Try Me: Promiscuous Inhibitors Still Allow for Selective Targeted Protein Degradation
2018; Elsevier BV; Volume: 25; Issue: 1 Linguagem: Inglês
10.1016/j.chembiol.2018.01.004
ISSN2451-9456
Autores Tópico(s)CAR-T cell therapy research
ResumoIn this issue of Cell Chemical Biology, Bondeson et al., 2018Bondeson D.P. Smith B.E. Burslem G.M. Buhimschi A.D. Hines J. Jaime-Figueroa S. Wang J. Hamman B.D. Ishchenko A. Crews C.M. Lessons in PROTAC design from selective degradation with a promiscuous warhead.Cell Chem Biol. 2018; 25 (this issue): 78-87Abstract Full Text Full Text PDF PubMed Scopus (384) Google Scholar, Burslem et al., 2018Burslem G.M. Smith B.E. Lai A.C. Jaime-Figueroa S. McQuaid D.C. Bondeson D.P. Toure M. Dong H. Qian Y. Wang J. et al.The advantages of targeted protein degradation over inhibition: an RTK case study.Cell Chem Biol. 2018; 25 (this issue): 67-77Abstract Full Text Full Text PDF PubMed Scopus (306) Google Scholar, and Huang et al., 2018Huang H.T. Dobrovolsky D. Paulk J. Yang G. Weisberg E.L. Doctor Z.M. Buckley D.L. Cho J.H. Ko E. Jang J. et al.A chemoproteomic approach to query the degradable kinome using a multi-kinase degrader.Cell Chem Biol. 2018; 25 (this issue): 88-99Abstract Full Text Full Text PDF PubMed Scopus (233) Google Scholar systematically characterize proteolysis-targeting chimeras (PROTACs) regarding their specificity and general advantages of targeted proteolysis of cellular proteins and provide interesting insights into possible future developments. In this issue of Cell Chemical Biology, Bondeson et al., 2018Bondeson D.P. Smith B.E. Burslem G.M. Buhimschi A.D. Hines J. Jaime-Figueroa S. Wang J. Hamman B.D. Ishchenko A. Crews C.M. Lessons in PROTAC design from selective degradation with a promiscuous warhead.Cell Chem Biol. 2018; 25 (this issue): 78-87Abstract Full Text Full Text PDF PubMed Scopus (384) Google Scholar, Burslem et al., 2018Burslem G.M. Smith B.E. Lai A.C. Jaime-Figueroa S. McQuaid D.C. Bondeson D.P. Toure M. Dong H. Qian Y. Wang J. et al.The advantages of targeted protein degradation over inhibition: an RTK case study.Cell Chem Biol. 2018; 25 (this issue): 67-77Abstract Full Text Full Text PDF PubMed Scopus (306) Google Scholar, and Huang et al., 2018Huang H.T. Dobrovolsky D. Paulk J. Yang G. Weisberg E.L. Doctor Z.M. Buckley D.L. Cho J.H. Ko E. Jang J. et al.A chemoproteomic approach to query the degradable kinome using a multi-kinase degrader.Cell Chem Biol. 2018; 25 (this issue): 88-99Abstract Full Text Full Text PDF PubMed Scopus (233) Google Scholar systematically characterize proteolysis-targeting chimeras (PROTACs) regarding their specificity and general advantages of targeted proteolysis of cellular proteins and provide interesting insights into possible future developments. The selective inhibition of certain proteins within cells is of major importance both for treatment of diseases and for understanding the role of a protein of interest (POI) in a cellular pathway. Such interference in protein function can be generally divided into two approaches: conventional occupancy-driven methods (e.g., small molecules that must bind to a target protein to inhibit the function) and event-driven strategies (e.g., intervention by RNAi or genome editing with CRISPR/Cas to reduce the concentration of a given protein) (Cromm and Crews, 2017Cromm P.M. Crews C.M. Targeted protein degradation: from chemical biology to drug discovery.Cell Chem Biol. 2017; 24: 1181-1190Abstract Full Text Full Text PDF PubMed Scopus (208) Google Scholar). An additional event-driven strategy is the targeted degradation of a protein, making use of the cellular degradation machinery (Bondeson et al., 2015Bondeson D.P. Mares A. Smith I.E.D. Ko E. Campos S. Miah A.H. Mulholland K.E. Routly N. Buckley D.L. Gustafson J.L. et al.Catalytic in vivo protein knockdown by small-molecule PROTACs.Nat. Chem. Biol. 2015; 11: 611-617Crossref PubMed Scopus (673) Google Scholar, Sakamoto et al., 2001Sakamoto K.M. Kim K.B. Kumagai A. Mercurio F. Crews C.M. Deshaies R.J. Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation.Proc. Natl. Acad. Sci. USA. 2001; 98: 8554-8559Crossref PubMed Scopus (999) Google Scholar, Winter et al., 2015Winter G.E. Buckley D.L. Paulk J. Roberts J.M. Souza A. Dhe-Paganon S. Bradner J.E. DRUG DEVELOPMENT. Phthalimide conjugation as a strategy for in vivo target protein degradation.Science. 2015; 348: 1376-1381Crossref PubMed Scopus (954) Google Scholar). This approach, called proteolysis-targeting chimeras (PROTACs), utilizes a heterobifunctional molecule consisting of a small molecule that binds to the POI and is linked to an E3 ligase-recruiting ligand via a flexible linker (Figure 1). This process allows specific targeting of the E3 ligase to the POI, thus leading to its ubiquitination and subsequent proteasomal degradation (reviewed in Lai and Crews, 2017Lai A.C. Crews C.M. Induced protein degradation: an emerging drug discovery paradigm.Nat. Rev. Drug Discov. 2017; 16: 101-114Crossref PubMed Scopus (704) Google Scholar). Occupancy-driven methods often suffer from the lengthy exposure of the target protein to high local concentrations of the inhibitor required for effective inhibition. Unfortunately, these high levels of compound also lead to nonspecific off-target binding and side effects. Possible strategies to overcome these limitations include allosteric modulators (Fang et al., 2013Fang Z. Grütter C. Rauh D. Strategies for the selective regulation of kinases with allosteric modulators: exploiting exclusive structural features.ACS Chem. Biol. 2013; 8: 58-70Crossref PubMed Scopus (147) Google Scholar), covalently bound inhibitors (Chaikuad et al., 2017Chaikuad A. Koch P. Laufer S. Knapp S. Targeting the protein kinases cysteinome.Angew. Chem. Int. Ed. 2017; https://doi.org/10.1002/anie.201707875Crossref PubMed Scopus (126) Google Scholar) and chemical genetics strategies (Blair et al., 2007Blair J.A. Rauh D. Kung C. Yun C.H. Fan Q.W. Rode H. Zhang C. Eck M.J. Weiss W.A. Shokat K.M. Structure-guided development of affinity probes for tyrosine kinases using chemical genetics.Nat. Chem. Biol. 2007; 3: 229-238Crossref PubMed Scopus (187) Google Scholar, Bührmann et al., 2017Bührmann M. Hardick J. Weisner J. Quambusch L. Rauh D. Covalent lipid pocket ligands targeting p38α MAPK mutants.Angew. Chem. Int. Ed. 2017; 56: 13232-13236Crossref PubMed Scopus (13) Google Scholar) as well as the aforementioned event-driven PROTAC approach (Cromm and Crews, 2017Cromm P.M. Crews C.M. Targeted protein degradation: from chemical biology to drug discovery.Cell Chem Biol. 2017; 24: 1181-1190Abstract Full Text Full Text PDF PubMed Scopus (208) Google Scholar). Moreover, PROTACs not only target enzymatic activities underlying the disease state, but they also perturb other important protein functions such as the scaffolding role of individual proteins. Small molecular ligands additionally do not need to bind specifically to the active site of a target protein to induce degradation, and specificity of the given ligand for a certain site (usually the active site) is not required. Therefore, proteins previously thought to be undruggable may well be druggable after all. Additionally, small molecule inhibitors do not readily address amplification of genes or overexpression of oncogenes as a primary cause of a disease or a secondary resistance mechanism, but these metabolic anomalies can be targeted with PROTACs. In this issue of Cell Chemical Biology, three publications describe an in-depth characterization of the PROTAC approach to further