guanidinium derivatives (p Ka 13) favors the formation of strong, hydrogen bonded ion pairs. In addition, carboxylate binding is further enhanced by additional amide hydrogen bond donors located at the five position of the pyrrole core. Moreover, the design has allowed for introducing secondary interactions between receptor side chains and guest molecules, which allows for optimizing binding specificity and selectivity. The spectroscopic data confirmed stabilization of guanidiniocarbonyl pyrrole/oxoanion complexes through a combination of ion pairing and multiple hydrogen bonding interactions. The key role of the ionic interaction in a polar solvent, is demonstrated by a zwitterion derivative of the guanidiniocarbonyl pyrrole, which self-assembles in both dimethyl sulfoxide and pure water with association constants of K > 1010 M-1 and K = 170 M-1, respectively. In this Account, we discuss strategies for making GCP functionalized compounds, in order to boost their ability to bind oxoanions. Then we explore how these building blocks have been incorporated into different synthetic molecules and peptide sequences, highlighting examples that demonstrated the versatility of this binding scaffold. For instance, the high oxoanion binding property of GCP-based compounds was exploited to generate a detectable signal for sensing applications, thus improving selectivity and sensitivity in aqueous solution. Moreover, peptides and molecules containing GCP have shown excellent gene transfections properties. Furthermore, the self-assembly and zwitterionic behavior of zwitterionic GCP analogues was used to develop variety of supramolecular architectures such as stable supramolecular β-helix structure, linear supramolecular oligomers, one-dimensional rods or two-dimension sheets, fibers, vesicles, soft nanospheres, as well as stimuli responsive supramolecular gels.
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Affiliation(s)
- Joydev Hatai
- Institut für Organische Chemie, Universität Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Carsten Schmuck
- Institut für Organische Chemie, Universität Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany
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7
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Sikder A, Ray D, Aswal VK, Ghosh S. Hydrogen‐Bonding‐Regulated Supramolecular Nanostructures and Impact on Multivalent Binding. Angew Chem Int Ed Engl 2018; 58:1606-1611. [DOI: 10.1002/anie.201812217] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Amrita Sikder
- School of Applied and Interdisciplinary SciencesIndian Association for the Cultivation of Science Kolkata- 700032 India
| | - Debes Ray
- Solid State Physics DivisionBhabha Atomic Research Centre Mumbai- 400085 India
| | - Vinod K. Aswal
- Solid State Physics DivisionBhabha Atomic Research Centre Mumbai- 400085 India
| | - Suhrit Ghosh
- School of Applied and Interdisciplinary SciencesIndian Association for the Cultivation of Science Kolkata- 700032 India
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8
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Sikder A, Ray D, Aswal VK, Ghosh S. Hydrogen‐Bonding‐Regulated Supramolecular Nanostructures and Impact on Multivalent Binding. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201812217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Amrita Sikder
- School of Applied and Interdisciplinary SciencesIndian Association for the Cultivation of Science Kolkata- 700032 India
| | - Debes Ray
- Solid State Physics DivisionBhabha Atomic Research Centre Mumbai- 400085 India
| | - Vinod K. Aswal
- Solid State Physics DivisionBhabha Atomic Research Centre Mumbai- 400085 India
| | - Suhrit Ghosh
- School of Applied and Interdisciplinary SciencesIndian Association for the Cultivation of Science Kolkata- 700032 India
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9
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Neal TA, Wang W, Zhiquan L, Peng R, Soni P, Xie H, Badjić JD. A Hexavalent Basket for Bottom‐Up Construction of Functional Soft Materials and Polyvalent Drugs through a “Click” Reaction. Chemistry 2018; 25:1242-1248. [PMID: 30466183 DOI: 10.1002/chem.201805246] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/19/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Taylor A. Neal
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue 43210 Columbus Ohio USA
| | - Weikun Wang
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue 43210 Columbus Ohio USA
| | - Lei Zhiquan
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue 43210 Columbus Ohio USA
| | - Ruojing Peng
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue 43210 Columbus Ohio USA
| | - Priti Soni
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue 43210 Columbus Ohio USA
| | - Han Xie
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue 43210 Columbus Ohio USA
| | - Jovica D. Badjić
- Department of Chemistry & Biochemistry The Ohio State University 100 West 18th Avenue 43210 Columbus Ohio USA
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10
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Ishiwari F, Shoji Y, Fukushima T. Supramolecular scaffolds enabling the controlled assembly of functional molecular units. Chem Sci 2018; 9:2028-2041. [PMID: 29719683 PMCID: PMC5896469 DOI: 10.1039/c7sc04340f] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/19/2018] [Indexed: 12/14/2022] Open
Abstract
To assemble functional molecular units into a desired structure while controlling positional and orientational order is a key technology for the development of high-performance organic materials that exhibit electronic, optoelectronic, biological and even dynamic functions. For this purpose, we cannot rely simply on the inherent self-assembly properties of the target functional molecular units, since it is difficult to predict, based solely on the molecular structure, what structure will be achieved upon assembly. To address this issue, it would be useful to employ molecular building blocks with self-assembly structures that can be clearly predicted and defined, to make target molecular units assemble into a desired structure. To date, various motifs of molecular assemblies, polymers, discrete and/or three-dimensional metal-organic complexes, nanoparticles and metal/metal oxide substrates have been developed to create materials with particular structures and dimensionalities. In this perspective, we define such assembly motifs as "supramolecular scaffolds". The structure of supramolecular scaffolds can be classified in terms of dimensionality, and they range in size from nano- to macroscopic scales. Functional molecular units, when attached to supramolecular scaffolds either covalently or non-covalently, can be assembled into specific structures, thus enabling the exploration of new properties, which cannot be achieved with the target molecular units alone. Through the classification and overview of reported examples, we shed new light on supramolecular scaffolds for the rational design of organic and polymeric materials.
