1
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Shchegravina ES, Tretiakova DS, Sitdikova AR, Usova SD, Boldyrev IA, Alekseeva AS, Svirshchevskaya EV, Vodovozova EL, Fedorov AY. Design and preparation of pH-sensitive cytotoxic liposomal formulations containing antitumor colchicine analogues for target release. J Liposome Res 2024; 34:399-410. [PMID: 37867342 DOI: 10.1080/08982104.2023.2274428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/18/2023] [Indexed: 10/24/2023]
Abstract
Herein, we describe the synthesis of pH-sensitive lipophilic colchicine prodrugs for liposomal bilayer inclusion, as well as preparation and characterization of presumably stealth PEGylated liposomes with above-mentioned prodrugs. These formulations liberate strongly cytotoxic colchicinoid derivatives selectively under slightly acidic tumor-associated conditions, ensuring tumor-targeted delivery of the compounds. The design of the prodrugs is addressed to pH-triggered release of active compounds in the slight acidic media, that corresponds to tumor microenvironment, while keeping sufficient stability of the whole formulation at physiological pH. Correlations between the structure of the conjugates, their hydrolytic stability, colloidal stability, ability of the prodrug retention in the lipid bilayer are described. Several formulations were found promising for further development and in vivo investigations.
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Affiliation(s)
- Ekaterina S Shchegravina
- Department of Organic Chemistry, UNN Lobachevsky University, Nizhny Novgorod, Russian Federation
| | - Daria S Tretiakova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | - Alsu R Sitdikova
- Department of Organic Chemistry, UNN Lobachevsky University, Nizhny Novgorod, Russian Federation
| | - Sofia D Usova
- N.D. Zelinsky Insitute of Organic Chemistry RAS, Moscow, Russian Federation
| | - Ivan A Boldyrev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | - Anna S Alekseeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | | | - Elena L Vodovozova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russian Federation
| | - Alexey Yu Fedorov
- Department of Organic Chemistry, UNN Lobachevsky University, Nizhny Novgorod, Russian Federation
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2
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Pal A, Das KM, Sau S, Thakur A. Co(II) Acetate-Assisted Direct Synthesis of Acyl Hydrazones from Acyl Hydrazides under Mild Conditions. Chem Asian J 2023; 18:e202300755. [PMID: 37814533 DOI: 10.1002/asia.202300755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/04/2023] [Accepted: 10/09/2023] [Indexed: 10/11/2023]
Abstract
Acyl hydrazones are a class of synthetically important organic compounds that are recurrently in high demand for synthesis and use in various fields of chemistry and biology. We report the first Co(II) catalyzed one-component one-pot sustainable synthesis of acyl hydrazones only from acyl hydrazides under mild reaction conditions. Traditional and contemporary methodologies use two components (usually acyl hydrazides and aldehydes/ketones/alcohols/styrene) as the coupling partners. Our protocol, on the other hand, involves the in situ generation of aldehyde intermediate (detected by gas chromatography) from the acyl hydrazide, which then undergoes condensation with another molecule of the same acyl hydrazide in the same pot to yield acyl hydrazones in presence of mild base K2 CO3 and low-cost Co(OAc)2 ⋅ 4H2 O as catalyst. This method shows good functional group tolerance with good to excellent yield of products. Furthermore, some of the resulting acyl hydrazones have been used as synthetic precursors and explored in various post-synthetic modifications to afford N-heterocyclic compounds. Furthermore, photoswitchable properties of few synthesized acyl hydrazones are also explored using their E/Z isomerization around the C=N bond, as realized by high-pressure liquid chromatography (HPLC) and UV-vis spectroscopic studies.
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Affiliation(s)
- Adwitiya Pal
- Department of Chemistry, Jadavpur University, Kolkata, 700032, West Bengal, India
| | - Krishna Mohan Das
- Department of Chemistry, Jadavpur University, Kolkata, 700032, West Bengal, India
| | - Subham Sau
- Department of Chemistry, Jadavpur University, Kolkata, 700032, West Bengal, India
| | - Arunabha Thakur
- Department of Chemistry, Jadavpur University, Kolkata, 700032, West Bengal, India
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3
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Hayamizu K, Koike K, Dodo K, Asanuma M, Egami H, Sodeoka M. Simple purification of small-molecule-labelled peptides via palladium enolate formation from β-ketoamide tags. Chem Sci 2023; 14:8249-8254. [PMID: 37564408 PMCID: PMC10411859 DOI: 10.1039/d2sc03112d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/04/2023] [Indexed: 08/12/2023] Open
Abstract
Palladium enolates derived from β-ketocarbonyl compounds serve as key intermediates in various catalytic asymmetric reactions. We found that the palladium enolate formed from β-ketoamide is stable in air and moisture and we applied this property to develop a peptide purification system using β-ketoamide as a small affinity tag in aqueous media. A solid-supported palladium complex successfully captured β-ketoamide-tagged molecules as palladium enolates and released them in high yield upon acid treatment. Optimum conditions for the catch and release of tagged peptides from a mixture of untagged peptides were established. To demonstrate the value of this methodology in identifying the binding site of a ligand to its target protein, we purified and identified a peptide containing the ligand-binding site from the tryptic digest of cathepsin B labelled with a covalent cathepsin B inhibitor containing a β-ketoamide tag.
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Affiliation(s)
- Kenji Hayamizu
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Kota Koike
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa Wako Saitama 351-0198 Japan
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa Wako Saitama 351-0198 Japan
| | - Miwako Asanuma
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa Wako Saitama 351-0198 Japan
| | - Hiromichi Egami
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research 2-1 Hirosawa Wako Saitama 351-0198 Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa Wako Saitama 351-0198 Japan
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4
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McCoy MA, Spicer D, Wells N, Hoogewijs K, Fiedler M, Baud MGJ. Biophysical Survey of Small-Molecule β-Catenin Inhibitors: A Cautionary Tale. J Med Chem 2022; 65:7246-7261. [PMID: 35581674 PMCID: PMC9150122 DOI: 10.1021/acs.jmedchem.2c00228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The canonical Wingless-related
integration site signaling pathway
plays a critical role in human physiology, and its dysregulation can
lead to an array of diseases. β-Catenin is a multifunctional
protein within this pathway and an attractive yet challenging therapeutic
target, most notably in oncology. This has stimulated the search for
potent small-molecule inhibitors binding directly to the β-catenin
surface to inhibit its protein–protein interactions and downstream
signaling. Here, we provide an account of the claimed (and some putative)
small-molecule ligands of β-catenin from the literature. Through
in silico analysis, we show that most of these molecules contain promiscuous
chemical substructures notorious for interfering with screening assays.
Finally, and in line with this analysis, we demonstrate using orthogonal
biophysical techniques that none of the examined small molecules bind
at the surface of β-catenin. While shedding doubts on their
reported mode of action, this study also reaffirms β-catenin
as a prominent target in drug discovery.
