Selective autophagy as the basis of autophagy-based degraders
نویسندگان
چکیده
Degrader technologies, which enable the chemical knockdown of disease-causing proteins, are promising for drug discovery. After two decades research, degraders using ubiquitin-proteasome system (UPS) currently in clinical trials. However, UPS substrates mainly limited to soluble proteins. Autophagy-targeting chimeras and autophagosome-tethering compounds that use autophagy, has functions complementary UPS. They can degrade organelles aggregate-prone making them treatments against age-related conditions such as mitochondrial dysfunction neurodegenerative diseases. The molecular mechanism selective autophagy is an ongoing research topic, explains why autophagy-based were not available until recently. In this review, we introduce four classifications mechanisms facilitate understanding degrader design. (UPS), a proteolytic pathway conserved among eukaryotes, degrades target proteins via large machine, 26S proteasome (Smalle Vierstra, 2004Smalle J. Vierstra R.D. ubiquitin 26s pathway.Annu. Rev. Plant Biol. 2004; 55: 555-590https://doi.org/10.1146/annurev.arplant.55.031903.141801Crossref PubMed Scopus (998) Google Scholar). UPS-based (e.g., proteolysis-targeting chimera [PROTAC] specific nongenetic inhibitor apoptosis protein [IAP]-dependent eraser [SNIPER]) some most popular new modalities discovery (Nalawansha Crews, 2020Nalawansha D.A. Crews C.M. PROTACs: emerging therapeutic modality precision medicine.Cell Chem. 2020; 27: 998-1014Abstract Full Text PDF (102) Scholar) (Figure 1A). These bind along with E3 ligase induce ubiquitination. Current only handful ligases, but human genome encodes more than 600 ligases (Machado et al., 2020Machado V. Carvalho R. Mendes J.J. Botelho periodontal disease: comprehensive review.Front. Dent. Med. https://doi.org/10.3389/fdmed.2020.613080Crossref Scholar), may provide researchers opportunity design target-specific or organ-specific variety uses. Autophagy another major degradation system, discoveries autophagy-related genes 1990s yeast (Tsukada Ohsumi, 1993Tsukada M. Ohsumi Y. Isolation characterization autophagy-defective mutants Saccharomyces cerevisiae.FEBS Lett. 1993; 333: 169-174Crossref (1354) enabled scientists understand roles (Dikic Elazar, 2018Dikic I. Elazar Z. Mechanism medical implications mammalian autophagy.Nat. Mol. Cell 2018; 19: 349-364Crossref (1130) 2). Researchers believed macroautophagy was nonselective responded amino acid starvation (Reggiori 2012Reggiori F. Komatsu Finley K. Simonsen A. Autophagy: pathway.Int. 2012; : 219625https://doi.org/10.1155/2012/219625Crossref (104) Scholar; Wu 2020Wu C. Yao W. Kai Liu Wang Li S. Chen X. L. al.Mitochondrial fusion machinery specifically involved energy deprivation-induced autophagy.Front. Dev. 8https://doi.org/10.3389/fcell.2020.00221Crossref (5) selectively clears harmful cargoes, impaired organelles, aggregates, pathogens (Kirkin Rogov, 2019Kirkin Rogov V.V. A diversity receptors determines specificity pathway.Mol. Cell. 2019; 76: 268-285Abstract (185) As will be focus few exist, reflects short history (Mizushima, 2018Mizushima N. brief from cell biology physiology disease.Nat. 20: 521-527Crossref (334) There crosstalk between UPS, they each other. Large cellular cargoes (organelles aggregates) nonprotein materials Therefore, development needed. PROTACs related proximity Figure 1B). categories degraders: glues (Han 2017Han T. Goralski Gaskill Capota E. Kim Ting T.C. Xie Williams N.S. Nijhawan D. Anticancer sulfonamides splicing by inducing RBM39 recruitment DCAF15.Science. 2017; 356https://doi.org/10.1126/science.aal3755Crossref (260) Uehara 2017Uehara Minoshima Sagane Sugi N.H. Mitsuhashi K.O. Yamamoto Kamiyama H. Takahashi Kotake Uesugi al.Selective factor CAPER? anticancer sulfonamides.Nat. 13: 675-680Crossref (191) Bussiere 2020Bussiere D.E. Srinivas Shu Burke Be Zhao Godbole King Karki R.G. al.Structural basis indisulam-mediated DCAF15 complex.Nat. 16: 15-23Crossref (76) heterobifunctional (Naito 2019Naito Ohoka Shibata SNIPERs—hijacking IAP activity degradation.Drug Discov. Today. 