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Affiliation(s)
- Fumitaka Ishiwari
- Laboratory for Chemistry and Life Science , Institute of Innovative Research , Tokyo Institute of Technology , 4259 Nagatsuta, Midori-ku , Yokohama 226-8503 , Japan .
| | - Yoshiaki Shoji
- Laboratory for Chemistry and Life Science , Institute of Innovative Research , Tokyo Institute of Technology , 4259 Nagatsuta, Midori-ku , Yokohama 226-8503 , Japan .
| | - Takanori Fukushima
- Laboratory for Chemistry and Life Science , Institute of Innovative Research , Tokyo Institute of Technology , 4259 Nagatsuta, Midori-ku , Yokohama 226-8503 , Japan .
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11
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Abstract
A key challenge in chemical biology is to identify small molecule regulators for every single protein. However, protein surfaces are notoriously difficult to recognise with synthetic molecules, often having large flat surfaces that are poorly matched to traditional small molecules. In the surface mimetic approach, a supramolecular scaffold is used to project recognition groups in such a manner as to make multivalent non-covalent contacts over a large area of protein surface. Metal based supramolecular scaffolds offer unique advantages over conventional organic molecules for protein binding, including greater stereochemical and geometrical diversity conferred through the metal centre and the potential for direct assessment of binding properties and even visualisation in cells without recourse to further functionalisation. This feature article will highlight the current state of the art in protein surface recognition using metal complexes as surface mimetics.
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Affiliation(s)
- Sarah H Hewitt
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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12
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Reader PP, Shaw AM. Kinetic Analysis of the Multivalent Ligand Binding Interaction between Protein A/G and IgG: A Standard System Setting. J Phys Chem B 2017; 121:8919-8925. [PMID: 28876067 DOI: 10.1021/acs.jpcb.7b06163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recombinant protein A/G (PAG) has a sequence coding for eight IgG binding sites and has enhanced interspecies affinity. High-frequency sampling of a PAG titration with IgG produces concentration profiles that are sensitive to the kinetic availability of the binding sites. The full kinetic model developed here for IgG binding sequentially to PAG shows only two distinct kinetic processes, describing an initial rapid association of two antibodies to PAG with a rate constant k-fast = (1.86 ± 0.08) × 106 M-1 s-1 and a slower antibody binding process to all remaining sites, k-slow = (1.24 ± 0.05) × 104 M-1 s-1. At equilibrium (after 1 h), the maximum IgG occupancy of PAG is 2.8 ± 0.5, conflicting with the genetic evidence of eight binding sites and suggesting significant steric hindrance of the neighboring IgG binding sites. The phosphate-buffered saline (PBS) solution defines a standard system setting, and this may be compared with other settings. The mean association rate of PAG-IgGn in the standard setting is 282 ± 20% higher than when PAG is tethered to a surface. A systems biology approach requires that a model parameter set that defines a system in a standard setting should be transferable to another system. The transfer of parameters between settings may be performed using activity coefficients characterizing an effective concentration of species in a system, ai = γici. The activity correction, γ, for the eight-site occupancy is γ = 0.35 ± 0.06, and mapping from the standard setting to the solution setting suggests γPAG-IgG = 0.4 ± 0.03. The role of activity coefficients and transferability of kinetic parameters between system settings is discussed.
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Affiliation(s)
- Peter P Reader
- University of Exeter Medical School, University of Exeter College of Life and Environmental Sciences, University of Exeter , Stocker Road, Exeter, EX4 4PB, U.K
| | - Andrew M Shaw
- University of Exeter Medical School, University of Exeter College of Life and Environmental Sciences, University of Exeter , Stocker Road, Exeter, EX4 4PB, U.K
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13
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Wilch C, Talbiersky P, Berchner‐Pfannschmidt U, Schaller T, Kirsch M, Klärner F, Schrader T. Molecular Tweezers Inhibit PARP‐1 by a New Mechanism. European J Org Chem 2017. [DOI: 10.1002/ejoc.201601596] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Constanze Wilch
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | - Peter Talbiersky
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | | | - Torsten Schaller
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | - Michael Kirsch
- Institute of Physiological Chemistry University Hospital Essen Hufelandstr. 55 45122 Essen Germany
| | - Frank‐Gerrit Klärner
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
| | - Thomas Schrader
- Faculty of Chemistry University of Duisburg‐Essen Universitätsstr. 7 45117 Essen Germany
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14
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Su X, Zhou X, Zhang N, Zhu M, Zhang H, Jayawickramarajah J. A stable bidentate protein binder achieved via DNA self-assembly driven ligand migration. Chem Commun (Camb) 2016. [PMID: 26225890 DOI: 10.1039/c5cc03213j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Herein we disclose the development of two complementary single stranded DNA-small molecule chimeras (DCs) that by themselves only bind weakly to a protein target (human serum albumin; HSA). However, upon self-assembly, the DC duplex facilitates a ligand migration reaction leading to a covalently fastened high-affinity, bidentate, protein-binder that resides at the terminus of only one of the DC strands. Due to this specific localization, the bidentate projection remains intact—and thus the system continues to strongly bind HSA—even under conditions that denature and degrade the DNA scaffolds.