define the inherent limitations and potential of altered protein degradation. Burslem et al. (2018) show that PROTACS can target not only soluble proteins, but also membrane-spanning medically relevant receptor tyrosine kinases (RTKs). Using the RTKs EGFR, Her2, and c-Met as well as mutants thereof as relevant model proteins, they convincingly show that lower concentrations of the bifunctional heterodimerizer targeting the POI are sufficient compared to conventional occupancy-driven inhibition, while simultaneously obtaining more sustained degradation as well as downregulation of signaling. Two additional publications further examine the effect of promiscuous inhibitors that target a whole family of proteins. Bonderson et al. (2018) analyze the effect of using the promiscuous kinase inhibitor foretinib that binds more than 130 different kinases. However, in the context of a PROTAC, only a small fraction of these kinases (< 10 kinases) are degraded. This finding could be well explained by putative direct interactions between the E3 ligase of choice and the POI to be degraded that are necessary for effective degradation. Interestingly, the affinity between the ligand and the targeted protein had only a minor influence and the MAP kinase p38α could be successfully degraded using an inhibitor with weak binding affinity (Bondeson et al., 2018Bondeson D.P. Smith B.E. Burslem G.M. Buhimschi A.D. Hines J. Jaime-Figueroa S. Wang J. Hamman B.D. Ishchenko A. Crews C.M. Lessons in PROTAC design from selective degradation with a promiscuous warhead.Cell Chem Biol. 2018; 25 (this issue): 78-87Abstract Full Text Full Text PDF PubMed Scopus (384) Google Scholar). In a similar approach, Huang et al. (2018) use a promiscuous diaminopyrimidine-based inhibitor and measure changes in the protein abundance in cells using a quantitative proteomic approach; this protocol defines kinases that could, in principle, be targeted with a given E3 ligase. In a subsequent second step, PROTACs were optimized to yield highly selective heterobifunctional degradation agents for the two medically relevant kinases FLT3 and BTK (Huang et al., 2018Huang H.T. Dobrovolsky D. Paulk J. Yang G. Weisberg E.L. Doctor Z.M. Buckley D.L. Cho J.H. Ko E. Jang J. et al.A chemoproteomic approach to query the degradable kinome using a multi-kinase degrader.Cell Chem Biol. 2018; 25 (this issue): 88-99Abstract Full Text Full Text PDF PubMed Scopus (233) Google Scholar). Within this optimization step, more selective inhibitors were tested in combination with different linkers and attachment sites for each respective kinase inhibitor. The findings described above suggest multiple future developments and applications of the PROTAC approach. The systematic investigation of possible reasons for the different susceptibilities of a protein (family) toward PROTAC-induced degradation may provide valuable information for future studies. The susceptibility of a protein toward degradation may result not only from necessary direct interactions between the E3 ligase and the POI, but rather may be multifactorial in nature. Possible underlying causes range from intrinsic stability of the POI toward degradation, availability of Lys residues for ubiquitin attachment, and interference by the attached linker, as well as involvement of the respective protein in large protein assemblies that limit accessibility of the E3 ligase (Bondeson et al., 2018Bondeson D.P. Smith B.E. Burslem G.M. Buhimschi A.D. Hines J. Jaime-Figueroa S. Wang J. Hamman B.D. Ishchenko A. Crews C.M. Lessons in PROTAC design from selective degradation with a promiscuous warhead.Cell Chem Biol. 2018; 25 (this issue): 78-87Abstract Full Text Full Text PDF PubMed Scopus (384) Google Scholar, Huang et al., 2018Huang H.T. Dobrovolsky D. Paulk