1
|
Gewering T, Waghray D, Parey K, Jung H, Tran NNB, Zapata J, Zhao P, Chen H, Januliene D, Hummer G, Urbatsch I, Moeller A, Zhang Q. Tracing the substrate translocation mechanism in P-glycoprotein. eLife 2024; 12:RP90174. [PMID: 38259172 PMCID: PMC10945689 DOI: 10.7554/elife.90174] [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: 01/24/2024] Open
Abstract
P-glycoprotein (Pgp) is a prototypical ATP-binding cassette (ABC) transporter of great biological and clinical significance.Pgp confers cancer multidrug resistance and mediates the bioavailability and pharmacokinetics of many drugs (Juliano and Ling, 1976; Ueda et al., 1986; Sharom, 2011). Decades of structural and biochemical studies have provided insights into how Pgp binds diverse compounds (Loo and Clarke, 2000; Loo et al., 2009; Aller et al., 2009; Alam et al., 2019; Nosol et al., 2020; Chufan et al., 2015), but how they are translocated through the membrane has remained elusive. Here, we covalently attached a cyclic substrate to discrete sites of Pgp and determined multiple complex structures in inward- and outward-facing states by cryoEM. In conjunction with molecular dynamics simulations, our structures trace the substrate passage across the membrane and identify conformational changes in transmembrane helix 1 (TM1) as regulators of substrate transport. In mid-transport conformations, TM1 breaks at glycine 72. Mutation of this residue significantly impairs drug transport of Pgp in vivo, corroborating the importance of its regulatory role. Importantly, our data suggest that the cyclic substrate can exit Pgp without the requirement of a wide-open outward-facing conformation, diverting from the common efflux model for Pgp and other ABC exporters. The substrate transport mechanism of Pgp revealed here pinpoints critical targets for future drug discovery studies of this medically relevant system.
Collapse
Affiliation(s)
- Theresa Gewering
- Osnabrück University, Department of Biology/Chemistry, Structural Biology SectionOsnabrückGermany
- Department of Structural Biology, Max Planck Institute of BiophysicsFrankfurtGermany
| | - Deepali Waghray
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Kristian Parey
- Osnabrück University, Department of Biology/Chemistry, Structural Biology SectionOsnabrückGermany
- Department of Structural Biology, Max Planck Institute of BiophysicsFrankfurtGermany
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs)OsnabrückGermany
| | - Hendrik Jung
- Department of Theoretical Biophysics, Max Planck Institute of BiophysicsFrankfurtGermany
| | - Nghi NB Tran
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbockUnited States
| | - Joel Zapata
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbockUnited States
| | - Pengyi Zhao
- Department of Chemistry & Environmental Science, New Jersey Institute of TechnologyNewarkUnited States
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of TechnologyNewarkUnited States
| | - Dovile Januliene
- Osnabrück University, Department of Biology/Chemistry, Structural Biology SectionOsnabrückGermany
- Department of Structural Biology, Max Planck Institute of BiophysicsFrankfurtGermany
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs)OsnabrückGermany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of BiophysicsFrankfurtGermany
- Institute for Biophysics, Goethe University FrankfurtFrankfurtGermany
| | - Ina Urbatsch
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbockUnited States
| | - Arne Moeller
- Osnabrück University, Department of Biology/Chemistry, Structural Biology SectionOsnabrückGermany
- Department of Structural Biology, Max Planck Institute of BiophysicsFrankfurtGermany
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs)OsnabrückGermany
| | - Qinghai Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| |
Collapse
|
2
|
Chiacchio MA, Legnani L, Fassi EMA, Roda G, Grazioso G. Development of AMBER Parameters for Molecular Simulations of Selected Boron-Based Covalent Ligands. Molecules 2023; 28:molecules28062866. [PMID: 36985837 PMCID: PMC10057150 DOI: 10.3390/molecules28062866] [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: 03/06/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Boron containing compounds (BCCs) aroused increasing interest in the scientific community due to their wide application as drugs in various fields. In order to design new compounds hopefully endowed with pharmacological activity and also investigate their conformational behavior, the support of computational studies is crucial. Nevertheless, the suitable molecular mechanics parameterization and the force fields needed to perform these simulations are not completely available for this class of molecules. In this paper, Amber force field parameters for phenyl-, benzyl-, benzylamino-, and methylamino-boronates, a group of boron-containing compounds involved in different branches of the medicinal chemistry, were created. The robustness of the obtained data was confirmed through molecular dynamics simulations on ligand/β-lactamases covalent complexes. The ligand torsional angles, populated over the trajectory frames, were confirmed by values found in the ligand geometries, located through optimizations at the DFT/B3LYP/6-31g(d) level, using water as a solvent. In summary, this study successfully provided a library of parameters, opening the possibility to perform molecular dynamics simulations of this class of boron-containing compounds.
Collapse
Affiliation(s)
- Maria Assunta Chiacchio
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Laura Legnani
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | | | - Gabriella Roda
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Chung CYS, Shin HR, Berdan CA, Ford B, Ward CC, Olzmann JA, Zoncu R, Nomura DK. Covalent targeting of the vacuolar H +-ATPase activates autophagy via mTORC1 inhibition. Nat Chem Biol 2019; 15:776-785. [PMID: 31285595 PMCID: PMC6641988 DOI: 10.1038/s41589-019-0308-4] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [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: 01/15/2019] [Accepted: 05/15/2019] [Indexed: 02/06/2023]
Abstract
Autophagy is a lysosomal degradation pathway that eliminates aggregated proteins and damaged organelles to maintain cellular homeostasis. A major route for activating autophagy involves inhibition of the mTORC1 kinase, but current mTORC1-targeting compounds do not allow complete and selective mTORC1 blockade. Here, we have coupled screening of a covalent ligand library with activity-based protein profiling to discover EN6, a small-molecule in vivo activator of autophagy that covalently targets cysteine 277 in the ATP6V1A subunit of the lysosomal v-ATPase, which activates mTORC1 via the Rag guanosine triphosphatases. EN6-mediated ATP6V1A modification decouples the v-ATPase from the Rags, leading to inhibition of mTORC1 signaling, increased lysosomal acidification and activation of autophagy. Consistently, EN6 clears TDP-43 aggregates, a causative agent in frontotemporal dementia, in a lysosome-dependent manner. Our results provide insight into how the v-ATPase regulates mTORC1, and reveal a unique approach for enhancing cellular clearance based on covalent inhibition of lysosomal mTORC1 signaling.
Collapse
Affiliation(s)
- Clive Yik-Sham Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
| | - Hijai R Shin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, Berkeley, CA, USA
| | - Charles A Berdan
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Breanna Ford
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Carl C Ward
- Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- The Paul F. Glenn Center for Aging Research at the University of California, Berkeley, 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.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA.
| |
Collapse
|