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Affiliation(s)
- Xiaoye Su
- Department of Chemistry, Tulane University, Louisiana 70118, USA.
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15
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Bartolami E, Bouillon C, Dumy P, Ulrich S. Bioactive clusters promoting cell penetration and nucleic acid complexation for drug and gene delivery applications: from designed to self-assembled and responsive systems. Chem Commun (Camb) 2016; 52:4257-73. [DOI: 10.1039/c5cc09715k] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recent developments in the (self-)assembly of cationic clusters promoting nucleic acids complexation and cell penetration open the door to applications in drug and gene delivery.
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Affiliation(s)
- Eline Bartolami
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Camille Bouillon
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247
- CNRS
- Université Montpellier
- ENSCM
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16
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Nissinkorn Y, Lahav‐Mankovski N, Rabinkov A, Albeck S, Motiei L, Margulies D. Sensing Protein Surfaces with Targeted Fluorescent Receptors. Chemistry 2015; 21:15981-7. [DOI: 10.1002/chem.201502069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Yael Nissinkorn
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Naama Lahav‐Mankovski
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Aharon Rabinkov
- Department of Biological Services, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Shira Albeck
- Israel Structural Proteomics Center, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science, 76100, Rehovot (Israel)
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17
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Dix A, Conroy JL, George Rosenker KM, Sibley DR, Appella DH. PNA-Based Multivalent Scaffolds Activate the Dopamine D2 Receptor. ACS Med Chem Lett 2015; 6:425-9. [PMID: 25893044 PMCID: PMC4394337 DOI: 10.1021/ml500478m] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/12/2015] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid scaffolds represent a promising tool to interrogate the multivalent effects of ligand binding to a membrane receptor. Dopamine D2 receptors (D2R) are a class of G-protein coupled receptors (GPCRs), and the formation of higher-ordered structures of these receptors has been associated with the progression of several neurological diseases. In this Letter, we describe the synthesis of a library of ligand-modified PNAs bearing a known D2R agonist, (±)-PPHT. The D2R activity for each construct was assessed, and the multivalent effects were evaluated.
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Affiliation(s)
- Andrew
V. Dix
- Laboratory of Bioorganic Chemistry, NIDDK, and Molecular Neuropharmacology Section,
NINDS, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jennie L. Conroy
- Laboratory of Bioorganic Chemistry, NIDDK, and Molecular Neuropharmacology Section,
NINDS, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kara M. George Rosenker
- Laboratory of Bioorganic Chemistry, NIDDK, and Molecular Neuropharmacology Section,
NINDS, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David R. Sibley
- Laboratory of Bioorganic Chemistry, NIDDK, and Molecular Neuropharmacology Section,
NINDS, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Daniel H. Appella
- Laboratory of Bioorganic Chemistry, NIDDK, and Molecular Neuropharmacology Section,
NINDS, National Institutes of Health, Bethesda, Maryland 20892, United States
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18
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Uccello-Barretta G, Balzano F, Aiello F, Vanni L, Mori M, Menta S, Calcaterra A, Botta B. Hydrolytic inhibition of α-chymotrypsin by 2,8,14,20-tetrakis(D-leucyl-D-valinamido)resorc[4]arenecarboxylic acid: a spectroscopic NMR and computational combined approach. Org Biomol Chem 2015; 13:916-24. [PMID: 25406985 DOI: 10.1039/c4ob01936a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The stereochemical features of 2,8,14,20-tetrakis(D-leucyl-D-valinamido)resorc[4]arenecarboxylic acid and the N-succinyl-L-alanyl-L-alanyl-L-prolyl-L-phenylalanine-4-nitroanilide polypeptide substrate were investigated by nuclear magnetic resonance spectroscopy. Proton selective relaxation parameters gave the basis for the inhibitory activity of resorcin[4]arene in the hydrolysis of the polypeptide substrate by α-chymotrypsin. Results showed that an interaction between the resorcin[4]arene and α-chymotrypsin does occur, and involves the hydrophobic moiety of the macrocycle. This interaction is further reinforced by polar groups located on the side chains of the resorcin[4]arene, whereas the macrocycle-polypeptide substrate interaction is negligible. Conformational analysis and interaction studies carried out by molecular modeling are in good agreement with the NMR data, thus providing an additional support to the rationalization of the inhibitory potential of resorcin[4]arenes on the α-chymotrypsin activity.
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Affiliation(s)
- Gloria Uccello-Barretta
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 3, 56124 Pisa, Italy.