31: 35-42Crossref (64) Sun 2019Sun Gao Yang He Song Tong Rao great opportunities academia industry.Signal. Transduct. Targeted Ther. 4: 64https://doi.org/10.1038/s41392-019-0101-6Crossref (201) latter often called chimeric molecules, PROTAC technology typical example. availability several tags makes rather straightforward: combine targeting ligand defining cargo selectivity, linker, tag. trickier, category obtained empirically. Mayor-Ruiz 2020Mayor-Ruiz Bauer Brand Kozicka Siklos Imrichova Kaltheuner I.H. Hahn Seiler Koren al.Rational glue scalable profiling.Nat. 1199-1207Crossref (79) Scholar recently developed strategy comparative screening hyponeddylated cells. This approach molecular-glue-based degraders. Because induction key property degraders, could also belong these categories. our current particularly regarding insufficient rationally main challenges low-molecular-weight and, importantly, identification appropriate binding tag hundreds Far participate UPS; however, principle one them, single must recruit entire achieve substrate degradation. Moreover, submechanisms no account entirely selectivity (Zaffagnini Martens, 2016Zaffagnini G. Martens Mechanisms autophagy.J. 2016; 428: 1714-1724Crossref (322) overview recent advances autophagy-targeting (AUTAC) (Takahashi Arimoto, 2020Takahashi Arimoto Targeting AUTAC degraders.Autophagy. 765-766Crossref (24) 2019Takahashi Moriyama Nakamura Miki Sato Akaike Itto-Nakama AUTACs: cargo-specific autophagy.Mol. 797-810.e10Abstract (131) compound (ATTEC) (Li 2019Li Zhu Sha Ma al.Allele-selective lowering mutant HTT HTT-LC3 linker compounds.Nature. 575: 203-209Crossref (135) Scholar, 2020Li Ding Fei Lu B. ATTEC: potential proteinopathies.Autophagy. 185-187Crossref (41) describe future perspectives field. One well-established subtypes clearance invading bacteria cytoplasm, first identified 2004 (Nakagawa 2004Nakagawa Amano Mizushima Yamaguchi Kamimoto Nara Funao Nakata Tsuda al.Autophagy defends cells group Streptococcus.Science. 306: 1037-1040Crossref (916) removes streptococci escape into cytoplasm host story began serendipitous guanine-modified accumulated around cytoplasmic streptococcus (Ito 2013Ito Saito Nozawa Fujii Sawa Inoue Matsunaga Khan Akashi Hashimoto al.Endogenous nitrated nucleotide mediator innate defense bacteria.Mol. 2013; 52: 794-804Abstract (70) We had previously 8-nitroguanosine 3?,5?-cyclic monophosphate (8-nitro-cGMP), reactive endogenous nucleotide, acts downstream nitric oxide oxygen species (Sawa 2007Sawa Zaki M.H. Okamoto Akuta Tokutomi Kim-Mitsuyama Ihara Kobayashi al.Protein S-guanylation biological signal monophosphate.Nat. 2007; 3: 727-735Crossref (203) production increases infected bacteria. It then reacts cysteine residues (by S-guanylation; 3A), resulting cGMP modification When investigating physiological role S-guanylation, observed S-guanylated noted robust correlation autophagic recognition bacterial important Salmonella (Khan 2018Khan Nishimura Ono Ida Ahmed K.A. Tsutsuki al.Reactive persulfides typhimurium downregulate autophagy-mediated immunity macrophages inhibiting electrophilic signaling.Cell 25: 1403-1413Abstract (18) during attempt (cysteine S-guanylation) unit 3). Following extensive efforts optimize efficiency, ribose moiety replaced 9-p-fluorobenzyl substituent 3B). AUTACs (p-fluorobenzyl guanine [FBnG] tag) decreased levels cytosolic successfully removed dysfunctional mitochondria through (mitophagy) Entire targets mitochondria. mitochondria-targeting (AUTAC4), therefore, opened avenue mitochondria-targeted chemotherapy 3C). Mitochondria dynamic equilibrium tubular fragment states due fission events, shifts fragmented form (Tilokani 2018Tilokani Nagashima Paupe Prudent Mitochondrial dynamics: mechanisms.Essays Biochem. 62: 341-360Crossref (434) Typical autophagosomes have diameter 0.5–1 ?m (Mizushima 2002Mizushima Yoshimori Autophagosome formation cells.Cell Struct. Funct. 