1
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Hillebrand L, Liang XJ, Serafim RAM, Gehringer M. Emerging and Re-emerging Warheads for Targeted Covalent Inhibitors: An Update. J Med Chem 2024; 67:7668-7758. [PMID: 38711345 DOI: 10.1021/acs.jmedchem.3c01825] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Covalent inhibitors and other types of covalent modalities have seen a revival in the past two decades, with a variety of new targeted covalent drugs having been approved in recent years. A key feature of such molecules is an intrinsically reactive group, typically a weak electrophile, which enables the irreversible or reversible formation of a covalent bond with a specific amino acid of the target protein. This reactive group, often called the "warhead", is a critical determinant of the ligand's activity, selectivity, and general biological properties. In 2019, we summarized emerging and re-emerging warhead chemistries to target cysteine and other amino acids (Gehringer, M.; Laufer, S. A. J. Med. Chem. 2019, 62, 5673-5724; DOI: 10.1021/acs.jmedchem.8b01153). Since then, the field has rapidly evolved. Here we discuss the progress on covalent warheads made since our last Perspective and their application in medicinal chemistry and chemical biology.
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Affiliation(s)
- Laura Hillebrand
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Xiaojun Julia Liang
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Ricardo A M Serafim
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
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2
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Hochegger P, Hermann T, Dolensky J, Seebacher W, Saf R, Pferschy-Wenzig EM, Kaiser M, Mäser P, Weis R. Structure-Activity Relationships and Antiplasmodial Potencies of Novel 3,4-Disubstituted 1,2,5-Oxadiazoles. Int J Mol Sci 2023; 24:14480. [PMID: 37833929 PMCID: PMC10572347 DOI: 10.3390/ijms241914480] [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: 08/30/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The 4-substituted 3-amino-1,2,5-oxadiazole 1 from the Malaria Box Project of the Medicines for Malaria Venture foundation shows very promising selectivity and in vitro activity against Plasmodium falciparum. Within the first series of new compounds, various 3-acylamino analogs were prepared. This paper now focuses on the investigation of the importance of the aromatic substituent in ring position 4. A number of new structure-activity relationships were elaborated, showing that antiplasmodial activity and selectivity strongly depend on the substitution pattern of the 4-phenyl moiety. In addition, physicochemical parameters relevant for drug development were calculated (logP and ligand efficiency) or determined experimentally (CYP3A4-inhibition and aqueous solubility). N-[4-(3-ethoxy-4-methoxyphenyl)-1,2,5-oxadiazol-3-yl]-3-methylbenzamide 51 showed high in vitro activity against the chloroquine-sensitive strain NF54 of P. falciparum (PfNF54 IC50 = 0.034 µM), resulting in a very promising selectivity index of 1526.
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Affiliation(s)
- Patrick Hochegger
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (P.H.); (J.D.); (W.S.); (R.W.)
| | - Theresa Hermann
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (P.H.); (J.D.); (W.S.); (R.W.)
| | - Johanna Dolensky
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (P.H.); (J.D.); (W.S.); (R.W.)
| | - Werner Seebacher
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (P.H.); (J.D.); (W.S.); (R.W.)
| | - Robert Saf
- Institute for Chemistry and Technology of Materials (ICTM), Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria;
| | - Eva-Maria Pferschy-Wenzig
- Institute of Pharmaceutical Sciences, Pharmacognosy, University of Graz, Beethovenstraße 8, A-8010 Graz, Austria;
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Kreuzstraße 2, CH-4123 Allschwil, Switzerland; (M.K.); (P.M.)
- Faculty of Philosophy and Natural Sciences, University of Basel, Swiss TPH, Petersplatz 1, CH-4003 Basel, Switzerland
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Kreuzstraße 2, CH-4123 Allschwil, Switzerland; (M.K.); (P.M.)
- Faculty of Philosophy and Natural Sciences, University of Basel, Swiss TPH, Petersplatz 1, CH-4003 Basel, Switzerland
| | - Robert Weis
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (P.H.); (J.D.); (W.S.); (R.W.)
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3
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Weierbach SM, Reynolds RP, Stephens SM, Vlasakakis KV, Ritter RT, White OM, Patel NH, Hayes EC, Dunmire S, Lambert KM. Chemoselective Oxidation of Thiols with Oxoammonium Cations. J Org Chem 2023; 88:11392-11410. [PMID: 35926190 DOI: 10.1021/acs.joc.2c01097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The oxidation of various aryl and aliphatic thiols with the commercially available and environmentally benign reagent Bobbitt's salt (1) has been investigated. The reaction affords the corresponding disulfide products in good to excellent yields (71-99%) and can be accomplished in water, methanol, or acetonitrile solvent. Moreover, the process is highly chemoselective, tolerating traditionally oxidation-labile groups such as free amines and alcohols. Combined experimental and computational studies reveal that the oxidation takes place via a polar two-electron process with concomitant and unexpected deoxygenation of the oxoammonium cation through homolysis of the weak N-O bond, differing from prototypical radical-based thiol couplings. This unusual consumption of the oxidant has significant implications for the development of new nitroxide-based radical traps for probing S-centered radicals, the advancement of new electrochemical or catalytic processes involving nitroxide/oxoammonium salt redox couples, and applications to biological systems.