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19
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Appelhans D, Klajnert-Maculewicz B, Janaszewska A, Lazniewska J, Voit B. Dendritic glycopolymers based on dendritic polyamine scaffolds: view on their synthetic approaches, characteristics and potential for biomedical applications. Chem Soc Rev 2015; 44:3968-96. [DOI: 10.1039/c4cs00339j] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The potential of dendritic glycopolymers based on dendritic polyamine scaffolds for biomedical applications is presented and compared with that of the structurally related anti-adhesive dendritic glycoconjugates.
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Affiliation(s)
- Dietmar Appelhans
- Leibniz-Institut für Polymerforschung Dresden e.V
- 01069 Dresden
- Germany
| | - Barbara Klajnert-Maculewicz
- Department of General Biophysics
- Faculty of Biology and Environmental Protection
- University of Lodz
- 90-236 Lodz
- Poland
| | - Anna Janaszewska
- Department of General Biophysics
- Faculty of Biology and Environmental Protection
- University of Lodz
- 90-236 Lodz
- Poland
| | - Joanna Lazniewska
- Department of General Biophysics
- Faculty of Biology and Environmental Protection
- University of Lodz
- 90-236 Lodz
- Poland
| | - Brigitte Voit
- Leibniz-Institut für Polymerforschung Dresden e.V
- 01069 Dresden
- Germany
- Organic Chemistry of Polymers
- Technische Universität Dresden
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20
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Kubota R, Hamachi I. Protein recognition using synthetic small-molecular binders toward optical protein sensing in vitro and in live cells. Chem Soc Rev 2015; 44:4454-71. [DOI: 10.1039/c4cs00381k] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review describes the recognition and sensing techniques of proteins and their building blocks by use of small synthetic binders.
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Affiliation(s)
- Ryou Kubota
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Katsura
- Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry
- Graduate School of Engineering
- Kyoto University
- Katsura
- Japan
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21
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Carta V, Pangerl M, Baur R, Puthenkalam R, Ernst M, Trauner D, Sigel E. A pentasymmetric open channel blocker for Cys-loop receptor channels. PLoS One 2014; 9:e106688. [PMID: 25184303 PMCID: PMC4153658 DOI: 10.1371/journal.pone.0106688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/31/2014] [Indexed: 11/30/2022] Open
Abstract
γ-Aminobutyric acid type A receptors (GABAA receptors) are chloride ion channels composed of five subunits, mediating fast synaptic and tonic inhibition in the mammalian brain. These receptors show near five-fold symmetry that is most pronounced in the second trans-membrane domain M2 lining the Cl- ion channel. To take advantage of this inherent symmetry, we screened a variety of aromatic anions with matched symmetry and found an inhibitor, pentacyanocyclopentdienyl anion (PCCP-) that exhibited all characteristics of an open channel blocker. Inhibition was strongly dependent on the membrane potential. Through mutagenesis and covalent modification, we identified the region α1V256-α1T261 in the rat recombinant GABAA receptor to be important for PCCP- action. Introduction of positive charges into M2 increased the affinity for PCCP- while PCCP- prevented the access of a positively charged molecule into M2. Interestingly, other anion selective cys-loop receptors were also inhibited by PCCP-, among them the Drosophila RDL GABAA receptor carrying an insecticide resistance mutation, suggesting that PCCP- could serve as an insecticide.
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Affiliation(s)
- Valentina Carta
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Michael Pangerl
- Department of Chemistry, Ludwig-Maximilians-Universität München and Center of Integrated Protein Science, Munich, Germany
| | - Roland Baur
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Roshan Puthenkalam
- Department of Biochemistry and Molecular Biology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Margot Ernst
- Department of Biochemistry and Molecular Biology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Dirk Trauner
- Department of Chemistry, Ludwig-Maximilians-Universität München and Center of Integrated Protein Science, Munich, Germany
| | - Erwin Sigel
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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22
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Latza P, Gilles P, Schaller T, Schrader T. Affinity Polymers Tailored for the Protein A Binding Site of Immunoglobulin G Proteins. Chemistry 2014; 20:11479-87. [DOI: 10.1002/chem.201402399] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Indexed: 01/01/2023]
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23
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Cereda M, Pozzoli U, Rot G, Juvan P, Schweitzer A, Clark T, Ule J. RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing. Genome Biol 2014; 15:R20. [PMID: 24485098 PMCID: PMC4054596 DOI: 10.1186/gb-2014-15-1-r20] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 01/31/2014] [Indexed: 12/16/2022] Open
Abstract
RNA-binding proteins (RBPs) regulate splicing according to position-dependent principles, which can be exploited for analysis of regulatory motifs. Here we present RNAmotifs, a method that evaluates the sequence around differentially regulated alternative exons to identify clusters of short and degenerate sequences, referred to as multivalent RNA motifs. We show that diverse RBPs share basic positional principles, but differ in their propensity to enhance or repress exon inclusion. We assess exons differentially spliced between brain and heart, identifying known and new regulatory motifs, and predict the expression pattern of RBPs that bind these motifs. RNAmotifs is available at https://bitbucket.org/rogrro/rna_motifs.
