DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Targeted protein degradation: from small molecules to complex organelles—a Keystone Symposia report

Journal Article · · Annals of the New York Academy of Sciences
DOI: https://doi.org/10.1111/nyas.14745 · OSTI ID:1863764
 [1];  [2];  [3];  [4];  [5];  [6];  [7];  [8];  [9];  [10];  [11];  [12];  [13];  [14];  [15];  [16];  [17];  [18];  [19];  [20] more »;  [21];  [22];  [23];  [24];  [25];  [26];  [27];  [28];  [29];  [30];  [6];  [31] « less
  1. PhD Science Writer, New York, NY (United States)
  2. ETH Zurich (Switzerland). Inst. of Molecular Biology and Biophysics
  3. Vienna BioCenter and Medical University of Vienna (Austria). Research Institute of Molecular Pathology (IMP)
  4. National Institutes of Health (NIH), Frederick MD (United States). National Cancer Inst., Center for Cancer Research, Center for Structural Biology
  5. Weizmann Institute of Science, Rehovot (Israel)
  6. Harvard Medical School, Boston, MA (United States)
  7. Univ. of California, Berkeley, CA (United States). Innovative Genomics Inst.
  8. Brigham and Women's Hospital (Harvard Medical School), Boston, MA (United States)
  9. Univ. of Toronto, ON (Canada). Princess Margaret Cancer Centre
  10. Univ. of Vienna (Austria). Vienna BioCenter (VBC), Max Perutz Labs
  11. Univ. of Oslo (Norway). Institute of Basic Medical Sciences, Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine; Oslo Univ. Hospital (Norway). Institute for Cancer Research
  12. Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA (United States)
  13. Chinese Academy of Sciences (CAS), Beijing (China). Inst. of Biophysics, CAS Center for Excellence in Biomacromolecules, National Laboratory of Biomacromolecules; University of Chinese Academy of Sciences, Beijing (China)
  14. Casma Therapeutics, Cambridge, MA (United States)
  15. Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (Italy)
  16. Univ. of California, Berkeley, CA (United States)
  17. Tsinghua Univ., Beijing (China); Tsinghua Univ.-Peking Univ. Joint Center for Life Sciences, Beijing (China). State Key Laboratory of Membrane Biology
  18. Max Planck Institute of Biochemistry, Martinsried (Germany)
  19. Amgen, Inc., Thousand Oaks, CA (United States)
  20. Goethe Univ., Frankfurt (Germany). Institute of Biochemistry, Buchmann Institute for Molecular Life Sciences
  21. Harvard Medical School, Boston, MA (United States). Blavatnik Inst.
  22. Genentech, Inc., South San Francisco, CA (United States); Bristol Myers Squibb, Brisbane, CA (United States)
  23. Friedrich Miescher Institute for Biomedical Research, Basel (Switzerland)
  24. Broad Institute of MIT and Harvard, Cambridge, MA (United States); Dana‐Farber Cancer Institute, Boston, MA (United States); German Cancer Research Center (DKFZ), Heidelberg (Germany); National Center for Tumor Diseases (NCT), Heidelberg (Germany)
  25. Biohub, San Francisco, CA (United States); Stanford Univ., CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States). Stanford Synchrotron Radiation Lightsource (SSRL)
  26. Univ. of Michigan, Ann Arbor, MI (United States)
  27. University of Tübingen (Germany). Interfaculty Institute of Biochemistry, German Center for Neurodegenerative Diseases (DZNE)
  28. Univ. of California San Diego, La Jolla, CA (United States)
  29. Howard Hughes Medical Inst., Stanford, CA (United States); Stanford Univ., CA (United States)
  30. Cornell Univ., Ithaca, NY (United States). Weill Institute of Cell and Molecular Biology
  31. University of Modena and Reggio Emilia (Italy)

Targeted protein degradation is critical for proper cellular function and development. Protein degradation pathways, such as the ubiquitin proteasomes system, autophagy, and endosome–lysosome pathway, must be tightly regulated to ensure proper elimination of misfolded and aggregated proteins and regulate changing protein levels during cellular differentiation, while ensuring that normal proteins remain unscathed. Protein degradation pathways have also garnered interest as a means to selectively eliminate target proteins that may be difficult to inhibit via other mechanisms. Additionally, on June 7 and 8, 2021, several experts in protein degradation pathways met virtually for the Keystone eSymposium “Targeting protein degradation: from small molecules to complex organelles.” The event brought together researchers working in different protein degradation pathways in an effort to begin to develop a holistic, integrated vision of protein degradation that incorporates all the major pathways to understand how changes in them can lead to disease pathology and, alternatively, how they can be leveraged for novel therapeutics.