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Affiliation(s)
- Michael A McCoy
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Dominique Spicer
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Neil Wells
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
| | - Kurt Hoogewijs
- National University of Ireland, University Road, Galway H91 TK33, Ireland
| | - Marc Fiedler
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Matthias G J Baud
- School of Chemistry, University of Southampton, Southampton SO17 1BJ, U.K
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5
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Hipper E, Blech M, Hinderberger D, Garidel P, Kaiser W. Photo-Oxidation of Therapeutic Protein Formulations: From Radical Formation to Analytical Techniques. Pharmaceutics 2021; 14:72. [PMID: 35056968 PMCID: PMC8779573 DOI: 10.3390/pharmaceutics14010072] [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: 10/07/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/25/2022] Open
Abstract
UV and ambient light-induced modifications and related degradation of therapeutic proteins are observed during manufacturing and storage. Therefore, to ensure product quality, protein formulations need to be analyzed with respect to photo-degradation processes and eventually protected from light exposure. This task usually demands the application and combination of various analytical methods. This review addresses analytical aspects of investigating photo-oxidation products and related mediators such as reactive oxygen species generated via UV and ambient light with well-established and novel techniques.
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Affiliation(s)
- Elena Hipper
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (E.H.); (D.H.)
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
| | - Dariush Hinderberger
- Institute of Chemistry, Martin-Luther-Universität Halle-Wittenberg, von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany; (E.H.); (D.H.)
| | - Patrick Garidel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
| | - Wolfgang Kaiser
- Boehringer Ingelheim Pharma GmbH & Co. KG, Innovation Unit, PDB, Birkendorfer Strasse 65, 88397 Biberach an der Riss, Germany;
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6
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Liu T, den Berk L, Wondergem JAJ, Tong C, Kwakernaak MC, Braak BT, Heinrich D, Water B, Kieltyka RE. Squaramide-Based Supramolecular Materials Drive HepG2 Spheroid Differentiation. Adv Healthc Mater 2021; 10:e2001903. [PMID: 33929772 DOI: 10.1002/adhm.202001903] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/19/2021] [Indexed: 12/12/2022]
Abstract
A major challenge in the use of HepG2 cell culture models for drug toxicity screening is their lack of maturity in 2D culture. 3D culture in Matrigel promotes the formation of spheroids that express liver-relevant markers, yet they still lack various primary hepatocyte functions. Therefore, alternative matrices where chemical composition and materials properties are controlled to steer maturation of HepG2 spheroids remain desired. Herein, a modular approach is taken based on a fully synthetic and minimalistic supramolecular matrix based on squaramide synthons outfitted with a cell-adhesive peptide, RGD for 3D HepG2 spheroid culture. Co-assemblies of RGD-functionalized squaramide-based and native monomers resulted in soft and self-recovering supramolecular hydrogels with a tunable RGD concentration. HepG2 spheroids are self-assembled and grown (≈150 µm) within the supramolecular hydrogels with high cell viability and differentiation over 21 days of culture. Importantly, significantly higher mRNA and protein expression levels of phase I and II metabolic enzymes, drug transporters, and liver markers are found for the squaramide hydrogels in comparison to Matrigel. Overall, the fully synthetic squaramide hydrogels are proven to be synthetically accessible and effective for HepG2 differentiation showcasing the potential of this supramolecular matrix to rival and replace naturally-derived materials classically used in high-throughput toxicity screening.
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Affiliation(s)
- Tingxian Liu
- Department of Supramolecular and Biomaterials Chemistry Leiden Institute of Chemistry Leiden University P.O. Box 9502 Leiden 2300 RA Netherlands
| | - Linda den Berk
- Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research Leiden University P.O. Box 9502 Leiden 2300 RA Netherlands
| | - Joeri A. J. Wondergem
- Department of Physics Huygens‐Kamerlingh Onnes Laboratory Leiden University Leiden 2300 RA Netherlands
- Fraunhofer Institute for Silicate Research ISC Neunerplatz 2 Würzburg 97082 Germany
| | - Ciqing Tong
- Department of Supramolecular and Biomaterials Chemistry Leiden Institute of Chemistry Leiden University P.O. Box 9502 Leiden 2300 RA Netherlands
| | - Markus C. Kwakernaak
- Department of Supramolecular and Biomaterials Chemistry Leiden Institute of Chemistry Leiden University P.O. Box 9502 Leiden 2300 RA Netherlands
| | - Bas ter Braak
- Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research Leiden University P.O. Box 9502 Leiden 2300 RA Netherlands
| | - Doris Heinrich
- Department of Physics Huygens‐Kamerlingh Onnes Laboratory Leiden University Leiden 2300 RA Netherlands
- Fraunhofer Institute for Silicate Research ISC Neunerplatz 2 Würzburg 97082 Germany
| | - Bob Water
- Division of Drug Discovery and Safety Leiden Academic Centre for Drug Research Leiden University P.O. Box 9502 Leiden 2300 RA Netherlands
| | - Roxanne E. Kieltyka
- Department of Supramolecular and Biomaterials Chemistry Leiden Institute of Chemistry Leiden University P.O. Box 9502 Leiden 2300 RA Netherlands
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7
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Dutson C, Allen E, Thompson MJ, Hedley JH, Murton HE, Williams DM. Synthesis of Polyanionic C5-Modified 2'-Deoxyuridine and 2'-Deoxycytidine-5'-Triphosphates and Their Properties as Substrates for DNA Polymerases. Molecules 2021; 26:molecules26082250. [PMID: 33924626 PMCID: PMC8069024 DOI: 10.3390/molecules26082250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
Modified 2′-deoxyribonucleotide triphosphates (dNTPs) have widespread applications in both existing and emerging biomolecular technologies. For such applications it is an essential requirement that the modified dNTPs be substrates for DNA polymerases. To date very few examples of C5-modified dNTPs bearing negatively charged functionality have been described, despite the fact that such nucleotides might potentially be valuable in diagnostic applications using Si-nanowire-based detection systems. Herein we have synthesised C5-modified dUTP and dCTP nucleotides each of which are labelled with an dianionic reporter group. The reporter group is tethered to the nucleobase via a polyethylene glycol (PEG)-based linkers of varying length. The substrate properties of these modified dNTPs with a variety of DNA polymerases have been investigated to study the effects of varying the length and mode of attachment of the PEG linker to the nucleobase. In general, nucleotides containing the PEG linker tethered to the nucleobase via an amide rather than an ether linkage proved to be the best substrates, whilst nucleotides containing PEG linkers from PEG6 to PEG24 could all be incorporated by one or more DNA polymerase. The polymerases most able to incorporate these modified nucleotides included Klentaq, Vent(exo-) and therminator, with incorporation by Klenow(exo-) generally being very poor.
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Affiliation(s)
- Claire Dutson
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield S3 7HF, UK; (C.D.); (E.A.); (M.J.T.)
| | - Esther Allen
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield S3 7HF, UK; (C.D.); (E.A.); (M.J.T.)
| | - Mark J. Thompson
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield S3 7HF, UK; (C.D.); (E.A.); (M.J.T.)
| | - Joseph H. Hedley
- QuantuMDx Group, Lugano Building, 57 Melbourne Street, Newcastle upon Tyne NE1 2JQ, UK; (J.H.H.); (H.E.M.)
| | - Heather E. Murton
- QuantuMDx Group, Lugano Building, 57 Melbourne Street, Newcastle upon Tyne NE1 2JQ, UK; (J.H.H.); (H.E.M.)
| | - David M. Williams
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield S3 7HF, UK; (C.D.); (E.A.); (M.J.T.)