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24
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Rusling JF, Bishop GW, Doan N, Papadimitrakopoulos F. Nanomaterials and biomaterials in electrochemical arrays for protein detection. J Mater Chem B 2014; 2:10.1039/C3TB21323D. [PMID: 24392222 PMCID: PMC3878175 DOI: 10.1039/c3tb21323d] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nanomaterials and biomaterials are important components of new electrochemical arrays designed for sensitive detection of proteins in biological fluids. Such multiplexed protein arrays are predicted to have an important future in personalized medical diagnostics, especially for cancer and heart disease. Sandwich immunoassays for proteins benefit greatly in sensitivity from the use of nanostructured sensor surfaces and multilabeled detection strategies involving nano- or microparticles. In these assays, capture agents such as antibodies or aptamers are attached to sensor surfaces in the array. Target proteins with large binding constants for the affinity agents are captured from liquid samples with high efficiency, either on the sensors or on magnetic bioconjugate particles decorated with many copies of labels and antibodies. After target proteins are captured on the sensor surfaces, the labels are detected by electrochemical techniques. This feature article begins with an overview of the recent history of nanoparticles in electrochemical protein sensors, then moves on to specific examples from our own laboratories. We discuss fabrication of nanostructured sensors and arrays with the aim of multiplexed detection as well as reusability. Following this, we describe systems that integrate particle-based protein sensing with microfluidics for multiplexed protein detection. We end with predictions on the diagnostic future of protein detection.
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Affiliation(s)
- James F Rusling
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA ; Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136, USA ; Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 06032, USA ; School of Chemistry, National University of Ireland at Galway, Ireland
| | - Gregory W Bishop
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA
| | - Nhi Doan
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA
| | - Fotios Papadimitrakopoulos
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269, USA ; Institute of Materials Science, University of Connecticut, Storrs, CT 06269-3136, USA
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25
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Ulrich S, Dumy P. Probing secondary interactions in biomolecular recognition by dynamic combinatorial chemistry. Chem Commun (Camb) 2014; 50:5810-25. [DOI: 10.1039/c4cc00263f] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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26
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Ulrich S, Boturyn D, Marra A, Renaudet O, Dumy P. Oxime Ligation: A Chemoselective Click-Type Reaction for Accessing Multifunctional Biomolecular Constructs. Chemistry 2013; 20:34-41. [DOI: 10.1002/chem.201302426] [Citation(s) in RCA: 176] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Ma X, Wang X, Zhou M, Fei H. A mitochondria-targeting gold-peptide nanoassembly for enhanced cancer-cell killing. Adv Healthc Mater 2013; 2:1638-43. [PMID: 23657942 DOI: 10.1002/adhm.201300037] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Indexed: 01/18/2023]
Abstract
Design and construction of multifunctional nanoparticles for effective delivery and therapeutic application remains a challenging task. It is desirable that nanoparticles can overcome multiple biological barriers and reach specific cellular locations to achieve maximum therapeutic effects. This aim often requires the fine tuning of nanoparticles' chemical and physical properties, as well as better understanding of their interaction with live cells. A peptide-modified gold-nanoparticle platform is designed, which consists of a 20-nm gold core stabilized with a layer of biotinylated CALNN-based peptides and a further layer of tetrameric streptavidins for functionalization with biotinylated molecules. The nanoassembly undergoes an efficient dynamin-dependent and caveolae-mediated endocytosis pathway, and displays highly specific localization to mitochondria, organelles of great therapeutic importance. When functionalized with a cytotoxic peptide (KLA: (KLAKLAK)2 ), the KLA-anchored nanoassembly exhibits dramatically enhanced anticancer activity, thousands of times stronger than that of the free KLA peptide, likely because of its improved cell entry efficiency, mitochondria-specific delivery, and the polyvalent effect of the nanoassembly. The study opens up the possibility of developing mitochondria-targeted nanomedicines.
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Affiliation(s)
- Xiaochuan Ma
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, 398 Ruoshui Road, Suzhou Industrial Park, Suzhou, Jiangsu, 215123, P. R. China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, P. R. China
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28
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Barnard A, Posocco P, Fermeglia M, Tschiche A, Calderon M, Pricl S, Smith DK. Double-degradable responsive self-assembled multivalent arrays--temporary nanoscale recognition between dendrons and DNA. Org Biomol Chem 2013; 12:446-55. [PMID: 24263553 DOI: 10.1039/c3ob42202j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This article reports self-assembling dendrons which bind DNA in a multivalent manner. The molecular design directly impacts on self-assembly which subsequently controls the way these multivalent nanostructures bind DNA--this can be simulated by multiscale modelling. Incorporation of an S-S linkage between the multivalent hydrophilic dendron and the hydrophobic units responsible for self-assembly allows these structures to undergo triggered reductive cleavage, with dithiothreitol (DTT) inducing controlled breakdown, enabling the release of bound DNA. As such, the high-affinity self-assembled multivalent binding is temporary. Furthermore, because the multivalent dendrons are constructed from esters, a second slow degradation step causes further breakdown of these structures. This two-step double-degradation mechanism converts a large self-assembling unit with high affinity for DNA into small units with no measurable binding affinity--demonstrating the advantage of self-assembled multivalency (SAMul) in achieving highly responsive nanoscale binding of biological targets.
