1
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Gowans FA, Thach DQ, Zhu Z, Wang Y, Altamirano Poblano BE, Dovala D, Tallarico JA, McKenna JM, Schirle M, Maimone TJ, Nomura DK. Ophiobolin A Covalently Targets Mitochondrial Complex IV Leading to Metabolic Collapse in Cancer Cells. ACS Chem Biol 2024. [PMID: 38739449 DOI: 10.1021/acschembio.4c00064] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Ophiobolin A (OPA) is a sesterterpenoid fungal natural product with broad anticancer activity. While OPA possesses multiple electrophilic moieties that can covalently react with nucleophilic amino acids on proteins, the proteome-wide targets and mechanism of OPA remain poorly understood in many contexts. In this study, we used covalent chemoproteomic platforms to map the proteome-wide reactivity of the OPA in a highly sensitive lung cancer cell line. Among several proteins that OPA engaged, we focused on two targets: lysine-72 of cytochrome c oxidase subunit 5A (COX5A) and cysteine-53 of mitochondrial hypoxia induced gene 1 domain family member 2A (HIGD2A). These two subunit proteins are part of complex IV (cytochrome C oxidase) within the electron transport chain and contributed significantly to the antiproliferative activity of OPA. OPA activated mitochondrial respiration in a COX5A- and HIGD2A-dependent manner, leading to an initial spike in mitochondrial ATP and heightened mitochondrial oxidative stress. OPA compromised mitochondrial membrane potential, ultimately leading to ATP depletion. We have used chemoproteomic strategies to discover a unique anticancer mechanism of OPA through activation of complex IV leading to compromised mitochondrial energetics and rapid cell death.
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Affiliation(s)
- Flor A Gowans
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720 United States
| | - Danny Q Thach
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States
| | - Zhouyang Zhu
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States
| | - Yangzhi Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
- Novartis Institutes for BioMedical Research, Basel CH-4056, Switzerland
| | - Belen E Altamirano Poblano
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
- Novartis Institutes for BioMedical Research, Basel CH-4056, Switzerland
| | - Dustin Dovala
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - John A Tallarico
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Jeffrey M McKenna
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Basel CH-4056, Switzerland
| | - Markus Schirle
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Thomas J Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720 United States
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2
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Hong SH, Divakaran A, Osa A, Huang OW, Wertz IE, Nomura DK. Exploiting the Cullin E3 Ligase Adaptor Protein SKP1 for Targeted Protein Degradation. ACS Chem Biol 2024; 19:442-450. [PMID: 38305738 PMCID: PMC10999000 DOI: 10.1021/acschembio.3c00642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Targeted protein degradation with proteolysis targeting chimeras (PROTACs) is a powerful therapeutic modality for eliminating disease-causing proteins through targeted ubiquitination and proteasome-mediated degradation. Most PROTACs have exploited substrate receptors of Cullin-RING E3 ubiquitin ligases such as cereblon and VHL. Whether core, shared, and essential components of the Cullin-RING E3 ubiquitin ligase complex can be used for PROTAC applications remains less explored. Here, we discovered a cysteine-reactive covalent recruiter EN884 against the SKP1 adapter protein of the SKP1-CUL1-F-box containing the SCF complex. We further showed that this recruiter can be used in PROTAC applications to degrade neo-substrate proteins such as BRD4 and the androgen receptor in a SKP1- and proteasome-dependent manner. Our studies demonstrate that core and essential adapter proteins within the Cullin-RING E3 ubiquitin ligase complex can be exploited for targeted protein degradation applications and that covalent chemoproteomic strategies can enable recruiter discovery against these targets.
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Affiliation(s)
- Seong Ho Hong
- Department of Chemistry, University of California, Berkeley, 2151 Berkeley Way, Room 312G, Berkeley, California 94720, United States
- Innovative Genomics Institute, 2151 Berkeley Way, Berkeley, California 94720, United States
| | - Anand Divakaran
- Department of Chemistry, University of California, Berkeley, 2151 Berkeley Way, Room 312G, Berkeley, California 94720, United States
- Innovative Genomics Institute, 2151 Berkeley Way, Berkeley, California 94720, United States
| | - Akane Osa
- Department of Chemistry, University of California, Berkeley, 2151 Berkeley Way, Room 312G, Berkeley, California 94720, United States
- Innovative Genomics Institute, 2151 Berkeley Way, Berkeley, California 94720, United States
| | - Oscar W Huang
- Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Ingrid E Wertz
- Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, 2151 Berkeley Way, Room 312G, Berkeley, California 94720, United States
- Innovative Genomics Institute, 2151 Berkeley Way, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, 2151 Berkeley Way, Room 312G, Berkeley, California 94720, United States
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3
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Shihadih D, Wang X, Zushin PJH, Khodakivskyi P, Park HM, Tso E, Shiblak J, Misic A, Louie SM, Ward C, Hellerstein M, Nomura DK, Goun E, Urigo F, Calvisi DF, Chen X, Stahl A. FATP5 is indispensable for the growth of intrahepatic cholangiocarcinoma. Mol Cancer Res 2024:734312. [PMID: 38358323 DOI: 10.1158/1541-7786.mcr-23-0389] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 11/13/2023] [Accepted: 02/13/2024] [Indexed: 02/16/2024]
Abstract
Altered lipid metabolism is a common hallmark of various cancers, including Intrahepatic Cholangiocarcinoma (ICC), a highly lethal carcinoma that lacks effective treatment options. To elucidate the lipid metabolism changes in ICC, we coupled the expression of the firefly luciferase gene (FFL) to AKT1 (AKT-FFL) via an IRES linker, and then hydrodynamically injected mice with AKT-FFL and Notch1 intracellular cytoplasmic domain (NICD) to establish a luciferase-positive ICC model. This model not only enabled us to monitor and quantify tumor growth by injecting the mice with luciferin, but also allowed us to assess the fatty acid uptake rate by injecting the mice with free fatty acid luciferin (FFA-Luc). The ICC model exhibited robust uptake of exogenous fatty acids compared with the HCC model induced by AKT-FFL/ neuroblastoma Ras (Ras). Lipidomics analysis showed a dramatically higher level of fatty acid in ICC, further supporting the increased fatty acids uptake. Mechanistic studies identified FATP5 as the predominant mediator of fatty acid uptake required for ICC growth using Fatp5 knockout mice and AAV-based shRNA silencing of Fatp5. Our study discovered a novel therapeutic target for the treatment of ICC and shed light on the contributions of lipid metabolism to ICC development. Implications: This study provides the first in vivo evidence that FATP5 is a potential therapeutic target for treating ICC.
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Affiliation(s)
| | - Xue Wang
- University of California, Berkeley, Berkeley, United States
| | | | | | - Hyo Min Park
- University of California, Berkeley, United States
| | - Emily Tso
- University of California, Berkeley, Berkeley, United States
| | - Jena Shiblak
- University of California, Berkeley, Berkeley, United States
| | - Angela Misic
- University of California, Berkeley, United States
| | | | | | | | | | | | | | | | - Xin Chen
- University of California, San Francisco, United States
| | - Andreas Stahl
- University of California, Berkeley, Berkeley, United States
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4
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Meyers M, Cismoski S, Panidapu A, Chie-Leon B, Nomura DK. Targeted Protein Degradation through Recruitment of the CUL4 Complex Adaptor Protein DDB1. ACS Chem Biol 2024; 19:58-68. [PMID: 38192078 PMCID: PMC11003717 DOI: 10.1021/acschembio.3c00487] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 01/10/2024]
Abstract
Targeted protein degradation has arisen as a powerful therapeutic modality for eliminating proteins. Thus far, most heterobifunctional proteolysis targeting chimeras (PROTACs) have utilized recruiters against substrate receptors of Cullin RING E3 ubiquitin ligases, such as cereblon and VHL. However, previous studies have surprisingly uncovered molecular glue degraders that exploit a CUL4 adaptor protein DDB1 to degrade neosubstrate proteins. Here, we sought to investigate whether DDB1 recruiters can be discovered that can be exploited for PROTAC applications. We utilized activity-based protein profiling and cysteine chemoproteomic screening to identify a covalent recruiter that targets C173 on DDB1 and exploited this recruiter to develop PROTACs against BRD4 and androgen receptor (AR). We demonstrated that the BRD4 PROTAC results in selective degradation of the short BRD4 isoform over the long isoform in a proteasome, NEDDylation, and DDB1-dependent manner. We also demonstrated degradation of AR with the AR PROTAC in prostate cancer cells. Our study demonstrated that covalent chemoproteomic approaches can be used to discover recruiters against Cullin RING adapter proteins and that these recruiters can be used for PROTAC applications to degrade neo-substrates.
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Affiliation(s)
- Margot Meyers
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Sabine Cismoski
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Barbara Chie-Leon
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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5
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Zhang L, Tang M, Tao X, Shao Q, Thomas V, Shimizu S, Kasano M, Ishikawa Y, Inukai T, Nomura DK. Covalent Targeting of Glutamate Cysteine Ligase to Inhibit Glutathione Synthesis. Chembiochem 2023; 24:e202300371. [PMID: 37756477 PMCID: PMC10739677 DOI: 10.1002/cbic.202300371] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 05/18/2023] [Revised: 09/24/2023] [Accepted: 09/27/2023] [Indexed: 09/29/2023]
Abstract
Dysregulated oxidative stress plays a major role in cancer pathogenesis and some types of cancer cells are particularly vulnerable to inhibition of their cellular antioxidant capacity. Glutamate-cysteine ligase (GCL) is the first and rate-limiting step in the synthesis of the major cellular antioxidant glutathione (GSH). Developing a GCL inhibitor may be an attractive therapeutic strategy for certain cancer types that are particularly sensitive to oxidative stress. In this study, we reveal a cysteine-reactive ligand, EN25, that covalently targets an allosteric cysteine C114 on GCLM, the modifier subunit of GCL, and leads to inhibition of GCL activity. This interaction also leads to reduced cellular GSH levels and impaired cell viability in ARID1A-deficient cancer cells, which are particularly vulnerable to glutathione depletion, but not in ARID1A-positive cancer cells. Our studies uncover a novel potential ligandable site within GCLM that can be targeted to inhibit GSH synthesis in vulnerable cancer cell types.
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Affiliation(s)
- Lydia Zhang
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Michelle Tang
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Xavier Tao
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Qian Shao
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Vienna Thomas
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Saki Shimizu
- Drug Discovery Technology, Ono Pharmaceutical Company, Ltd., Osaka 618-858 Japan
| | - Miki Kasano
- Drug Discovery Technology, Ono Pharmaceutical Company, Ltd., Osaka 618-858 Japan
| | - Yoshinori Ishikawa
- Research Center of Oncology, Ono Pharmaceutical Company, Ltd., Osaka 618-8585 Japan
| | - Takayuki Inukai
- Drug Discovery Chemistry, Ono Pharmaceutical Company, Ltd., Osaka 618-858 Japan
| | - Daniel K. Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
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6
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Shao Q, Duong TN, Park I, Nomura DK. Covalent 14-3-3 Molecular Glues and Heterobifunctional Molecules Against Nuclear Transcription Factors and Regulators. bioRxiv 2023:2023.11.06.565850. [PMID: 37986959 PMCID: PMC10659333 DOI: 10.1101/2023.11.06.565850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
14-3-3 proteins have the unique ability to bind and sequester a multitude of diverse phosphorylated signaling proteins and transcription factors. Many previous studies have shown that 14-3-3 interactions with specific phosphorylated substrate proteins can be enhanced through small-molecule natural product or fully synthetic molecular glue interactions. However, enhancing 14-3-3 interactions with both therapeutically intractable transcription factor substrates as well as potential neo-substrates to sequester and inhibit their function has remained elusive. One of the 14-3-3 proteins, 14-3-3σ or SFN, has a cysteine C38 at the substrate binding interface near sites where previous 14-3-3 molecular glues have been found to bind. In this study, we screened a fully synthetic cysteine-reactive covalent ligand library to identify molecular glues that enhance interaction of 14-3-3σ with not only druggable transcription factors such as estrogen receptor (ERα), but also challenging oncogenic transcription factors such as YAP and TAZ that are part of the Hippo transducer pathway. We identified a hit EN171 that covalently targets 14-3-3 to enhance 14-3-3 interactions with ERα, YAP, and TAZ leading to impaired estrogen receptor and Hippo pathway transcriptional activity. We further demonstrate that EN171 could not only be used as a molecular glue to enhance native protein interactions, but also could be used as a covalent 14-3-3 recruiter in heterobifunctional molecules to sequester nuclear neo-substrates such as BRD4 into the cytosol. Overall, our study reveals a covalent ligand that acts as a novel 14-3-3 molecular glue for challenging transcription factors such as YAP and TAZ and also demonstrates that these glues can be potentially utilized in heterobifunctional molecules to sequester nuclear neo-substrates out of the nucleus and into the cytosol to enable targeted protein localization.
