Targeted Protein Degradation: Principles, Strategies, and Applications

Protein degradation is a general process to maintain cell homeostasis. The intracellular protein quality control system mainly includes the ubiquitin-proteasome system and the lysosome pathway. Inspired by the physiological process, strategies to degrade specific proteins have developed, which emerge as potent and effective tools in biological research and drug discovery. This review focuses on recent advances in targeted protein degradation techniques, summarizing the principles, advantages, and challenges. Moreover, the potential applications and future direction in biological science and clinics are also discussed.

[1]  A. Tong,et al.  Targeted protein degradation: mechanisms, strategies and application , 2022, Signal Transduction and Targeted Therapy.

[2]  Peng Huang,et al.  Design, Synthesis, and Evaluation of VHL-Based EZH2 Degraders to Enhance Therapeutic Activity against Lymphoma. , 2021, Journal of medicinal chemistry.

[3]  Zhenghua Lv,et al.  Development of photocontrolled BRD4 PROTACs for tongue squamous cell carcinoma (TSCC). , 2021, European journal of medicinal chemistry.

[4]  Qiaojun He,et al.  Discovery of a first-in-class CDK2 selective degrader for AML differentiation therapy , 2021, Nature Chemical Biology.

[5]  H. Handa,et al.  ARID2 is a pomalidomide-dependent CRL4CRBN substrate in multiple myeloma cells , 2020, Nature Chemical Biology.

[6]  D. Dimitrov,et al.  Hematopoietic Progenitor Kinase1 (HPK1) Mediates T Cell Dysfunction and Is a Druggable Target for T Cell-Based Immunotherapies. , 2020, Cancer cell.

[7]  Kin F. Chan,et al.  Functional characterization of a PROTAC directed against BRAF mutant V600E , 2020, Nature Chemical Biology.

[8]  J. Zuber,et al.  Rational discovery of molecular glue degraders via scalable chemical profiling , 2020, Nature Chemical Biology.

[9]  Jason D. Ray,et al.  Bifunctional small molecules that mediate the degradation of extracellular proteins , 2020, Nature Chemical Biology.

[10]  Carolyn R. Bertozzi,et al.  Lysosome-targeting chimaeras for degradation of extracellular proteins , 2020, Nature.

[11]  Mingyao Liu,et al.  In vivo target protein degradation induced by PROTACs based on E3 ligase DCAF15 , 2020, Signal Transduction and Targeted Therapy.

[12]  Hye Jin Nam,et al.  Augmentation of the antitumor effects of PARP inhibitors in triple-negative breast cancer via degradation by hydrophobic tagging modulation. , 2020, European journal of medicinal chemistry.

[13]  H. Nakatogawa.  Mechanisms governing autophagosome biogenesis , 2020, Nature Reviews Molecular Cell Biology.

[14]  T. Golub,et al.  The CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K , 2020, Nature.

[15]  Huatai Xu,et al.  Glia-to-Neuron Conversion by CRISPR-CasRx Alleviates Symptoms of Neurological Disease in Mice , 2020, Cell.

[16]  S. Schreiber,et al.  Unifying principles of bifunctional, proximity-inducing small molecules , 2020, Nature Chemical Biology.

[17]  Jun Yin,et al.  Protein Engineering in the Ubiquitin System: Tools for Discovery and Beyond , 2020, Pharmacological Reviews.

[18]  B. Liu,et al.  pSILAC method coupled with two complementary digestion approaches reveals PRPF39 as a new E7070-dependent DCAF15 substrate. , 2020, Journal of proteomics.

[19]  Boxun Lu,et al.  ATTEC: a potential new approach to target proteinopathies , 2020, Autophagy.

[20]  V. Kirkin.  History of the Selective Autophagy Research: How Did It Begin and Where Does It Stand Today? , 2020, Journal of molecular biology.

[21]  H. Crawford,et al.  Interleukin 22 Signaling Regulates Acinar Cell Plasticity to Promote Pancreatic Tumor Development in Mice. , 2019, Gastroenterology.

[22]  A. Laganà,et al.  Discovery of a first-in-class EZH2 selective degrader , 2019, Nature Chemical Biology.