2002; 421-429Crossref (741) Scholar); favors smaller substrates. Mitophagy easy monitor mitochondria-localizing pH-sensitive probes, mito-Rosella (Sargsyan 2015Sargsyan Cai Fandino L.B. Labasky M.E. Forostyan Colosimo L.K. Thompson S.J. Graham T.E. Rapid parallel measurements mitophagy fluorescent biosensor.Sci. Rep. 2015; 5: 12397https://doi.org/10.1038/srep12397Crossref (26) mito-Keima (Kogure 2006Kogure Karasawa Araki Kinjo Miyawaki variant stony coral Montipora facilitates dual-color single-laser fluorescence cross-correlation spectroscopy.Nat. Biotechnol. 2006; 24: 577-581Crossref (254) 3D). probes visualization degraded acidic lysosomal environment. treatment Down syndrome-derived fibroblasts extensively AUTAC4 accelerated improved morphology (such membrane ATP production) suppresses preventing cytochrome c release well caspase activation. Of note, AUTAC4-mediated independent Parkin-phosphate tensin homolog (PTEN)-induced putative kinase 1 (PINK1) technique applicable Parkinson's disease because mutations Parkin PINK1 cases familial (Jiang Mizushima, 2014Jiang P. diseases.Cell Res. 2014; 69-79Crossref (567) Although dysfunctions common diseases, lack essential remedies (DiMauro 2006DiMauro Hirano Schon E.A. Approaches diseases.Muscle Nerve. 34: 265-283Crossref (108) existing mitophagy-activating chemicals toxins, FCCP (carbonyl cyanide-p-trifluoromethoxyphenylhydrazone), study process damaging (Georgakopoulos 2017Georgakopoulos N.D. Wells Campanella pharmacological regulation mitophagy.Nat. 136-146Crossref (149) Unfortunately, toxic suitable use, other treat (Svenning Johansen, 2013Svenning Johansen Selective autophagy.Essays 79-92Crossref elimination been studied representative example Sharma 2018Sharma Verma Seranova Sarkar Kumar xenophagy infection disease.Front. 6https://doi.org/10.3389/fcell.2018.00147Crossref (119) Geisler 2010Geisler Holmström K.M. Skujat Fiesel F.C. Rothfuss O.C. Kahle P.J. Springer PINK1/Parkin-mediated dependent on VDAC1 p62/SQSTM1.Nat. 2010; 12: 119-131Crossref (1940) derived Another screen based generalized mechanisms, those remain unclear. next briefly explain their possible applications technologies. adaptors (or receptors) polyvalent link isolation processes (Gatica 2018Gatica Lahiri Klionsky D.J. Cargo 233-242Crossref (484) 2014Rogov Dötsch Kirkin Interactions ubiquitin-like 53: 167-178Abstract (647) Major recognition. On membrane, commonly LC3 4) GABARAP/Gate-16 (the Atg8). Substrates adaptor marked (Kabeya 2000Kabeya Ueno Kirisako Noda Kominami LC3, homologue Apg8p, localized autophagosome membranes after processing.EMBO 2000; 5720-5728Crossref (5301) Most known LC3-interaction region (LIR) (Birgisdottir 2013Birgisdottir Å.B. Lamark LIR motif—crucial Sci. 126: 3237-3247Crossref (524) 4A). For example, NIX, localizes outer mediates (Schwarten 2009Schwarten Mohrlüder Stoldt Thielmann Stangler Hersch Hoffmann Merkel Willbold Nix directly binds GABARAP: autophagy.Autophagy. 2009; 690-698Crossref (180) 2017Rogov Suzuki Marinkovi? Lang Kato Kawasaki Buljubaši? Šprung Rogova Wakatsuki al.Phosphorylation receptor enhances its interaction proteins.Sci. 7: 1131https://doi.org/10.1038/s41598-017-01258-6Crossref (123) adaptor-mediated stimulated different ways. substitute function. named links huntingtin (mHTT) 4B). mHTT aggregation likely causes Huntington's (Scherzinger 1997Scherzinger Lurz Turmaine Mangiarini Hollenbach Hasenbank Bates G.P. Davies S.W. Lehrach Wanker E.E. Huntingtin-encoded polyglutamine expansions amyloid-like aggregates vitro vivo.Cell. 1997; 90: 549-558Abstract (1072) 2015Bates Dorsey Gusella J.F. Hayden M.R. Kay Leavitt B.R. Nance Ross C.A. Scahill R.I. Wetzel al.Huntington Dis. Primers. 