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Affiliation(s)
- Qian Shao
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Tuong Nghi Duong
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Inji Park
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Daniel K Nomura
- Departments of Chemistry and Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
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Pham VN, Bruemmer KJ, Toh JDW, Ge EJ, Tenney L, Ward CC, Dingler FA, Millington CL, Garcia-Prieto CA, Pulos-Holmes MC, Ingolia NT, Pontel LB, Esteller M, Patel KJ, Nomura DK, Chang CJ. Formaldehyde regulates S-adenosylmethionine biosynthesis and one-carbon metabolism. Science 2023; 382:eabp9201. [PMID: 37917677 DOI: 10.1126/science.abp9201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 09/24/2023] [Indexed: 11/04/2023]
Abstract
One-carbon metabolism is an essential branch of cellular metabolism that intersects with epigenetic regulation. In this work, we show how formaldehyde (FA), a one-carbon unit derived from both endogenous sources and environmental exposure, regulates one-carbon metabolism by inhibiting the biosynthesis of S-adenosylmethionine (SAM), the major methyl donor in cells. FA reacts with privileged, hyperreactive cysteine sites in the proteome, including Cys120 in S-adenosylmethionine synthase isoform type-1 (MAT1A). FA exposure inhibited MAT1A activity and decreased SAM production with MAT-isoform specificity. A genetic mouse model of chronic FA overload showed a decrease n SAM and in methylation on selected histones and genes. Epigenetic and transcriptional regulation of Mat1a and related genes function as compensatory mechanisms for FA-dependent SAM depletion, revealing a biochemical feedback cycle between FA and SAM one-carbon units.
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Affiliation(s)
- Vanha N Pham
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kevin J Bruemmer
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joel D W Toh
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Eva J Ge
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Logan Tenney
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carl C Ward
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Felix A Dingler
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Christopher L Millington
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Carlos A Garcia-Prieto
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Mia C Pulos-Holmes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lucas B Pontel
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Calle Monforte de Lemos, Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluis Companys, Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Feixa Llarga, l'Hospitalet de Llobregat, Spain
| | - Ketan J Patel
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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8
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Gowans FA, Forte N, Hatcher J, Huang OW, Wang Y, Poblano BEA, Wertz IE, Nomura DK. Covalent Degrader of the Oncogenic Transcription Factor β-Catenin. bioRxiv 2023:2023.10.31.565018. [PMID: 37961622 PMCID: PMC10635039 DOI: 10.1101/2023.10.31.565018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
β-catenin (CTNNB1) is an oncogenic transcription factor that is important in cell-cell adhesion and transcription of cell proliferation and survival genes that drives the pathogenesis of many different types of cancers. However, direct pharmacological targeting of CTNNB1 has remained challenging deeming this transcription factor as "undruggable." Here, we have performed a screen with a library of cysteine-reactive covalent ligands to identify a monovalent degrader EN83 that depletes CTNNB1 in a ubiquitin-proteasome-dependent manner. We show that EN83 directly and covalently targets CTNNB1 through targeting four distinct cysteines within the armadillo repeat domain-C439, C466, C520, and C619-leading to a destabilization of CTNNB1. Using covalent chemoproteomic approaches, we show that EN83 directly engages CTNNB1 in cells with a moderate degree of selectivity. We further demonstrate that direct covalent targeting of three of these four cysteines--C466, C520, and C619--in cells contributes to CTNNB1 degradation in cells. We also demonstrate that EN83 can be further optimized to yield more potent CTNNB1 binders and degraders. Our results show that chemoproteomic approaches can be used to covalently target and degrade challenging transcription factors like CTNNB1 through a destabilization-mediated degradation.
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Affiliation(s)
- Flor A. Gowans
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Nafsika Forte
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Justin Hatcher
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | | | - Yangzhi Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Belen E. Altamirano Poblano
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | | | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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9
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Hong SH, Osa A, Huang OW, Wertz IE, Nomura DK. Exploiting the Cullin E3 Ligase Adaptor Protein SKP1 for Targeted Protein Degradation. bioRxiv 2023:2023.10.20.563371. [PMID: 37904950 PMCID: PMC10614948 DOI: 10.1101/2023.10.20.563371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Targeted protein degradation with Proteolysis Targeting Chimeras (PROTACs) is a powerful therapeutic modality for eliminating disease-causing proteins through targeted ubiquitination and proteasome-mediated degradation. Most PROTACs have exploited substrate receptors of Cullin-RING E3 ubiquitin ligases such as cereblon and VHL. Whether core, shared, and essential components of the Cullin-RING E3 ubiquitin ligase complex can be used for PROTAC applications remains less explored. Here, we discovered a cysteine-reactive covalent recruiter EN884 against the SKP1 adapter protein of the SKP1-CUL1-F-box containing SCF complex. We further showed that this recruiter can be used in PROTAC applications to degrade neo-substrate proteins such as BRD4 and the androgen receptor in a SKP1- and proteasome-dependent manner. Our studies demonstrate that core and essential adapter proteins within the Cullin-RING E3 ubiquitin ligase complex can be exploited for targeted protein degradation applications and that covalent chemoproteomic strategies can enable recruiter discovery against these targets.
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Affiliation(s)
- Seong Ho Hong
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Akane Osa
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | | | | | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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10
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Davis MA, Yu VY, Fu B, Wen M, Koleski EJ, Silverman J, Berdan CA, Nomura DK, Chang MCY. A cellular platform for production of C 4 monomers. Chem Sci 2023; 14:11718-11726. [PMID: 37920356 PMCID: PMC10619544 DOI: 10.1039/d3sc02773b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/21/2023] [Indexed: 11/04/2023] Open
Abstract
Living organisms carry out a wide range of remarkable functions, including the synthesis of thousands of simple and complex chemical structures for cellular growth and maintenance. The manipulation of this reaction network has allowed for the genetic engineering of cells for targeted chemical synthesis, but it remains challenging to alter the program underlying their fundamental chemical behavior. By taking advantage of the unique ability of living systems to use evolution to find solutions to complex problems, we have achieved yields of up to ∼95% for three C4 commodity chemicals, n-butanol, 1,3-butanediol, and 4-hydroxy-2-butanone. Genomic sequencing of the evolved strains identified pcnB and rpoBC as two gene loci that are able to alter carbon flow by remodeling the transcriptional landscape of the cell, highlighting the potential of synthetic pathways as a tool to identify metabolic control points.
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Affiliation(s)
- Matthew A Davis
- Department of Molecular & Cellular Biology, University of California Berkeley CA 94720-3200 USA
| | - Vivian Yaci Yu
- Department of Molecular & Cellular Biology, University of California Berkeley CA 94720-3200 USA
| | - Beverly Fu
- Department of Chemistry, University of California Berkeley CA 94720-1460 USA
| | - Miao Wen
- Department of Chemistry, University of California Berkeley CA 94720-1460 USA
| | - Edward J Koleski
- Department of Chemistry, University of California Berkeley CA 94720-1460 USA
| | - Joshua Silverman
- Calysta 1900 Alameda de las Pulgas Suite 200 San Mateo CA 94404 USA
| | - Charles A Berdan
- Department of Chemistry, University of California Berkeley CA 94720-1460 USA
| | - Daniel K Nomura
- Department of Molecular & Cellular Biology, University of California Berkeley CA 94720-3200 USA
- Department of Chemistry, University of California Berkeley CA 94720-1460 USA
- Department of Nutritional Sciences & Toxicology, University of California Berkeley CA 94720-3104 USA
| | - Michelle C Y Chang
- Department of Molecular & Cellular Biology, University of California Berkeley CA 94720-3200 USA
- Department of Chemistry, University of California Berkeley CA 94720-1460 USA
- Department of Chemical & Biomolecular Engineering, University of California Berkeley CA 94720-1462 USA
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11
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Henning NJ, Manford AG, Spradlin JN, Brittain SM, Zhang E, McKenna JM, Tallarico JA, Schirle M, Rape M, Nomura DK. Correction to "Discovery of a Covalent FEM1B Recruiter for Targeted Protein Degradation Applications". J Am Chem Soc 2023; 145:21142. [PMID: 37708357 DOI: 10.1021/jacs.3c09174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
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12
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Wright AT, Nomura DK. Call for Papers: Special Issue on Chemical Biology Approaches for Investigating Toxicological Mechanisms. Chem Res Toxicol 2023; 36:1440. [PMID: 37589968 DOI: 10.1021/acs.chemrestox.3c00235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Affiliation(s)
- Aaron T Wright
- Biology, Baylor University, Baylor Science Building, One Bear Place, Waco, Texas 76798-7151, United States
| | - Daniel K Nomura
- University of California Berkeley, 2151 Berkeley Way, Room 312G, Berkeley, California 94720, United States
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13
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Toriki ES, Papatzimas JW, Nishikawa K, Dovala D, Frank AO, Hesse MJ, Dankova D, Song JG, Bruce-Smythe M, Struble H, Garcia FJ, Brittain SM, Kile AC, McGregor LM, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Correction to "Rational Chemical Design of Molecular Glue Degraders". ACS Cent Sci 2023; 9:1702. [PMID: 37637749 PMCID: PMC10450871 DOI: 10.1021/acscentsci.3c00844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Indexed: 08/29/2023]
Abstract
[This corrects the article DOI: 10.1021/acscentsci.2c01317.].
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14
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Meyers M, Cismoski S, Panidapu A, Chie-Leon B, Nomura DK. Targeted Protein Degradation through Recruitment of the CUL4A Complex Adaptor Protein DDB1. bioRxiv 2023:2023.08.11.553046. [PMID: 37614621 PMCID: PMC10443223 DOI: 10.1101/2023.08.11.553046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Targeted protein degradation has arisen as a powerful therapeutic modality for eliminating proteins. Thus far, most heterobifunctional Proteolysis Targeting Chimeras (PROTACs) have utilized recruiters against substrate receptors of Cullin RING E3 ubiquitin ligases, such as cereblon and VHL. However, previous studies have surprisingly uncovered molecular glue degraders that exploit a CUL4A adaptor protein DDB1 to degrade neosubstrate proteins. Here, we sought to investigate whether DDB1 recruiters can be discovered that can be exploited for PROTAC applications. We utilized activity-based protein profiling and cysteine chemoproteomic screening to identify a covalent recruiter that targets C173 on DDB1 and exploited this recruiter to develop PROTACs against BRD4 and androgen receptor (AR). We demonstrated that the BRD4 PROTAC results in selective degradation of the short BRD4 isoform over the long isoform in a proteasome, NEDDylation, and DDB1-dependent manner. We also demonstrated degradation of AR with the AR PROTAC in prostate cancer cells. Our study demonstrated that covalent chemoproteomic approaches can be used to discover recruiters against Cullin RING adapter proteins and that these recruiters can be used for PROTAC applications to degrade neo-substrates.
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Affiliation(s)
- Margot Meyers
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Sabine Cismoski
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Barbara Chie-Leon
- Novartis-Berkeley Translational Chemical Biology Institute
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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15
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Koo TY, Lai H, Nomura DK, Chung CYS. N-Acryloylindole-alkyne (NAIA) enables imaging and profiling new ligandable cysteines and oxidized thiols by chemoproteomics. Nat Commun 2023; 14:3564. [PMID: 37322008 PMCID: PMC10272157 DOI: 10.1038/s41467-023-39268-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 10/30/2022] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Cysteine has been exploited as the binding site of covalent drugs. Its high sensitivity to oxidation is also important for regulating cellular processes. To identify new ligandable cysteines which can be hotspots for therapy and to better study cysteine oxidations, we develop cysteine-reactive probes, N-acryloylindole-alkynes (NAIAs), which have superior cysteine reactivity owing to delocalization of π electrons of the acrylamide warhead over the whole indole scaffold. This allows NAIAs to probe functional cysteines more effectively than conventional iodoacetamide-alkyne, and to image oxidized thiols by confocal fluorescence microscopy. In mass spectrometry experiments, NAIAs successfully capture new oxidized cysteines, as well as a new pool of ligandable cysteines and proteins. Competitive activity-based protein profiling experiments further demonstrate the ability of NAIA to discover lead compounds targeting these cysteines and proteins. We show the development of NAIAs with activated acrylamide for advancing proteome-wide profiling and imaging ligandable cysteines and oxidized thiols.