[23]  T. Akaike,et al.  AUTACs: Cargo-Specific Degraders Using Selective Autophagy. , 2019, Molecular cell.

[24]  Liu Liu,et al.  A Potent and Selective Small-Molecule Degrader of STAT3 Achieves Complete Tumor Regression In Vivo. , 2019, Cancer cell.

[25]  Margaret A. Goralski,et al.  Aryl Sulfonamides Degrade RBM39 and RBM23 by Recruitment to CRL4-DCAF15. , 2019, Cell reports.

[26]  A. Ferrando,et al.  A selective BCL-XL PROTAC degrader achieves safe and potent antitumor activity , 2019, Nature Medicine.

[27]  Tomomi Sato,et al.  p63 is a cereblon substrate involved in thalidomide teratogenicity , 2019, Nature Chemical Biology.

[28]  Z. Pan,et al.  Light-induced protein degradation with photo-caged PROTACs. , 2019, Journal of the American Chemical Society.

[29]  Matthieu Schapira,et al.  Targeted protein degradation: expanding the toolbox , 2019, Nature Reviews Drug Discovery.

[30]  Derek S. Tan,et al.  Structural basis for adenylation and thioester bond formation in the ubiquitin E1 , 2019, Proceedings of the National Academy of Sciences.

[31]  John A. Tallarico,et al.  Covalent Ligand Screening Uncovers a RNF4 E3 Ligase Recruiter for Targeted Protein Degradation Applications , 2018, bioRxiv.

[32]  C. Lengner,et al.  In vivo neuronal gene editing via CRISPR–Cas9 amphiphilic nanocomplexes alleviates deficits in mouse models of Alzheimer’s disease , 2019, Nature Neuroscience.

[33]  Benjamin L Ebert,et al.  Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN , 2018, Science.

[34]  B. Cravatt,et al.  Electrophilic PROTACs that degrade nuclear proteins by engaging DCAF16 , 2018, bioRxiv.

[35]  John A. Tallarico,et al.  Harnessing the Anti-Cancer Natural Product Nimbolide for Targeted Protein Degradation , 2018, bioRxiv.

[36]  N. Pedersen,et al.  Concerted ESCRT and clathrin recruitment waves define the timing and morphology of intraluminal vesicle formation , 2018, Nature Communications.

[37]  I. Dikic,et al.  Mechanism and medical implications of mammalian autophagy , 2018, Nature reviews. Molecular cell biology.

[38]  Nobuhiro Nakamura,et al.  Ubiquitin System , 2018, International journal of molecular sciences.

[39]  D. Klionsky,et al.  Cargo recognition and degradation by selective autophagy , 2018, Nature Cell Biology.

[40]  Jing Wang,et al.  The Advantages of Targeted Protein Degradation Over Inhibition: An RTK Case Study. , 2017, Cell chemical biology.

[41]  A. Ciechanover,et al.  The Ubiquitin Code in the Ubiquitin-Proteasome System and Autophagy. , 2017, Trends in biochemical sciences.

[42]  I. Ng,et al.  Histone methyltransferase G9a promotes liver cancer development by epigenetic silencing of tumor suppressor gene RARRES3. , 2017, Journal of hepatology.

[43]  I. Dikič.  Proteasomal and Autophagic Degradation Systems. , 2017, Annual review of biochemistry.

[44]  M. Naito,et al.  Development of Protein Degradation Inducers of Androgen Receptor by Conjugation of Androgen Receptor Ligands and Inhibitor of Apoptosis Protein Ligands. , 2017, Journal of medicinal chemistry.

[45]  M. Naito,et al.  Development of protein degradation inducers of oncogenic BCR‐ABL protein by conjugation of ABL kinase inhibitors and IAP ligands , 2017, Cancer science.

[46]  Michael B. Stadler,et al.  pSILAC mass spectrometry reveals ZFP91 as IMiD-dependent substrate of the CRL4CRBN ubiquitin ligase , 2017, Nature Communications.

[47]  Margaret A. Goralski,et al.  Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15 , 2017, Science.

[48]  L. Hedstrom,et al.  Boc3Arg-Linked Ligands Induce Degradation by Localizing Target Proteins to the 20S Proteasome. , 2016, ACS chemical biology.

