Extended pharmacodynamic responses observed upon PROTAC-mediated degradation of RIPK2.
Animals
Anti-Inflammatory Agents
/ administration & dosage
Colitis, Ulcerative
/ drug therapy
Crohn Disease
/ drug therapy
Cytokines
/ metabolism
Dose-Response Relationship, Drug
Drug Design
Enzyme Stability
Female
Humans
Inflammation
/ enzymology
Inflammation Mediators
/ metabolism
Injections, Intravenous
Leukocytes, Mononuclear
/ drug effects
Male
Proteasome Endopeptidase Complex
/ metabolism
Proteolysis
Rats, Sprague-Dawley
Rats, Wistar
Receptor-Interacting Protein Serine-Threonine Kinase 2
/ metabolism
THP-1 Cells
Tissue Culture Techniques
Ubiquitin-Protein Ligases
/ metabolism
Ubiquitination
Journal
Communications biology
ISSN: 2399-3642
Titre abrégé: Commun Biol
Pays: England
ID NLM: 101719179
Informations de publication
Date de publication:
20 03 2020
20 03 2020
Historique:
received:
07
11
2019
accepted:
02
03
2020
entrez:
22
3
2020
pubmed:
22
3
2020
medline:
16
6
2021
Statut:
epublish
Résumé
Proteolysis-Targeting Chimeras (PROTACs) are heterobifunctional small-molecules that can promote the rapid and selective proteasome-mediated degradation of intracellular proteins through the recruitment of E3 ligase complexes to non-native protein substrates. The catalytic mechanism of action of PROTACs represents an exciting new modality in drug discovery that offers several potential advantages over traditional small-molecule inhibitors, including the potential to deliver pharmacodynamic (PD) efficacy which extends beyond the detectable pharmacokinetic (PK) presence of the PROTAC, driven by the synthesis rate of the protein. Herein we report the identification and development of PROTACs that selectively degrade Receptor-Interacting Serine/Threonine Protein Kinase 2 (RIPK2) and demonstrate in vivo degradation of endogenous RIPK2 in rats at low doses and extended PD that persists in the absence of detectable compound. This disconnect between PK and PD, when coupled with low nanomolar potency, offers the potential for low human doses and infrequent dosing regimens with PROTAC medicines.
Identifiants
pubmed: 32198438
doi: 10.1038/s42003-020-0868-6
pii: 10.1038/s42003-020-0868-6
pmc: PMC7083851
doi:
Substances chimiques
Anti-Inflammatory Agents
0
Cytokines
0
Inflammation Mediators
0
Ubiquitin-Protein Ligases
EC 2.3.2.27
RIPK2 protein, human
EC 2.7.11.1
Receptor-Interacting Protein Serine-Threonine Kinase 2
EC 2.7.11.1
Proteasome Endopeptidase Complex
EC 3.4.25.1
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
140Références
Burslem, G. M. & Crews, C. M. Small-molecule modulation of protein homeostasis. Chem. Rev. 117, 11269–11301 (2017).
doi: 10.1021/acs.chemrev.7b00077
Mainolfi, N. & Rasmusson, T. Targeted protein degradation. Annu. Rep. Med. Chem. 50, 301–334 (2017).
Churcher, I. Protac-induced protein degradation in drug discovery: breaking the rules or just making new ones? J. Med. Chem. 61, 444–452 (2018).
doi: 10.1021/acs.jmedchem.7b01272
Sakamoto, K. M. et al. Protacs: chimeric molecules that target proteins to the Skp1–Cullin–F box complex for ubiquitination and degradation. Proc. Natl Acad. Sci. USA 98, 8554–8559 (2001).
doi: 10.1073/pnas.141230798
Buckley, D. L. et al. Targeting the von Hippel–Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1α interaction. J. Am. Chem. Soc. 134, 4465–4468 (2012).
doi: 10.1021/ja209924v
Galdeano, C. et al. Structure-guided design and optimization of small molecules targeting the protein–protein interaction between the von Hippel–Lindau (VHL) E3 ubiquitin ligase and the hypoxia inducible factor (HIF) alpha subunit with in vitro nanomolar affinities. J. Med. Chem. 57, 8657–8663 (2014).
doi: 10.1021/jm5011258
Fischer, E. S. et al. Structure of the DDB1-CRBN E3 ubiquitin ligase in complex with thalidomide. Nature 512, 49–53 (2014).