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Affiliation(s)
- Tin-Yan Koo
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Hinyuk Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Clive Yik-Sham Chung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China.
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, P. R. China.
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong, P. R. China.
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16
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Bajaj T, Wehri E, Suryawanshi RK, King E, Pardeshi KS, Behrouzi K, Khodabakhshi Z, Schulze-Gahmen U, Kumar GR, Mofrad MRK, Nomura DK, Ott M, Schaletzky J, Murthy N. Mercapto-pyrimidines are reversible covalent inhibitors of the papain-like protease (PLpro) and inhibit SARS-CoV-2 (SCoV-2) replication. RSC Adv 2023; 13:17667-17677. [PMID: 37312993 PMCID: PMC10259201 DOI: 10.1039/d3ra01915b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/01/2023] [Indexed: 06/15/2023] Open
Abstract
The papain-like protease (PLpro) plays a critical role in SARS-CoV-2 (SCoV-2) pathogenesis and is essential for viral replication and for allowing the virus to evade the host immune response. Inhibitors of PLpro have great therapeutic potential, however, developing them has been challenging due to PLpro's restricted substrate binding pocket. In this report, we screened a 115 000-compound library for PLpro inhibitors and identified a new pharmacophore, based on a mercapto-pyrimidine fragment that is a reversible covalent inhibitor (RCI) of PLpro and inhibits viral replication in cells. Compound 5 had an IC50 of 5.1 μM for PLpro inhibition and hit optimization yielded a derivative with increased potency (IC50 0.85 μM, 6-fold higher). Activity based profiling of compound 5 demonstrated that it reacts with PLpro cysteines. We show here that compound 5 represents a new class of RCIs, which undergo an addition elimination reaction with cysteines in their target proteins. We further show that their reversibility is catalyzed by exogenous thiols and is dependent on the size of the incoming thiol. In contrast, traditional RCIs are all based upon the Michael addition reaction mechanism and their reversibility is base-catalyzed. We identify a new class of RCIs that introduces a more reactive warhead with a pronounced selectivity profile based on thiol ligand size. This could allow the expansion of RCI modality use towards a larger group of proteins important for human disease.
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Affiliation(s)
- Teena Bajaj
- Graduate Program of Comparative Biochemistry, University of California Berkeley CA USA
| | - Eddie Wehri
- The Henry Wheeler Center of Emerging and Neglected Diseases 344 Li Ka Shing Berkeley CA USA
| | | | - Elizabeth King
- Chemical Biology Graduate Program, University of California Berkeley CA USA
| | | | - Kamyar Behrouzi
- Department of Mechanical Engineering, University of California Berkeley CA USA
| | | | | | - G Renuka Kumar
- Gladstone Institute of Virology Gladstone Institutes San Francisco CA USA
| | | | - Daniel K Nomura
- Department of Chemistry, University of California Berkeley CA USA
| | - Melanie Ott
- Gladstone Institute of Virology Gladstone Institutes San Francisco CA USA
- Department of Medicine, University of California San Francisco CA USA
- Chan Zuckerberg Biohub San Francisco CA USA
| | - Julia Schaletzky
- The Henry Wheeler Center of Emerging and Neglected Diseases 344 Li Ka Shing Berkeley CA USA
| | - Niren Murthy
- Department of Bioengineering, University of California Berkeley CA USA
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17
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Toriki E, Papatzimas JW, Nishikawa K, Dovala D, Frank AO, Hesse MJ, Dankova D, Song JG, Bruce-Smythe M, Struble H, Garcia FJ, Brittain SM, Kile AC, McGregor LM, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Rational Chemical Design of Molecular Glue Degraders. ACS Cent Sci 2023; 9:915-926. [PMID: 37252349 PMCID: PMC10214506 DOI: 10.1021/acscentsci.2c01317] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Indexed: 05/31/2023]
Abstract
Targeted protein degradation with molecular glue degraders has arisen as a powerful therapeutic modality for eliminating classically undruggable disease-causing proteins through proteasome-mediated degradation. However, we currently lack rational chemical design principles for converting protein-targeting ligands into molecular glue degraders. To overcome this challenge, we sought to identify a transposable chemical handle that would convert protein-targeting ligands into molecular degraders of their corresponding targets. Using the CDK4/6 inhibitor ribociclib as a prototype, we identified a covalent handle that, when appended to the exit vector of ribociclib, induced the proteasome-mediated degradation of CDK4 in cancer cells. Further modification of our initial covalent scaffold led to an improved CDK4 degrader with the development of a but-2-ene-1,4-dione ("fumarate") handle that showed improved interactions with RNF126. Subsequent chemoproteomic profiling revealed interactions of the CDK4 degrader and the optimized fumarate handle with RNF126 as well as additional RING-family E3 ligases. We then transplanted this covalent handle onto a diverse set of protein-targeting ligands to induce the degradation of BRD4, BCR-ABL and c-ABL, PDE5, AR and AR-V7, BTK, LRRK2, HDAC1/3, and SMARCA2/4. Our study undercovers a design strategy for converting protein-targeting ligands into covalent molecular glue degraders.
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Affiliation(s)
- Ethan
S. Toriki
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - James W. Papatzimas
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Kaila Nishikawa
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Dustin Dovala
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Andreas O. Frank
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Matthew J. Hesse
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daniela Dankova
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Jae-Geun Song
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Megan Bruce-Smythe
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Heidi Struble
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Francisco J. Garcia
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Scott M. Brittain
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Andrew C. Kile
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Lynn M. McGregor
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Jeffrey M. McKenna
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A. Tallarico
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Daniel K. Nomura
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
- Department
of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, California 94720, United States
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18
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King EA, Cho Y, Hsu NS, Dovala D, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Chemoproteomics-enabled discovery of a covalent molecular glue degrader targeting NF-κB. Cell Chem Biol 2023; 30:394-402.e9. [PMID: 36898369 PMCID: PMC10121878 DOI: 10.1016/j.chembiol.2023.02.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [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: 05/18/2022] [Revised: 01/11/2023] [Accepted: 02/16/2023] [Indexed: 03/11/2023]
Abstract
Targeted protein degradation has arisen as a powerful therapeutic modality for degrading disease targets. While proteolysis-targeting chimera (PROTAC) design is more modular, the discovery of molecular glue degraders has been more challenging. Here, we have coupled the phenotypic screening of a covalent ligand library with chemoproteomic approaches to rapidly discover a covalent molecular glue degrader and associated mechanisms. We have identified a cysteine-reactive covalent ligand EN450 that impairs leukemia cell viability in a NEDDylation and proteasome-dependent manner. Chemoproteomic profiling revealed covalent interaction of EN450 with an allosteric C111 in the E2 ubiquitin-conjugating enzyme UBE2D. Quantitative proteomic profiling revealed the degradation of the oncogenic transcription factor NFKB1 as a putative degradation target. Our study thus puts forth the discovery of a covalent molecular glue degrader that uniquely induced the proximity of an E2 with a transcription factor to induce its degradation in cancer cells.
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Affiliation(s)
- Elizabeth A King
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Yoojin Cho
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Nathan S Hsu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94704, USA
| | - Dustin Dovala
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Emeryville, CA 94608, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - John A Tallarico
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94704, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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19
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Moon P, Zammit C, Shao Q, Boike L, Dovala D, Henning NJ, Knapp M, Spradlin JN, Ward CC, Wolleb H, Fuller D, Blake G, Murphy JP, Wang F, Lu Y, Moquin SA, Tandeske L, Hesse MJ, McKenna JM, Tallarico JA, Schirle M, Toste FD, Nomura DK. Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors. Chembiochem 2023:e202300116. [PMID: 37069799 DOI: 10.1002/cbic.202300116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/19/2023]
Abstract
Among the various genes and proteins encoded by all coronaviruses, one particularly "druggable" or relatively easy-to-drug target is the coronavirus Main Protease (3CLproor Mpro), an enzyme that is involved in cleaving a long peptide translated by the viral genome into its individual protein components that are then assembled into the virus to enable viral replication in the cell. Inhibiting Mpro with a small-molecule antiviral would effectively stop the ability of the virus to replicate, providing therapeutic benefit. In this study, we have utilized activity-based protein profiling (ABPP)-based chemoproteomic approaches to discover and further optimize cysteine-reactive pyrazoline-based covalent inhibitors for the SARS-CoV-2 Mpro. Structure-guided medicinal chemistry and modular synthesis of di- and tri-substituted pyrazolines bearing either chloroacetamide or vinyl sulfonamide cysteine-reactive warheads enabled the expedient exploration of structure-activity relationships (SAR), yielding nanomolar potency inhibitors against Mpro from not only SARS-CoV-2, but across many other coronaviruses. Our studies highlight promising chemical scaffolds that may contribute to future pan-coronavirus inhibitors.
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Affiliation(s)
- Patrick Moon
- University of California Berkeley, Chemistry, UNITED STATES
| | | | - Qian Shao
- UC Berkeley: University of California Berkeley, Chemistry, UNITED STATES
| | - Lydia Boike
- University of California Berkeley, Chemistry, UNITED STATES
| | - Dustin Dovala
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | | | - Mark Knapp
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | | | - Carl C Ward
- University of California Berkeley, Chemistry, UNITED STATES
| | - Helene Wolleb
- University of California Berkeley, Chemistry, UNITED STATES
| | - Daniel Fuller
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Gabrielle Blake
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Jason P Murphy
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Feng Wang
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Yipin Lu
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Stephanie A Moquin
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Laura Tandeske
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Matthew J Hesse
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, UNITED STATES
| | - Jeffrey M McKenna
- Novartis Institutes for BioMedical Research Basel, Global Discovery Chemistry, UNITED STATES
| | - John A Tallarico
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - Markus Schirle
- Novartis Institutes for BioMedical Research Basel, Chemical Biology and Therapeutics, UNITED STATES
| | - F Dean Toste
- University of California Berkeley, Chemistry, UNITED STATES
| | - Daniel K Nomura
- University of California, Berkeley, Chemistry, 127 Morgan Hall, 94720, Berkeley, UNITED STATES
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20
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Belcher BP, Machicao PA, Tong B, Ho E, Friedli J, So B, Bui H, Isobe Y, Maimone TJ, Nomura DK. Chemoproteomic Profiling Reveals that Anti-Cancer Natural Product Dankastatin B Covalently Targets Mitochondrial VDAC3. Chembiochem 2023:e202300111. [PMID: 36964942 DOI: 10.1002/cbic.202300111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Chlorinated gymnastatin and dankastatin alkaloids derived from the fungal strain Gymnascella dankaliensis have been reported to possess significant anti-cancer activity but their mode of action is unknown. These members possess electrophilic functional groups that may undergo covalent bond formation with specific proteins to exert their biological activity. To better understand the mechanism of action of this class of natural products, we mapped the proteome-wide cysteine-reactivity of the most potent of these alkaloids, dankastatin B, using activity-based protein profiling chemoproteomic approaches. We identified a primary target of dankastatin B in breast cancer cells as cysteine C65 of the voltage-dependent anion selective channel on the outer mitochondrial membrane VDAC3. We demonstrated direct and covalent interaction of dankastatin B with VDAC3. VDAC3 knockdown conferred hyper-sensitivity to dankastatin B-mediated anti-proliferative effects in breast cancer cells indicating that VDAC3 was at least partially involved in the anti-cancer effects of this natural product. Our study reveals a potential mode of action of dankastatin B through covalent targeting of VDAC3 and highlight the utility of chemoproteomic approaches in gaining mechanistic understanding of electrophilic natural products.
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Affiliation(s)
| | | | - Binqi Tong
- University of California Berkeley, Chemistry, UNITED STATES
| | - Emily Ho
- University of California Berkeley, Chemistry, UNITED STATES
| | - Julia Friedli
- University of California Berkeley, Chemistry, UNITED STATES
| | - Brian So
- University of California Berkeley, Chemistry, UNITED STATES
| | - Helen Bui
- University of California Berkeley, Chemistry, UNITED STATES
| | - Yosuke Isobe
- University of California Berkeley, Chemistry, UNITED STATES
| | | | - Daniel K Nomura
- University of California, Berkeley, Chemistry, 127 Morgan Hall, 94720, Berkeley, UNITED STATES
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21
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Abstract
Targeted protein degradation (TPD) with proteolysis targeting chimeras (PROTACs), heterobifunctional compounds consisting of protein targeting ligands linked to recruiters of E3 ubiquitin ligases, has arisen as a powerful therapeutic modality to induce the proximity of target proteins with E3 ligases to ubiquitinate and degrade specific proteins in cells. Thus far, PROTACs have primarily exploited the recruitment of E3 ubiquitin ligases or their substrate adapter proteins but have not exploited the recruitment of more core components of the ubiquitin-proteasome system (UPS). In this study, we used covalent chemoproteomic approaches to discover a covalent recruiter against the E2 ubiquitin conjugating enzyme UBE2D─EN67─that targets an allosteric cysteine, C111, without affecting the enzymatic activity of the protein. We demonstrated that this UBE2D recruiter could be used in heterobifunctional degraders to degrade neo-substrate targets in a UBE2D-dependent manner, including BRD4 and the androgen receptor. Overall, our data highlight the potential for the recruitment of core components of the UPS machinery, such as E2 ubiquitin conjugating enzymes, for TPD, and underscore the utility of covalent chemoproteomic strategies for identifying novel recruiters for additional components of the UPS.