[49]  S. Zhou,et al.  Clinical Pharmacokinetics and Pharmacodynamics of Lenalidomide , 2016, Clinical Pharmacokinetics.

[50]  Chin-Chun Lu,et al.  A novel cereblon modulator recruits GSPT1 to the CRL4CRBN ubiquitin ligase , 2016, Nature.

[51]  Guinevere L. Grice,et al.  The recognition of ubiquitinated proteins by the proteasome , 2016, Cellular and Molecular Life Sciences.

[52]  J. Joung,et al.  Defining and improving the genome-wide specificities of CRISPR–Cas9 nucleases , 2016, Nature Reviews Genetics.

[53]  G. Petzold,et al.  Structural basis of lenalidomide-induced CK1α degradation by the CRL4CRBN ubiquitin ligase , 2016, Nature.

[54]  Eunhwa Ko,et al.  Modular PROTAC Design for the Degradation of Oncogenic BCR-ABL. , 2016, Angewandte Chemie.

[55]  Dennis L. Buckley,et al.  Small-Molecule-Mediated Degradation of the Androgen Receptor through Hydrophobic Tagging. , 2015, Angewandte Chemie.

[56]  I. E. Smith,et al.  Catalytic in vivo protein knockdown by small-molecule PROTACs. , 2015, Nature chemical biology.

[57]  James E. Bradner,et al.  Phthalimide conjugation as a strategy for in vivo target protein degradation , 2015, Science.

[58]  C. Crews,et al.  Hijacking the E3 Ubiquitin Ligase Cereblon to Efficiently Target BRD4. , 2015, Chemistry & biology.

[59]  A. Ciechanover.  The unravelling of the ubiquitin system , 2015, Nature Reviews Molecular Cell Biology.

[60]  M. Kirschner,et al.  Substrate degradation by the proteasome: A single-molecule kinetic analysis , 2015, Science.

[61]  Yong Tae Kwon,et al.  Degradation of misfolded proteins in neurodegenerative diseases: therapeutic targets and strategies , 2015, Experimental & Molecular Medicine.

[62]  G. von Heijne,et al.  Tissue-based map of the human proteome , 2015, Science.

[63]  J. Doudna,et al.  The new frontier of genome engineering with CRISPR-Cas9 , 2014, Science.

[64]  M. Naito,et al.  Cancer cell death induced by novel small molecules degrading the TACC3 protein via the ubiquitin–proteasome pathway , 2014, Cell Death and Disease.

[65]  P. Jänne,et al.  Pharmacological Targeting of the Pseudokinase Her3 , 2014, Nature chemical biology.

[66]  Friedrich Förster,et al.  Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome , 2014, Proceedings of the National Academy of Sciences.

[67]  S. Carr,et al.  Lenalidomide Causes Selective Degradation of IKZF1 and IKZF3 in Multiple Myeloma Cells , 2014, Science.

[68]  Keiji Tanaka,et al.  Endogenous nitrated nucleotide is a key mediator of autophagy and innate defense against bacteria. , 2013, Molecular cell.

[69]  Y. Ohsumi.  Historical landmarks of autophagy research , 2013, Cell Research.

[70]  H. Handa,et al.  Immunomodulatory agents lenalidomide and pomalidomide co-stimulate T cells by inducing degradation of T cell repressors Ikaros and Aiolos via modulation of the E3 ubiquitin ligase complex CRL4CRBN , 2013, British journal of haematology.

[71]  M. Naito,et al.  Development of hybrid small molecules that induce degradation of estrogen receptor‐alpha and necrotic cell death in breast cancer cells , 2013, Cancer science.

[72]  Andreas Martin,et al.  Reconstitution of the 26S proteasome reveals functional asymmetries in its AAA+ unfoldase , 2013, Nature Structural &Molecular Biology.

[73]  G. Montelione,et al.  A bidirectional system for the dynamic small molecule control of intracellular fusion proteins. , 2013, ACS chemical biology.

[74]  T. Corson,et al.  Posttranslational protein knockdown coupled to receptor tyrosine kinase activation with phosphoPROTACs , 2013, Proceedings of the National Academy of Sciences.