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Affiliation(s)
- Shayne M Weierbach
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Robert P Reynolds
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Shannon M Stephens
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Kostantinos V Vlasakakis
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Ramsey T Ritter
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Olivia M White
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Nishi H Patel
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Eric C Hayes
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Sydney Dunmire
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
| | - Kyle M Lambert
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia 23529, United States
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4
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Niu Y, Chen Z, Jiang Z, Yang Y, Liu G, Cheng X, Jiang Z, Zhang G, Tong L, Tang B. Detection of Cysteine Sulfenic Acid on E. coli Proteins with a Biotin-Benzoboroxole Probe. ACS Chem Biol 2023; 18:1351-1359. [PMID: 37260364 DOI: 10.1021/acschembio.3c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
S-sulfenylation of cysteine residues on proteins can effectively change protein structures and accordingly regulate their functions in vivo. Investigation of S-sulfenylation in different biological environments is thus vital for a systematic understanding of cellular redox regulation. In this work, a functional probe, biotin-benzoboroxole (Bio-ben), was designed for the detection of cysteine sulfenic acid (Cys-SOH). The performance of Bio-ben was characterized by small-molecule sulfenic acid, protein models, and proteome tests via mass spectra and western blotting. The results showed that Bio-ben was validated for cysteine sulfenic acid on proteins with good capture efficiency even at low concentrations. Compared with commonly used probes such as dimedone, the current probe has significantly shortened labeling time and exhibited comparable sensitivity. The proposed method provides a new approach for exploring S-sulfenylation in the oxidative modification of proteins and is helpful for related biological and clinical applications.
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Affiliation(s)
- Yaxin Niu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Zhenzhen Chen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Zhongyao Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Guangzhao Liu
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Xiufen Cheng
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Zhenhao Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Guanglu Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Lili Tong
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan 250014, People's Republic of China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, People's Republic of China
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5
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Li M, Cai Z, Li M, Chen L, Zeng W, Yuan H, Liu C. The dual detection of formaldehydes and sulfenic acids with a reactivity fluorescent probe in cells and in plants. Anal Chim Acta 2023; 1239:340734. [PMID: 36628774 DOI: 10.1016/j.aca.2022.340734] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
In order to reveal the inter-relationship between protein sulfenic acid (RSOH) and formaldehyde (FA) in different physiological processes, development of tools that are capable of respective and continuous detection for both species is highly valuable. Herein, we reported an "off-on" sensor NA-SF for dual detection of RSOH and FA in cells and plant tissues. Importantly, the highly desirable attribute of the probe NA-SF combined with TCEP, makes it possible to monitor endogenous both RSOH and FA in living cells and plants tissues. NA-SF has been applied successfully in detecting RSOH and FA at physiological concentrations in HeLa, HepG2, A549 cells. Furthermore, the application of NA-SF in evaluating the RSOH and FA level in Arabidopsis thaliana roots of different growth stages are performed. The results show that the level of RSOH and FA in Arabidopsis thaliana roots correlates well with their growth stages, which suggests that both RSOH and FA might play important roles in promoting plant growth and roots elongation. And it also implied a potential application for the biological and pathological research of RSOH and FA, especially in plant physiology. Therefore, we expect NA-SF could provide a convenient and robust tool for better understanding the physiological and pathological roles of RSOH and FA.
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Affiliation(s)
- Man Li
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, School of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Zhiyi Cai
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, School of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Mengzhao Li
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, School of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Linfeng Chen
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, School of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Weili Zeng
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, School of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Hong Yuan
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, School of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Chunrong Liu
- Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensing Technology and Health, School of Chemistry, Central China Normal University, Wuhan, 430079, China.
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6
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Melodia D, Di Pietro Z, Cao C, Stenzel MH, Chapman R. Traceless pH-Sensitive Antibody Conjugation Inspired by Citraconic Anhydride. Biomacromolecules 2022; 23:5322-5329. [PMID: 36395470 DOI: 10.1021/acs.biomac.2c01125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We introduce a pH-sensitive amide bond, inspired by citraconic anhydride, for the reversible conjugation of polymers to the lysine residues of proteins and antibodies. The pH sensitivity arises from a conformation lock at the end of the polymer, which we introduce by means of a Diels-Alder reaction, that positions a carboxylic acid close to the amide after conjugation occurs. The amide is stable over weeks at pH 7.4 but sensitive to hydrolysis at pH 5.5 and below, returning the amine to its original state. The pH sensitivity can be tuned by positioning secondary amide groups nearby. We use this approach to PEGylate an antibody to human serum albumin at high dilution and demonstrate successful recovery of the activity after hydrolysis at pH 5.5. These results offer a convenient and traceless approach to protein and antibody functionalization.