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Affiliation(s)
- Nafsika Forte
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Innovative Genomics Institute, Berkeley, California 94704, United States
| | - Dustin Dovala
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Matthew J Hesse
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Novartis Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Jeffrey M McKenna
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A Tallarico
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, California 94720, United States.,Innovative Genomics Institute, Berkeley, California 94704, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
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22
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Gowans FA, Thach DQ, Wang Y, Altamirano Poblano BE, Dovala D, Tallarico JA, McKenna JM, Schirle M, Maimone TJ, Nomura DK. Ophiobolin A Covalently Targets Complex IV Leading to Mitochondrial Metabolic Collapse in Cancer Cells. bioRxiv 2023:2023.03.09.531918. [PMID: 36945520 PMCID: PMC10029012 DOI: 10.1101/2023.03.09.531918] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Ophiobolin A (OPA) is a sesterterpenoid fungal natural product with broad anti-cancer activity. While OPA possesses multiple electrophilic moieties that can covalently react with nucleophilic amino acids on proteins, the proteome-wide targets and mechanism of OPA remain poorly understood in many contexts. In this study, we used covalent chemoproteomic platforms to map the proteome-wide reactivity of OPA in a highly sensitive lung cancer cell line. Among several proteins that OPA engaged, we focused on two targets-cysteine C53 of HIG2DA and lysine K72 of COX5A-that are part of complex IV of the electron transport chain and contributed significantly to the anti-proliferative activity. OPA activated mitochondrial respiration in a HIG2DA and COX5A-dependent manner, led to an initial spike in mitochondrial ATP, but then compromised mitochondrial membrane potential leading to ATP depletion. We have used chemoproteomic strategies to discover a unique anti-cancer mechanism of OPA through activation of complex IV leading to compromised mitochondrial energetics and rapid cell death.
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Affiliation(s)
- Flor A. Gowans
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Danny Q. Thach
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
| | - Yangzhi Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Belen E. Altamirano Poblano
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Dustin Dovala
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Emeryville, CA 94608 USA
| | - John A. Tallarico
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Jeffrey M. McKenna
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Markus Schirle
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Thomas J. Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
| | - Daniel K. Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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23
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Benjamin DI, Brett JO, Both P, Benjamin JS, Ishak HL, Kang J, Kim S, Chung M, Arjona M, Nutter CW, Tan JH, Krishnan AK, Dulay H, Louie SM, de Morree A, Nomura DK, Rando TA. Multiomics reveals glutathione metabolism as a driver of bimodality during stem cell aging. Cell Metab 2023; 35:472-486.e6. [PMID: 36854304 PMCID: PMC10015599 DOI: 10.1016/j.cmet.2023.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/14/2022] [Accepted: 02/01/2023] [Indexed: 03/02/2023]
Abstract
With age, skeletal muscle stem cells (MuSCs) activate out of quiescence more slowly and with increased death, leading to defective muscle repair. To explore the molecular underpinnings of these defects, we combined multiomics, single-cell measurements, and functional testing of MuSCs from young and old mice. The multiomics approach allowed us to assess which changes are causal, which are compensatory, and which are simply correlative. We identified glutathione (GSH) metabolism as perturbed in old MuSCs, with both causal and compensatory components. Contrary to young MuSCs, old MuSCs exhibit a population dichotomy composed of GSHhigh cells (comparable with young MuSCs) and GSHlow cells with impaired functionality. Mechanistically, we show that antagonism between NRF2 and NF-κB maintains this bimodality. Experimental manipulation of GSH levels altered the functional dichotomy of aged MuSCs. These findings identify a novel mechanism of stem cell aging and highlight glutathione metabolism as an accessible target for reversing MuSC aging.
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Affiliation(s)
- Daniel I Benjamin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jamie O Brett
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University School of Medicine, Stanford, CA, USA; Medical Scientist Training Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Pieter Both
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Joel S Benjamin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Heather L Ishak
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jengmin Kang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Soochi Kim
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Mingyu Chung
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Marina Arjona
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher W Nutter
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Jenna H Tan
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Ananya K Krishnan
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Hunter Dulay
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Sharon M Louie
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA; Neurology Service, Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA, USA.
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24
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Belcher BP, Machicao PA, Tong B, Ho E, Friedli J, So B, Bui H, Isobe Y, Maimone TJ, Nomura DK. Chemoproteomic Profiling Reveals that Anti-Cancer Natural Product Dankastatin B Covalently Targets Mitochondrial VDAC3. bioRxiv 2023:2023.02.11.528139. [PMID: 36798342 PMCID: PMC9934694 DOI: 10.1101/2023.02.11.528139] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Chlorinated gymnastatin and dankastatin alkaloids derived from the fungal strain Gymnascella dankaliensis have been reported to possess significant anti-cancer activity but their mode of action is unknown. These members possess electrophilic functional groups that may undergo covalent bond formation with specific proteins to exert their biological activity. To better understand the mechanism of action of this class of natural products, we mapped the proteome-wide cysteine-reactivity of the most potent of these alkaloids, dankastatin B, using activitybased protein profiling chemoproteomic approaches. We identified a primary target of dankastatin B in breast cancer cells as cysteine C65 of the voltage-dependent anion selective channel on the outer mitochondrial membrane VDAC3. We demonstrated direct and covalent interaction of dankastatin B with VDAC3. VDAC3 knockdown conferred hyper-sensitivity to dankastatin B-mediated anti-proliferative effects in breast cancer cells indicating that VDAC3 was at least partially involved in the anti-cancer effects of this natural product. Our study reveals a potential mode of action of dankastatin B through covalent targeting of VDAC3 and highlight the utility of chemoproteomic approaches in gaining mechanistic understanding of electrophilic natural products.
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Affiliation(s)
- Bridget P. Belcher
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Paulo A. Machicao
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Binqi Tong
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Emily Ho
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Julia Friedli
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Brian So
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Helen Bui
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Yosuke Isobe
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Thomas J. Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
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25
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Abstract
Targeted protein degradation (TPD) using proteolysis targeting chimeras (PROTACs) and molecular glue degraders has arisen as a powerful therapeutic modality for eliminating disease-causing proteins from cells. PROTACs and molecular glue degraders employ heterobifunctional or monovalent small molecules, respectively, to chemically induce the proximity of target proteins with E3 ubiquitin ligases to ubiquitinate and degrade specific proteins via the proteasome. Whereas TPD is an attractive therapeutic strategy for expanding the druggable proteome, only a relatively small number of E3 ligases out of the >600 E3 ligases encoded by the human genome have been exploited by small molecules for TPD applications. Here we review the existing E3 ligases that have thus far been successfully exploited for TPD and discuss chemoproteomics-enabled covalent screening strategies for discovering new E3 ligase recruiters. We also provide a chemoproteomic map of reactive cysteines within hundreds of E3 ligases that may represent potential ligandable sites that can be pharmacologically interrogated to uncover additional E3 ligase recruiters.
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Affiliation(s)
- Bridget P. Belcher
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720,Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Carl C. Ward
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720,Innovative Genomics Institute, Berkeley, CA 94720 USA,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720,Innovative Genomics Institute, Berkeley, CA 94720 USA,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA,correspondence to
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26
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Han H, Gracia AV, Røise JJ, Boike L, Leon K, Schulze-Gahmen U, Stentzel MR, Bajaj T, Chen D, Li IC, He M, Behrouzi K, Khodabakhshi Z, Nomura DK, Mofrad MRK, Kumar GR, Ott M, Murthy N. A covalent inhibitor targeting the papain-like protease from SARS-CoV-2 inhibits viral replication †. RSC Adv 2023; 13:10636-10641. [PMID: 37025664 PMCID: PMC10072198 DOI: 10.1039/d3ra00426k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/27/2023] [Indexed: 04/07/2023] Open
Abstract
Covalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-2 have great potential as antivirals, but their non-specific reactivity with thiols has limited their development. In this report, we performed an 8000 molecule electrophile screen against PLpro and identified an α-chloro amide fragment, termed compound 1, which inhibited SARS-CoV-2 replication in cells, and also had low non-specific reactivity with thiols. Compound 1 covalently reacts with the active site cysteine of PLpro, and had an IC50 of 18 μM for PLpro inhibition. Compound 1 also had low non-specific reactivity with thiols and reacted with glutathione 1–2 orders of magnitude slower than other commonly used electrophilic warheads. Finally, compound 1 had low toxicity in cells and mice and has a molecular weight of only 247 daltons and consequently has great potential for further optimization. Collectively, these results demonstrate that compound 1 is a promising lead fragment for future PLpro drug discovery campaigns. Compound 1 is a covalent inhibitor of SARS-CoV-2 PLpro that inhibits viral replication and has low non-specific reactivity with thiols.![]()
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Affiliation(s)
- Hesong Han
- Department of Bioengineering, University of California at BerkeleyBerkeleyCAUSA
| | | | - Joachim J. Røise
- Department of Bioengineering, University of California at BerkeleyBerkeleyCAUSA
- Department of Chemistry, University of CaliforniaBerkeleyCAUSA
| | - Lydia Boike
- Department of Chemistry, University of CaliforniaBerkeleyCAUSA
- Innovative Genomics InstituteBerkeleyCAUSA
- Novartis-Berkeley Center for Proteomics and Chemistry TechnologiesBerkeleyCAUSA
| | - Kristoffer Leon
- Gladstone Institute of Virology, Gladstone InstitutesSan FranciscoCAUSA
- Department of Medicine, University of CaliforniaSan FranciscoCAUSA
| | | | - Michael R. Stentzel
- Department of Bioengineering, University of California at BerkeleyBerkeleyCAUSA
| | - Teena Bajaj
- Graduate Program of Comparativ Biochemistry, University of California at BerkeleyBerkeleyCAUSA
| | - Dake Chen
- Department of Bioengineering, University of California at BerkeleyBerkeleyCAUSA
| | - I.-Che Li
- Department of Bioengineering, University of California at BerkeleyBerkeleyCAUSA
| | - Maomao He
- Department of Bioengineering, University of California at BerkeleyBerkeleyCAUSA
| | - Kamyar Behrouzi
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of CaliforniaBerkeleyCAUSA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National LaboratoryBerkeleyUSA
| | - Zahra Khodabakhshi
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of CaliforniaBerkeleyCAUSA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National LaboratoryBerkeleyUSA
| | - Daniel K. Nomura
- Department of Chemistry, University of CaliforniaBerkeleyCAUSA
- Innovative Genomics InstituteBerkeleyCAUSA
- Novartis-Berkeley Center for Proteomics and Chemistry TechnologiesBerkeleyCAUSA
- Department of Molecular and Cell Biology, University of CaliforniaBerkeleyCAUSA
- Department of Nutritional Sciences and Toxicology, University of CaliforniaBerkeleyCAUSA
| | - Mohammad R. K. Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of CaliforniaBerkeleyCAUSA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National LaboratoryBerkeleyUSA
| | - G. Renuka Kumar
- Gladstone Institute of Virology, Gladstone InstitutesSan FranciscoCAUSA
| | - Melanie Ott
- Gladstone Institute of Virology, Gladstone InstitutesSan FranciscoCAUSA
- Department of Medicine, University of CaliforniaSan FranciscoCAUSA
- Chan Zuckerberg BiohubSan FranciscoCAUSA
| | - Niren Murthy
- Department of Bioengineering, University of California at BerkeleyBerkeleyCAUSA
- Innovative Genomics InstituteBerkeleyCAUSA
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27
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Abstract
Covalent drugs have been used to treat diseases for more than a century, but tools that facilitate the rational design of covalent drugs have emerged more recently. The purposeful addition of reactive functional groups to existing ligands can enable potent and selective inhibition of target proteins, as demonstrated by the covalent epidermal growth factor receptor (EGFR) and Bruton's tyrosine kinase (BTK) inhibitors used to treat various cancers. Moreover, the identification of covalent ligands through 'electrophile-first' approaches has also led to the discovery of covalent drugs, such as covalent inhibitors for KRAS(G12C) and SARS-CoV-2 main protease. In particular, the discovery of KRAS(G12C) inhibitors validates the use of covalent screening technologies, which have become more powerful and widespread over the past decade. Chemoproteomics platforms have emerged to complement covalent ligand screening and assist in ligand discovery, selectivity profiling and target identification. This Review showcases covalent drug discovery milestones with emphasis on the lessons learned from these programmes and how an evolving toolbox of covalent drug discovery techniques facilitates success in this field.
