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Krammer L, Breinbauer R. Activity‐Based Protein Profiling of Oxidases and Reductases. Isr J Chem 2023. [DOI: 10.1002/ijch.202200086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Leo Krammer
- Institute of Organic Chemistry Graz University of Technology Stremayrgasse 9 A-8010 Graz Austria
| | - Rolf Breinbauer
- Institute of Organic Chemistry Graz University of Technology Stremayrgasse 9 A-8010 Graz Austria
- BIOTECHMED Graz A-8010 Graz Austria
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2
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McKenna SM, Fay EM, McGouran JF. Flipping the Switch: Innovations in Inducible Probes for Protein Profiling. ACS Chem Biol 2021; 16:2719-2730. [PMID: 34779621 PMCID: PMC8689647 DOI: 10.1021/acschembio.1c00572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Over the past two
decades, activity-based probes have enabled a
range of discoveries, including the characterization of new enzymes
and drug targets. However, their suitability in some labeling experiments
can be limited by nonspecific reactivity, poor membrane permeability,
or high toxicity. One method for overcoming these issues is through
the development of “inducible” activity-based probes.
These probes are added to samples in an unreactive state and require in situ transformation to their active form before labeling
can occur. In this Review, we discuss a variety of approaches to inducible
activity-based probe design, different means of probe activation,
and the advancements that have resulted from these applications. Additionally,
we highlight recent developments which may provide opportunities for
future inducible activity-based probe innovations.
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Affiliation(s)
- Sean M. McKenna
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC), Bernal Institute, Limerick V94 T9PX, Ireland
| | - Ellen M. Fay
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
| | - Joanna F. McGouran
- School of Chemistry and Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse St, Dublin 2, Ireland
- Synthesis and Solid State Pharmaceutical Centre (SSPC), Bernal Institute, Limerick V94 T9PX, Ireland
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3
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Chen D, Xiao Z, Guo H, Gogishvili D, Setroikromo R, van der Wouden PE, Dekker FJ. Identification of a Bromodomain-like Region in 15-Lipoxygenase-1 Explains Its Nuclear Localization. Angew Chem Int Ed Engl 2021; 60:21875-21883. [PMID: 34388301 PMCID: PMC8518382 DOI: 10.1002/anie.202106968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Indexed: 01/17/2023]
Abstract
Lipoxygenase (LOX) activity provides oxidative lipid metabolites, which are involved in inflammatory disorders and tumorigenesis. Activity-based probes to detect the activity of LOX enzymes in their cellular context provide opportunities to explore LOX biology and LOX inhibition. Here, we developed Labelox B as a potent covalent LOX inhibitor for one-step activity-based labeling of proteins with LOX activity. Labelox B was used to establish an ELISA-based assay for affinity capture and antibody-based detection of specific LOX isoenzymes. Moreover, Labelox B enabled efficient activity-based labeling of endogenous LOXs in living cells. LOX proved to localize in the nucleus, which was rationalized by identification of a functional bromodomain-like consensus motif in 15-LOX-1. This indicates that 15-LOX-1 is not only involved in oxidative lipid metabolism, but also in chromatin binding, which suggests a potential role in chromatin modifications.
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Affiliation(s)
- Deng Chen
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Zhangping Xiao
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Hao Guo
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Dea Gogishvili
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Rita Setroikromo
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Petra E. van der Wouden
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
| | - Frank J. Dekker
- Department Chemical and Pharmaceutical BiologyGroningen Research Institute of Pharmacy (GRIP)University of GroningenAntonius Deusinglaan 19713AVGroningenThe Netherlands
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4
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Chen D, Xiao Z, Guo H, Gogishvili D, Setroikromo R, Wouden PE, Dekker FJ. Identification of a Bromodomain‐like Region in 15‐Lipoxygenase‐1 Explains Its Nuclear Localization. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Deng Chen
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Zhangping Xiao
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Hao Guo
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Dea Gogishvili
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Rita Setroikromo
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Petra E. Wouden
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
| | - Frank J. Dekker
- Department Chemical and Pharmaceutical Biology Groningen Research Institute of Pharmacy (GRIP) University of Groningen Antonius Deusinglaan 1 9713 AV Groningen The Netherlands
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5
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Cahn JKB, Piel J. Anwendungen von Einzelzellmethoden in der mikrobiellen Naturstoffforschung. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.201900532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jackson K. B. Cahn
- Institut für Mikrobiologie Eidgenössische Technische Hochschule Zürich (ETH) 8093 Zürich Schweiz
| | - Jörn Piel
- Institut für Mikrobiologie Eidgenössische Technische Hochschule Zürich (ETH) 8093 Zürich Schweiz
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6
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Cahn JKB, Piel J. Opening up the Single-Cell Toolbox for Microbial Natural Products Research. Angew Chem Int Ed Engl 2021; 60:18412-18428. [PMID: 30748086 DOI: 10.1002/anie.201900532] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Indexed: 02/06/2023]
Abstract
The diverse microbes that produce natural products represent an important source of novel therapeutics, drug leads, and scientific tools. However, the vast majority have not been grown in axenic culture and are members of complex communities. While meta-'omic methods such as metagenomics, -transcriptomics, and -proteomics reveal collective molecular features of this "microbial dark matter", the study of individual microbiome members can be challenging. To address these limits, a number of techniques with single-bacterial resolution have been developed in the last decade and a half. While several of these are embraced by microbial ecologists, there has been less use by researchers interested in mining microbes for natural products. In this review, we discuss the available and emerging techniques for targeted single-cell analysis with a particular focus on applications to the discovery and study of natural products.