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Affiliation(s)
- Daniele Melodia
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Zachary Di Pietro
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Cheng Cao
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia
| | | | - Robert Chapman
- School of Chemistry, UNSW Sydney, Kensington, NSW 2052, Australia.,School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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7
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Garrido Ruiz D, Sandoval-Perez A, Rangarajan AV, Gunderson EL, Jacobson MP. Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation. Biochemistry 2022; 61:2165-2176. [PMID: 36161872 PMCID: PMC9583617 DOI: 10.1021/acs.biochem.2c00349] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cysteine side chains
can exist in distinct oxidation
states depending
on the pH and redox potential of the environment, and cysteine oxidation
plays important yet complex regulatory roles. Compared with the effects
of post-translational modifications such as phosphorylation, the effects
of oxidation of cysteine to sulfenic, sulfinic, and sulfonic acid
on protein structure and function remain relatively poorly characterized.
We present an analysis of the role of cysteine reactivity as a regulatory
factor in proteins, emphasizing the interplay between electrostatics
and redox potential as key determinants of the resulting oxidation
state. A review of current computational approaches suggests underdeveloped
areas of research for studying cysteine reactivity through molecular
simulations.
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Affiliation(s)
- Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Angelica Sandoval-Perez
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Amith Vikram Rangarajan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Emma L Gunderson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
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8
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Lunzer M, Maryasin B, Zandrini T, Baudis S, Ovsianikov A, Liska R. A disulfide-based linker for thiol-norbornene conjugation: formation and cleavage of hydrogels by the use of light. Polym Chem 2022; 13:1158-1168. [PMID: 35341220 PMCID: PMC8886483 DOI: 10.1039/d1py00914a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/03/2022] [Indexed: 11/21/2022]
Abstract
Photolabile groups are the key components of photo-responsive polymers, dynamically tunable materials with multiple applications in materials and life sciences. They usually consist of a chromophore and a labile bond and are inherently light sensitive. An exception are disulfides, simple reversible linkages, which become photocleavable upon addition of a photoinitiator. Despite their practical features, disulfides are rarely utilized due to their impractical formation. Here, we report a disulfide-based linker series bearing norbornene terminals for facile crosslinking of thiol-functionalized macromers via light-triggered thiol-ene conjugation (TEC). Besides finding a highly reactive lead compound, we also identify an unexpected TEC-retardation, strongly dependent on the molecular linker structure and affecting hydrogel stability. Finally, we present a useful method for localized disulfide cleavage by two-photon irradiation permitting micropatterning of disulfide-crosslinked networks.
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Affiliation(s)
- Markus Lunzer
- Institute of Applied Synthetic Chemistry, Technische Universität Wien Getreidemarkt 9/E163 1060 Vienna Austria
- Institute of Materials Science and Technology, Technische Universität Wien Getreidemarkt 9/E308 1060 Vienna Austria
| | - Boris Maryasin
- Institute of Organic Chemistry, University of Vienna Währinger Strasse 38 1090 Vienna Austria
- Institute of Theoretical Chemistry, University of Vienna Währinger Strasse 17 1090 Vienna Austria
| | - Tommaso Zandrini
- Institute of Materials Science and Technology, Technische Universität Wien Getreidemarkt 9/E308 1060 Vienna Austria
| | - Stefan Baudis
- Institute of Applied Synthetic Chemistry, Technische Universität Wien Getreidemarkt 9/E163 1060 Vienna Austria
| | - Aleksandr Ovsianikov
- Institute of Materials Science and Technology, Technische Universität Wien Getreidemarkt 9/E308 1060 Vienna Austria
| | - Robert Liska
- Institute of Applied Synthetic Chemistry, Technische Universität Wien Getreidemarkt 9/E163 1060 Vienna Austria
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9
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Shi Y, Carroll KS. Parallel evaluation of nucleophilic and electrophilic chemical probes for sulfenic acid: Reactivity, selectivity and biocompatibility. Redox Biol 2021; 46:102072. [PMID: 34298464 PMCID: PMC8321940 DOI: 10.1016/j.redox.2021.102072] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/11/2021] [Accepted: 07/14/2021] [Indexed: 12/19/2022] Open
Abstract
Cysteine sulfenic acids (Cys-SOH) are pivotal modifications in thiol-based redox signaling and central intermediates en route to disulfide and sulfinic acid states. A core mission in our lab is to develop bioorthogonal chemical tools with the potential to answer mechanistic questions involving cysteine oxidation. Our group, among others, has contributed to the development of nucleophilic chemical probes for detecting sulfenic acids in living cells. Recently, another class of Cys-SOH probes based on strained alkene and alkyne electrophiles has emerged. However, the use of different models of sulfenic acid and methodologies, has confounded clear comparison of these probes with respect to chemical reactivity, kinetics, and selectivity. Here, we perform a parallel evaluation of nucleophilic and electrophilic chemical probes for Cys-SOH. Among the key findings, we demonstrate that a probe for Cys-SOH based on the norbornene scaffold does not react with any of the validated sulfenic acid models in this study. Furthermore, we show that purported cross-reactivity of dimedone-like probes with electrophiles, like aldehydes and cyclic sulfenamides, is a not meaningful in a biological setting. In summary, nucleophilic probes remain the most viable tools for bioorthogonal detection of Cys-SOH.
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Affiliation(s)
- Yunlong Shi
- Department of Chemistry, Scripps Research, Jupiter, FL 33458, USA
| | - Kate S Carroll
- Department of Chemistry, Scripps Research, Jupiter, FL 33458, USA.