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Affiliation(s)
- Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
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28
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Shin HR, Citron YR, Wang L, Tribouillard L, Goul CS, Stipp R, Sugasawa Y, Jain A, Samson N, Lim CY, Davis OB, Castaneda-Carpio D, Qian M, Nomura DK, Perera RM, Park E, Covey DF, Laplante M, Evers AS, Zoncu R. Lysosomal GPCR-like protein LYCHOS signals cholesterol sufficiency to mTORC1. Science 2022; 377:1290-1298. [PMID: 36007018 PMCID: PMC10023259 DOI: 10.1126/science.abg6621] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Lysosomes coordinate cellular metabolism and growth upon sensing of essential nutrients, including cholesterol. Through bioinformatic analysis of lysosomal proteomes, we identified lysosomal cholesterol signaling (LYCHOS, previously annotated as G protein-coupled receptor 155), a multidomain transmembrane protein that enables cholesterol-dependent activation of the master growth regulator, the protein kinase mechanistic target of rapamycin complex 1 (mTORC1). Cholesterol bound to the amino-terminal permease-like region of LYCHOS, and mutating this site impaired mTORC1 activation. At high cholesterol concentrations, LYCHOS bound to the GATOR1 complex, a guanosine triphosphatase (GTPase)-activating protein for the Rag GTPases, through a conserved cytoplasm-facing loop. By sequestering GATOR1, LYCHOS promotes cholesterol- and Rag-dependent recruitment of mTORC1 to lysosomes. Thus, LYCHOS functions in a lysosomal pathway for cholesterol sensing and couples cholesterol concentrations to mTORC1-dependent anabolic signaling.
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Affiliation(s)
- Hijai R. Shin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Y. Rose Citron
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lei Wang
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Laura Tribouillard
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, G1R 3S3, Canada
| | - Claire S. Goul
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Robin Stipp
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yusuke Sugasawa
- Department of Anesthesiology and Pain Medicine, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Aakriti Jain
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nolwenn Samson
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, G1R 3S3, Canada
| | - Chun-Yan Lim
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Oliver B. Davis
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - David Castaneda-Carpio
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mingxing Qian
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Daniel K. Nomura
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Rushika M. Perera
- Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA
| | - Eunyong Park
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Douglas F. Covey
- Department of Developmental Biology and Biochemistry, Washington University School of Medicine, St Louis, MO 63110, USA
- The Taylor Family Institute for Innovative Psychiatric Research, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Mathieu Laplante
- Centre de recherche sur le cancer de l’Université Laval, Université Laval, Québec, QC, G1R 3S3, Canada
| | - Alex S. Evers
- Department of Anesthesiology, Washington University School of Medicine, St Louis, MO 63110, USA
- Department of Developmental Biology and Biochemistry, Washington University School of Medicine, St Louis, MO 63110, USA
- The Taylor Family Institute for Innovative Psychiatric Research, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
- Innovative Genomics Initiative at the University of California, Berkeley, Berkeley, CA 94720, USA
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29
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Maza J, García-Almedina DM, Boike LE, Hamlish NX, Nomura DK, Francis MB. Tyrosinase-Mediated Synthesis of Nanobody-Cell Conjugates. ACS Cent Sci 2022; 8:955-962. [PMID: 35912347 PMCID: PMC9335918 DOI: 10.1021/acscentsci.1c01265] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A convenient enzymatic strategy is reported for the modification of cell surfaces. Using a tyrosinase enzyme isolated from Agaricus bisporus, unique tyrosine residues introduced at the C-termini of nanobodies can be site-selectively oxidized to reactive o-quinones. These reactive intermediates undergo rapid modification with nucleophilic thiol, amine, and imidazole residues present on cell surfaces, producing novel nanobody-cell conjugates that display targeted antigen binding. We extend this approach toward the synthesis of nanobody-NK cell conjugates for targeted immunotherapy applications. The resulting NK cell conjugates exhibit targeted cell binding and elicit targeted cell death.
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Affiliation(s)
- Johnathan
C. Maza
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | | | - Lydia E. Boike
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Novartis-Berkeley
Center for Proteomics and Chemistry Technologies, Cambridge, Massachusetts 02139, United States
| | - Noah X. Hamlish
- Department
of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, California 94720, United States
| | - Daniel K. Nomura
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Novartis-Berkeley
Center for Proteomics and Chemistry Technologies, Cambridge, Massachusetts 02139, United States
- Department
of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, California 94720, United States
- Department
of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94720, United States
| | - Matthew B. Francis
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Materials
Sciences Division, Lawrence Berkeley National
Laboratories, Berkeley, California 94720,United States
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30
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Benjamin DI, Both P, Benjamin JS, Nutter CW, Tan JH, Kang J, Machado LA, Klein JDD, de Morree A, Kim S, Liu L, Dulay H, Feraboli L, Louie SM, Nomura DK, Rando TA. Fasting induces a highly resilient deep quiescent state in muscle stem cells via ketone body signaling. Cell Metab 2022; 34:902-918.e6. [PMID: 35584694 PMCID: PMC9177797 DOI: 10.1016/j.cmet.2022.04.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 12/15/2021] [Accepted: 04/25/2022] [Indexed: 01/11/2023]
Abstract
Short-term fasting is beneficial for the regeneration of multiple tissue types. However, the effects of fasting on muscle regeneration are largely unknown. Here, we report that fasting slows muscle repair both immediately after the conclusion of fasting as well as after multiple days of refeeding. We show that ketosis, either endogenously produced during fasting or a ketogenic diet or exogenously administered, promotes a deep quiescent state in muscle stem cells (MuSCs). Although deep quiescent MuSCs are less poised to activate, slowing muscle regeneration, they have markedly improved survival when facing sources of cellular stress. Furthermore, we show that ketone bodies, specifically β-hydroxybutyrate, directly promote MuSC deep quiescence via a nonmetabolic mechanism. We show that β-hydroxybutyrate functions as an HDAC inhibitor within MuSCs, leading to acetylation and activation of an HDAC1 target protein p53. Finally, we demonstrate that p53 activation contributes to the deep quiescence and enhanced resilience observed during fasting.
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Affiliation(s)
- Daniel I Benjamin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pieter Both
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA; Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joel S Benjamin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christopher W Nutter
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jenna H Tan
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jengmin Kang
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leo A Machado
- Biology of the Neuromuscular System, INSERM IMRB U955-E10, UPEC, ENVA, EFS, Creteil 94000, France
| | - Julian D D Klein
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Antoine de Morree
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Soochi Kim
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ling Liu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hunter Dulay
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ludovica Feraboli
- Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sharon M Louie
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thomas A Rando
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA; Paul F. Glenn Laboratories for the Biology of Aging, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Healthcare System, Palo Alto, CA 94304, USA; Neurology Service, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
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31
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Henning NJ, Boike L, Spradlin JN, Ward CC, Liu G, Zhang E, Belcher BP, Brittain SM, Hesse MJ, Dovala D, McGregor LM, Valdez Misiolek R, Plasschaert LW, Rowlands DJ, Wang F, Frank AO, Fuller D, Estes AR, Randal KL, Panidapu A, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Deubiquitinase-targeting chimeras for targeted protein stabilization. Nat Chem Biol 2022; 18:412-421. [PMID: 35210618 PMCID: PMC10125259 DOI: 10.1038/s41589-022-00971-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [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: 04/30/2021] [Accepted: 01/09/2022] [Indexed: 12/12/2022]
Abstract
Many diseases are driven by proteins that are aberrantly ubiquitinated and degraded. These diseases would be therapeutically benefited by targeted protein stabilization (TPS). Here we present deubiquitinase-targeting chimeras (DUBTACs), heterobifunctional small molecules consisting of a deubiquitinase recruiter linked to a protein-targeting ligand, to stabilize the levels of specific proteins degraded in a ubiquitin-dependent manner. Using chemoproteomic approaches, we discovered the covalent ligand EN523 that targets a non-catalytic allosteric cysteine C23 in the K48-ubiquitin-specific deubiquitinase OTUB1. We showed that a DUBTAC consisting of our EN523 OTUB1 recruiter linked to lumacaftor, a drug used to treat cystic fibrosis that binds ΔF508-cystic fibrosis transmembrane conductance regulator (CFTR), robustly stabilized ΔF508-CFTR protein levels, leading to improved chloride channel conductance in human cystic fibrosis bronchial epithelial cells. We also demonstrated stabilization of the tumor suppressor kinase WEE1 in hepatoma cells. Our study showcases covalent chemoproteomic approaches to develop new induced proximity-based therapeutic modalities and introduces the DUBTAC platform for TPS.
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Affiliation(s)
- Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Carl C Ward
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gang Liu
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Bridget P Belcher
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Matthew J Hesse
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Dustin Dovala
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Lynn M McGregor
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | | | - Feng Wang
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Andreas O Frank
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Daniel Fuller
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Abigail R Estes
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Katelyn L Randal
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Anoohya Panidapu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Innovative Genomics Institute, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA.
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32
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Page ACS, Scholz SO, Keenan KN, Spradlin JN, Belcher BP, Brittain SM, Tallarico JA, McKenna JM, Schirle M, Nomura DK, Toste FD. Photo-Brook rearrangement of acyl silanes as a strategy for photoaffinity probe design. Chem Sci 2022; 13:3851-3856. [PMID: 35432890 PMCID: PMC8966736 DOI: 10.1039/d2sc00426g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/02/2022] [Indexed: 01/14/2023] Open
Abstract
Photoaffinity labeling (PAL) is a powerful tool for the identification of non-covalent small molecule–protein interactions that are critical to drug discovery and medicinal chemistry, but this approach is limited to only a small subset of robust photocrosslinkers. The identification of new photoreactive motifs capable of covalent target capture is therefore highly desirable. Herein, we report the design, synthesis, and evaluation of a new class of PAL warheads based on the UV-triggered 1,2-photo-Brook rearrangement of acyl silanes, which hitherto have not been explored for PAL workflows. Irradiation of a series of probes in cell lysate revealed an iPr-substituted acyl silane with superior photolabeling and minimal thermal background labeling compared to other substituted acyl silanes. Further, small molecule (+)-JQ1- and rapamycin-derived iPr acyl silanes were shown to selectively label recombinant BRD4-BD1 and FKBP12, respectively, with minimal background. Together, these data highlight the untapped potential of acyl silanes as a novel, tunable scaffold for photoaffinity labeling. Irradiation initiated 1,2-photo Brook rearrangement of acyl silanes generated α-siloxycarbene intermediates that were used for photoaffinity labeling. Optimization of the acyl silane group produced a probe capable of capturing small molecule–protein interactions.![]()
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Affiliation(s)
- Annika C S Page
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
| | - Spencer O Scholz
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
| | - Katherine N Keenan
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Innovative Genomics Institute, University of California Berkeley California 94720 USA
| | - Bridget P Belcher
- Department of Chemistry, University of California Berkeley California 94720 USA .,Innovative Genomics Institute, University of California Berkeley California 94720 USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Novartis Institute for BioMedical Research Cambridge Massachusetts 02139 USA
| | - Daniel K Nomura
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA.,Innovative Genomics Institute, University of California Berkeley California 94720 USA.,Department of Molecular and Cellular Biology, University of California Berkeley California 94720 USA
| | - F Dean Toste
- Department of Chemistry, University of California Berkeley California 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California Berkeley California 94720 USA
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33
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Henning NJ, Manford AG, Spradlin JN, Brittain SM, Zhang E, McKenna JM, Tallarico JA, Schirle M, Rape M, Nomura DK. Discovery of a Covalent FEM1B Recruiter for Targeted Protein Degradation Applications. J Am Chem Soc 2022; 144:701-708. [PMID: 34994556 PMCID: PMC8928484 DOI: 10.1021/jacs.1c03980] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [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] [Indexed: 12/12/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs), heterobifunctional compounds that consist of protein-targeting ligands linked to an E3 ligase recruiter, have arisen as a powerful therapeutic modality for targeted protein degradation (TPD). Despite the popularity of TPD approaches in drug discovery, only a small number of E3 ligase recruiters are available for the >600 E3 ligases that exist in human cells. Here, we have discovered a cysteine-reactive covalent ligand, EN106, that targets FEM1B, an E3 ligase recently discovered as the critical component of the cellular response to reductive stress. By targeting C186 in FEM1B, EN106 disrupts recognition of the key reductive stress substrate of FEM1B, FNIP1. We further establish that EN106 can be used as a covalent recruiter for FEM1B in TPD applications by demonstrating that a PROTAC linking EN106 to the BET bromodomain inhibitor JQ1 or the kinase inhibitor dasatinib leads to the degradation of BRD4 and BCR-ABL, respectively. Our study showcases a covalent ligand that targets a natural E3 ligase-substrate binding site and highlights the utility of covalent ligand screening in expanding the arsenal of E3 ligase recruiters suitable for TPD applications.