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Affiliation(s)
- Jackson K B Cahn
- Instit. of Microbiol., Eidgenössische Technische Hochschule Zürich (ETH), 8093, Zurich, Switzerland
| | - Jörn Piel
- Instit. of Microbiol., Eidgenössische Technische Hochschule Zürich (ETH), 8093, Zurich, Switzerland
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7
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Fuerst R, Breinbauer R. Activity-Based Protein Profiling (ABPP) of Oxidoreductases. Chembiochem 2021; 22:630-638. [PMID: 32881211 PMCID: PMC7894341 DOI: 10.1002/cbic.202000542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/02/2020] [Indexed: 12/20/2022]
Abstract
Over the last two decades, activity-based protein profiling (ABPP) has been established as a tremendously useful proteomic tool for measuring the activity of proteins in their cellular context, annotating the function of uncharacterized proteins, and investigating the target profile of small-molecule inhibitors. Unlike hydrolases and other enzyme classes, which exhibit a characteristic nucleophilic residue, oxidoreductases have received much less attention in ABPP. In this minireview, the state of the art of ABPP of oxidoreductases is described and the scope and limitations of the existing approaches are discussed. It is noted that several ABPP probes have been described for various oxidases, but none so far for a reductase, which gives rise to opportunities for future research.
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Affiliation(s)
- Rita Fuerst
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
| | - Rolf Breinbauer
- Institute of Organic ChemistryGraz University of TechnologyStremayrgasse 98010GrazAustria
- BIOTECHMEDGrazAustria
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8
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Davis TD, Michaud JM, Burkart MD. Active site labeling of fatty acid and polyketide acyl-carrier protein transacylases. Org Biomol Chem 2020; 17:4720-4724. [PMID: 31044196 DOI: 10.1039/c8ob03229g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Metabolic engineering of fatty acids and polyketides remains challenging due to unresolved protein-protein interactions that are essential to synthase activity. While several chemical probes have been developed to capture and visualize protein interfaces in these systems, acyl carrier protein (ACP) transacylase (AT) domains remain elusive. Herein, we combine a mutational strategy with fluorescent probe design to expedite the study of AT domains from fatty acid and polyketide synthases. We describe the design and evaluation of inhibitor-inspired and substrate-mimetic reporters containing sulfonyl fluoride and β-lactone warheads. Moreover, specific active-site labeling occurs by optimizing pH, time, and probe concentration, and selective labeling is achieved in the presence of inhibitors of competing domains. These findings provide a panel of AT-targeting probes and set the stage for future combinatorial biosynthetic and drug discovery initiatives.
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Affiliation(s)
- Tony D Davis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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9
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Vickery CR, McCulloch IP, Sonnenschein EC, Beld J, Noel JP, Burkart MD. Dissecting modular synthases through inhibition: A complementary chemical and genetic approach. Bioorg Med Chem Lett 2020; 30:126820. [PMID: 31812466 DOI: 10.1016/j.bmcl.2019.126820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 11/08/2019] [Accepted: 11/09/2019] [Indexed: 01/23/2023]
Abstract
Modular synthases, such as fatty acid, polyketide, and non-ribosomal peptide synthases (NRPSs), are sophisticated machineries essential in both primary and secondary metabolism. Various techniques have been developed to understand their genetic background and enzymatic abilities. However, uncovering the actual biosynthetic pathways remains challenging. Herein, we demonstrate a pipeline to study an assembly line synthase by interrogating the enzymatic function of each individual enzymatic domain of BpsA, a NRPS that produces the blue 3,3'-bipyridyl pigment indigoidine. Specific inhibitors for each biosynthetic domain of BpsA were obtained or synthesized, and the enzymatic performance of BpsA upon addition of each inhibitor was monitored by pigment development in vitro and in living bacteria. The results were verified using genetic mutants to inactivate each domain. Finally, the results complemented the currently proposed biosynthetic pathway of BpsA.
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Affiliation(s)
- Christopher R Vickery
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ian P McCulloch
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Eva C Sonnenschein
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Joris Beld
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Joseph P Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 248] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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