1: 15005https://doi.org/10.1038/nrdp.2015.5Crossref (678) removal consensus disorder. ATTEC category; it surprisingly straightforward affinity-based both does wild-type HTT. reduced expression level mouse model. increased mTORC1 inhibition barely affected ATTEC-induced rate interesting increase number should LC3-attachable cargoes. Only lipidated (on inner faces), whereas unlipidated exists cytoplasm. i.e., LC3-I, advantage low weight compared (often >1,000 Da). Further uses eagerly awaited. attempted (ER Golgi apparatus) so far failed transport lysosome (Loos 2019Loos Sica Bravo-San Pedro J.M. Souquère Pierron Lachkar Sauvat Petrazzuolo Jimenez A.J. al.Artificial tethering p62 sufficient trigger autophagy.Cell Death 10: 771https://doi.org/10.1038/s41419-019-2011-5Crossref (11) second binders. at Frontier Medicines (USA) used covalent binder warhead heterobifunctional-type (Nomura 2019Nomura, D., Zoncu, R., Ward, C., Fung, S., Varma, Fontaine, (2019). Methods Compounds Autophagy. PCT International Patent WO 2019183600A1, application filed March 22, 2019 published 26 September, 2019.Google BMF-1-64 comprises chloroacetyl covalently p62, JQ1, noncovalently bromodomain 4C). p62/sqstm1 accelerate patent documents information full p62-targeting degraders; autophagy-inducing together appears further BMF-1-141 disease-related earliest established autophagy; influential concept modifications regulate proteasome-dependent wide range functions, transduction, DNA repair, trafficking, degradation, autophagy-lysosome (Zhu 2020Zhu Xia Xiong Yin Q. Rui Roles ubiquitination deubiquitination regulating dendritic maturation function.Front. Immunol. 11: 586613https://doi.org/10.3389/fimmu.2020.586613Crossref (8) 2020Yin Popelka Lei mediating autophagy.Cells. 9: 2025https://doi.org/10.3390/cells9092025Crossref (33) ubiquitin-linkage types ubiquitin-binding enables perform 5A). homotypic polyubiquitin chains, C-terminal glycine linked seven lysine (K48-, K63-, K6-, K11-, K27-, K29-, K33-linked chains) N-terminal amine methionine (M1-linked chain). K48- K11-linked chains markers proteasomal (Komander Rape, 2012Komander Rape code.Ann. 81: 203-229Crossref (2051) ubiquitylated before (Khaminets 2016Khaminets Behl Dikic Ubiquitin-dependent signals autophagy.Trends 26: 6-16Abstract (436) Gatica adaptors, p62/sqstm-1, motifs, aforementioned 2018
منابع مشابه
Selective autophagy.
During the last decade it has become evident that autophagy is not simply a non-selective bulk degradation pathway for intracellular components. On the contrary, the discovery and characterization of autophagy receptors which target specific cargo for lysosomal degradation by interaction with ATG8 (autophagy-related protein 8)/LC3 (light-chain 3) has accelerated our understanding of selective a...
متن کاملStructural basis for sorting mechanism of p62 in selective autophagy.
Impairment of autophagic degradation of the ubiquitin- and LC3-binding protein "p62" leads to the formation of cytoplasmic inclusion bodies. However, little is known about the sorting mechanism of p62 to autophagic degradation. Here we identified a motif of murine p62 consisting of 11 amino acids (Ser334-Ser344) containing conserved acidic and hydrophobic residues across species, as an LC3 reco...
متن کاملSelective Types of Autophagy
1Department of Cell Biology and Institute of Biomembranes, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands 2Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan 3BioScience Center, San Diego State University, San Diego, CA 92182, USA 4Department of Biochemistry, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo,...
متن کاملSelective Autophagy in Drosophila
Autophagy is an evolutionarily conserved process of cellular self-eating and is a major pathway for degradation of cytoplasmic material by the lysosomal machinery. Autophagy functions as a cellular response in nutrient starvation, but it is also associated with the removal of protein aggregates and damaged organelles and therefore plays an important role in the quality control of proteins and o...
متن کاملSnapShot: Selective Autophagy
A t g 8 A t g 8 A t g 8 A t g 8 A t g 8 A t g 8 A t g 8 A t g 8 A t g 8 A t g 8 A t g 8 A t g 8 Atg19 A tg 1 9 prApe1 Ape1 complex
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Cell chemical biology
سال: 2021
ISSN: ['2451-9456', '2451-9448']
DOI: https://doi.org/10.1016/j.chembiol.2021.05.006