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Julio AR, Shikwana F, Truong C, Burton NR, Dominguez E, Turmon AC, Cao J, Backus K. Pervasive aggregation and depletion of host and viral proteins in response to cysteine-reactive electrophilic compounds. bioRxiv 2023:2023.10.30.564067. [PMID: 38014036 PMCID: PMC10680658 DOI: 10.1101/2023.10.30.564067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Protein homeostasis is tightly regulated, with damaged or misfolded proteins quickly eliminated by the proteasome and autophagosome pathways. By co-opting these processes, targeted protein degradation technologies enable pharmacological manipulation of protein abundance. Recently, cysteine-reactive molecules have been added to the degrader toolbox, which offer the benefit of unlocking the therapeutic potential of 'undruggable' protein targets. The proteome-wide impact of these molecules remains to be fully understood and given the general reactivity of many classes of cysteine-reactive electrophiles, on- and off-target effects are likely. Using chemical proteomics, we identified a cysteine-reactive small molecule degrader of the SARS-CoV-2 non- structural protein 14 (nsp14), which effects degradation through direct modification of cysteines in both nsp14 and in host chaperones together with activation of global cell stress response pathways. We find that cysteine-reactive electrophiles increase global protein ubiquitylation, trigger proteasome activation, and result in widespread aggregation and depletion of host proteins, including components of the nuclear pore complex. Formation of stress granules was also found to be a remarkably ubiquitous cellular response to nearly all cysteine-reactive compounds and degraders. Collectively, our study sheds light on complexities of covalent target protein degradation and highlights untapped opportunities in manipulating and characterizing proteostasis processes via deciphering the cysteine-centric regulation of stress response pathways.
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Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Nguyễn KB, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. Cell Chem Biol 2023; 30:811-827.e7. [PMID: 37419112 PMCID: PMC10510412 DOI: 10.1016/j.chembiol.2023.06.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 04/01/2023] [Accepted: 06/07/2023] [Indexed: 07/09/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxICAT, Biotin Switch, and SP3-Rox, these methods typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. Here we establish the local cysteine capture (Cys-LoC) and local cysteine oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole-cell proteomic analysis. Application of the Cys-LOx method to LPS-stimulated immortalized murine bone marrow-derived macrophages (iBMDM), revealed previously unidentified, mitochondrially localized cysteine oxidative modifications upon pro-inflammatory activation, including those associated with oxidative mitochondrial metabolism.
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Affiliation(s)
- Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Ashley R Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Andréa B Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Lisa M Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Alexandra C Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA
| | - Kaitlyn B Nguyễn
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Stephanie L Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Heta S Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los A ngeles, CA 90095, USA
| | - Keriann M Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA; DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
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Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Yen SL, Desai HS, Divakaruni AS, Backus KM. Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. bioRxiv 2023:2023.01.22.525042. [PMID: 36711448 PMCID: PMC9882296 DOI: 10.1101/2023.01.22.525042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Proteinaceous cysteines function as essential sensors of cellular redox state. Consequently, defining the cysteine redoxome is a key challenge for functional proteomic studies. While proteome-wide inventories of cysteine oxidation state are readily achieved using established, widely adopted proteomic methods such as OxiCat, Biotin Switch, and SP3-Rox, they typically assay bulk proteomes and therefore fail to capture protein localization-dependent oxidative modifications. To obviate requirements for laborious biochemical fractionation, here, we develop and apply an unprecedented two step cysteine capture method to establish the Local Cysteine Capture (Cys-LoC), and Local Cysteine Oxidation (Cys-LOx) methods, which together yield compartment-specific cysteine capture and quantitation of cysteine oxidation state. Benchmarking of the Cys-LoC method across a panel of subcellular compartments revealed more than 3,500 cysteines not previously captured by whole cell proteomic analysis. Application of the Cys-LOx method to LPS stimulated murine immortalized bone marrow-derived macrophages (iBMDM), revealed previously unidentified mitochondria-specific inflammation-induced cysteine oxidative modifications including those associated with oxidative phosphorylation. These findings shed light on post-translational mechanisms regulating mitochondrial function during the cellular innate immune response.
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Affiliation(s)
- Tianyang Yan
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Ashley R. Julio
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Miranda Villanueva
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Anthony E. Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Andréa B. Ball
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Lisa M. Boatner
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Alexandra C. Turmon
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA
| | - Stephanie L. Yen
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Heta S. Desai
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA
| | - Ajit S. Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA
| | - Keriann M. Backus
- Biological Chemistry Department, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, USA.,Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA, 90095, USA.,Molecular Biology Institute, UCLA, Los Angeles, CA, 90095, USA.,DOE Institute for Genomics and Proteomics, UCLA, Los Angeles, CA, 90095, USA.,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA, 90095, USA
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Klein VG, Bray WM, Wang HY, Edmondson Q, Schwochert J, Ono S, Naylor MR, Turmon AC, Faris JH, Okada O, Taunton J, Lokey RS. Identifying the Cellular Target of Cordyheptapeptide A and Synthetic Derivatives. ACS Chem Biol 2021; 16:1354-1364. [PMID: 34251165 DOI: 10.1021/acschembio.1c00094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cordyheptapeptide A is a lipophilic cyclic peptide from the prized Cordyceps fungal genus that shows potent cytotoxicity in multiple cancer cell lines. To better understand the bioactivity and physicochemical properties of cordyheptapeptide A with the ultimate goal of identifying its cellular target, we developed a solid-phase synthesis of this multiply N-methylated cyclic heptapeptide which enabled rapid access to both side chain- and backbone-modified derivatives. Removal of one of the backbone amide N-methyl (N-Me) groups maintained bioactivity, while membrane permeability was also preserved due to the formation of a new intramolecular hydrogen bond in a low dielectric solvent. Based on its cytotoxicity profile in the NCI-60 cell line panel, as well as its phenotype in a microscopy-based cytological assay, we hypothesized that cordyheptapeptide was acting on cells as a protein synthesis inhibitor. Further studies revealed the molecular target of cordyheptapeptide A to be the eukaryotic translation elongation factor 1A (eEF1A), a target shared by other lipophilic cyclic peptide natural products. This work offers a strategy to study and improve cyclic peptide natural products while highlighting the ability of these lipophilic compounds to effectively inhibit intracellular disease targets.