Research Organization:
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
Grant/Contract Number:
AC02-76SF00515
OSTI ID:
1863764
Journal Information:
Annals of the New York Academy of Sciences, Journal Name: Annals of the New York Academy of Sciences Journal Issue: 1 Vol. 1510; ISSN 0077-8923
Publisher:
WileyCopyright Statement
Country of Publication:
United States
Language:
English

References (130)

Mitochondrial dynamics, mitophagy and biogenesis in neonatal hypoxic-ischaemic brain injury journal December 2017
NIMA-related kinase 9–mediated phosphorylation of the microtubule-associated LC3B protein at Thr-50 suppresses selective autophagy of p62/sequestosome 1 journal January 2020
Ump1p Is Required for Proper Maturation of the 20S Proteasome and Becomes Its Substrate upon Completion of the Assembly journal February 1998
Cdc48–Ufd1–Npl4: Stuck in the Middle with Ub journal May 2002
A Dynamic Role of HAUSP in the p53-Mdm2 Pathway journal March 2004
Selective autophagy as a potential therapeutic target for neurodegenerative disorders journal September 2018
A bis-Benzylidine Piperidone Targeting Proteasome Ubiquitin Receptor RPN13/ADRM1 as a Therapy for Cancer journal December 2013
SEPA-1 Mediates the Specific Recognition and Degradation of P Granule Components by Autophagy in C. elegans journal January 2009
C. elegans Screen Identifies Autophagy Genes Specific to Multicellular Organisms journal June 2010
Dual Specificity Kinase DYRK3 Couples Stress Granule Condensation/Dissolution to mTORC1 Signaling journal February 2013
Two Distinct Types of E3 Ligases Work in Unison to Regulate Substrate Ubiquitylation journal August 2016
mTOR Regulates Phase Separation of PGL Granules to Modulate Their Autophagic Degradation journal September 2018
The Selective Autophagy Receptor p62 Forms a Flexible Filamentous Helical Scaffold journal May 2015
iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation journal August 2021
Physical and Functional Analysis of the Putative Rpn13 Inhibitor RA190 journal November 2020
Mechanistic Studies of the Multiple Myeloma and Melanoma Cell-Selective Toxicity of the Rpn13-Binding Peptoid KDT-11 journal November 2020
Interplay between the virus and the ubiquitin–proteasome system: molecular mechanism of viral pathogenesis journal April 2016
LC3B phosphorylation regulates FYCO1 binding and directional transport of autophagosomes journal August 2021
A distinct structural region of the prokaryotic ubiquitin-like protein (Pup) is recognized by the N-terminal domain of the proteasomal ATPase Mpa journal September 2009
Mechanisms of Selective Autophagy journal May 2016
Repair or Lysophagy: Dealing with Damaged Lysosomes journal January 2020
Arginine Methylation Modulates Autophagic Degradation of PGL Granules in C. elegans journal November 2013
Phosphorylation of LC3 by the Hippo Kinases STK3/STK4 Is Essential for Autophagy journal January 2015
A Surveillance Function of the HSPB8-BAG3-HSP70 Chaperone Complex Ensures Stress Granule Integrity and Dynamism journal September 2016
ZFAND1 Recruits p97 and the 26S Proteasome to Promote the Clearance of Arsenite-Induced Stress Granules journal June 2018
ZNF598 Is a Quality Control Sensor of Collided Ribosomes journal November 2018
FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates journal April 2019
The G3BP1-Family-USP10 Deubiquitinase Complex Rescues Ubiquitinated 40S Subunits of Ribosomes Stalled in Translation from Lysosomal Degradation journal March 2020
Structure of HHARI, a RING-IBR-RING Ubiquitin Ligase: Autoinhibition of an Ariadne-Family E3 and Insights into Ligation Mechanism journal June 2013
ER-Phagy: Quality Control and Turnover of Endoplasmic Reticulum journal May 2020
Beyond Autophagy: The Expanding Roles of ATG8 Proteins journal August 2021
Eating the unknown: Xenophagy and ER-phagy are cytoprotective defenses against pathogens journal November 2020
Covalent Rpn13-Binding Inhibitors for the Treatment of Ovarian Cancer journal September 2018
A Reversible and Highly Selective Inhibitor of the Proteasomal Ubiquitin Receptor Rpn13 Is Toxic to Multiple Myeloma Cells journal May 2015
TRIAD1 and HHARI bind to and are activated by distinct neddylated Cullin-RING ligase complexes journal September 2013
Targeting proteasome ubiquitin receptor Rpn13 in multiple myeloma journal April 2016
Disruption of HAUSP gene stabilizes p53 journal April 2004
Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction journal May 2008
Proteasome subunit Rpn13 is a novel ubiquitin receptor journal May 2008
An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer journal April 2009