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10
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Abstract
Click chemistry has been established rapidly as one of the most valuable methods for the chemical transformation of complex molecules. Due to the rapid rates, clean conversions to the products, and compatibility of the reagents and reaction conditions even in complex settings, it has found applications in many molecule-oriented disciplines. From the vast landscape of click reactions, approaches have emerged in the past decade centered around oxidative processes to generate in situ highly reactive synthons from dormant functionalities. These approaches have led to some of the fastest click reactions know to date. Here, we review the various methods that can be used for such oxidation-induced "one-pot" click chemistry for the transformation of small molecules, materials, and biomolecules. A comprehensive overview is provided of oxidation conditions that induce a click reaction, and oxidation conditions are orthogonal to other click reactions so that sequential "click-oxidation-click" derivatization of molecules can be performed in one pot. Our review of the relevant literature shows that this strategy is emerging as a powerful approach for the preparation of high-performance materials and the generation of complex biomolecules. As such, we expect that oxidation-induced "one-pot" click chemistry will widen in scope substantially in the forthcoming years.
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Affiliation(s)
- Bauke Albada
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands
| | - Jordi F Keijzer
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands.,School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, China.,Department of Chemical and Materials Engineering, Faculty of Engineering, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Floris van Delft
- Laboratory of Organic Chemistry, Wageningen University & Research, Stippeneng 4, 6807 WE Wageningen, The Netherlands.,Synaffix BV, Industrielaan 63, 5349 AE, Oss, The Netherlands
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11
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Hermann T, Hochegger P, Dolensky J, Seebacher W, Saf R, Kaiser M, Mäser P, Weis R. New Acyl Derivatives of 3-Aminofurazanes and Their Antiplasmodial Activities. Pharmaceuticals (Basel) 2021; 14:ph14050412. [PMID: 33925485 PMCID: PMC8145535 DOI: 10.3390/ph14050412] [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: 03/29/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 11/16/2022] Open
Abstract
An N-acylated furazan-3-amine of a Medicines for Malaria Venture (MMV) project has shown activity against different strains of Plasmodium falciparum. Seventeen new derivatives were prepared and tested in vitro for their activities against blood stages of two strains of Plasmodium falciparum. Several structure-activity relationships were revealed. The activity strongly depended on the nature of the acyl moiety. Only benzamides showed promising activity. The substitution pattern of their phenyl ring affected the activity and the cytotoxicity of compounds. In addition, physicochemical parameters were calculated (log P, log D, ligand efficiency) or determined experimentally (permeability) via a PAMPA. The N-(4-(3,4-diethoxyphenyl)-1,2,5-oxadiazol-3-yl)-3-(trifluoromethyl)benzamide possessed good physicochemical properties and showed high antiplasmodial activity against a chloroquine-sensitive strain (IC50(NF54) = 0.019 µM) and even higher antiplasmodial activity against a multiresistant strain (IC50(K1) = 0.007 µM). Compared to the MMV compound, the permeability and the activity against the multiresistant strain were improved.
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Affiliation(s)
- Theresa Hermann
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (T.H.); (J.D.); (W.S.); (R.W.)
| | - Patrick Hochegger
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (T.H.); (J.D.); (W.S.); (R.W.)
- Correspondence: ; Tel.: +43-316-380-5379; Fax: +43-316-380-9846
| | - Johanna Dolensky
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (T.H.); (J.D.); (W.S.); (R.W.)
| | - Werner Seebacher
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (T.H.); (J.D.); (W.S.); (R.W.)
| | - Robert Saf
- Institute for Chemistry and Technology of Materials (ICTM), Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria;
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute, Socinstraße 57, CH-4002 Basel, Switzerland; (M.K.); (P.M.)
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, Socinstraße 57, CH-4002 Basel, Switzerland; (M.K.); (P.M.)
| | - Robert Weis
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, Schubertstraße 1, A-8010 Graz, Austria; (T.H.); (J.D.); (W.S.); (R.W.)
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12
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Jones D, Wang F, Winkler D, Brunger M. The electronic structure of bicyclo[2.2.2]octa-2,5-dione. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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A critical evaluation of probes for cysteine sulfenic acid. Curr Opin Chem Biol 2020; 60:55-65. [PMID: 32866852 DOI: 10.1016/j.cbpa.2020.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/18/2020] [Accepted: 07/24/2020] [Indexed: 12/31/2022]
Abstract
Cysteine oxidation is important in cellular redox regulation, signaling, and biocatalysis. To understand the biological relevance of cysteine oxidation, it is desirable to identify the proteins involved, the site of the oxidized cysteine, and the relevant oxidation states. Because the thiol of cysteine can be converted to a wide range of oxidation states, mapping these oxidative modifications is challenging. The dynamic and reversible nature of many cysteine oxidation states compounds the difficulty in such proteomic analyses. In this review, we examine methods to detect cysteine sulfenic acid - a particularly challenging functional group to analyze because of its reactive nature. We focus on the selectivity of recently reported probes and discuss some challenges and opportunities in this field.