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Affiliation(s)
- Nathaniel J. Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Andrew G. Manford
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Jessica N. Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Scott M. Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
| | - Jeffrey M. McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - John A. Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139 USA
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94704 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720 USA
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34
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Biering SB, Van Dis E, Wehri E, Yamashiro LH, Nguyenla X, Dugast-Darzacq C, Graham TGW, Stroumza JR, Golovkine GR, Roberts AW, Fines DM, Spradlin JN, Ward CC, Bajaj T, Dovala D, Schulze-Gamen U, Bajaj R, Fox DM, Ott M, Murthy N, Nomura DK, Schaletzky J, Stanley SA. Screening a Library of FDA-Approved and Bioactive Compounds for Antiviral Activity against SARS-CoV-2. ACS Infect Dis 2021; 7:2337-2351. [PMID: 34129317 PMCID: PMC8231672 DOI: 10.1021/acsinfecdis.1c00017] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has emerged as a major global health threat. The COVID-19 pandemic has resulted in over 168 million cases and 3.4 million deaths to date, while the number of cases continues to rise. With limited therapeutic options, the identification of safe and effective therapeutics is urgently needed. The repurposing of known clinical compounds holds the potential for rapid identification of drugs effective against SARS-CoV-2. Here, we utilized a library of FDA-approved and well-studied preclinical and clinical compounds to screen for antivirals against SARS-CoV-2 in human pulmonary epithelial cells. We identified 13 compounds that exhibit potent antiviral activity across multiple orthogonal assays. Hits include known antivirals, compounds with anti-inflammatory activity, and compounds targeting host pathways such as kinases and proteases critical for SARS-CoV-2 replication. We identified seven compounds not previously reported to have activity against SARS-CoV-2, including B02, a human RAD51 inhibitor. We further demonstrated that B02 exhibits synergy with remdesivir, the only antiviral approved by the FDA to treat COVID-19, highlighting the potential for combination therapy. Taken together, our comparative compound screening strategy highlights the potential of drug repurposing screens to identify novel starting points for development of effective antiviral mono- or combination therapies to treat COVID-19.
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Affiliation(s)
- Scott B. Biering
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
| | - Erik Van Dis
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Eddie Wehri
- The Henry Wheeler Center for Emerging and
Neglected Diseases, 344 Li Ka Shing, Berkeley, California 94720,
United States
| | - Livia H. Yamashiro
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Xammy Nguyenla
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, Division of
Biochemistry, Biophysics and Structural Biology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Thomas G. W. Graham
- Department of Molecular and Cell Biology, Division of
Biochemistry, Biophysics and Structural Biology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Julien R. Stroumza
- The Henry Wheeler Center for Emerging and
Neglected Diseases, 344 Li Ka Shing, Berkeley, California 94720,
United States
| | - Guillaume R. Golovkine
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Allison W. Roberts
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Daniel M. Fines
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Jessica N. Spradlin
- Departments of Chemistry, Molecular and Cell Biology,
and Nutritional Sciences and Toxicology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Carl C. Ward
- Departments of Chemistry, Molecular and Cell Biology,
and Nutritional Sciences and Toxicology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Teena Bajaj
- Department of Bioengineering, University of
California, Berkeley, Berkeley, California 94720, United
States
| | - Dustin Dovala
- Novartis Institutes for BioMedical
Research, Emeryville, California 94608, United
States
| | - Ursula Schulze-Gamen
- QBI Coronavirus Research Group Structural Biology
Consortium, University of California, San Francisco, California
94158, United States
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences,
University of California, San Francisco, San Francisco,
California 94158, United States
| | - Douglas M. Fox
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Melanie Ott
- Department of Medicine, Medical Scientist Training
Program, Biomedical Sciences Graduate Program, University of California, San
Francisco, San Francisco, California 94143, United
States
- J. David Gladstone
Institutes, San Francisco, California 94158, United
States
| | - Niren Murthy
- Department of Bioengineering, University of
California, Berkeley, Berkeley, California 94720, United
States
- Innovative Genomics Institute
(IGI), 2151 Berkeley Way, Berkeley, California 94704, United
States
| | - Daniel K. Nomura
- Departments of Chemistry, Molecular and Cell Biology,
and Nutritional Sciences and Toxicology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Julia Schaletzky
- The Henry Wheeler Center for Emerging and
Neglected Diseases, 344 Li Ka Shing, Berkeley, California 94720,
United States
| | - Sarah A. Stanley
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
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Vepřek NA, Peitsinis Z, Zhang Y, Trauner D, Fischer C, Rühmann KP, Yang C, Spradlin JN, Dovala D, Nomura DK. De novo Design of SARS-CoV-2 Main Protease Inhibitors. Synlett 2021; 33:458-463. [DOI: 10.1055/a-1582-0243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThe COVID-19 pandemic prompted many scientists to investigate remedies against SARS-CoV-2 and related viruses that are likely to appear in the future. As the main protease of the virus, MPro, is highly conserved among coronaviruses, it has emerged as a prime target for developing inhibitors. Using a combination of virtual screening and molecular modeling, we identified small molecules that were easily accessible and could be quickly diversified. Biochemical assays confirmed a class of pyridones as low micromolar noncovalent inhibitors of the viral main protease.
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Affiliation(s)
- Nynke A. Vepřek
- Department of Chemistry, New York University
- Department of Chemistry, Ludwig-Maximilians-University Munich
| | | | | | | | | | | | - Chao Yang
- Department of Chemistry, New York University
| | | | | | - Daniel K. Nomura
- Innovative Genomics Institute, University of California Berkeley
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Tharp KM, Higuchi-Sanabria R, Timblin GA, Ford B, Garzon-Coral C, Schneider C, Muncie JM, Stashko C, Daniele JR, Moore AS, Frankino PA, Homentcovschi S, Manoli SS, Shao H, Richards AL, Chen KH, Hoeve JT, Ku GM, Hellerstein M, Nomura DK, Saijo K, Gestwicki J, Dunn AR, Krogan NJ, Swaney DL, Dillin A, Weaver VM. Adhesion-mediated mechanosignaling forces mitohormesis. Cell Metab 2021; 33:1322-1341.e13. [PMID: 34019840 PMCID: PMC8266765 DOI: 10.1016/j.cmet.2021.04.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 02/09/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022]
Abstract
Mitochondria control eukaryotic cell fate by producing the energy needed to support life and the signals required to execute programed cell death. The biochemical milieu is known to affect mitochondrial function and contribute to the dysfunctional mitochondrial phenotypes implicated in cancer and the morbidities of aging. However, the physical characteristics of the extracellular matrix are also altered in cancerous and aging tissues. Here, we demonstrate that cells sense the physical properties of the extracellular matrix and activate a mitochondrial stress response that adaptively tunes mitochondrial function via solute carrier family 9 member A1-dependent ion exchange and heat shock factor 1-dependent transcription. Overall, our data indicate that adhesion-mediated mechanosignaling may play an unappreciated role in the altered mitochondrial functions observed in aging and cancer.
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Affiliation(s)
- Kevin M Tharp
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ryo Higuchi-Sanabria
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94597, USA
| | - Greg A Timblin
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Breanna Ford
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA; Novartis, Berkeley Center for Proteomics and Chemistry Technologies and Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Carlos Garzon-Coral
- Chemical Engineering Department, Stanford University, Stanford, CA 94305, USA
| | - Catherine Schneider
- Novartis, Berkeley Center for Proteomics and Chemistry Technologies and Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jonathon M Muncie
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Connor Stashko
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph R Daniele
- MD Anderson Cancer Center, South Campus Research, Houston, CA 77054, USA
| | - Andrew S Moore
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Phillip A Frankino
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94597, USA
| | - Stefan Homentcovschi
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94597, USA
| | - Sagar S Manoli
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hao Shao
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alicia L Richards
- Quantitative Biosciences Institute (QBI), J. David Gladstone Institutes, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kuei-Ho Chen
- Quantitative Biosciences Institute (QBI), J. David Gladstone Institutes, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Johanna Ten Hoeve
- UCLA Metabolomics Center, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gregory M Ku
- Diabetes Center, Division of Endocrinology and Metabolism, Department of Medicine, UCSF, San Francisco, CA 94143, USA
| | - Marc Hellerstein
- Novartis, Berkeley Center for Proteomics and Chemistry Technologies and Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA; Novartis, Berkeley Center for Proteomics and Chemistry Technologies and Department of Chemistry, University of California Berkeley, Berkeley, CA 94720, USA
| | - Karou Saijo
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Jason Gestwicki
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alexander R Dunn
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), J. David Gladstone Institutes, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI), J. David Gladstone Institutes, Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Andrew Dillin
- Department of Molecular & Cellular Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, CA 94597, USA
| | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences and Department of Radiation Oncology, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and The Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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Affiliation(s)
| | - Mishtu Dey
- Senior Scientific Editor, Cell Chemical Biology
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38
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Kilinc S, Paisner R, Camarda R, Gupta S, Momcilovic O, Kohnz RA, Avsaroglu B, L'Etoile ND, Perera RM, Nomura DK, Goga A. Oncogene-regulated release of extracellular vesicles. Dev Cell 2021; 56:1989-2006.e6. [PMID: 34118203 DOI: 10.1016/j.devcel.2021.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 03/24/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022]
Abstract
Oncogenes can alter metabolism by changing the balance between anabolic and catabolic processes. However, how oncogenes regulate tumor cell biomass remains poorly understood. Using isogenic MCF10A cells transformed with nine different oncogenes, we show that specific oncogenes reduce the biomass of cancer cells by promoting extracellular vesicle (EV) release. While MYC and AURKB elicited the highest number of EVs, each oncogene selectively altered the protein composition of released EVs. Likewise, oncogenes alter secreted miRNAs. MYC-overexpressing cells require ceramide, whereas AURKB requires ESCRT to release high levels of EVs. We identify an inverse relationship between MYC upregulation and activation of the RAS/MEK/ERK signaling pathway for regulating EV release in some tumor cells. Finally, lysosome genes and activity are downregulated in the context of MYC and AURKB, suggesting that cellular contents, instead of being degraded, were released via EVs. Thus, oncogene-mediated biomass regulation via differential EV release is a new metabolic phenotype.