- Correspondence: ; Tel.: +44-114-222-9502
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8
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Gaffney A, Nangarlia A, Ang CG, Gossert S, Rashad Ahmed AA, Hossain MA, Abrams CF, Smith AB, Chaiken I. HIV-1 Env-Dependent Cell Killing by Bifunctional Small-Molecule/Peptide Conjugates. ACS Chem Biol 2021; 16:440-442. [PMID: 33535751 DOI: 10.1021/acschembio.1c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Althea Gaffney
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Aakansha Nangarlia
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Charles G. Ang
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Steven Gossert
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Adel Ahmed Rashad Ahmed
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Md Alamgir Hossain
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Cameron F. Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Irwin Chaiken
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
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9
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Gaffney A, Nangarlia A, Ang CG, Gossert S, Rashad Ahmed AA, Hossain MA, Abrams CF, Smith AB, Chaiken I. HIV-1 Env-Dependent Cell Killing by Bifunctional Small-Molecule/Peptide Conjugates. ACS Chem Biol 2021; 16:193-204. [PMID: 33410670 DOI: 10.1021/acschembio.0c00888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A strategy has been established for the synthesis of a family of bifunctional HIV-1 inhibitor covalent conjugates with the potential to bind simultaneously to both the gp120 and gp41 subunits of the HIV-1 envelope glycoprotein trimeric complex (Env). One component of the conjugates is derived from BNM-III-170, a small-molecule CD4 mimic that binds to gp120. The second component, comprised of the peptide DKWASLWNW ("Trp3"), was derived from the N-terminus of the HIV-1 gp41 Membrane Proximal External Region (MPER) and found previously to bind to the gp41 subunit of Env. The resulting bifunctional conjugates were shown to inhibit virus cell infection with low micromolar potency and to induce lysis of the HIV-1 virion. Crucially, virolysis was found to be dependent on the covalent linkage of the BNM-III-170 and Trp3 domains, as coadministration of a mixture of the un-cross-linked components proved to be nonlytic. However, a significant magnitude of lytic activity was observed in Env-negative and other control pseudoviruses, suggesting parallel mechanisms of action of the conjugates involving Env interaction and direct membrane disruption. Computational modeling suggested strong membrane-binding activity of BNM-III-170, which may underly the nonspecific virolytic effects of the conjugates. To investigate the scope of the membrane effect, cell-based cytotoxicity and membrane permeability assays were performed employing flow cytometry. Here, we observed a dose-dependent and specific cytotoxic effect on HIV-1 Env-expressing cells by the small-molecule bifunctional inhibitor. Most importantly, Env-negative cells were not susceptible to the cytotoxic effect upon exposure to this construct at concentrations where cell-killing effects were observed for Env-positive cells. Computational structural modeling supports a mechanism in which the bifunctional inhibitors bind to the gp120 and gp41 subunits in tandem in open-state Env trimers and induce relative motion of the gp120 subunits consistent with models of Env inactivation. This observation supports the idea that the cell-killing effect of the small-molecule bifunctional inhibitor is due to specific Env conformational triggering. This work lays important groundwork to advance a small-molecule bifunctional inhibitor approach for eliminating Env-expressing infected cells and the eradication of HIV-1.
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Affiliation(s)
- Althea Gaffney
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Aakansha Nangarlia
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Charles G. Ang
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Steven Gossert
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Adel Ahmed Rashad Ahmed
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Md Alamgir Hossain
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
| | - Cameron F. Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Amos B. Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Irwin Chaiken
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19102, United States
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10
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Anichini C, Aliprandi A, Gali SM, Liscio F, Morandi V, Minoia A, Beljonne D, Ciesielski A, Samorì P. Ultrafast and Highly Sensitive Chemically Functionalized Graphene Oxide-Based Humidity Sensors: Harnessing Device Performances via the Supramolecular Approach. ACS APPLIED MATERIALS & INTERFACES 2020; 12:44017-44025. [PMID: 32880164 DOI: 10.1021/acsami.0c11236] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Humidity sensors have been gaining increasing attention because of their relevance for well-being. To meet the ever-growing demand for new cost-efficient materials with superior performances, graphene oxide (GO)-based relative humidity sensors have emerged recently as low-cost and highly sensitive devices. However, current GO-based sensors suffer from important drawbacks including slow response and recovery, as well as poor stability. Interestingly, reduced GO (rGO) exhibits higher stability, yet accompanied by a lower sensitivity to humidity due to its hydrophobic nature. With the aim of improving the sensing performances of rGO, here we report on a novel generation of humidity sensors based on a simple chemical modification of rGO with hydrophilic moieties, i.e., triethylene glycol chains. Such a hybrid material exhibits an outstandingly improved sensing performance compared to pristine rGO such as high sensitivity (31% increase in electrical resistance when humidity is shifted from 2 to 97%), an ultrafast response (25 ms) and recovery in the subsecond timescale, low hysteresis (1.1%), excellent repeatability and stability, as well as high selectivity toward moisture. Such highest-key-performance indicators demonstrate the full potential of two-dimensional (2D) materials when decorated with suitably designed supramolecular receptors to develop the next generation of chemical sensors of any analyte of interest.
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Affiliation(s)
- Cosimo Anichini
- Université de Strasbourg, CNRS, ISIS, 8 alleé Gaspard Monge, 67000 Strasbourg, France
| | - Alessandro Aliprandi
- Université de Strasbourg, CNRS, ISIS, 8 alleé Gaspard Monge, 67000 Strasbourg, France
| | - Sai Manoj Gali
- CMN, Université de Mons, Place du Parc 20, 7000 Mons, Belgium
| | - Fabiola Liscio
- Istituto per la Microelettronica e Microsistemi (IMM)-CNR, via Gobetti 101, 40129 Bologna, Italy
| | - Vittorio Morandi
- Istituto per la Microelettronica e Microsistemi (IMM)-CNR, via Gobetti 101, 40129 Bologna, Italy
| | - Andrea Minoia
- CMN, Université de Mons, Place du Parc 20, 7000 Mons, Belgium
| | - David Beljonne
- CMN, Université de Mons, Place du Parc 20, 7000 Mons, Belgium
| | - Artur Ciesielski
- Université de Strasbourg, CNRS, ISIS, 8 alleé Gaspard Monge, 67000 Strasbourg, France
| | - Paolo Samorì
- Université de Strasbourg, CNRS, ISIS, 8 alleé Gaspard Monge, 67000 Strasbourg, France
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11
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Morisaki T, Shigenaga A, Otaka A. Development of a Turn-On Fluorescent Traceable Linker Employing N-Sulfanylethylcoumarinyl Amide for the Enrichment and Visualization of Target Proteins. Chem Pharm Bull (Tokyo) 2020; 68:216-219. [PMID: 32115528 DOI: 10.1248/cpb.c19-00726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A turn-on fluorescent traceable linker based on N-sulfanylethylcoumarinyl amide (SECmide) has been developed as an advanced cleavable linker. It was successfully employed for the enrichment and selective visualization of a target protein in cell lysate. The results demonstrated that the SECmide-based traceable linker is potentially applicable to the identification of low molecular weight target proteins, a factor which has been problematic for a previously developed N-sulfanylethylanilide-based traceable linker.