[75]  C. Lima,et al.  Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer. , 2013, Molecular cell.

[76]  J. Lieberman,et al.  Efficient and specific gene knockdown by small interfering RNAs produced in bacteria , 2013, Nature Biotechnology.

[77]  Nobutaka Hattori,et al.  PINK1-mediated phosphorylation of the Parkin ubiquitin-like domain primes mitochondrial translocation of Parkin and regulates mitophagy , 2012, Scientific Reports.

[78]  W. L. Jorgensen,et al.  Small-molecule inhibitors of the interaction between the E3 ligase VHL and HIF1α. , 2012, Angewandte Chemie.

[79]  M. Prata,et al.  A shortcut to the lysosome: the mannose-6-phosphate-independent pathway. , 2012, Molecular genetics and metabolism.

[80]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[81]  L. Shihabuddin,et al.  Sustained Therapeutic Reversal of Huntington's Disease by Transient Repression of Huntingtin Synthesis , 2012, Neuron.

[82]  Miratul M. K. Muqit,et al.  PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65 , 2012, Open Biology.

[83]  L. Hedstrom,et al.  Inhibitor mediated protein degradation. , 2012, Chemistry & biology.

[84]  Gabriel C. Lander,et al.  Complete subunit architecture of the proteasome regulatory particle , 2011, Nature.

[85]  N. Mizushima,et al.  The role of Atg proteins in autophagosome formation. , 2011, Annual review of cell and developmental biology.

[86]  Ari Helenius,et al.  Endosome maturation , 2011, The EMBO journal.

[87]  Min Jae Lee,et al.  An asymmetric interface between the regulatory particle and core particle of the proteasome , 2011, Nature Structural &Molecular Biology.

[88]  Ivan Dikic,et al.  The spatial and temporal organization of ubiquitin networks , 2011, Nature Reviews Molecular Cell Biology.

[89]  T. Corson,et al.  Small-Molecule Hydrophobic Tagging Induced Degradation of HaloTag Fusion Proteins , 2011, Nature Chemical Biology.

[90]  R. Youle,et al.  Mitochondrial membrane potential regulates PINK1 import and proteolytic destabilization by PARL , 2010, The Journal of cell biology.

[91]  Dimitri Krainc,et al.  The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy. , 2010, Molecular cell.

[92]  N. Hattori,et al.  PINK1 stabilized by mitochondrial depolarization recruits Parkin to damaged mitochondria and activates latent Parkin for mitophagy , 2010, The Journal of cell biology.

[93]  Minoru Ishikawa,et al.  Protein knockdown using methyl bestatin-ligand hybrid molecules: design and synthesis of inducers of ubiquitination-mediated degradation of cellular retinoic acid-binding proteins. , 2010, Journal of the American Chemical Society.

[94]  G. Bjørkøy,et al.  p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy , 2010, Autophagy.

[95]  Toshihiko Ogura,et al.  Identification of a Primary Target of Thalidomide Teratogenicity , 2010, Science.

[96]  Atsushi Tanaka,et al.  PINK1 Is Selectively Stabilized on Impaired Mitochondria to Activate Parkin , 2010, PLoS biology.

[97]  D. Finley,et al.  Recognition and processing of ubiquitin-protein conjugates by the proteasome. , 2009, Annual review of biochemistry.

[98]  R. Deshaies,et al.  RING domain E3 ubiquitin ligases. , 2009, Annual review of biochemistry.

[99]  J. Bonifacino,et al.  Sorting of lysosomal proteins. , 2009, Biochimica et biophysica acta.

[100]  Harald Stenmark,et al.  The ESCRT machinery in endosomal sorting of ubiquitylated membrane proteins , 2009, Nature.

[101]  M. Komatsu,et al.  A role for NBR1 in autophagosomal degradation of ubiquitinated substrates. , 2009, Molecular cell.

[102]  R. Deshaies,et al.  Targeting steroid hormone receptors for ubiquitination and degradation in breast and prostate cancer , 2008, Oncogene.

[103]  Jennifer Lippincott-Schwartz,et al.  Ubiquitin signals autophagic degradation of cytosolic proteins and peroxisomes , 2008, Proceedings of the National Academy of Sciences.