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Affiliation(s)
- Seda Kilinc
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Rebekka Paisner
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Roman Camarda
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Suprit Gupta
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Olga Momcilovic
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rebecca A Kohnz
- Departments of Chemistry and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Baris Avsaroglu
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Noelle D L'Etoile
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rushika M Perera
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel K Nomura
- Departments of Chemistry and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrei Goga
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
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Tong B, Belcher BP, Nomura DK, Maimone TJ. Chemical investigations into the biosynthesis of the gymnastatin and dankastatin alkaloids. Chem Sci 2021; 12:8884-8891. [PMID: 34257889 PMCID: PMC8246081 DOI: 10.1039/d1sc02613e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/31/2021] [Indexed: 12/25/2022] Open
Abstract
Electrophilic natural products have provided fertile ground for understanding how nature inhibits protein function using covalent bond formation. The fungal strain Gymnascella dankaliensis has provided an especially interesting collection of halogenated cytotoxic agents derived from tyrosine which feature an array of reactive functional groups. Herein we explore chemical and potentially biosynthetic relationships between architecturally complex gymnastatin and dankastatin members, finding conditions that favor formation of a given scaffold from a common intermediate. Additionally, we find that multiple natural products can also be formed from aranorosin, a non-halogenated natural product also produced by Gymnascella sp. fungi, using simple chloride salts thus offering an alternative hypothesis for the origins of these compounds in nature. Finally, growth inhibitory activity of multiple members against human triple negative breast cancer cells is reported. Total synthesis sheds light on biosynthetic relationships among the chlorinated gymnastatin and dankastatin alkaloids.![]()
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Affiliation(s)
- Bingqi Tong
- Department of Chemistry, University of California-Berkeley Berkeley CA 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California-Berkeley Berkeley CA 94720 USA
| | - Bridget P Belcher
- Department of Chemistry, University of California-Berkeley Berkeley CA 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California-Berkeley Berkeley CA 94720 USA
| | - Daniel K Nomura
- Department of Chemistry, University of California-Berkeley Berkeley CA 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California-Berkeley Berkeley CA 94720 USA.,Departments of Nutritional Science and Toxicology, Cell and Molecular Biology, The Innovative Genomics Institute, University of California-Berkeley Berkeley CA 94720 USA
| | - Thomas J Maimone
- Department of Chemistry, University of California-Berkeley Berkeley CA 94720 USA .,Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California-Berkeley Berkeley CA 94720 USA
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Timblin GA, Tharp KM, Ford B, Winchester JM, Wang J, Zhu S, Khan RI, Louie SK, Iavarone AT, Ten Hoeve J, Nomura DK, Stahl A, Saijo K. Mitohormesis reprogrammes macrophage metabolism to enforce tolerance. Nat Metab 2021; 3:618-635. [PMID: 34031590 PMCID: PMC8162914 DOI: 10.1038/s42255-021-00392-w] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 04/15/2021] [Indexed: 02/03/2023]
Abstract
Macrophages generate mitochondrial reactive oxygen species and mitochondrial reactive electrophilic species as antimicrobials during Toll-like receptor (TLR)-dependent inflammatory responses. Whether mitochondrial stress caused by these molecules impacts macrophage function is unknown. Here, we demonstrate that both pharmacologically driven and lipopolysaccharide (LPS)-driven mitochondrial stress in macrophages triggers a stress response called mitohormesis. LPS-driven mitohormetic stress adaptations occur as macrophages transition from an LPS-responsive to LPS-tolerant state wherein stimulus-induced pro-inflammatory gene transcription is impaired, suggesting tolerance is a product of mitohormesis. Indeed, like LPS, hydroxyoestrogen-triggered mitohormesis suppresses mitochondrial oxidative metabolism and acetyl-CoA production needed for histone acetylation and pro-inflammatory gene transcription, and is sufficient to enforce an LPS-tolerant state. Thus, mitochondrial reactive oxygen species and mitochondrial reactive electrophilic species are TLR-dependent signalling molecules that trigger mitohormesis as a negative feedback mechanism to restrain inflammation via tolerance. Moreover, bypassing TLR signalling and pharmacologically triggering mitohormesis represents a new anti-inflammatory strategy that co-opts this stress response to impair epigenetic support of pro-inflammatory gene transcription by mitochondria.
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Affiliation(s)
- Greg A Timblin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA, USA.
| | - Kevin M Tharp
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Breanna Ford
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies and Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Janet M Winchester
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jerome Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Stella Zhu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Rida I Khan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Shannon K Louie
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Anthony T Iavarone
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA, USA
| | - Johanna Ten Hoeve
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging and UCLA Metabolomics Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies and Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Andreas Stahl
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Kaoru Saijo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
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Abstract
One of the biggest bottlenecks in modern drug discovery efforts is in tackling the undruggable proteome. Currently, over 85% of the proteome is still considered undruggable because most proteins lack well-defined binding pockets that can be functionally targeted with small molecules. Tackling the undruggable proteome necessitates innovative approaches for ligand discovery against undruggable proteins as well as the development of new therapeutic modalities to functionally manipulate proteins of interest. Chemoproteomic platforms, in particular activity-based protein profiling (ABPP), have arisen to tackle the undruggable proteome by using reactivity-based chemical probes and advanced quantitative mass spectrometry-based proteomic approaches to enable the discovery of "ligandable hotspots" or proteome-wide sites that can be targeted with small-molecule ligands. These sites can subsequently be pharmacologically targeted with covalent ligands to rapidly discover functional or nonfunctional binders against therapeutic proteins of interest. Chemoproteomic approaches have also revealed unique insights into ligandability such as the discovery of unique allosteric sites or intrinsically disordered regions of proteins that can be pharmacologically and selectively targeted for biological modulation and therapeutic benefit. Chemoproteomic platforms have also expanded the scope of emerging therapeutic modalities for targeted protein degradation and proteolysis-targeting chimeras (PROTACs) through the discovery of several new covalent E3 ligase recruiters. Looking into the future, chemoproteomic approaches will unquestionably have a major impact in further expansion of existing efforts toward proteome-wide ligandability mapping, targeted ligand discovery efforts against high-value undruggable therapeutic targets, further expansion of the scope of targeted protein degradation platforms, the discovery of new molecular glue scaffolds that enable unique modulation of protein function, and perhaps most excitingly the development of next-generation small-molecule induced-proximity-based therapeutic modalities that go beyond degradation. Exciting days lie ahead in this field as chemical biology becomes an increasingly major driver in drug discovery, and chemoproteomic approaches are sure to be a mainstay in developing next-generation therapeutics.
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Affiliation(s)
- Jessica N. Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, California 94720, United States
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, California 94720, United States
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, California 94720, United States
- Departments of Molecular and Cell Biology and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
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Cho H, Shen Q, Zhang LH, Okumura M, Kawakami A, Ambrose J, Sigoillot F, Miller HR, Gleim S, Cobos-Correa A, Wang Y, Piechon P, Roma G, Eggimann F, Moore C, Aspesi P, Mapa FA, Burks H, Ross NT, Krastel P, Hild M, Maimone TJ, Fisher DE, Nomura DK, Tallarico JA, Canham SM, Jenkins JL, Forrester WC. CYP27A1-dependent anti-melanoma activity of limonoid natural products targets mitochondrial metabolism. Cell Chem Biol 2021; 28:1407-1419.e6. [PMID: 33794192 DOI: 10.1016/j.chembiol.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/24/2021] [Accepted: 03/09/2021] [Indexed: 01/18/2023]
Abstract
Three limonoid natural products with selective anti-proliferative activity against BRAF(V600E) and NRAS(Q61K)-mutation-dependent melanoma cell lines were identified. Differential transcriptome analysis revealed dependency of compound activity on expression of the mitochondrial cytochrome P450 oxidase CYP27A1, a transcriptional target of melanogenesis-associated transcription factor (MITF). We determined that CYP27A1 activity is necessary for the generation of a reactive metabolite that proceeds to inhibit cellular proliferation. A genome-wide small interfering RNA screen in combination with chemical proteomics experiments revealed gene-drug functional epistasis, suggesting that these compounds target mitochondrial biogenesis and inhibit tumor bioenergetics through a covalent mechanism. Our work suggests a strategy for melanoma-specific targeting by exploiting the expression of MITF target gene CYP27A1 and inhibiting mitochondrial oxidative phosphorylation in BRAF mutant melanomas.
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Affiliation(s)
- Hyelim Cho
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Qiong Shen
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Lydia H Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Mikiko Okumura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Akinori Kawakami
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jessi Ambrose
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Frederic Sigoillot
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Howard R Miller
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Scott Gleim
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Amanda Cobos-Correa
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Ying Wang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Philippe Piechon
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Fabian Eggimann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Charles Moore
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Peter Aspesi
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Felipa A Mapa
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Heather Burks
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Nathan T Ross
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Marc Hild
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Thomas J Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - David E Fisher
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA
| | - John A Tallarico
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Stephen M Canham
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Jeremy L Jenkins
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - William C Forrester
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
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Moldavski O, Zushin PJH, Berdan CA, Van Eijkeren RJ, Jiang X, Qian M, Ory DS, Covey DF, Nomura DK, Stahl A, Weiss EJ, Zoncu R. 4β-Hydroxycholesterol is a prolipogenic factor that promotes SREBP1c expression and activity through the liver X receptor. J Lipid Res 2021; 62:100051. [PMID: 33631213 PMCID: PMC8042401 DOI: 10.1016/j.jlr.2021.100051] [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] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/06/2021] [Accepted: 02/12/2021] [Indexed: 12/16/2022] Open
Abstract
Oxysterols are oxidized derivatives of cholesterol that play regulatory roles in lipid biosynthesis and homeostasis. How oxysterol signaling coordinates different lipid classes such as sterols and triglycerides remains incompletely understood. Here, we show that 4β-hydroxycholesterol (HC) (4β-HC), a liver and serum abundant oxysterol of poorly defined functions, is a potent and selective inducer of the master lipogenic transcription factor, SREBP1c, but not the related steroidogenic transcription factor SREBP2. By correlating tracing of lipid synthesis with lipogenic gene expression profiling, we found that 4β-HC acts as a putative agonist for the liver X receptor (LXR), a sterol sensor and transcriptional regulator previously linked to SREBP1c activation. Unique among the oxysterol agonists of the LXR, 4β-HC induced expression of the lipogenic program downstream of SREBP1c and triggered de novo lipogenesis both in primary hepatocytes and in the mouse liver. In addition, 4β-HC acted in parallel to insulin-PI3K–dependent signaling to stimulate triglyceride synthesis and lipid-droplet accumulation. Thus, 4β-HC is an endogenous regulator of de novo lipogenesis through the LXR-SREBP1c axis.
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Affiliation(s)
- Ofer Moldavski
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; The Paul F. Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA, USA; Cardiovascular Research Institute, UCSF, San Francisco, CA, USA
| | - Peter-James H Zushin
- Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA, USA
| | - Charles A Berdan
- Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA, USA
| | - Robert J Van Eijkeren
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; The Paul F. Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA, USA
| | - Xuntian Jiang
- Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St Louis, MO, USA
| | - Mingxing Qian
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel S Ory
- Diabetic Cardiovascular Disease Center, Washington University School of Medicine, St Louis, MO, USA
| | - Douglas F Covey
- Department of Developmental Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Daniel K Nomura
- Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA, USA
| | - Andreas Stahl
- Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA, USA
| | - Ethan J Weiss
- Cardiovascular Research Institute, UCSF, San Francisco, CA, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; The Paul F. Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA, USA.
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44
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Tošić I, Heppler LN, Egusquiaguirre SP, Boehnke N, Correa S, Costa DF, Moore EAG, Pal S, Richardson DS, Ivanov AR, Haas-Kogan DA, Nomura DK, Hammond PT, Frank DA. Lipidome-based Targeting of STAT3-driven Breast Cancer Cells Using Poly-l-glutamic Acid-coated Layer-by-Layer Nanoparticles. Mol Cancer Ther 2021; 20:726-738. [PMID: 33536189 DOI: 10.1158/1535-7163.mct-20-0505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/29/2020] [Accepted: 01/26/2021] [Indexed: 11/16/2022]
Abstract
The oncogenic transcription factor STAT3 is aberrantly activated in 70% of breast cancers, including nearly all triple-negative breast cancers (TNBCs). Because STAT3 is difficult to target directly, we considered whether metabolic changes driven by activated STAT3 could provide a therapeutic opportunity. We found that STAT3 prominently modulated several lipid classes, with most profound effects on N-acyl taurine and arachidonic acid, both of which are involved in plasma membrane remodeling. To exploit these metabolic changes therapeutically, we screened a library of layer-by-layer (LbL) nanoparticles (NPs) differing in the surface layer that modulates interactivity with the cell membrane. We found that poly-l-glutamic acid (PLE)-coated NPs bind to STAT3-transformed breast cancer cells with 50% greater efficiency than to nontransformed cells, and the heightened PLE-NP binding to TNBC cells was attenuated by STAT3 inhibition. This effect was also observed in densely packed three-dimensional breast cancer organoids. As STAT3-transformed cells show greater resistance to cytotoxic agents, we evaluated whether enhanced targeted delivery via PLE-NPs would provide a therapeutic advantage. We found that cisplatin-loaded PLE-NPs induced apoptosis of STAT3-driven cells at lower doses compared with both unencapsulated cisplatin and cisplatin-loaded nontargeted NPs. In addition, because radiation is commonly used in breast cancer treatment, and may alter cellular lipid distribution, we analyzed its effect on PLE-NP-cell binding. Irradiation of cells enhanced the STAT3-targeting properties of PLE-NPs in a dose-dependent manner, suggesting potential synergies between these therapeutic modalities. These findings suggest that cellular lipid changes driven by activated STAT3 may be exploited therapeutically using unique LbL NPs.