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Affiliation(s)
- Anna Barnard
- Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
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29
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Xiao X, Sun J, Jiang J. X-ray Structure of a Porphyrin-Tetramethylcucurbit[6]uril Supramolecular Polymer. Chemistry 2013; 19:16891-6. [DOI: 10.1002/chem.201303530] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Indexed: 11/11/2022]
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30
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Mignani S, El Kazzouli S, Bousmina MM, Majoral JP. Dendrimer Space Exploration: An Assessment of Dendrimers/Dendritic Scaffolding as Inhibitors of Protein–Protein Interactions, a Potential New Area of Pharmaceutical Development. Chem Rev 2013; 114:1327-42. [DOI: 10.1021/cr400362r] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Serge Mignani
- Laboratoire de Chimie et de
Biochimie Pharmacologiques
et Toxicologiques, CNRS UMR 8601, Université Paris Descartes, Sorbonne Paris Cité, 45 rue des Saints Pères, 75006 Paris, France
| | - Saïd El Kazzouli
- Euro-Mediterranean University of Fez, Fès-Shore, Route de Sidi harazem, Fès, Morocco
| | - Mosto M. Bousmina
- Euro-Mediterranean University of Fez, Fès-Shore, Route de Sidi harazem, Fès, Morocco
- Hassan II Academy of Science and Technology, Avenue Mohammed
VI, 10222 Rabat, Morocco
| | - Jean-Pierre Majoral
- Laboratoire
de Chimie de Coordination, Centre National de la Recherche Scientifique, 205 route de Narbonne, 31077 Toulouse Cedex 4, France
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31
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Trush VV, Cherenok SO, Tanchuk VY, Kukhar VP, Kalchenko VI, Vovk AI. Calix[4]arene methylenebisphosphonic acids as inhibitors of protein tyrosine phosphatase 1B. Bioorg Med Chem Lett 2013; 23:5619-23. [DOI: 10.1016/j.bmcl.2013.08.040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 11/24/2022]
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32
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Battle C, Chu X, Jayawickramarajah J. Oligonucleotide-Based Systems for Input-Controlled and Non-Covalently Regulated Protein-Binding. Supramol Chem 2013; 25. [PMID: 24187478 DOI: 10.1080/10610278.2013.810337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Supramolecular chemists continuously take inspiration from complex biological systems to develop functional molecules involved in molecular recognition and self-assembly. In this regard, "smart" synthetic molecules that emulate allosteric proteins are both exciting and challenging, since many allosteric proteins can be considered as molecular switches that bind to other protein targets in a non-covalent fashion, and importantly, are capable of having their output activity controlled by prior binding to input molecules. This review discusses the foundations and passage toward the development of non-covalently operated oligonucleotide-based systems with protein-binding capacity that can be precisely regulated in an input-controlled manner.
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Affiliation(s)
- Cooper Battle
- Department of Chemistry, Tulane University, New Orleans, LA, USA
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33
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Gaeta C, Talotta C, Neri P. The calixarene p-bromodienone route: from a chemical curiosity to an useful synthetic tool. J INCL PHENOM MACRO 2013. [DOI: 10.1007/s10847-013-0343-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Molecular tweezers modulate 14-3-3 protein–protein interactions. Nat Chem 2013; 5:234-9. [DOI: 10.1038/nchem.1570] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 01/10/2013] [Indexed: 12/12/2022]
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35
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Luczkowiak J, Muñoz A, Sánchez-Navarro M, Ribeiro-Viana R, Ginieis A, Illescas BM, Martín N, Delgado R, Rojo J. Glycofullerenes Inhibit Viral Infection. Biomacromolecules 2013; 14:431-7. [DOI: 10.1021/bm3016658] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Joanna Luczkowiak
- Laboratorio de Microbiología
Molecular, Instituto de Investigación Hospital, 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Antonio Muñoz
- Departamento de
Química Orgánica, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain
| | - Macarena Sánchez-Navarro
- Glycosystems
Laboratory, Instituto de Investigaciones Químicas (IIQ), CSIC − Universidad de Sevilla, Av. Américo
Vespucio 49, Seville 41092 Spain
| | - Renato Ribeiro-Viana
- Glycosystems
Laboratory, Instituto de Investigaciones Químicas (IIQ), CSIC − Universidad de Sevilla, Av. Américo
Vespucio 49, Seville 41092 Spain
| | - Anthony Ginieis
- Glycosystems
Laboratory, Instituto de Investigaciones Químicas (IIQ), CSIC − Universidad de Sevilla, Av. Américo
Vespucio 49, Seville 41092 Spain
| | - Beatriz M. Illescas
- Departamento de
Química Orgánica, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain
| | - Nazario Martín
- Departamento de
Química Orgánica, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain
- IMDEA-Nanoscience, Campus Cantoblanco, 28049 Madrid, Spain
| | - Rafael Delgado
- Laboratorio de Microbiología
Molecular, Instituto de Investigación Hospital, 12 de Octubre (imas12), 28041 Madrid, Spain
| | - Javier Rojo
- Glycosystems
Laboratory, Instituto de Investigaciones Químicas (IIQ), CSIC − Universidad de Sevilla, Av. Américo
Vespucio 49, Seville 41092 Spain
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36
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Ulrich S, Dumy P, Boturyn D, Renaudet O. Engineering of biomolecules for sensing and imaging applications. J Drug Deliv Sci Technol 2013. [DOI: 10.1016/s1773-2247(13)50001-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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37
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Jiang QQ, Bartsch L, Sicking W, Wich PR, Heider D, Hoffmann D, Schmuck C. A new approach to inhibit human β-tryptase by protein surface binding of four-armed peptide ligands with two different sets of arms. Org Biomol Chem 2013; 11:1631-9. [DOI: 10.1039/c3ob27302d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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38