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Affiliation(s)
- Takuya Morisaki
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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12
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Borsari C, Trader DJ, Tait A, Costi MP. Designing Chimeric Molecules for Drug Discovery by Leveraging Chemical Biology. J Med Chem 2020; 63:1908-1928. [PMID: 32023055 PMCID: PMC7997565 DOI: 10.1021/acs.jmedchem.9b01456] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
After the first seed concept introduced in the 18th century, different disciplines have attributed different names to dual-functional molecules depending on their application, including bioconjugates, bifunctional compounds, multitargeting molecules, chimeras, hybrids, engineered compounds. However, these engineered constructs share a general structure: a first component that targets a specific cell and a second component that exerts the pharmacological activity. A stable or cleavable linker connects the two modules of a chimera. Herein, we discuss the recent advances in the rapidly expanding field of chimeric molecules leveraging chemical biology concepts. This Perspective is focused on bifunctional compounds in which one component is a lead compound or a drug. In detail, we discuss chemical features of chimeric molecules and their use for targeted delivery and for target engagement studies.
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Affiliation(s)
- Chiara Borsari
- Department of Biomedicine, University of Basel, Mattenstrasse 28, 4058 Basel, Switzerland
| | - Darci J Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 610 Purdue Mall, West Lafayette, Indiana 47907, United States
| | - Annalisa Tait
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
| | - Maria P Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy
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13
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Shigenaga A. Development of Chemical Biology Tools Focusing on Peptide/Amide Bond Cleavage Reaction. Chem Pharm Bull (Tokyo) 2019; 67:1171-1178. [PMID: 31685746 DOI: 10.1248/cpb.c19-00285] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peptides and proteins are involved in almost all biological events. In this review, three chemical biology tools, which were developed for peptide/protein sciences from a viewpoint of peptide/amide bond cleavage, are overviewed. First, study on an artificial amino acid that enables stimulus-responsive functional control of peptides/proteins is briefly described. Two N-S acyl transfer reaction-based tools, one a linker molecule for facile identification of target proteins of bioactive compounds and the other a reagent for selective labeling of proteins of interest, are then discussed.
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Affiliation(s)
- Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University
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14
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Wang R, Ding J, Zhang Y. Naphthalimide/benzimide-based excited-state intramolecular proton transfer active luminogens: aggregation-induced enhanced emission and potential for chemical modification. NEW J CHEM 2019. [DOI: 10.1039/c9nj01685f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two ESIPT- and AIEE-active molecules, HPIBT, which is superior to HNIBT, and HPIBT-yl can be further modified through high-efficiency click chemistry.
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Affiliation(s)
- Rong Wang
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling
- P. R. China
| | - Ju Ding
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling
- P. R. China
| | - Yanrong Zhang
- College of Chemistry & Pharmacy
- Northwest A&F University
- Yangling
- P. R. China
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15
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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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16
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Hagen SE, Liu K, Jin Y, Piersimoni L, Andrews PC, Showalter HD. Synthesis of CID-cleavable protein crosslinking agents containing quaternary amines for structural mass spectrometry. Org Biomol Chem 2018; 16:8245-8248. [PMID: 29537042 PMCID: PMC6138586 DOI: 10.1039/c8ob00329g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Two novel cyclic quaternary amine crosslinking probes are synthesized for structural mass spectrometry of protein complexes in solution and for analysis of protein interactions in organellar and whole cell extracts. Each exhibits high aqueous solubility, excellent protein crosslinking efficiencies, low collision induced dissociation (CID) energy fragmentation efficiencies, high stoichiometries of reaction, increased charges of crosslinked peptide ions, and maintenance of overall surface charge balance of crosslinked proteins.
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Affiliation(s)
- Susan E Hagen
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
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17
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Meyer A, Vasseur JJ, Dumy P, Morvan F. Phthalimide-Oxy Derivatives for 3′- or 5′-Conjugation of Oligonucleotides by Oxime Ligation and Circularization of DNA by “Bis- or Tris-Click” Oxime Ligation. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Albert Meyer
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
| | - François Morvan
- Institut des Biomolécules Max Mousseron; IBMM, UMR 5247; Université Montpellier, CNRS, ENSCM; 34095 Montpellier Cedex 5 France
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18
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Cowell J, Buck M, Essa AH, Clarke R, Vollmer W, Vollmer D, Hilkens CM, Isaacs JD, Hall MJ, Gray J. Traceless Cleavage of Protein-Biotin Conjugates under Biologically Compatible Conditions. Chembiochem 2017; 18:1688-1691. [PMID: 28581639 PMCID: PMC5708275 DOI: 10.1002/cbic.201700214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Indexed: 12/14/2022]
Abstract
Biotinylation of amines is widely used to conjugate biomolecules, but either the resulting label is non-removable or its removal leaves a tag on the molecule of interest, thus affecting downstream processes. We present here a set of reagents (RevAmines) that allow traceless, reversible biotinylation under biologically compatible, mild conditions. Release following avidin-based capture is achieved through the cleavage of a (2-(alkylsulfonyl)ethyl) carbamate linker under mild conditions (200 mm ammonium bicarbonate, pH 8, 16-24 h, room temperature) that regenerates the unmodified amine. The capture and release of biotinylated proteins and peptides from neutravidin, fluorescent labelling through reversible biotinylation at the cell surface and the selective enrichment of proteins from bacterial periplasm are demonstrated. The tags are easily prepared, stable and offer the potential for future application in proteomics, activity-based protein profiling, affinity chromatography and bio-molecule tagging and purification.
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Affiliation(s)
- Joseph Cowell
- School of ChemistryNewcastle UniversityNewcastle upon TyneNE2 7RUUK
| | - Matthew Buck
- Musculoskeletal Research GroupInstitute of Cellular MedicineNewcastle UniversityNewcastle upon TyneNE2 4HHUK
| | - Ali H. Essa
- School of ChemistryNewcastle UniversityNewcastle upon TyneNE2 7RUUK
- Department of ChemistryCollege of ScienceUniversity of BasrahBasrahIraq
| | - Rebecca Clarke
- School of ChemistryNewcastle UniversityNewcastle upon TyneNE2 7RUUK
| | - Waldemar Vollmer
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneNE2 4HHUK
| | - Daniela Vollmer
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneNE2 4HHUK
| | - Catharien M. Hilkens
- Musculoskeletal Research GroupInstitute of Cellular MedicineNewcastle UniversityNewcastle upon TyneNE2 4HHUK
| | - John D. Isaacs
- Musculoskeletal Research GroupInstitute of Cellular MedicineNewcastle UniversityNewcastle upon TyneNE2 4HHUK
| | - Michael J. Hall
- School of ChemistryNewcastle UniversityNewcastle upon TyneNE2 7RUUK
| | - Joe Gray
- Institute for Cell and Molecular BiosciencesNewcastle UniversityNewcastle upon TyneNE2 4HHUK
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19
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Synthesis of Novel Saccharin Derivatives. Molecules 2017; 22:molecules22040516. [PMID: 28333118 PMCID: PMC6153755 DOI: 10.3390/molecules22040516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 03/20/2017] [Accepted: 03/20/2017] [Indexed: 11/16/2022] Open
Abstract
The synthesis of saccharin (1,2-benzisothiazol-3-one-1,1-dioxide) derivatives substituted on the benzene ring has seen limited development despite the longevity of this compound’s use as an artificial sweetener. This type of saccharin derivative would however present attractive properties for the development of new bioactive, drug-like small molecule compounds. Here we report the derivatisation of the benzene ring of saccharin using Cu(I)-catalyzed azide alkyne cycloaddition (CuAAC) to synthesise a diverse library of novel saccharin-1,2,3-triazole conjugates. All library compounds retain the capability for interactions with biomolecules via the unmodified sulfonamide and lactam groups of the parent saccharin core heterocycle. The compounds also encompass alternate orientations of the 1,2,3-triazole heterocycle, thus further adding diversity to the potential hydrogen bonding interactions of these compounds with biomolecules of therapeutic interest. Our findings demonstrate that specifically functionalized derivatives of saccharin may be prepared from either saccharin azide or saccharin alkyne building blocks in high yield using CuAAC.