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14
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Alcock LJ, Langini M, Stühler K, Remke M, Perkins MV, Bernardes GJL, Chalker JM. Proteome‐Wide Survey of Cysteine Oxidation by Using a Norbornene Probe. Chembiochem 2020; 21:1329-1334. [DOI: 10.1002/cbic.201900729] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Lisa J. Alcock
- Flinders University College of Science and Engineering Sturt Road Bedford Park South Australia 5042 Australia
- Flinders University Institute for Nanoscale Science and Technology Sturt Road Bedford Park South Australia 5042 Australia
| | - Maike Langini
- Molecular Proteomics Laboratory (MPL) Biomedical Research Center (BMFZ) Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Division of Pediatric Neuro-Oncogenomics German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) Partner site University Hospital Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
- Department of Pediatric Oncology, Hematology and Clinical Immunology Medical Faculty Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Institute of Neuropathology Medical Faculty Heinrich Heine University Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
| | - Kai Stühler
- Molecular Proteomics Laboratory (MPL) Biomedical Research Center (BMFZ) Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Institute of Molecular Medicine University Hospital Düsseldorf Universitätsstrasse 1 40225 Düsseldorf Germany
| | - Marc Remke
- Division of Pediatric Neuro-Oncogenomics German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK) Partner site University Hospital Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
- Department of Pediatric Oncology, Hematology and Clinical Immunology Medical Faculty Heinrich Heine University Universitätsstrasse 1 40225 Düsseldorf Germany
- Institute of Neuropathology Medical Faculty Heinrich Heine University Düsseldorf Moorenstrasse 5 40225 Düsseldorf Germany
| | - Michael V. Perkins
- Flinders University College of Science and Engineering Sturt Road Bedford Park South Australia 5042 Australia
| | - Gonçalo J. L. Bernardes
- University of Cambridge Department of Chemistry Lensfield Road Cambridge CB2 1EW UK
- Instituto de Medicina Molecular Faculdade de Medicina Universidade de Lisboa Avenida Professor Egas Moniz 1649-028 Lisboa Portugal
| | - Justin M. Chalker
- Flinders University College of Science and Engineering Sturt Road Bedford Park South Australia 5042 Australia
- Flinders University Institute for Nanoscale Science and Technology Sturt Road Bedford Park South Australia 5042 Australia
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15
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Shi Y, Carroll KS. Activity-Based Sensing for Site-Specific Proteomic Analysis of Cysteine Oxidation. Acc Chem Res 2020; 53:20-31. [PMID: 31869209 DOI: 10.1021/acs.accounts.9b00562] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Oxidative post-translational modifications (OxiPTMs) of cysteine residues are the molecular foundation of thiol-based redox regulation that modulates physiological events such as cell proliferation, differentiation, and migration and, when dysregulated, can lead to biomolecule damage and cell death. Common OxiPTMs of cysteine thiols (-SH) include reversible modifications such as S-sulfenylation (-SOH), S-glutathionylation (-SSG), disulfide formation (-SSR), S-nitrosylation (-SNO), and S-sulfhydration (-SSH) as well as more biologically stable modifications like S-sulfinylation (-SO2H) and S-sulfonylation (-SO3H). In the past decade, our laboratory has developed first-in-class chemistry-based tools and proteomic methods to advance the field of thiol-based redox biology and oxidative stress. In this Account, we take the reader through the historical aspects of probe development and application in our laboratory, highlighting key advances in our understanding of sulfur chemistry, in the test tube and in living systems. Offering superior resolution, throughput, accuracy, and reproducibility, mass spectrometry (MS)-based proteomics coupled to chemoselective "activity-based" small-molecule probes is the most rigorous technique for global mapping of cysteine OxiPTMs. Herein, we describe the evolution of this field from indirect detection to state-of-the-art site-centric quantitative chemoproteomic approaches that enable mapping of physiological and pathological changes in cysteine oxidation. These methods enable protein and site-level identification, mechanistic studies, mapping fold-changes, and modification stoichiometry. In particular, this Account focuses on activity-based methods for profiling S-sulfenylation, S-sulfinylation, and S-sulfhydration with an eye toward new reactions and methodologies developed in our group as well as their applications that have shed new light on fundamental processes of redox biology. Among several classes of sulfenic acid probes, dimedone-based C-nucleophiles possess superior chemical selectivity and compatibility with tandem MS. Cell-permeable dimedone derivatives with a bioconjugation handle are capable of detecting of S-sulfenylation in living cells. In-depth screening of a C-nucleophile library has yielded several entities with significantly enhanced reactivity over dimedone while maintaining selectivity, and reversible linear C-nucleophiles that enable controlled target release. C-Nucleophiles have also been implemented in tag-switch methods to detect S-sulfhydration. Most recently, activity-based detection of protein S-sulfinylation with electrophilic nitrogen species (ENS), such as C-nitroso compounds and electron deficient diazines, offers significant advantages in simplicity-of-use and target specificity compared to label-free methods. When feasible, the rich information provided by site-centric quantitative proteomics should not be tainted by oxidation artifacts from cell lysis. Therefore, chemoselective probes that function in a native environment with low cytotoxicity, good cell-permeability, and competitive kinetics are desired in modern redox chemoproteomics approaches. As our understanding of sulfur chemistry and redox signaling evolves, newly discovered cysteine OxiPTMs in microorganisms, plants, cells, tissues, and disease models should innovatively promote mechanistic and therapeutic research.