Members of the H3K4 trimethylation complex regulate lifespan in a germline-dependent manner in C. elegans journal June 2010
Transgenerational epigenetic inheritance of longevity in Caenorhabditis elegans journal October 2011
Structural basis of lenalidomide-induced CK1α degradation by the CRL4CRBN ubiquitin ligase journal February 2016
Arginine phosphorylation marks proteins for degradation by a Clp protease journal October 2016
CMTM6 maintains the expression of PD-L1 and regulates anti-tumour immunity journal August 2017
Conformational stabilization of ubiquitin yields potent and selective inhibitors of USP7 journal November 2012
Structure of the Rpn13-Rpn2 complex provides insights for Rpn13 and Uch37 as anticancer targets journal June 2017
In vivo gene silencing identifies the Mycobacterium tuberculosis proteasome as essential for the bacteria to persist in mice journal December 2007
Real-time imaging of the intracellular glutathione redox potential journal May 2008
Genetically encoded fluorescent indicator for intracellular hydrogen peroxide journal March 2006
LUBAC-synthesized linear ubiquitin chains restrict cytosol-invading bacteria by activating autophagy and NF-κB journal May 2017
Linear ubiquitination of cytosolic Salmonella Typhimurium activates NF-κB and restricts bacterial proliferation journal May 2017
Bacterial ubiquitin-like modifier Pup is deamidated and conjugated to substrates by distinct but homologous enzymes journal May 2009
Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation journal October 2010
Mitochondrial ClpP serine protease-biological function and emerging target for cancer therapy journal October 2020
A complex of C9ORF72 and p62 uses arginine methylation to eliminate stress granules by autophagy journal July 2018
Proximity labeling proteomics reveals critical regulators for inner nuclear membrane protein degradation in plants journal June 2020
The complex structure of GRL0617 and SARS-CoV-2 PLpro reveals a hot spot for antiviral drug discovery journal January 2021
20S proteasomes secreted by the malaria parasite promote its growth journal February 2021
Reconstitution defines the roles of p62, NBR1 and TAX1BP1 in ubiquitin condensate formation and autophagy initiation journal September 2021
GAK and PRKCD are positive regulators of PRKN-independent mitophagy journal October 2021
Structure-guided bifunctional molecules hit a DEUBAD-lacking hRpn13 species upregulated in multiple myeloma journal December 2021
Autophagy as a promoter of longevity: insights from model organisms journal July 2018
Distinct proteostasis circuits cooperate in nuclear and cytoplasmic protein quality control journal October 2018
Developmental ROS individualizes organismal stress resistance and lifespan journal December 2019
Multispecific drugs herald a new era of biopharmaceutical innovation journal April 2020
Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors journal April 2020
The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K journal June 2020
Extracellular proteostasis prevents aggregation during pathogenic attack journal July 2020
Lysosome-targeting chimaeras for degradation of extracellular proteins journal July 2020
Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity journal July 2020
Small-molecule-induced polymerization triggers degradation of BCL6 journal November 2020
Ubiquitin ligation to F-box protein targets by SCF–RBR E3–E3 super-assembly journal February 2021
HIP1R targets PD-L1 to lysosomal degradation to alter T cell–mediated cytotoxicity journal November 2018
Structure of McsB, a protein kinase for regulated arginine phosphorylation journal April 2019
Rational discovery of molecular glue degraders via scalable chemical profiling journal August 2020
LYTACs that engage the asialoglycoprotein receptor for targeted protein degradation journal March 2021
A gel phase promotes condensation of liquid P granules in Caenorhabditis elegans embryos journal March 2019
Structures of chaperone-associated assembly intermediates reveal coordinated mechanisms of proteasome biogenesis journal April 2021
Autophagy in healthy aging and disease journal August 2021
Autophagosome-associated variant isoforms of cytosolic enzymes journal December 2000
A noncovalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication journal October 2008
FYCO1 Contains a C-terminally Extended, LC3A/B-preferring LC3-interacting Region (LIR) Motif Required for Efficient Maturation of Autophagosomes during Basal Autophagy journal October 2015
The Proteasome Ubiquitin Receptor hRpn13 and Its Interacting Deubiquitinating Enzyme Uch37 Are Required for Proper Cell Cycle Progression journal April 2016
Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism journal July 2017
Proteasomal Protein Degradation in Mycobacteria Is Dependent upon a Prokaryotic Ubiquitin-like Protein journal January 2009
Interplay of the nuclear envelope with chromatin in physiology and pathology journal January 2020
FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end–directed vesicle transport journal January 2010
Rsp5 Ubiquitin ligase–mediated quality control system clears membrane proteins mistargeted to the vacuole membrane journal October 2018
Liquid–liquid phase separation in autophagy journal June 2020
Four Genome-Wide Association Studies Identify New Extreme Longevity Variants journal March 2017
Erythroid Differentiation: A Matter of Proteome Remodeling journal January 2018
Cellular Strategies of Protein Quality Control journal July 2011
The crystal structure of mouse LC3B in complex with the FYCO1 LIR reveals the importance of the flanking region of the LIR motif journal February 2017
Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti–COVID-19 drug design journal October 2020
Reconstitution of cargo-induced LC3 lipidation in mammalian selective autophagy journal April 2021
GABARAP sequesters the FLCN-FNIP tumor suppressor complex to couple autophagy with lysosomal biogenesis journal October 2021
The Proteasome of Mycobacterium tuberculosis Is Required for Resistance to Nitric Oxide journal December 2003
In Vivo Activation of the p53 Pathway by Small-Molecule Antagonists of MDM2 journal February 2004
Ubiquitin-Like Protein Involved in the Proteasome Pathway of Mycobacterium tuberculosis journal October 2008
McsB Is a Protein Arginine Kinase That Phosphorylates and Inhibits the Heat-Shock Regulator CtsR journal June 2009
Phosphorylation of the Autophagy Receptor Optineurin Restricts Salmonella Growth journal May 2011
UBE2O remodels the proteome during terminal erythroid differentiation journal August 2017
Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN journal November 2018
ESCRTs offer repair service journal April 2018
Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors journal March 2020
Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease journal April 2020
Impact of Losing hRpn13 Pru or UCHL5 on Proteasome Clearance of Ubiquitinated Proteins and RA190 Cytotoxicity journal August 2020
The Biology of Proteostasis in Aging and Disease journal June 2015
Cullin-RING Ubiquitin Ligase Regulatory Circuits: A Quarter Century Beyond the F-Box Hypothesis journal June 2021
The Genomic Landscape of SMARCA4 Alterations and Associations with Outcomes in Patients with Lung Cancer journal July 2020
Widespread Protein Aggregation as an Inherent Part of Aging in C. elegans journal August 2010
Genetic Determinants of Human Health Span and Life Span: Progress and New Opportunities journal July 2007
Genetic Signatures of Exceptional Longevity in Humans journal January 2012
Ubiquitin-Mediated Response to Microsporidia and Virus Infection in C. elegans journal June 2014
p62 filaments capture and present ubiquitinated cargos for autophagy journal January 2018
Collided ribosomes form a unique structural interface to induce Hel2‐driven quality control pathways journal January 2019
Hsp90‐mediated regulation of DYRK3 couples stress granule disassembly and growth via mTORC1 signaling journal March 2021
Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER‐phagy, and Collagen quality control journal August 2021
Aging and the aggregating proteome journal January 2012
Dysregulation of the Ubiquitin Proteasome System in Human Malignancies: A Window for Therapeutic Intervention journal March 2021
Immunomodulatory Drugs for the Treatment of B Cell Malignancies journal August 2021
Methods to Study Changes in Inherent Protein Aggregation with Age in Caenorhabditis elegans journal January 2017
FYCO1: Linking autophagosomes to microtubule plus end-directing molecular motors journal May 2010
Chronic optogenetic induction of stress granules is cytotoxic and reveals the evolution of ALS-FTD pathology journal March 2019
Intrinsically aggregation-prone proteins form amyloid-like aggregates and contribute to tissue aging in Caenorhabditis elegans journal May 2019
Distinct regulatory ribosomal ubiquitylation events are reversible and hierarchically organized journal February 2020
Discovery of a molecular glue promoting CDK12-DDB1 interaction to trigger cyclin K degradation journal August 2020
McsB forms a gated kinase chamber to mark aberrant bacterial proteins for degradation journal July 2021
Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy journal September 2021