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39
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Welsh DJ, Posocco P, Pricl S, Smith DK. Self-assembled multivalent RGD-peptide arrays – morphological control and integrin binding. Org Biomol Chem 2013; 11:3177-86. [DOI: 10.1039/c3ob00034f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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40
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Cagnoni AJ, Varela O, Uhrig ML, Kovensky J. Efficient Synthesis of Thiolactoside Glycoclusters by Ruthenium-Catalyzed Cycloaddition Reaction of Disubstituted Alkynes on Carbohydrate Scaffolds. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201412] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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41
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Reinwarth M, Glotzbach B, Tomaszowski M, Fabritz S, Avrutina O, Kolmar H. Oxidative folding of peptides with cystine-knot architectures: kinetic studies and optimization of folding conditions. Chembiochem 2012; 14:137-46. [PMID: 23229141 DOI: 10.1002/cbic.201200604] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Indexed: 11/07/2022]
Abstract
Bioactive peptides often contain several disulfide bonds that provide the main contribution to conformational rigidity and structural, thermal, or biological stability. Among them, cystine-knot peptides-commonly named "knottins"-make up a subclass with several thousand natural members. Hence, they are considered promising frameworks for peptide-based pharmaceuticals. Although cystine-knot peptides are available through chemical and recombinant synthetic routes, oxidative folding to afford the bioactive isomers still remains a crucial step. We therefore investigated the oxidative folding of ten protease-inhibiting peptides from two knottin families, as well as that of an HIV entry inhibitor and of aprotinin, under two conventional sets of folding conditions and by a newly developed procedure. Kinetic studies identified folding conditions that resulted in correctly folded miniproteins with high rates of conversion even for highly hydrophobic and aggregation-prone peptides in concentrated solutions.
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Affiliation(s)
- Michael Reinwarth
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Petersenstr. 22, 64287 Darmstadt, Germany
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42
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Mani V, Wasalathanthri DP, Joshi AA, Kumar CV, Rusling JF. Highly efficient binding of paramagnetic beads bioconjugated with 100,000 or more antibodies to protein-coated surfaces. Anal Chem 2012; 84:10485-91. [PMID: 23121341 PMCID: PMC3514570 DOI: 10.1021/ac3028257] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here the first kinetic characterization of 1 μm diameter superparamagnetic particles (MP) decorated with over 100,000 antibodies binding to protein antigens attached to flat surfaces. Surface plasmon resonance (SPR) was used to show that these antibody-derivatized MPs (MP-Ab(2)) exhibit irreversible binding with 100-fold increased association rates compared to free antibodies. The estimated upper limit for the dissociation constant of MP-Ab(2) from the SPR sensor surface is 5 fM, compared to 3-8 nM for the free antibodies. These results are explained by up to 2000 interactions of MP-Ab(2) with protein-decorated surfaces. Findings are consistent with highly efficient capture of protein antigens in solution by the MP-Ab(2) and explain in part the utility of these beads for ultrasensitive protein detection into the fM and aM range. Aggregation of these particles on the SPR chip, probably due to residual magnetic microdomains in the particles, also contributes to ultrasensitive detection and may also help drive the irreversible binding.
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Affiliation(s)
- Vigneshwaran Mani
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, CT, 06269, USA
| | - Dhanuka P. Wasalathanthri
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, CT, 06269, USA
| | - Amit A. Joshi
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, CT, 06269, USA
| | - Challa V. Kumar
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, CT, 06269, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - James F. Rusling
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, CT, 06269, USA
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, 06032, USA
- School of Chemistry, National University of Ireland at Galway, Ireland
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43
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Ou HD, Kwiatkowski W, Deerinck TJ, Noske A, Blain KY, Land HS, Soria C, Powers CJ, May AP, Shu X, Tsien RY, Fitzpatrick JA, Long JA, Ellisman MH, Choe S, O’Shea CC. A structural basis for the assembly and functions of a viral polymer that inactivates multiple tumor suppressors. Cell 2012; 151:304-19. [PMID: 23063122 PMCID: PMC3681303 DOI: 10.1016/j.cell.2012.08.035] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 05/10/2012] [Accepted: 08/16/2012] [Indexed: 12/21/2022]
Abstract
Evolution of minimal DNA tumor virus' genomes has selected for small viral oncoproteins that hijack critical cellular protein interaction networks. The structural basis for the multiple and dominant functions of adenovirus oncoproteins has remained elusive. E4-ORF3 forms a nuclear polymer and simultaneously inactivates p53, PML, TRIM24, and MRE11/RAD50/NBS1 (MRN) tumor suppressors. We identify oligomerization mutants and solve the crystal structure of E4-ORF3. E4-ORF3 forms a dimer with a central β core, and its structure is unrelated to known polymers or oncogenes. E4-ORF3 dimer units coassemble through reciprocal and nonreciprocal exchanges of their C-terminal tails. This results in linear and branched oligomer chains that further assemble in variable arrangements to form a polymer network that partitions the nuclear volume. E4-ORF3 assembly creates avidity-driven interactions with PML and an emergent MRN binding interface. This reveals an elegant structural solution whereby a small protein forms a multivalent matrix that traps disparate tumor suppressors.
