Homolog-Selective Degradation as a Strategy to Probe the Function of CDK6 in AML

Brand, Matthias; Jiang, Baishan; Bauer, Sophie; Donovan, Katherine A.; Liang, Yanke; Wang, Eric S.; Nowak, Radosław P.; Yuan, Jingting; Zhang, Tinghu; Kwiatkowski, Nicholas; Müller, André C.; Fischer, Eric S.; Gray, Nathanael S.; Ciulli, Alessio

doi:10.1016/j.chembiol.2018.11.006

Cited by 204 publications

(208 citation statements)

References 26 publications

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“…In both assays, levels of FKBP12 F36V -fusion degradation with dTAG V -1 were comparable to CRBN-recruiting dTAG molecules (dTAG-13 and dTAG-47). 13 Use of dTAG V -1-NEG abrogated these effects comparably to the matched heterobifunctional negative control compounds that cannot bind and recruit CRBN 19, 20 (dTAG-13-NEG and dTAG-47-NEG) (Supplementary Fig. 1b-e).…”

Section: Resultsmentioning

confidence: 89%

Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules

Nabet

Ferguson

Seong

et al. 2020

Preprint

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35Chemical biology strategies for directly perturbing protein homeostasis including the 36 degradation tag (dTAG) system provide temporal advantages over genetic approaches and 37 improved selectivity over small molecule inhibitors. We describe dTAG V -1, an exclusively 38 selective VHL-recruiting dTAG molecule, to rapidly degrade FKBP12 F36V -tagged proteins. 39 dTAG V -1 overcomes a limitation of previously reported CRBN-recruiting dTAG molecules to 40 degrade recalcitrant oncogenes, supports combination degrader studies and facilitates 41 investigations of protein function in cells and mice. 42 43 We next evaluated the utility of dTAG V -1 for combinatorial degrader studies. dTAG V -1 94 was effectively combined with THAL-SNS-032, a previously reported CRBN-recruiting CDK9 95 degrader 21 (Fig. 1e). Pronounced degradation of LACZ-FKBP12 F36V and CDK9 was observed to 96 levels comparable to those with treatment of each degrader alone, avoiding potential substrate 97 competition effects. 22 To confirm the utility of dTAG V -1 for target validation, we evaluated 98 KRAS G12V degradation, an oncogenic driver of PDAC, in PATU-8902 FKBP12 F36V -KRAS G12V ;; 99 KRAS -/cells. 17 dTAG V -1 treatment led to rapid KRAS G12V degradation, which was rescued by 100 use of dTAG V -1-NEG, pre-treatment with proteasome-inhibitor (carfilzomib) or Nedd8 activating 101 enzyme inhibitor (MLN4924), and VHL knockout, consistent with the mechanism of action of a 102 VHL-recruiting degrader ( Fig. 1f-g and Supplementary Fig. 2a-b). We also observed the 103 expected collapse in cellular signaling and diminished cell proliferation in 2D-monolayer and 3D-104 spheroid cultures upon FKBP12 F36V -KRAS G12V degradation with dTAG V -1 treatment, to levels 105 comparable to CRBN-recruiting dTAG molecules ( Fig. 1h and Supplementary Fig. 2c-e). 106To confirm the in vivo applicability of dTAG V -1, we characterized the pharmacokinetic 107 (PK) and pharmacodynamic (PD) profile of dTAG V -1 in mice. dTAG V -1 demonstrated improved 108properties compared to dTAG-13, with a longer half-life (T1/2 = 4.43, 2.41 h respectively) and 109 greater exposure (AUCinf = 18517, 6140 hr*ng mL -1 respectively) by intraperitoneal 110 administration at 10 mg/kg ( Supplementary Table 1). To report on the PD profile of dTAG 111 molecules, we employed MV4;;11 luciferase-FKBP12 F36V (luc-FKBP12 F36V ) cells 6 that allow non-112 invasive monitoring of bioluminescent signal upon dTAG molecule administration in mice. 113Following tail vein injection of MV4;;11 luc-FKBP12 F36V cells and establishment of leukemic 114 burden, we performed daily bioluminescent measurements 4 h after vehicle, 35 mg/kg dTAG-13 115 or 35 mg/kg dTAG V -1 administration. Striking loss of bioluminescent signal was achieved 4 h 116 after the first administration of dTAG V -1 ( Fig. 1i and Supplementary Fig. 3). Consistent loss of 117 bioluminescent signal was observed 4 h after each of the three dTAG-13 or dTAG V -1 118 administrations. Compared to dTAG-13, improved duration of degradation w...