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Affiliation(s)
- Yunlong Shi
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Kate S. Carroll
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida 33458, United States
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16
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de Vries RH, Viel JH, Oudshoorn R, Kuipers OP, Roelfes G. Selective Modification of Ribosomally Synthesized and Post-Translationally Modified Peptides (RiPPs) through Diels-Alder Cycloadditions on Dehydroalanine Residues. Chemistry 2019; 25:12698-12702. [PMID: 31361053 PMCID: PMC6790694 DOI: 10.1002/chem.201902907] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 07/29/2019] [Indexed: 11/08/2022]
Abstract
We report the late‐stage chemical modification of ribosomally synthesized and post‐translationally modified peptides (RIPPs) by Diels–Alder cycloadditions to naturally occurring dehydroalanines. The tail region of the thiopeptide thiostrepton could be modified selectively and efficiently under microwave heating and transition‐metal‐free conditions. The Diels–Alder adducts were isolated and the different site‐ and endo/exo isomers were identified by 1D/2D 1H NMR. Via efficient modification of the thiopeptide nosiheptide and the lanthipeptide nisin Z the generality of the method was established. Minimum inhibitory concentration (MIC) assays of the purified thiostrepton Diels–Alder products against thiostrepton‐susceptible strains displayed high activities comparable to that of native thiostrepton. These Diels–Alder products were also subjected successfully to inverse‐electron‐demand Diels–Alder reactions with a variety of functionalized tetrazines, demonstrating the utility of this method for labeling of RiPPs.
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Affiliation(s)
- Reinder H de Vries
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Jakob H Viel
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Ruben Oudshoorn
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
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17
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Diastereoselective Opening of Bridged Anhydrides by Amidoximes Providing Access to 1,2,4-Oxadiazole/Norborna(e)ne Hybrids. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900843] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Scinto SL, Ekanayake O, Seneviratne U, Pigga JE, Boyd SJ, Taylor MT, Liu J, Am Ende CW, Rozovsky S, Fox JM. Dual-Reactivity trans-Cyclooctenol Probes for Sulfenylation in Live Cells Enable Temporal Control via Bioorthogonal Quenching. J Am Chem Soc 2019; 141:10932-10937. [PMID: 31246462 DOI: 10.1021/jacs.9b01164] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sulfenylation (RSH → RSOH) is a post-translational protein modification associated with cellular mechanisms for signal transduction and the regulation of reactive oxygen species. Protein sulfenic acids are challenging to identify and study due to their electrophilic and transient nature. Described here are sulfenic acid modifying trans-cycloocten-5-ol (SAM-TCO) probes for labeling sulfenic acid functionality in live cells. These probes enable a new mode of capturing sulfenic acids via transannular thioetherification, whereas "ordinary" trans-cyclooctenes react only slowly with sulfenic acids. SAM-TCOs combine with sulfenic acid forms of a model peptide and proteins to form stable adducts. Analogously, SAM-TCO with the selenenic acid form of a model protein leads to a selenoetherification product. Control experiments illustrate the need for the transannulation process coupled with the activated trans-cycloalkene functionality. Bioorthogonal quenching of excess unreacted SAM-TCOs with tetrazines in live cells provides both temporal control and a means of preventing artifacts caused by cellular-lysis. A SAM-TCO biotin conjugate was used to label protein sulfenic acids in live cells, and subsequent quenching by tetrazine prevented further labeling even under harshly oxidizing conditions. A cell-based proteomic study validates the ability of SAM-TCO probes to identify and quantify known sulfenic acid redox proteins as well as targets not captured by dimedone-based probes.
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Affiliation(s)
- Samuel L Scinto
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Oshini Ekanayake
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Uthpala Seneviratne
- Pfizer Worldwide Research and Development , Cambridge , Massachusetts 02139 , United States
| | - Jessica E Pigga
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Samantha J Boyd
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Michael T Taylor
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Jun Liu
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Christopher W Am Ende
- Pfizer Worldwide Research and Development , Groton , Connecticut 06340 , United States
| | - Sharon Rozovsky
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Joseph M Fox
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
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19
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Naveen K, Perumal PT, Cho DH. Domino Palladium-Catalyzed Double Norbornene Insertion/Annulation Reaction: Expeditious Synthesis of Overcrowded Tetrasubstituted Olefins. Org Lett 2019; 21:4350-4354. [DOI: 10.1021/acs.orglett.9b01543] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Kanagaraj Naveen
- Advanced Industrial Chemistry Research Centre, Korea Research Institute of Chemical Technology, 45, Jongga-ro, Jung-gu, Ulsan 44412, Republic of Korea
- Organic and Bio-organic Chemistry, Central Leather Research Institute (CSIR), Adyar, Chennai 600 020, India
| | | | - Deug-Hee Cho
- Advanced Industrial Chemistry Research Centre, Korea Research Institute of Chemical Technology, 45, Jongga-ro, Jung-gu, Ulsan 44412, Republic of Korea
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20
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Alcock LJ, Oliveira BL, Deery MJ, Pukala TL, Perkins MV, Bernardes GJL, Chalker JM. Norbornene Probes for the Detection of Cysteine Sulfenic Acid in Cells. ACS Chem Biol 2019; 14:594-598. [PMID: 30893551 DOI: 10.1021/acschembio.8b01104] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Norbornene derivatives were validated as probes for cysteine sulfenic acid on proteins and in live cells. Trapping sulfenic acids with norbornene probes is highly selective and revealed a different reactivity profile than the traditional dimedone reagent. The norbornene probe also revealed a superior chemoselectivity when compared to a commonly used dimedone probe. Together, these results advance the study of cysteine oxidation in biological systems.