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Affiliation(s)
- Horng D. Ou
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Witek Kwiatkowski
- Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Thomas J. Deerinck
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Andrew Noske
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Katie Y. Blain
- Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hannah S. Land
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Conrado Soria
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Colin J. Powers
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Andrew P. May
- Fluidigm Corporation, 7000 Shoreline Court, Suite 100, South San Francisco, CA 94080, USA
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry and Cardiovascular Research Institute, University of California at San Francisco, 555 Mission Bay Blvd South, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Roger Y. Tsien
- Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Pharmacology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Departments of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - James A.J. Fitzpatrick
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jeff A. Long
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Mark H. Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
- Department of Neurosciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Senyon Choe
- Structural Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Clodagh C. O’Shea
- Molecular and Cell Biology Laboratory Salk Institute for Biological Studies 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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44
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Ariga K, Ito H, Hill JP, Tsukube H. Molecular recognition: from solution science to nano/materials technology. Chem Soc Rev 2012; 41:5800-35. [PMID: 22773130 DOI: 10.1039/c2cs35162e] [Citation(s) in RCA: 332] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In the 25 years since its Nobel Prize in chemistry, supramolecular chemistry based on molecular recognition has been paid much attention in scientific and technological fields. Nanotechnology and the related areas seek breakthrough methods of nanofabrication based on rational organization through assembly of constituent molecules. Advanced biochemistry, medical applications, and environmental and energy technologies also depend on the importance of specific interactions between molecules. In those current fields, molecular recognition is now being re-evaluated. In this review, we re-examine current trends in molecular recognition from the viewpoint of the surrounding media, that is (i) the solution phase for development of basic science and molecular design advances; (ii) at nano/materials interfaces for emerging technologies and applications. The first section of this review includes molecular recognition frontiers, receptor design based on combinatorial approaches, organic capsule receptors, metallo-capsule receptors, helical receptors, dendrimer receptors, and the future design of receptor architectures. The following section summarizes topics related to molecular recognition at interfaces including fundamentals of molecular recognition, sensing and detection, structure formation, molecular machines, molecular recognition involving polymers and related materials, and molecular recognition processes in nanostructured materials.
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Affiliation(s)
- Katsuhiko Ariga
- Japan Science and Technology Agency, Core Research for Evolutional Science and Technology, Go-bancho, Chiyoda-ku, Tokyo 102-0076, Japan
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45
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Hollenbeck JJ, Danner DJ, Landgren RM, Rainbolt TK, Roberts DS. Designed ankyrin repeat proteins as scaffolds for multivalent recognition. Biomacromolecules 2012; 13:1996-2002. [PMID: 22681396 DOI: 10.1021/bm300455f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ankyrin repeat (AR) proteins are composed of tandem repeats of a basic structural motif of ca. 33 amino acid residues that form a β-turn followed by two antiparallel α-helices. Multiple repeats stack together in a modular fashion to form a scaffold that is ideally suited for the presentation of multiple functional groups and/or recognition elements. Here we describe a biosynthetic strategy that takes advantage of the modular nature of these proteins to generate multivalent ligands that are both chemically homogeneous and structurally well-defined. Glycosylated AR proteins cluster the tetrameric lectin concanavalin A (Con A) at a rate that is comparable to the rate of Con A aggregation mediated by globular protein conjugates and variable density linear polymers. Thus, AR proteins define a new class of multivalent ligand scaffolds that have significant potential application in the study and control of a variety of multivalent interactions.
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Affiliation(s)
- Jessica J Hollenbeck
- Department of Chemistry, Trinity University, San Antonio, Texas 78212, United States.
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46
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Barnard A, Smith DK. Selbstorganisierte Multivalenz: dynamische Ligandenanordnungen für hochaffine Bindungen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201200076] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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47
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Barnard A, Smith DK. Self-assembled multivalency: dynamic ligand arrays for high-affinity binding. Angew Chem Int Ed Engl 2012; 51:6572-81. [PMID: 22689381 DOI: 10.1002/anie.201200076] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Indexed: 12/12/2022]
Abstract
Multivalency is a powerful strategy for achieving high-affinity molecular recognition in biological systems. Recently, attention has begun to focus on using self-assembly rather than covalent scaffold synthesis to organize multiple ligands. This approach has a number of advantages, including ease of synthesis/assembly, tunability of nanostructure morphology and ligands, potential to incorporate multiple active units, and the responsive nature of self-assembly. We suggest that self-assembled multivalency is a strategy of fundamental importance in the design of synthetic nanosystems to intervene in biological pathways and has potential applications in nanomedicine.
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Affiliation(s)
- Anna Barnard
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
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48
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Biros S, Hof F. Supramolecular Approaches to Medicinal Chemistry. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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49
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Lindhorst TK, Kubik S. Supramolecular Approaches to the Study of Glycobiology. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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50
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Conley MP, Valero J, de Mendoza J. Guanidinium-Based Receptors for Oxoanions. Supramol Chem 2012. [DOI: 10.1002/9780470661345.smc061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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