[104]  C. Crews,et al.  Targeted intracellular protein degradation induced by a small molecule: En route to chemical proteomics. , 2008, Bioorganic & medicinal chemistry letters.

[105]  Ivan Dikic,et al.  Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction , 2008, Nature.

[106]  Ivan Dikic,et al.  Proteasome subunit Rpn13 is a novel ubiquitin receptor , 2008, Nature.

[107]  Yifan Cheng,et al.  Mechanism of gate opening in the 20S proteasome by the proteasomal ATPases. , 2008, Molecular cell.

[108]  C. Thompson,et al.  Autophagy: basic principles and relevance to disease. , 2008, Annual review of pathology.

[109]  P. Saftig,et al.  LIMP-2 Is a Receptor for Lysosomal Mannose-6-Phosphate-Independent Targeting of β-Glucocerebrosidase , 2007, Cell.

[110]  Masayuki Yamamoto,et al.  Protein S-guanylation by the biological signal 8-nitroguanosine 3',5'-cyclic monophosphate. , 2007, Nature chemical biology.

[111]  J. Paul Luzio,et al.  Lysosomes: fusion and function , 2007, Nature Reviews Molecular Cell Biology.

[112]  Y. Shaul,et al.  20S proteasomes and protein degradation "by default". , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[113]  S. Akira,et al.  Sequence-specific potent induction of IFN-α by short interfering RNA in plasmacytoid dendritic cells through TLR7 , 2005, Nature Medicine.

[114]  Harald Stenmark,et al.  Alfy, a novel FYVE-domain-containing protein associated with protein granules and autophagic membranes , 2004, Journal of Cell Science.

[115]  Francesco Scaravilli,et al.  Inhibition of mTOR induces autophagy and reduces toxicity of polyglutamine expansions in fly and mouse models of Huntington disease , 2004, Nature Genetics.

[116]  Michael A. Koldobskiy,et al.  Chemical genetic control of protein levels: selective in vivo targeted degradation. , 2004, Journal of the American Chemical Society.

[117]  B. Li,et al.  Expression profiling reveals off-target gene regulation by RNAi , 2003, Nature Biotechnology.

[118]  S. Kornfeld,et al.  Mannose 6-phosphate receptors: new twists in the tale , 2003, Nature Reviews Molecular Cell Biology.

[119]  T. Yao,et al.  A cryptic protease couples deubiquitination and degradation by the proteasome , 2002, Nature.

[120]  L. Aravind,et al.  Role of Rpn11 Metalloprotease in Deubiquitination and Degradation by the 26S Proteasome , 2002, Science.

[121]  Ottoline Leyser,et al.  Auxin regulates SCFTIR1-dependent degradation of AUX/IAA proteins , 2001, Nature.

[122]  Li Chen,et al.  Ubiquitin‐associated (UBA) domains in Rad23 bind ubiquitin and promote inhibition of multi‐ubiquitin chain assembly , 2001, EMBO reports.

[123]  R. Deshaies,et al.  Protacs: Chimeric molecules that target proteins to the Skp1–Cullin–F box complex for ubiquitination and degradation , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[124]  C. Hill,et al.  Structural basis for the activation of 20S proteasomes by 11S regulators , 2000, Nature.

[125]  R. Huber,et al.  Structure of 20S proteasome from yeast at 2.4Å resolution , 1997, Nature.

[126]  F. Hartl,et al.  Pharmacologic shifting of a balance between protein refolding and degradation mediated by Hsp90. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[127]  S. Mayor,et al.  Sorting of membrane components from endosomes and subsequent recycling to the cell surface occurs by a bulk flow process , 1993, The Journal of cell biology.

[128]  D. Finley,et al.  Gates, Channels, and Switches: Elements of the Proteasome Machine. , 2016, Trends in biochemical sciences.

[129]  M. Hayden,et al.  Huntington disease , 2015, Nature Reviews Disease Primers.

[130]  F. Maxfield,et al.  Endocytic recycling , 2004, Nature Reviews Molecular Cell Biology.

[131]  C. Pickart,et al.  Mechanisms underlying ubiquitination. , 2001, Annual review of biochemistry.