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Section: Resultsmentioning

confidence: 89%

Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules

Nabet

Ferguson

Seong

et al. 2020

Preprint

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“…Methylation of the glutarimide prevented the degradation of BRD4 as previously demonstrated ( fig. S8) (30).…”

Section: Optical Control Of Brd2-4 With Photacsmentioning

confidence: 99%

PHOTACs enable optical control of protein degradation

et al. 2020

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PROTACs (PROteolysis TArgeting Chimeras) are bifunctional molecules that target proteins for ubiquitylation by an E3 ligase complex and subsequent degradation by the proteasome. They have emerged as powerful tools to control the levels of specific cellular proteins. We now introduce photoswitchable PROTACs that can be activated with the spatiotemporal precision that light provides. These trifunctional molecules, which we named PHOTACs (PHOtochemically TArgeting Chimeras), consist of a ligand for an E3 ligase, a photoswitch, and a ligand for a protein of interest. We demonstrate this concept by using PHOTACs that target either BET family proteins (BRD2,3,4) or FKBP12. Our lead compounds display little or no activity in the dark but can be reversibly activated with different wavelengths of light. Our modular approach provides a method for the optical control of protein levels with photopharmacology and could lead to new types of precision therapeutics that avoid undesired systemic toxicity. RESULTS Design, synthesis, and photophysical characterizationThe design of our PHOTACs was guided by a desire to render our molecules as diversifiable and modular as possible while ensuring

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“…This has been shown recently in several studies. For example, Brand et al () generated a potent PROTAC against CDK6 that was not adequately selective as two IMiD substrates, IKZF1 and IKZF3, were also degraded. However, modifications in the linker region resulted in a PROTAC with no observed degradation of these Ikaros proteins.…”

Section: Opportunity To Develop “Safer” Protacsmentioning

confidence: 99%

“…Many studies have shown that PROTACs are not entirely selective and can degrade proteins other than the primary target (Bai et al, 2017;Bondeson et al, 2018;Brand et al, 2019;Matyskiela et al, 2016;Yang et al, 2019;Zorba et al, 2018). Degradation of a protein that is not directly bound by the PROTAC can arise as a consequence of "bystander degradation" where the degradation of a protein that is not directly bound by the PROTAC becomes ubiquitinated and hence degraded as part of the same complex with the PROTAC POI (Hsu et al, 2019;Maniaci et al, 2017;Potjewyd et al, 2019).…”

Section: Off-target Protein Degradationmentioning

confidence: 99%

Proteolysis‐targeting chimeras in drug development: A safety perspective

Moreau

Coen

Zhang

et al. 2020

British J Pharmacology

124

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Proteolysis‐targeting chimeras are a new drug modality that exploits the endogenous ubiquitin proteasome system to degrade a protein of interest for therapeutic benefit. As the first‐generation of proteolysis‐targeting chimeras have now entered clinical trials for oncology indications, it is timely to consider the theoretical safety risks inherent with this modality which include off‐target degradation, intracellular accumulation of natural substrates for the E3 ligases used in the ubiquitin proteasome system, proteasome saturation by ubiquitinated proteins, and liabilities associated with the “hook effect” of proteolysis‐targeting chimeras This review describes in vitro and non‐clinical in vivo data that provide mechanistic insight of these safety risks and approaches being used to mitigate these risks in the next generation of proteolysis‐targeting chimera molecules to extend therapeutic applications beyond life‐threatening diseases.

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Homolog-Selective Degradation as a Strategy to Probe the Function of CDK6 in AML

Cited by 204 publications

References 26 publications

Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules

Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules

PHOTACs enable optical control of protein degradation

Proteolysis‐targeting chimeras in drug development: A safety perspective

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