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Affiliation(s)
- Victoria G. Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Walter M. Bray
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Hao-Yuan Wang
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, 94158, United States
| | - Quinn Edmondson
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Satoshi Ono
- Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Kanagawa 227-0033, Japan
| | - Matthew R. Naylor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Alexandra C. Turmon
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Justin H. Faris
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
| | - Okimasa Okada
- Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Kanagawa 227-0033, Japan
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, 94158, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, United States
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Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug-Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side-Chain Lipophilicity. Angew Chem Int Ed Engl 2020; 59:21571-21577. [PMID: 32789999 PMCID: PMC7719619 DOI: 10.1002/anie.202004550] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/10/2020] [Indexed: 12/22/2022]
Abstract
Large macrocyclic peptides can achieve surprisingly high membrane permeability, although the properties that govern permeability in this chemical space are only beginning to come into focus. We generated two libraries of cyclic decapeptides with stable cross-β conformations, and found that peptoid substitutions within the β-turns of the macrocycle preserved the rigidity of the parent scaffold, whereas peptoid substitutions in the opposing β-strands led to "chameleonic" species that were rigid in nonpolar media but highly flexible in water. Both rigid and chameleonic compounds showed high permeability over a wide lipophilicity range, with peak permeabilities differing significantly depending on scaffold rigidity. Our findings indicate that modulating lipophilicity can be used to engineer favorable ADME properties into both rigid and flexible macrocyclic peptides, and that scaffold rigidity can be used to tune optimal lipophilicity.
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Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Joshua Schwochert
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd., 1-2-58, Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Alexandra C. Turmon
- Unnatural Products, Inc., 250 Natural Bridges Drive, Santa Cruz, CA 95060 USA
| | - Victoria G. Klein
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - Okimasa Okada
- Discovery Technology Laboratories, Mitsubishi Tanabe Pharma Corporation, Yokohama, 227-0033, Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry, University of California Santa Cruz, Santa Cruz, CA 96064 USA
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6
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Furukawa A, Schwochert J, Pye CR, Asano D, Edmondson QD, Turmon AC, Klein VG, Ono S, Okada O, Lokey RS. Drug‐Like Properties in Macrocycles above MW 1000: Backbone Rigidity versus Side‐Chain Lipophilicity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Akihiro Furukawa
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Joshua Schwochert
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Cameron R. Pye
- Unnatural Products, Inc. 250 Natural Bridges Drive Santa Cruz CA 95060 USA
| | - Daigo Asano
- Daiichi Sankyo Co., Ltd. 1-2-58, Hiromachi, Shinagawa-ku Tokyo 140-8710 Japan
| | - Quinn D. Edmondson
- Department of Pharmaceutical Chemistry University of California, San Francisco San Francisco California 94158 USA
| | | | - Victoria G. Klein
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
| | - Satoshi Ono
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - Okimasa Okada
- Discovery Technology Laboratories Mitsubishi Tanabe Pharma Corporation Yokohama 227-0033 Japan
| | - R. Scott Lokey
- Department of Chemistry & Biochemistry University of California Santa Cruz Santa Cruz CA 96064 USA
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Naylor MR, Ly AM, Handford MJ, Ramos DP, Pye CR, Furukawa A, Klein VG, Noland RP, Edmondson Q, Turmon AC, Hewitt WM, Schwochert J, Townsend CE, Kelly CN, Blanco MJ, Lokey RS. Lipophilic Permeability Efficiency Reconciles the Opposing Roles of Lipophilicity in Membrane Permeability and Aqueous Solubility. J Med Chem 2018; 61:11169-11182. [DOI: 10.1021/acs.jmedchem.8b01259] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Matthew R. Naylor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Andrew M. Ly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Mason J. Handford
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Daniel P. Ramos
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Cameron R. Pye
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Akihiro Furukawa
- Modality Research Laboratories, Daiichi Sankyo Company, Ltd., 1-2-58 Hiromachi, Shingawa-ku, Tokyo 140-8710, Japan
| | - Victoria G. Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Ryan P. Noland
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Quinn Edmondson
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Alexandra C. Turmon
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - William M. Hewitt
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chad E. Townsend
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Colin N. Kelly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Maria-Jesus Blanco
- Sage Therapeutics, 215 First Street, Suite 220, Cambridge, Massachusetts 02142, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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