doi: 10.1038/nature13527
Ito, T. et al. Identification of a primary target of thalidomide teratogenicity. Science 327, 1345–1350 (2010).
doi: 10.1126/science.1177319
Bondeson, D. P. et al. Catalytic in vivo protein knockdown by small-molecule PROTACs. Nat. Chem. Biol. 11, 611–617 (2015).
doi: 10.1038/nchembio.1858
Winter, G. E. et al. Phthalimide conjugation as a strategy for in vivo target protein degradation. Science 348, 1376–1381 (2015).
doi: 10.1126/science.aab1433
Han, X. et al. Discovery of highly potent and efficient PROTAC degraders of androgen receptor (AR) by employing weak binding affinity VHL E3 ligase ligands. J. Med. Chem. https://doi.org/10.1021/acs.jmedchem.9b01393 (2019).
Pillow, T. H. et al. Antibody conjugation of a chimeric BET degrader enables in vivo activity. ChemMedChem, https://doi.org/10.1002/cmdc.201900497 (2019).
Watt, G. F., Scott-Stevens, P. & Gaohua, L. Targeted protein degradation in vivo with Proteolysis Targeting Chimeras: Current status and future considerations. Drug Discov. Today Technol. 31, 69–80 (2019).
doi: 10.1016/j.ddtec.2019.02.005
Bertin, J. et al. Human CARD4 protein is a novel CED-4/Apaf-1 cell death family member that activates NF-kappaB. J. Biol. Chem. 274, 12955–12958 (1999).
doi: 10.1074/jbc.274.19.12955
Girardin, S. E. et al. Nod1 detects a unique muropeptide from gram-negative bacterial peptidoglycan. Science 300, 1584–1587 (2003).
doi: 10.1126/science.1084677
Biswas, A. et al. Induction and rescue of Nod2-dependent Th1-driven granulomatous inflammation of the ileum. Proc. Natl Acad. Sci. USA 107, 14739–14744 (2010).
doi: 10.1073/pnas.1003363107
Jamontt, J., Petit, S., Clark, N., Parkinson, S. J. & Smith, P. Nucleotide-binding oligomerization domain 2 signaling promotes hyperresponsive macrophages and colitis in IL-10-deficient mice. J. Immunol. 190, 2948–2958 (2013).
doi: 10.4049/jimmunol.1201332
Sato, H. et al. CARD15/NOD2 polymorphisms are associated with severe pulmonary sarcoidosis. Eur. Respir. J. 35, 324–330 (2010).
doi: 10.1183/09031936.00010209
Shaw, P. J. et al. Signaling via the RIP2 adaptor protein in central nervous system-infiltrating dendritic cells promotes inflammation and autoimmunity. Immunity 34, 75–84 (2011).
doi: 10.1016/j.immuni.2010.12.015
Doherty, M. K., Hammond, D. E., Clague, M. J., Gaskell, S. J. & Beynon, R. J. Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC. J. Proteome Res. 8, 104–112 (2009).
doi: 10.1021/pr800641v
Mathieson, T. et al. Systematic analysis of protein turnover in primary cells. Nat. Commun. 9, 689 (2018).
doi: 10.1038/s41467-018-03106-1
Bhattachar, S. N., Wesley, J. A. & Seadeek, C. Evaluation of the chemiluminescent nitrogen detector for solubility determinations to support drug discovery. J. Pharm. Biomed. Anal. 41, 152–157 (2006).
doi: 10.1016/j.jpba.2005.11.009
Kestranek, A., Chervenak, A., Longenberger, J. & Placko, S. Chemiluminescent nitrogen detection (CLND) to measure kinetic aqueous solubility. Curr. Protoc. Chem. Biol. 5, 269–280 (2013).
doi: 10.1002/9780470559277.ch130145
Young, R. J., Green, D. V., Luscombe, C. N. & Hill, A. P. Getting physical in drug discovery II: the impact of chromatographic hydrophobicity measurements and aromaticity. Drug Discov. Today 16, 822–830 (2011).
doi: 10.1016/j.drudis.2011.06.001
Haile, P. A. et al. The identification and pharmacological characterization of 6-(tert-Butylsulfonyl)-N-(5-fluoro-1H-indazol-3-yl)quinolin-4-amine (GSK583), a highly potent and selective inhibitor of RIP2 kinase. J. Med Chem. 59, 4867–4880 (2016).