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20
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Shigenaga A, Yamamoto J, Kohiki T, Inokuma T, Otaka A. Invention of stimulus-responsive peptide-bond-cleaving residue (Spr) and its application to chemical biology tools. J Pept Sci 2017; 23:505-513. [PMID: 28105728 DOI: 10.1002/psc.2961] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 01/04/2023]
Abstract
Elucidation of biological functions of peptides and proteins is essential for understanding peptide/protein-related biological events and developing drugs. Caged peptides and proteins that release a parent active peptide/protein by photo-irradiation have successfully been employed to elucidate the functions. Whereas the usual caged peptide/protein enables conversion of an inactive form to an active form (OFF-to-ON conversion) by photo-induced deprotection, photo-triggered main chain cleavage is reported to be applicable to ON-to-OFF conversion. These peptides and proteins are photo-responsive; however, if peptides and proteins could respond to other stimuli such as disease-related environment or enzymes, their range of application should be widened. To convert the photo-responsive peptide/protein into other stimulus-responsive peptide/protein, quite laborious de novo design and synthesis of the stimulus-responsive unit are required. In this context, we designed a stimulus-responsive peptide-bond-cleaving residue (Spr) in which the stimuli available for the main chain cleavage vary according to the choice of protecting groups on the residue. In this review, design and synthesis of Spr are introduced, and challenges to apply Spr to other fields to enable, for example, functional control, localization control, delivery of cargos, labeling of a protein of interest in living cells, and identification of target proteins of bioactive ligands are discussed. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Akira Shigenaga
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan.,PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Jun Yamamoto
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Taiki Kohiki
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Tsubasa Inokuma
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
| | - Akira Otaka
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, 770-8505, Japan
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21
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Abstract
The discovery of the protein targets of small molecule probes is a crucial aspect of activity-based protein profiling and chemical biology. Mass spectrometry is the primary method for target identification, and in the last decade, cleavable linkers have become a popular strategy to facilitate protein enrichment and identification. In this chapter, we provide an overview of cleavable linkers used in chemical proteomics approaches, discuss their different chemistries, and describe how they aid in protein identification.
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Affiliation(s)
- Yinliang Yang
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Marko Fonović
- Department of Biochemistry, Molecular and Structural Biology, Jožef Stefan Institute, Jamova cesta 39, Ljubljana, Slovenia
| | - Steven H L Verhelst
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestr. 49 box 802, 3000 Leuven, Belgium, 3000, Leuven, Belgium.
- Leibniz Institute for AnalyticalSciences ISAS, Otto-Hahn-Str. 6b, 44227, Dortmund, Germany.
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22
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Godde B, Jouaiti A, Fluck A, Kyritsakas N, Mauro M, Hosseini MW. Symmetrical or non-symmetrical luminescent turnstiles based on hydroquinone stators and rotors bearing pyridyl or p-dimethylaminopyridyl coordinating units. Dalton Trans 2017; 46:14897-14906. [DOI: 10.1039/c7dt02762a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Luminescent symmetrical and non-symmetrical molecular turnstiles based on hydroquinone stators and rotors bearing coordinating units are reported.
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Affiliation(s)
- Bérangère Godde
- Molecular Tectonics Laboratory
- UMR UdS-CNRS 7140
- University of Strasbourg
- F-67000 Strasbourg
- France
| | - Abdelaziz Jouaiti
- Molecular Tectonics Laboratory
- UMR UdS-CNRS 7140
- University of Strasbourg
- F-67000 Strasbourg
- France
| | - Audrey Fluck
- Molecular Tectonics Laboratory
- UMR UdS-CNRS 7140
- University of Strasbourg
- F-67000 Strasbourg
- France
| | - Nathalie Kyritsakas
- Molecular Tectonics Laboratory
- UMR UdS-CNRS 7140
- University of Strasbourg
- F-67000 Strasbourg
- France
| | - Matteo Mauro
- Molecular Tectonics Laboratory
- UMR UdS-CNRS 7140
- University of Strasbourg
- F-67000 Strasbourg
- France
| | - Mir Wais Hosseini
- Molecular Tectonics Laboratory
- UMR UdS-CNRS 7140
- University of Strasbourg
- F-67000 Strasbourg
- France
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23
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Morisaki T, Denda M, Yamamoto J, Tsuji D, Inokuma T, Itoh K, Shigenaga A, Otaka A. An N-sulfanylethylanilide-based traceable linker for enrichment and selective labelling of target proteins. Chem Commun (Camb) 2016; 52:6911-3. [PMID: 27146590 DOI: 10.1039/c6cc01229a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
An N-sulfanylethylanilide-based traceable linker, developed to facilitate identification of target proteins of bioactive compounds, was introduced into an alkynylated target protein. Subsequent adsorption onto streptavidin beads allowed it to be treated with a cysteine-fluorophore conjugate in the presence of phosphate. This induced the N-S acyl transfer reaction of the N-sulfanylethylanilide unit. The subsequent native chemical ligation of the fluorophore resulted in cleavage of the linker for target elution and fluorescence labelling of the target, allowing it to be distinguished from non-target proteins.
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Affiliation(s)
- Takuya Morisaki
- Institute of Biomedical Sciences and Graduate School of Pharmaceutical Sciences, Tokushima University, Shomachi, Tokushima 770-8505, Japan.
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24
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Huang YC, Fang GM, Liu L. Chemical synthesis of proteins using hydrazide intermediates. Natl Sci Rev 2015. [DOI: 10.1093/nsr/nwv072] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Protein chemical synthesis offers useful and otherwise-difficulty-to-obtain biomacromolecules for biological and pharmaceutical studies. Recently, the hydrazide chemistry has drawn attentions in this field as peptide or protein hydrazides can be used as key intermediates for different synthesis and modification purposes. Besides being a traditional bioorthogonal chemical handle, a hydrazide group can serve as a readily accessible precursor of a thioester. This strategy significantly improves the efficiency and scope of native chemical ligation for protein chemical synthesis. Here we review the chemical transformations of peptide or protein hydrazides and total/semi/enzymatic protein synthesis methods involving peptide or protein hydrazides. Several examples of protein chemical synthesis using peptide hydrazides as key intermediates are described.