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Affiliation(s)
- Isidora Tošić
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Biochemistry, Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | - Lisa N Heppler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | | | - Natalie Boehnke
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Santiago Correa
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Daniel F Costa
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Elizabeth A Grossman Moore
- Department of Chemistry, Molecular and Cell Biology, University of California at Berkeley, Berkeley, Massachusetts
| | - Sharmistha Pal
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Douglas S Richardson
- Harvard Center for Biological Imaging, Harvard University, Cambridge, Massachusetts
| | - Alexander R Ivanov
- Department of Chemistry and Chemical Biology, Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts
| | - Daphne A Haas-Kogan
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Daniel K Nomura
- Department of Chemistry, Molecular and Cell Biology, University of California at Berkeley, Berkeley, Massachusetts
| | - Paula T Hammond
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Institute for Soldier Nanotechnology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - David A Frank
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. .,Harvard Medical School, Boston, Massachusetts
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45
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Luo M, Spradlin JN, Boike L, Tong B, Brittain SM, McKenna JM, Tallarico JA, Schirle M, Maimone TJ, Nomura DK. Chemoproteomics-enabled discovery of covalent RNF114-based degraders that mimic natural product function. Cell Chem Biol 2021; 28:559-566.e15. [PMID: 33513350 DOI: 10.1016/j.chembiol.2021.01.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 12/10/2020] [Accepted: 01/05/2021] [Indexed: 12/26/2022]
Abstract
The translation of functionally active natural products into fully synthetic small-molecule mimetics has remained an important process in medicinal chemistry. We recently discovered that the terpene natural product nimbolide can be utilized as a covalent recruiter of the E3 ubiquitin ligase RNF114 for use in targeted protein degradation-a powerful therapeutic modality within modern-day drug discovery. Using activity-based protein profiling-enabled covalent ligand-screening approaches, here we report the discovery of fully synthetic RNF114-based recruiter molecules that can also be exploited for PROTAC applications, and demonstrate their utility in degrading therapeutically relevant targets, such as BRD4 and BCR-ABL, in cells. The identification of simple and easily manipulated drug-like scaffolds that can mimic the function of a complex natural product is beneficial in further expanding the toolbox of E3 ligase recruiters, an area of great importance in drug discovery and chemical biology.
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Affiliation(s)
- Mai Luo
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA
| | - Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA
| | - Bingqi Tong
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA
| | - Scott M Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Thomas J Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA.
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Cambridge, MA 02139, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, Univerity of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA.
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46
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Manford AG, Rodríguez-Pérez F, Shih KY, Shi Z, Berdan CA, Choe M, Titov DV, Nomura DK, Rape M. A Cellular Mechanism to Detect and Alleviate Reductive Stress. Cell 2020; 183:46-61.e21. [PMID: 32941802 DOI: 10.1016/j.cell.2020.08.034] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [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: 12/18/2019] [Revised: 05/28/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022]
Abstract
Metazoan organisms rely on conserved stress response pathways to alleviate adverse conditions and preserve cellular integrity. Stress responses are particularly important in stem cells that provide lifetime support for tissue formation and repair, but how these protective systems are integrated into developmental programs is poorly understood. Here we used myoblast differentiation to identify the E3 ligase CUL2FEM1B and its substrate FNIP1 as core components of the reductive stress response. Reductive stress, as caused by prolonged antioxidant signaling or mitochondrial inactivity, reverts the oxidation of invariant Cys residues in FNIP1 and allows CUL2FEM1B to recognize its target. The ensuing proteasomal degradation of FNIP1 restores mitochondrial activity to preserve redox homeostasis and stem cell integrity. The reductive stress response is therefore built around a ubiquitin-dependent rheostat that tunes mitochondrial activity to redox needs and implicates metabolic control in coordination of stress and developmental signaling.
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Affiliation(s)
- Andrew G Manford
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley CA 94720, USA
| | - Fernando Rodríguez-Pérez
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley CA 94720, USA
| | - Karen Y Shih
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley CA 94720, USA
| | - Zhuo Shi
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley CA 94720, USA
| | - Charles A Berdan
- Department of Nutritional Science and Toxicology, University of California at Berkeley, Berkeley CA 94720, USA
| | - Mangyu Choe
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley CA 94720, USA; Department of Nutritional Science and Toxicology, University of California at Berkeley, Berkeley CA 94720, USA; Center for Computational Biology, University of California at Berkeley, Berkeley CA 94720, USA
| | - Denis V Titov
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley CA 94720, USA; Department of Nutritional Science and Toxicology, University of California at Berkeley, Berkeley CA 94720, USA; Center for Computational Biology, University of California at Berkeley, Berkeley CA 94720, USA
| | - Daniel K Nomura
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley CA 94720, USA; Department of Nutritional Science and Toxicology, University of California at Berkeley, Berkeley CA 94720, USA; Department of Chemistry, University of California at Berkeley, CA 94720, USA
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley CA 94720, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley CA 94720, USA; California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA 94720, USA.
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47
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Tong B, Luo M, Xie Y, Spradlin JN, Tallarico JA, McKenna JM, Schirle M, Maimone TJ, Nomura DK. Bardoxolone conjugation enables targeted protein degradation of BRD4. Sci Rep 2020; 10:15543. [PMID: 32968148 PMCID: PMC7511954 DOI: 10.1038/s41598-020-72491-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/27/2020] [Indexed: 02/08/2023] Open
Abstract
Targeted protein degradation (TPD) has emerged as a powerful tool in drug discovery for the perturbation of protein levels using heterobifunctional small molecules. E3 ligase recruiters remain central to this process yet relatively few have been identified relative to the ~ 600 predicted human E3 ligases. While, initial recruiters have utilized non-covalent chemistry for protein binding, very recently covalent engagement to novel E3's has proven fruitful in TPD application. Herein we demonstrate efficient proteasome-mediated degradation of BRD4 by a bifunctional small molecule linking the KEAP1-Nrf2 activator bardoxolone to a BRD4 inhibitor JQ1.
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Affiliation(s)
- Bingqi Tong
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Mai Luo
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Yi Xie
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Jessica N Spradlin
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA
| | - Thomas J Maimone
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA.
- Departments of Molecular and Cell Biology and Nutritional Sciences and Toxicology, University of California, Berkeley, CA, 94720, USA.
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48
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Boike L, Cioffi AG, Majewski FC, Co J, Henning NJ, Jones MD, Liu G, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Discovery of a Functional Covalent Ligand Targeting an Intrinsically Disordered Cysteine within MYC. Cell Chem Biol 2020; 28:4-13.e17. [PMID: 32966806 DOI: 10.1016/j.chembiol.2020.09.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 08/14/2020] [Accepted: 09/01/2020] [Indexed: 12/21/2022]
Abstract
MYC is a major oncogenic transcriptional driver of most human cancers that has remained intractable to direct targeting because much of MYC is intrinsically disordered. Here, we have performed a cysteine-reactive covalent ligand screen to identify compounds that could disrupt the binding of MYC to its DNA consensus sequence in vitro and also impair MYC transcriptional activity in situ in cells. We have identified a covalent ligand, EN4, that targets cysteine 171 of MYC within a predicted intrinsically disordered region of the protein. We show that EN4 directly targets MYC in cells, reduces MYC and MAX thermal stability, inhibits MYC transcriptional activity, downregulates multiple MYC transcriptional targets, and impairs tumorigenesis. We also show initial structure-activity relationships of EN4 and identify compounds that show improved potency. Overall, we identify a unique ligandable site within an intrinsically disordered region of MYC that leads to inhibition of MYC transcriptional activity.
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Affiliation(s)
- Lydia Boike
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Alexander G Cioffi
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Felix C Majewski
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Jennifer Co
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Nathaniel J Henning
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Michael D Jones
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Gang Liu
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Jeffrey M McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - John A Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA.
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49
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Tong B, Spradlin JN, Novaes LFT, Zhang E, Hu X, Moeller M, Brittain SM, McGregor LM, McKenna JM, Tallarico JA, Schirle M, Maimone TJ, Nomura DK. A Nimbolide-Based Kinase Degrader Preferentially Degrades Oncogenic BCR-ABL. ACS Chem Biol 2020; 15:1788-1794. [PMID: 32568522 DOI: 10.1021/acschembio.0c00348] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Targeted protein degradation (TPD) and proteolysis-targeting chimeras (PROTACs) have arisen as powerful therapeutic modalities for degrading specific proteins in a proteasome-dependent manner. However, a major limitation of TPD is the lack of E3 ligase recruiters. Recently, we discovered the natural product nimbolide as a covalent recruiter for the E3 ligase RNF114. Here, we show the broader utility of nimbolide as an E3 ligase recruiter for TPD applications. We demonstrate that a PROTAC linking nimbolide to the kinase and BCR-ABL fusion oncogene inhibitor dasatinib, BT1, selectively degrades BCR-ABL over c-ABL in leukemia cancer cells, compared to previously reported cereblon or VHL-recruiting BCR-ABL degraders that show opposite selectivity or, in some cases, inactivity. Thus, we further establish nimbolide as an additional general E3 ligase recruiter for PROTACs, and we demonstrate the importance of expanding upon the arsenal of E3 ligase recruiters, as such molecules confer differing selectivity for the degradation of neo-substrate proteins.
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Affiliation(s)
- Bingqi Tong
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Jessica N. Spradlin
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Luiz F. T. Novaes
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Erika Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Xirui Hu
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Malte Moeller
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Scott M. Brittain
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Lynn M. McGregor
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Jeffrey M. McKenna
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A. Tallarico
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Thomas J. Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, California 94720, United States
- Innovative Genomics Institute, Berkeley, California 94704, United States
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50
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Sponton CH, Hosono T, Taura J, Jedrychowski MP, Yoneshiro T, Wang Q, Takahashi M, Matsui Y, Ikeda K, Oguri Y, Tajima K, Shinoda K, Pradhan RN, Chen Y, Brown Z, Roberts LS, Ward CC, Taoka H, Yokoyama Y, Watanabe M, Karasawa H, Nomura DK, Kajimura S. The regulation of glucose and lipid homeostasis via PLTP as a mediator of BAT-liver communication. EMBO Rep 2020; 21:e49828. [PMID: 32672883 DOI: 10.15252/embr.201949828] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 06/09/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022] Open
Abstract
While brown adipose tissue (BAT) is well-recognized for its ability to dissipate energy in the form of heat, recent studies suggest multifaced roles of BAT in the regulation of glucose and lipid homeostasis beyond stimulating thermogenesis. One of the functions involves interorgan communication with metabolic organs, such as the liver, through BAT-derived secretory factors, a.k.a., batokine. However, the identity and the roles of such mediators remain insufficiently understood. Here, we employed proteomics and transcriptomics in human thermogenic adipocytes and identified previously unappreciated batokines, including phospholipid transfer protein (PLTP). We found that increased circulating levels of PLTP, via systemic or BAT-specific overexpression, significantly improve glucose tolerance and insulin sensitivity, increased energy expenditure, and decrease the circulating levels of cholesterol, phospholipids, and sphingolipids. Such changes were accompanied by increased bile acids in the circulation, which in turn enhances glucose uptake and thermogenesis in BAT. Our data suggest that PLTP is a batokine that contributes to the regulation of systemic glucose and lipid homeostasis as a mediator of BAT-liver interorgan communication.
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Affiliation(s)
- Carlos H Sponton
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Takashi Hosono
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Junki Taura
- End-Organ Disease Laboratories, Daiichi-Sankyo Co., Ltd., Tokyo, Japan
| | | | - Takeshi Yoneshiro
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Qiang Wang
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Makoto Takahashi
- Drug Metabolism & Pharmacokinetics Research Laboratories, Daiichi-Sankyo Co., Ltd., Tokyo, Japan
| | - Yumi Matsui
- Protein Production Research Group, Biological Research Department, Daiichi-Sankyo RD Novare Co., Ltd., Tokyo, Japan
| | - Kenji Ikeda
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Yasuo Oguri
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Kazuki Tajima
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Kosaku Shinoda
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Rachana N Pradhan
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Yong Chen
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Zachary Brown
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Lindsay S Roberts
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Carl C Ward
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Hiroki Taoka
- Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| | - Yoko Yokoyama
- Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| | - Mitsuhiro Watanabe
- Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| | - Hiroshi Karasawa
- End-Organ Disease Laboratories, Daiichi-Sankyo Co., Ltd., Tokyo, Japan
| | - Daniel K Nomura
- Departments of Chemistry, Molecular and Cell Biology, and Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Shingo Kajimura
- Diabetes Center, University of California, San Francisco, CA, USA.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA.,Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
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