doi: 10.1021/acs.jmedchem.6b00211
Haile, P. A. et al. Discovery of a first-in-class receptor interacting protein 2 (RIP2) kinase specific clinical candidate, 2-((4-(benzo[d]thiazol-5-ylamino)-6-(tert-butylsulfonyl)quinazolin-7-yl)oxy)ethyl dihydrogen phosphate, for the treatment of inflammatory diseases. J. Med. Chem. https://doi.org/10.1021/acs.jmedchem.9b00575 (2019).
Rosenzweig, H. L. et al. Activation of NOD2 in vivo induces IL-1beta production in the eye via caspase-1 but results in ocular inflammation independently of IL-1 signaling. J. Leukoc. Biol. 84, 529–536 (2008).
doi: 10.1189/jlb.0108015
Bantscheff, M. et al. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat. Biotechnol. 25, 1035–1044 (2007).
doi: 10.1038/nbt1328
Kruse, U. et al. Chemoproteomics-based kinome profiling and target deconvolution of clinical multi-kinase inhibitors in primary chronic lymphocytic leukemia cells. Leukemia 25, 89–100 (2011).
doi: 10.1038/leu.2010.233
Becher, I. et al. Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat. Nat. Chem. Biol. 12, 908–910 (2016).
doi: 10.1038/nchembio.2185
Reinhard, F. B. et al. Thermal proteome profiling monitors ligand interactions with cellular membrane proteins. Nat. Methods 12, 1129–1131 (2015).
pubmed: 26524241
pmcid: 26524241
Savitski, M. M. et al. Multiplexed proteome dynamics profiling reveals mechanisms controlling protein homeostasis. Cell 173, 260–274.e225 (2018).
doi: 10.1016/j.cell.2018.02.030
Zoppi, V. et al. Iterative design and optimization of initially inactive Proteolysis Targeting Chimeras (PROTACs) identify VZ185 as a potent, fast and selective von Hippel-Lindau (VHL)-based dual degrader probe of BRD9 and BRD7. J. Med. Chem. https://doi.org/10.1021/acs.jmedchem.8b01413 (2018).
doi: 10.1021/acs.jmedchem.8b01413
pubmed: 30540463
pmcid: 6348446
Nowak, R. P. et al. Plasticity in binding confers selectivity in ligand-induced protein degradation. Nat. Chem. Biol. 14, 706–714 (2018).
doi: 10.1038/s41589-018-0055-y
Brand, M. et al. Homolog-selective degradation as a strategy to probe the function of CDK6 in AML. Cell Chem. Biol. https://doi.org/10.1016/j.chembiol.2018.11.006 (2018).
Gadd, M. S. et al. Structural basis of PROTAC cooperative recognition for selective protein degradation. Nat. Chem. Biol. 13, 514–521 (2017).
doi: 10.1038/nchembio.2329
Haile, P. A. et al. Identification of quinoline-based RIP2 kinase inhibitors with an improved therapeutic index to the hERG ion channel. ACS Med. Chem. Lett. 9, 1039–1044 (2018).
doi: 10.1021/acsmedchemlett.8b00344
Sun, B. et al. BET protein proteolysis targeting chimera (PROTAC) exerts potent lethal activity against mantle cell lymphoma cells. Leukemia 32, 343–352 (2018).
doi: 10.1038/leu.2017.207
Sun, X. et al. A chemical approach for global protein knockdown from mice to non-human primates. Cell Discov. 5, 10 (2019).
doi: 10.1038/s41421-018-0079-1
Chen, C. Impact of dosing schedule in animal experiments on compound progression decisions. Drug Discov. Today 24, 371–376 (2019).
doi: 10.1016/j.drudis.2018.11.006
Sturm, N., Desaphy, J., Quinn, R. J., Rognan, D. & Kellenberger, E. Structural insights into the molecular basis of the ligand promiscuity. J. Chem. Inf. Model 52, 2410–2421 (2012).
doi: 10.1021/ci300196g
Savitski, M. M. et al. Measuring and managing ratio compression for accurate iTRAQ/TMT quantification. J. Proteome Res. 12, 3586–3598 (2013).
doi: 10.1021/pr400098r