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25
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Ali B, Shamim A, Vasconcelos SN, Stefani HA. Synthesis and applications of 4-substituted 1-(4-iodophenyl)pyrrolidine-2,5-diones. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.05.066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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26
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Mauri E, Rossi F, Sacchetti A. Simple and efficient strategy to synthesize PEG-aldehyde derivatives for hydrazone orthogonal chemistry. POLYM ADVAN TECHNOL 2015. [DOI: 10.1002/pat.3578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Emanuele Mauri
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; via Mancinelli 7 20131 Milan Italy
| | - Filippo Rossi
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; via Mancinelli 7 20131 Milan Italy
| | - Alessandro Sacchetti
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”; Politecnico di Milano; via Mancinelli 7 20131 Milan Italy
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27
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Yamamoto J, Denda M, Maeda N, Kita M, Komiya C, Tanaka T, Nomura W, Tamamura H, Sato Y, Yamauchi A, Shigenaga A, Otaka A. Development of a traceable linker containing a thiol-responsive amino acid for the enrichment and selective labelling of target proteins. Org Biomol Chem 2015; 12:3821-6. [PMID: 24806338 DOI: 10.1039/c4ob00622d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A traceable linker that is potentially applicable to identification of a target protein of bioactive compounds was developed. It enabled not only thiol-induced cleavage of the linker for enrichment of the target protein but also selective labelling to pick out the target from contaminated non-target proteins for facile identification.
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Affiliation(s)
- Jun Yamamoto
- Institute of Health Biosciences and Graduate School of Pharmaceutical Sciences, The University of Tokushima, Shomachi, Tokushima 770-8505, Japan.
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28
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Bi C, Jiang R, He X, Chen L, Zhang Y. Synthesis of a hydrophilic maltose functionalized Au NP/PDA/Fe3O4-RGO magnetic nanocomposite for the highly specific enrichment of glycopeptides. RSC Adv 2015. [DOI: 10.1039/c5ra06911d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel approach was developed to synthesize a hydrophilic thiol-terminated maltose-functionalized Au NP/PDA/Fe3O4-RGO nanocomposite which exhibited high selectivity and detection sensitivity in the enrichment of glycopeptides from complex samples.
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Affiliation(s)
- Changfen Bi
- Research Center for Analytical Sciences
- College of Chemistry
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
| | - Ruidong Jiang
- Research Center for Analytical Sciences
- College of Chemistry
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
| | - Xiwen He
- Research Center for Analytical Sciences
- College of Chemistry
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
| | - Langxing Chen
- Research Center for Analytical Sciences
- College of Chemistry
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
| | - Yukui Zhang
- Research Center for Analytical Sciences
- College of Chemistry
- Tianjin Key Laboratory of Biosensing and Molecular Recognition
- State Key Laboratory of Medicinal Chemical Biology
- Nankai University
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29
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Xu Y, Xu L, Xia Y, Guan CJ, Guo QX, Fu Y, Wang C, Li YM. Fast and catalyst-free hydrazone ligation via ortho-halo-substituted benzaldehydes for protein C-terminal labeling at neutral pH. Chem Commun (Camb) 2015. [DOI: 10.1039/c5cc04382d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Rapid and catalyst-free hydrazone ligation reaction between ortho-halobenzaldehyde derivatives and peptide/protein hydrazides was observed at neutral pH and room temperature.
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Affiliation(s)
- Yang Xu
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
- China
- School of Medical Engineering
| | - Ling Xu
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
- China
| | - Yuan Xia
- Zhejiang Key Laboratory of Alternative Technologies for Fine Chemicals Process
- Shaoxing University
- Shaoxing 312000
- China
| | - Chao-Jian Guan
- School of Medical Engineering
- Hefei University of Technology
- Hefei
- China
| | - Qing-Xiang Guo
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
- China
| | - Yao Fu
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
- China
| | - Chen Wang
- Zhejiang Key Laboratory of Alternative Technologies for Fine Chemicals Process
- Shaoxing University
- Shaoxing 312000
- China
| | - Yi-Ming Li
- Department of Chemistry
- University of Science and Technology of China
- Hefei 230026
- China
- School of Medical Engineering
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30
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Yamamoto J, Maeda N, Komiya C, Tanaka T, Denda M, Ebisuno K, Nomura W, Tamamura H, Sato Y, Yamauchi A, Shigenaga A, Otaka A. Development of a fluoride-responsive amide bond cleavage device that is potentially applicable to a traceable linker. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.05.110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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31
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Miyazaki A, Asanuma M, Dodo K, Egami H, Sodeoka M. A "catch-and-release" protocol for alkyne-tagged molecules based on a resin-bound cobalt complex for peptide enrichment in aqueous media. Chemistry 2014; 20:8116-28. [PMID: 24788842 DOI: 10.1002/chem.201400056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Indexed: 01/09/2023]
Abstract
The development of new and mild protocols for the specific enrichment of biomolecules is of significant interest from the perspective of chemical biology. A cobalt-phosphine complex immobilised on a solid-phase resin has been found to selectively bind to a propargyl carbamate tag, that is, "catch", under dilute aqueous conditions (pH 7) at 4 °C. Upon acidic treatment of the resulting resin-bound alkyne-cobalt complex, the Nicholas reaction was induced to "release" the alkyne-tagged molecule from the resin as a free amine. Model studies revealed that selective enrichment of the alkyne-tagged molecule could be achieved with high efficiency at 4 °C. The proof-of-concept was applied to an alkyne-tagged amino acid and dipeptide. Studies using an alkyne-tagged dipeptide proved that this protocol is compatible with various amino acids bearing a range of functionalities in the side-chain. In addition, selective enrichment and detection of an amine derived from the "catch and release" of an alkyne-tagged dipeptide in the presence of various peptides has been accomplished under highly dilute conditions, as determined by mass spectrometry.
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Affiliation(s)
- Ayako Miyazaki
- Sodeoka Live Cell Chemistry Project, ERATO, Japan Science and Technology Agency (JST), 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan) and Synthetic Organic Chemistry Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Current address: Institute of Transformative, Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan)
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32
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Zigon N, Kyritsakas N, Hosseini MW. Organometallic turnstiles: acid and base locking and unlocking. Dalton Trans 2014; 43:152-7. [DOI: 10.1039/c3dt51996a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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33
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An H, Statsyuk AV. Development of activity-based probes for ubiquitin and ubiquitin-like protein signaling pathways. J Am Chem Soc 2013; 135:16948-62. [PMID: 24138456 DOI: 10.1021/ja4099643] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ubiquitin and ubiquitin-like (UBL) proteins regulate a vast variety of cellular functions. Some UBL proteins are present in all cell types, while others are expressed only in certain cells or under certain environmental conditions. This highlights the central role of UBL systems in regulation of ubiquitous as well as specific cellular functions. UBL proteins share little amino acid sequence identity to each other, yet they share similar 3D shapes, which is exemplified by the β-grasp fold. Central to UBL protein signaling pathways are UBL protein-activating E1 enzymes that activate the C-terminus of UBL proteins for subsequent conjugation to the protein substrates. Due to their critical roles in biology, E1 enzymes have been recognized as emerging drug targets to treat human diseases. In spite of their biological significance, however, methods to discover UBL proteins and to monitor the intracellular activity of E1 enzymes are lacking. Thus, there is a critical need for methods to evaluate the intracellular mechanisms of action of E1 enzyme inhibitors. Here we describe the development of a mechanism-based small-molecule probe, ABP1, that can be used to discover and to detect active UBL proteins, and to monitor the intracellular activity of E1 enzymes inside intact cells. The developed probe can also be used to profile the selectivity of E1 enzyme-targeting drugs in vitro and inside intact cells.