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Affiliation(s)
- Lisa J. Alcock
- Flinders University, College of Science and Engineering, Sturt Road, Bedford Park, South Australia 5042, Australia
- Flinders University, Institute for NanoScale Science and Technology, Sturt Road, Bedford Park, South Australia 5042, Australia
| | - Bruno L. Oliveira
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Tara L. Pukala
- The University of Adelaide, School of Physical Sciences, Adelaide, South Australia 5005, Australia
| | - Michael V. Perkins
- Flinders University, College of Science and Engineering, Sturt Road, Bedford Park, South Australia 5042, Australia
| | - Gonçalo J. L. Bernardes
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028, Lisboa, Portugal
| | - Justin M. Chalker
- Flinders University, College of Science and Engineering, Sturt Road, Bedford Park, South Australia 5042, Australia
- Flinders University, Institute for NanoScale Science and Technology, Sturt Road, Bedford Park, South Australia 5042, Australia
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21
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Reactive-cysteine profiling for drug discovery. Curr Opin Chem Biol 2019; 50:29-36. [PMID: 30897495 DOI: 10.1016/j.cbpa.2019.02.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 01/10/2023]
Abstract
The recognition that only a small percentage of known human gene products are druggable using traditional modes of non-covalent ligand design, has led to a resurgence in targeted covalent inhibitors. Covalent inhibitors offer advantages over non-covalent inhibitors in engaging otherwise challenging targets. Reactive cysteine residues on proteins are a common target for covalent inhibitors, whereby the high nucleophilicity of the cysteine thiol under physiological conditions provides an ideal anchoring site for electrophilic small molecules. A chemical-proteomic platform, termed isoTOP-ABPP, allows for profiling cysteine reactivity in complex proteomes and is one of many techniques that can aid in two aspects of the covalent-inhibitor development process: (1) to identify functional cysteines that lead to modulation of protein activity through covalent modification; and, (2) to determine cellular targets and evaluate promiscuity of electrophilic fragments, small molecules, and natural products. Herein, we discuss recent advances in isoTOP-ABPP and potential applications of this technology in the drug-discovery pipeline.
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22
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Chang X, Sun XS, Che C, Hu YZ, Tao HY, Wang CJ. Copper(I)-Catalyzed Kinetic Resolution of exo-3-Oxodicyclopentadienes and endo-3-Oxodicyclopentadiene. Org Lett 2019; 21:1191-1196. [PMID: 30707591 DOI: 10.1021/acs.orglett.9b00136] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The first example of highly efficient kinetic resolution of exo-3-oxodicyclopentadienes and endo-3-oxodicyclopentadiene has been developed by means of Cu(I)-catalyzed asymmetric 1,3-dipolar cycloaddition of azomethine ylide. Compared with the existing methodologies for those synthetically important optically active convex molecules, the current protocol provides an alternative but more practical approach from the readily available racemic starting materials, which is free from the repetitive reduction/oxidation steps in the enzymatic resolution or the indispensable stoichiometric amount of chirality-induction reagents.
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Affiliation(s)
- Xin Chang
- College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , China
| | - Xi-Shang Sun
- College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , China
| | - Chao Che
- College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , China
| | - Yuan-Zheng Hu
- College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , China
| | - Hai-Yan Tao
- College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , China
| | - Chun-Jiang Wang
- College of Chemistry and Molecular Sciences , Wuhan University , Wuhan 430072 , China.,State Key Laboratory of Elemento-organic Chemistry , Nankai University , Tianjin 300071 , China
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23
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Gehringer M, Laufer SA. Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology. J Med Chem 2019; 62:5673-5724. [PMID: 30565923 DOI: 10.1021/acs.jmedchem.8b01153] [Citation(s) in RCA: 396] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Targeted covalent inhibitors (TCIs) are designed to bind poorly conserved amino acids by means of reactive groups, the so-called warheads. Currently, targeting noncatalytic cysteine residues with acrylamides and other α,β-unsaturated carbonyl compounds is the predominant strategy in TCI development. The recent ascent of covalent drugs has stimulated considerable efforts to characterize alternative warheads for the covalent-reversible and irreversible engagement of noncatalytic cysteine residues as well as other amino acids. This Perspective article provides an overview of warheads-beyond α,β-unsaturated amides-recently used in the design of targeted covalent ligands. Promising reactive groups that have not yet demonstrated their utility in TCI development are also highlighted. Special emphasis is placed on the discussion of reactivity and of case studies illustrating applications in medicinal chemistry and chemical biology.