J. Yang G. Weisberg E.L. Doctor Z.M. Buckley D.L. Cho J.H. Ko E. Jang J. et al.A chemoproteomic approach to query the degradable kinome using a multi-kinase degrader.Cell Chem Biol. 2018; 25 (this issue): 88-99Abstract Full Text Full Text PDF PubMed Scopus (233) Google Scholar). While on the one hand this may complicate the design of PROTACs for a given protein, it may have the beneficial effect of sparing proteins that bind nonspecifically to the PROTAC from unintended degradation (Lai and Crews, 2017Lai A.C. Crews C.M. Induced protein degradation: an emerging drug discovery paradigm.Nat. Rev. Drug Discov. 2017; 16: 101-114Crossref PubMed Scopus (704) Google Scholar). The rational design of PROTACs is further complicated because the mere affinity of the ligand for a target protein is not necessarily a predictor of the PROTAC's ability to induce degradation and is of minor importance compared to occupancy driven methods (Bondeson et al., 2018Bondeson D.P. Smith B.E. Burslem G.M. Buhimschi A.D. Hines J. Jaime-Figueroa S. Wang J. Hamman B.D. Ishchenko A. Crews C.M. Lessons in PROTAC design from selective degradation with a promiscuous warhead.Cell Chem Biol. 2018; 25 (this issue): 78-87Abstract Full Text Full Text PDF PubMed Scopus (384) Google Scholar). On the positive side, however, resistance mutations that lower the affinity are less likely to affect the induction of degradation, and certain resistance mutations might still be targetable with known inhibitors that, on their own, do not effectively inhibit the mutant protein anymore. In summary, these studies show that systematic testing in combination with careful design of bifunctional heterodimerizers not only has the potential to overcome the limitations, but will allow for higher selectivity than was originally conceived. The design of additional specific E3 ligase-recruiting molecules will further expand the numbers of targetable intracellular medically relevant proteins (Lai et al., 2016Lai A.C. Toure M. Hellerschmied D. Salami J. Jaime-Figueroa S. Ko E. Hines J. Crews C.M. Modular PROTAC design for the degradation of oncogenic BCR-ABL.Angew. Chem. Int. Ed. 2016; 55: 807-810Crossref PubMed Scopus (375) Google Scholar). We are looking forward to a new year full of equally interesting novel ideas and developments. A Chemoproteomic Approach to Query the Degradable Kinome Using a Multi-kinase DegraderHuang et al.Cell Chemical BiologyNovember 9, 2017In BriefHeterobifunctional protein degrader is an emerging pharmacological strategy. Using a multi-kinase degrader, Huang et al. greatly expanded the number of known degradable kinases, and demonstrated an efficient approach to triage a gene family for actionable targets with potential therapeutic impacts. Full-Text PDF Open ArchiveThe Advantages of Targeted Protein Degradation Over Inhibition: An RTK Case StudyBurslem et al.Cell Chemical BiologyNovember 9, 2017In BriefBurslem, Smith et al. describe the development of PROTACs capable of degrading transmembrane receptor tyrosine kinases and further highlight the advantages of degradation over inhibition in terms of potency, duration of effect, and combating compensatory signaling. Full-Text PDF Open ArchiveLessons in PROTAC Design from Selective Degradation with a Promiscuous WarheadBondeson et al.Cell Chemical BiologyNovember 9, 2017In BriefBondeson, Smith et al. examined the degradation selectivity of promiscuous PROTACs, heterobifunctional small molecules based on E3 ligase-recruiting molecules conjugated to a non-selective kinase inhibitor. Despite binding to well over 50 kinases, these compounds selectively degrade <15 due to unique protein-protein interactions between the E3 ligase and degraded targets. Full-Text PDF Open Archive
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