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Affiliation(s)
- Heeseon An
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, Chemistry of Life Processes Institute, Northwestern University , Silverman Hall, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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Detection of electrophile-sensitive proteins. Biochim Biophys Acta Gen Subj 2013; 1840:913-22. [PMID: 24021887 DOI: 10.1016/j.bbagen.2013.09.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 08/22/2013] [Accepted: 09/03/2013] [Indexed: 01/01/2023]
Abstract
BACKGROUND Redox signaling is an important emerging mechanism of cellular function. Dysfunctional redox signaling is increasingly implicated in numerous pathologies, including atherosclerosis, diabetes, and cancer. The molecular messengers in this type of signaling are reactive species which can mediate the post-translational modification of specific groups of proteins, thereby effecting functional changes in the modified proteins. Electrophilic compounds comprise one class of reactive species which can participate in redox signaling. Electrophiles modulate cell function via formation of covalent adducts with proteins, particularly cysteine residues. SCOPE OF REVIEW This review will discuss the commonly used methods of detection for electrophile-sensitive proteins, and will highlight the importance of identifying these proteins for studying redox signaling and developing novel therapeutics. MAJOR CONCLUSIONS There are several methods which can be used to detect electrophile-sensitive proteins. These include the use of tagged model electrophiles, as well as derivatization of endogenous electrophile-protein adducts. GENERAL SIGNIFICANCE In order to understand the mechanisms by which electrophiles mediate redox signaling, it is necessary to identify electrophile-sensitive proteins and quantitatively assess adduct formation. Strengths and limitations of these methods will be discussed. This article is part of a Special Issue entitled Current methods to study reactive oxygen species - pros and cons and biophysics of membrane proteins. Guest Editor: Christine Winterbourn.
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Qian Y, Martell J, Pace NJ, Ballard TE, Johnson DS, Weerapana E. An isotopically tagged azobenzene-based cleavable linker for quantitative proteomics. Chembiochem 2013; 14:1410-4. [PMID: 23861326 DOI: 10.1002/cbic.201300396] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Indexed: 01/03/2023]
Abstract
Putting a number on it: Cleavable linkers are widely utilized in proteomics applications. In particular, the azobenzene-based linker cleaves under mild conditions that are mass-spectrometry-compatible. Here, we adapt this linker for quantitative proteomic applications by incorporating an isotopic label. These light- and heavy-tagged linkers enable the identification and quantitation of labeled peptides from multiple proteomes.
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Affiliation(s)
- Yu Qian
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02467, USA
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36
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Gupta V, Carroll KS. Sulfenic acid chemistry, detection and cellular lifetime. Biochim Biophys Acta Gen Subj 2013; 1840:847-75. [PMID: 23748139 DOI: 10.1016/j.bbagen.2013.05.040] [Citation(s) in RCA: 296] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 05/24/2013] [Accepted: 05/26/2013] [Indexed: 02/03/2023]
Abstract
BACKGROUND Reactive oxygen species-mediated cysteine sulfenic acid modification has emerged as an important regulatory mechanism in cell signaling. The stability of sulfenic acid in proteins is dictated by the local microenvironment and ability of antioxidants to reduce this modification. Several techniques for detecting this cysteine modification have been developed, including direct and in situ methods. SCOPE OF REVIEW This review presents a historical discussion of sulfenic acid chemistry and highlights key examples of this modification in proteins. A comprehensive survey of available detection techniques with advantages and limitations is discussed. Finally, issues pertaining to rates of sulfenic acid formation, reduction, and chemical trapping methods are also covered. MAJOR CONCLUSIONS Early chemical models of sulfenic acid yielded important insights into the unique reactivity of this species. Subsequent pioneering studies led to the characterization of sulfenic acid formation in proteins. In parallel, the discovery of oxidant-mediated cell signaling pathways and pathological oxidative stress has led to significant interest in methods to detect these modifications. Advanced methods allow for direct chemical trapping of protein sulfenic acids directly in cells and tissues. At the same time, many sulfenic acids are short-lived and the reactivity of current probes must be improved to sample these species, while at the same time, preserving their chemical selectivity. Inhibitors with binding scaffolds can be rationally designed to target sulfenic acid modifications in specific proteins. GENERAL SIGNIFICANCE Ever increasing roles for protein sulfenic acids have been uncovered in physiology and pathology. A more complete understanding of sulfenic acid-mediated regulatory mechanisms will continue to require rigorous and new chemical insights. This article is part of a Special Issue entitled Current methods to study reactive oxygen species - pros and cons and biophysics of membrane proteins. Guest Editor: Christine Winterbourn.
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Affiliation(s)
- Vinayak Gupta
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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37
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Zigon N, Guenet A, Graf E, Kyritsakas N, Hosseini MW. A platinum turnstile with a palladium lock. Dalton Trans 2013; 42:9740-5. [PMID: 23685676 DOI: 10.1039/c3dt50809a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
An organometallic molecular turnstile composed of a stator based on an α,ω-diphosphine bearing, in a symmetric fashion, the 2,6-pyridyl diamide moiety as a central tridentate chelating unit and a rotor composed of Pt(II) equipped with two pyridyl groups in trans configuration was designed. The switching between its open and closed states using Pd(II) was investigated both in solution and in the solid state.
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Affiliation(s)
- Nicolas Zigon
- Molecular Tectonic Laboratory, UMR UDS-CNRS 7140, Université de Strasbourg, Institut Le Bel, 4, rue Blaise Pascal, F-67000 Strasbourg, France
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Ziegler S, Pries V, Hedberg C, Waldmann H. Identifizierung der Zielproteine bioaktiver Verbindungen: Die Suche nach der Nadel im Heuhaufen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208749] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Ziegler S, Pries V, Hedberg C, Waldmann H. Target identification for small bioactive molecules: finding the needle in the haystack. Angew Chem Int Ed Engl 2013; 52:2744-92. [PMID: 23418026 DOI: 10.1002/anie.201208749] [Citation(s) in RCA: 356] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Indexed: 01/10/2023]
Abstract
Identification and confirmation of bioactive small-molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state-of-the-art. Among the techniques currently available, protein affinity isolation using suitable small-molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.
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Affiliation(s)
- Slava Ziegler
- Max-Planck-Institut für molekulare Physiologie, Abt. Chemische Biologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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Trippier PC. Synthetic strategies for the biotinylation of bioactive small molecules. ChemMedChem 2013; 8:190-203. [PMID: 23303486 DOI: 10.1002/cmdc.201200498] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 12/07/2012] [Indexed: 01/19/2023]
Abstract
Biotinylation, the functional appendage of a biotin moiety to a bioactive compound (including small molecules and biological macromolecules), represents a common technique for identification of the intracellular binding partners that underlie the foundation of observed biological activity. Introduction of an attachment tether to the framework of a compound of interest must be planned at an early stage of development, and many considerations apply: 1) region of attachment, so as not to impede the pharmacophore; 2) stability of the parent molecular architecture to biotinylation conditions; 3) regioselectivity for the chosen tethering location over other reactive functionalities; 4) toxicity of reagents if biotinylation is to be performed in vitro; and 5) overall ease of synthesis. This review is intended to serve as a guide for the selection of appropriate tethering modalities. Examples of the common techniques used to affix biotin, including amide bond formation, [3+2] cycloadditions through "click" chemistry, Staudinger ligation, and thioether formation will be discussed, along with analysis of the wider applications of synthetic methodology that have been applied toward the biotinylation of small molecules.
