Isotopic tagging of oxidized and reduced cysteines (iTORC) for detecting and quantifying sulfenic acids, disulfides, and free thiols in cells

Albertolle, Matthew E.; Glass, Sarah M.; Trefts, Elijah; Guengerich, F. Peter

doi:10.1074/jbc.ac118.007225

Cited by 9 publications

(7 citation statements)

References 34 publications

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“…Importantly, only redox-sensitive Cys149 exhibited an increase in the fraction of sulfenic acid modification in response to H 2 O 2 . In an elegant modification of this chemical strategy, Guengerich and co-workers prepared BTD and iodo-BTD derivatives 13 C 6 d 7 -pBTD, d 7 -ipBTD, and d 0 -ipBTD to quantify sulfenic acids, free thiols, and reversible OxiPTMs in complex proteomes (Figure b) . A relatively low number (∼600) of sulfenylated peptides can be attributed to the lack of an enrichment handle.…”

Section: Site-centric Quantitative Proteomicsmentioning

confidence: 99%

Activity-Based Sensing for Site-Specific Proteomic Analysis of Cysteine Oxidation

2019

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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 (─SO 2 H) and S-sulfonylation (─SO 3 H). 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 foldchanges, 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 *

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Section: Site-centric Quantitative Proteomicsmentioning

confidence: 99%

Activity-Based Sensing for Site-Specific Proteomic Analysis of Cysteine Oxidation

2019

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“…recently reported an alternative approach that uses isotope‐substituted BTD (pBTD) and iodo‐BTD (ipBTD) probes to tag SOH, free thiols, and disulfides (after TCEP reduction). The so‐called isotopic tagging of oxidized and reduced cysteines (iTORC) method [89] allows one to assess SOH and total thiol oxidation stoichiometry. Mouse hepatocyte lysates were incubated with 13 C 6 ‐d 7 ‐pBTD first to directly label SOH, followed by d 7 ‐ipBTD to label SH.…”

Section: Chemoselective Probe‐based Methodsmentioning

confidence: 99%

Thiol redox proteomics: Characterization of thiol‐based post‐translational modifications

Gluth

Zhang

et al. 2023

Proteomics

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Redox post-translational modifications on cysteine thiols (redox PTMs) have profound effects on protein structure and function, thus enabling regulation of various biological processes. Redox proteomics approaches aim to characterize the landscape of redox PTMs at the systems level. These approaches facilitate studies of condition-specific, dynamic processes implicating redox PTMs and have furthered our understanding of redox signaling and regulation. Mass spectrometry (MS) is a powerful tool for such analyses which has been demonstrated by significant advances in redox proteomics during the last decade. A group of well-established approaches involves the initial blocking of free thiols followed by selective reduction of oxidized PTMs and subsequent enrichment for downstream detection. Alternatively, novel chemoselective probe-based approaches have been developed for various redox PTMs. Direct detection of redox PTMs without any enrichment has also been demonstrated given the sensitivity of contemporary MS instruments. This review discusses the general principles behind different analytical strategies and covers recent advances in redox proteomics. Several applications of redox proteomics are also highlighted to illustrate how large-scale redox proteomics data can lead to novel biological insights.

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“…reactive oxygen species (O2•¯, H2O2). Some P450s (e.g., 4A11) appear to be very sensitive to this phenomenon, with conversion of the thiolate group normally liganded to the heme being oxidized to a sulfenic acid (Albertolle et al, 2017(Albertolle et al, , 2018(Albertolle et al, , 2019.…”

Section: Types Of Inhibitionmentioning

confidence: 99%

Inhibition of Cytochrome P450 Enzymes by Drugs-Molecular Basis and Practical Applications

Guengerich

2022

Biomol Ther (Seoul)

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Drug-drug interactions are important and accordingly are a major issue in the advancement of new chemical entities to patients. In one study (Montané et al., 2018), drug-related deaths accounted for 7% of all deaths in hospital settings. Drug-drug interactions are an issue in this regard. Although some pharmacodynamic issues are involved, a large fraction of the drug-drug interactions is pharmacokinetic in nature.A general overview of the interactions of a chemical with an enzyme is shown in Fig. 1A, where an enzyme involved in the metabolism of a drug is considered. The drug is converted to a product, often called a metabolite. With respect to the parent drug molecule, the product may have unaltered pharmacological activity, lose some or all of its pharmacological activity, be even more active, or be toxic. In the interactions of two drugs, one is sometimes termed the "perpetrator" and one the "victim" (Fig. 1B). In some cases, drug interaction due to enhanced metabolism by induction or allosteric activation may be seen and have clinical consequences (Bolt et al., 1977), but the focus here will be on competitive and irreversible inhibitors that attenuate drug metabolism (as "perpetrators").Recently Yu et al. (2018) evaluated drug-drug interactions in 103 recent drug approvals by the United States Food and Drug Administration (FDA). Of these, 45 were involved as victims (substrates) in interactions with marketed drugs (perpetrators). The therapeutic classes are shown in Fig. 2A, with cancer treatments accounting for more than 1/4. The enzymes involved are primarily cytochrome P450 and transporter enzymes (Fig. 2B), with P450 3A4/5 involved in ~2/3 of the interactions. Of the 103 new drugs, 20 were acting as perpetrators to some extent (Yu et al., 2018), with P450 3A4/5 and P-glycoprotein again being the most prominent enzymes (Fig. 1B). Accordingly, this review will focus on issues of inhibition of P450 3A4 (In general P450 3A4 and 3A5 have similar substrate specificity and are sensitive to the same inhibitors, with some important exceptions (Hardy et al., 2014;Zhu et al., 2014;Kramlinger et al., 2015), but many experiments with drugs were done only with P450 3A4-or 3A4 and 3A5 were not discriminated-and will be referred to as 3A4 in that context). BACKGROUND ON P450SP450s enzymes are the main catalysts involved in the oxidation of chemicals in general (Rendic and Guengerich, 2015), including drugs. The same is true for involvement in Please cite this article in press as: Guengerich, Inhibition of Cytochrome P450 Enzymes by Drugs-Molecular Basis and Practical Applications, Biomol. Ther.

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Isotopic tagging of oxidized and reduced cysteines (iTORC) for detecting and quantifying sulfenic acids, disulfides, and free thiols in cells

Cited by 9 publications

References 34 publications

Activity-Based Sensing for Site-Specific Proteomic Analysis of Cysteine Oxidation

Activity-Based Sensing for Site-Specific Proteomic Analysis of Cysteine Oxidation

Thiol redox proteomics: Characterization of thiol‐based post‐translational modifications

Inhibition of Cytochrome P450 Enzymes by Drugs-Molecular Basis and Practical Applications

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