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Affiliation(s)
- Matthias Gehringer
- Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , Germany
| | - Stefan A Laufer
- Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , Germany
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24
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Lackmann JW, Wende K, Verlackt C, Golda J, Volzke J, Kogelheide F, Held J, Bekeschus S, Bogaerts A, Schulz-von der Gathen V, Stapelmann K. Chemical fingerprints of cold physical plasmas - an experimental and computational study using cysteine as tracer compound. Sci Rep 2018; 8:7736. [PMID: 29769633 PMCID: PMC5955931 DOI: 10.1038/s41598-018-25937-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/19/2018] [Indexed: 12/13/2022] Open
Abstract
Reactive oxygen and nitrogen species released by cold physical plasma are being proposed as effectors in various clinical conditions connected to inflammatory processes. As these plasmas can be tailored in a wide range, models to compare and control their biochemical footprint are desired to infer on the molecular mechanisms underlying the observed effects and to enable the discrimination between different plasma sources. Here, an improved model to trace short-lived reactive species is presented. Using FTIR, high-resolution mass spectrometry, and molecular dynamics computational simulation, covalent modifications of cysteine treated with different plasmas were deciphered and the respective product pattern used to generate a fingerprint of each plasma source. Such, our experimental model allows a fast and reliable grading of the chemical potential of plasmas used for medical purposes. Major reaction products were identified to be cysteine sulfonic acid, cystine, and cysteine fragments. Less-abundant products, such as oxidized cystine derivatives or S-nitrosylated cysteines, were unique to different plasma sources or operating conditions. The data collected point at hydroxyl radicals, atomic O, and singlet oxygen as major contributing species that enable an impact on cellular thiol groups when applying cold plasma in vitro or in vivo.
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Affiliation(s)
- J-W Lackmann
- Biomedical Applications of Plasma Technology, Ruhr University Bochum, Universitätsstr 150, 44780, Bochum, Germany. .,ZIK plasmatis, Leibniz-Institute for Plasma Science and Technology, Felix-Hausdorff-Str. 2, 17489, Greifswald, Germany.
| | - K Wende
- ZIK plasmatis, Leibniz-Institute for Plasma Science and Technology, Felix-Hausdorff-Str. 2, 17489, Greifswald, Germany.
| | - C Verlackt
- PLASMANT, University of Antwerp, Universiteitsplein 1, 2610, Antwerp-Wilrijk, Belgium
| | - J Golda
- Experimental Physics II, Ruhr University Bochum, Universitätsstr 150, 44780, Bochum, Germany
| | - J Volzke
- ZIK plasmatis, Leibniz-Institute for Plasma Science and Technology, Felix-Hausdorff-Str. 2, 17489, Greifswald, Germany
| | - F Kogelheide
- Biomedical Applications of Plasma Technology, Ruhr University Bochum, Universitätsstr 150, 44780, Bochum, Germany
| | - J Held
- Experimental Physics II, Ruhr University Bochum, Universitätsstr 150, 44780, Bochum, Germany
| | - S Bekeschus
- ZIK plasmatis, Leibniz-Institute for Plasma Science and Technology, Felix-Hausdorff-Str. 2, 17489, Greifswald, Germany
| | - A Bogaerts
- PLASMANT, University of Antwerp, Universiteitsplein 1, 2610, Antwerp-Wilrijk, Belgium
| | - V Schulz-von der Gathen
- Experimental Physics II, Ruhr University Bochum, Universitätsstr 150, 44780, Bochum, Germany
| | - K Stapelmann
- Biomedical Applications of Plasma Technology, Ruhr University Bochum, Universitätsstr 150, 44780, Bochum, Germany.,Department of Nuclear Engineering, Plasma for Life Sciences, North Carolina State University, Raleigh, NC, 27695, USA
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25
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Alcock LJ, Perkins MV, Chalker JM. Chemical methods for mapping cysteine oxidation. Chem Soc Rev 2018; 47:231-268. [DOI: 10.1039/c7cs00607a] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Methods to characterise oxidative modifications of cysteine help clarify their role in protein function in both healthy and diseased cells.
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Affiliation(s)
- Lisa J. Alcock
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
| | - Michael V. Perkins
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
| | - Justin M. Chalker
- College of Science and Engineering
- Flinders University
- South Australia
- Australia
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26
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Abstract
Cysteine thiols are involved in a diverse set of biological transformations, including nucleophilic and redox catalysis, metal coordination and formation of both dynamic and structural disulfides. Often posttranslationally modified, cysteines are also frequently alkylated by electrophilic compounds, including electrophilic metabolites, drugs, and natural products, and are attractive sites for covalent probe and drug development. Quantitative proteomics combined with activity-based protein profiling has been applied to annotate cysteine reactivity, susceptibility to posttranslational modifications, and accessibility to chemical probes, uncovering thousands of functional and small-molecule targetable cysteines across a diverse set of proteins, proteome-wide in an unbiased manner. Reactive cysteines have been targeted by high-throughput screening and fragment-based ligand discovery efforts. New cysteine-reactive electrophiles and compound libraries have been synthesized to enable inhibitor discovery broadly and to minimize nonspecific toxicity and off-target activity of compounds. With the recent blockbuster success of several covalent inhibitors, and the development of new chemical proteomic strategies to broadly identify reactive, ligandable and posttranslationally modified cysteines, cysteine profiling is poised to enable the development of new potent and selective chemical probes and even, in some cases, new drugs.
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