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Affiliation(s)
- Paul C Trippier
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, TX, USA.
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41
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Baell JB, Ferrins L, Falk H, Nikolakopoulos G. PAINS: Relevance to Tool Compound Discovery and Fragment-Based Screening. Aust J Chem 2013. [DOI: 10.1071/ch13551] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pan assay interference compounds (PAINS) are readily discovered in any bioassay and can appear to give selective and optimisable hits. The most common PAINS can be readily recognised by their structure. However, there are compounds that closely resemble PAINS that are not specifically recognised by the PAINS filters. In addition, highly reactive compounds are not encoded for in the PAINS filters because they were excluded from the high-throughput screening (HTS) library used to develop the filters and so were never present to provide indicting data. A compounding complication in the area is that very occasionally a PAINS compound may serve as a viable starting point for progression. Despite such an occasional example, the literature is littered with an overwhelming number of examples of compounds that fail to progress and were probably not optimisable in the first place, nor useful tool compounds. Thus it is with great caution and diligence that compounds possessing a known PAINS core should be progressed through to medicinal chemistry optimisation, if at all, as the chances are very high that the hits will be found to be non-progressable, often after a significant waste of resources.
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42
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Yang Y, Verhelst SHL. Cleavable trifunctional biotin reagents for protein labelling, capture and release. Chem Commun (Camb) 2013; 49:5366-8. [DOI: 10.1039/c3cc42076k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Kramer JR, Deming TJ. Reversible chemoselective tagging and functionalization of methionine containing peptides. Chem Commun (Camb) 2013; 49:5144-6. [DOI: 10.1039/c3cc42214c] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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44
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Maurer A, Zeyher C, Amin B, Kalbacher H. A Periodate-Cleavable Linker for Functional Proteomics under Slightly Acidic Conditions: Application for the Analysis of Intracellular Aspartic Proteases. J Proteome Res 2012; 12:199-207. [DOI: 10.1021/pr300758c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Andreas Maurer
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Claus Zeyher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Bushra Amin
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tuebingen, Ob dem Himmelreich 7, 72074
Tuebingen, Germany
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45
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Bielski R, Witczak Z. Strategies for Coupling Molecular Units if Subsequent Decoupling Is Required. Chem Rev 2012; 113:2205-43. [DOI: 10.1021/cr200338q] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Roman Bielski
- Value Recovery, Inc., 510 Heron Drive, Suite 301, Bridgeport, New Jersey
08014, United States
| | - Zbigniew Witczak
- Department
of Pharmaceutical
Sciences, Nesbitt School of Pharmacy, Wilkes University, Wilkes-Barre, Pennsylvania 18766, United States
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46
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Yang Y, Hahne H, Kuster B, Verhelst SHL. A simple and effective cleavable linker for chemical proteomics applications. Mol Cell Proteomics 2012; 12:237-44. [PMID: 23028061 DOI: 10.1074/mcp.m112.021014] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The study of metabolically labeled or probe-modified proteins is an important area in chemical proteomics. Isolation and purification of the protein targets is a necessary step before MS identification. The biotin-streptavidin system is widely used in this process, but the harsh denaturing conditions also release natively biotinylated proteins and non-selectively bound proteins. A cleavable linker strategy is a promising approach for solving this problem. Though several cleavable linkers have been developed and tested, an efficient, easily synthesized, and inexpensive cleavable linker is a desirable addition to the proteomics toolbox. Here, we describe the chemical proteomics application of a vicinal diol cleavable linker. Through easy-to-handle chemistry we incorporate this linker into an activity-based probe and a biotin alkyne tag amenable for bioorthogonal ligation. With these reagents, background protein identifications are significantly reduced relative to standard on-bead digestion.
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Affiliation(s)
- Yinliang Yang
- Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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47
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Serim S, Haedke U, Verhelst SHL. Activity-based probes for the study of proteases: recent advances and developments. ChemMedChem 2012; 7:1146-59. [PMID: 22431376 DOI: 10.1002/cmdc.201200057] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/28/2012] [Indexed: 11/11/2022]
Abstract
Proteases are important targets for the treatment of human disease. Several protease inhibitors have failed in clinical trials due to a lack of in vivo specificity, indicating the need for studies of protease function and inhibition in complex, disease-related models. The tight post-translational regulation of protease activity complicates protease analysis by traditional proteomics methods. Activity-based protein profiling is a powerful technique that can resolve this issue. It uses small-molecule tools-activity-based probes-to label and analyze active enzymes in lysates, cells, and whole animals. Over the last twelve years, a wide variety of protease activity-based probes have been developed. These synthetic efforts have enabled techniques ranging from real-time in vivo imaging of protease activity to high-throughput screening of uncharacterized proteases. This Review introduces the general principles of activity-based protein profiling and describes the recent advancements in probe design and analysis techniques, which have increased the knowledge of protease biology and will aid future protease drug discovery.
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Affiliation(s)
- Sevnur Serim
- Center for Integrated Protein Science Munich (CIPS(M)), Lehrstuhl für Chemie der Biopolymere, Technische Universität München, Weihenstephaner Berg 3, 85354 Freising, Germany
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48
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Cleavable linkers in chemical biology. Bioorg Med Chem 2012; 20:571-82. [DOI: 10.1016/j.bmc.2011.07.048] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 07/08/2011] [Accepted: 07/23/2011] [Indexed: 01/11/2023]
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49
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Temming RP, van Scherpenzeel M, te Brinke E, Schoffelen S, Gloerich J, Lefeber DJ, van Delft FL. Protein enrichment by capture–release based on strain-promoted cycloaddition of azide with bicyclononyne (BCN). Bioorg Med Chem 2012; 20:655-61. [DOI: 10.1016/j.bmc.2011.07.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 07/22/2011] [Accepted: 07/23/2011] [Indexed: 11/26/2022]
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50
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Egami H, Kamisuki S, Dodo K, Asanuma M, Hamashima Y, Sodeoka M. Catch and release of alkyne-tagged molecules in water by a polymer-supported cobalt complex. Org Biomol Chem 2011; 9:7667-70. [PMID: 21935565 DOI: 10.1039/c1ob06123b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A cobalt-phosphine complex supported on PS-PEG beads was found to react with a propargyl carbamate tag, and the tagged molecules immobilized on the beads could be released by acidic treatment through the Nicholas reaction pathway. These reactions work in aqueous media at 4 °C, so that this catch and release procedure is compatible with conditions generally used in biochemical experiments.
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Affiliation(s)
- Hiromichi Egami
- Sodeoka Live Cell Chemistry Project, ERATO, Japan Science and Technology, Wako-shi, Saitama 351-0198, Japan
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