scholarly journals Predator: A novel method for targeted protein degradation

2020 ◽  
Author(s):  
Chuanyang Liu ◽  
Jingyu Kuang ◽  
Xinyuan Qiu ◽  
Lu Min ◽  
Wenying Li ◽  
...  

AbstractProtein expression and degradation are fundamental to cell function and physiological status of organisms. Interfering with protein expression not only provides powerful strategies to analyze the function of proteins but also inspires effective treatment methods for diseases caused by protein dysfunction. Recently, harnessing the power of the ubiquitin-proteasome system for targeted protein degradation (TPD) has become the focus of researches. Over the past two decades, TPD technologies, such as E3 ligase modification, PROTACs, and the Trim-Away method, have successfully re-oriented the ubiquitin-proteasome pathway and thus degraded many pathogenic proteins and even "undruggable" targets. However, A low-cost, convenient, and modularized TPD method is currently not available. Herein, we proposed a synthetic biology TPD method, termed Predator, by integrating the classic function of E3 ligase Trim21 and the expression of a bifunctional fusion protein that links Trim21 and the target protein, which leads to the formation of a ternary complex inside mammalian cells and therefore induce the ubiquitination and subsequent proteasome-dependent degradation of the target protein. We first proved this concept by using nanobody and scFv as the targeting module for the Predator system to degrade free GFP and membrane protein ErbB3, respectively. Then, we give an example of how the engineered Predator system can be developed towards biomedical solutions in the context of diabetes mellitus. Ligands-receptor interaction and adenovirus-mediated gene delivery were introduced to the Predator system, and we found this bifunctional fusion protein, in which glucagon was selected to function as the targeting module, downregulated the endogenous glucagon receptor (GCGR) and attenuated glucagon-stimulated glucose production in primary hepatocytes. Although preliminarily, our results showed that this Predator system is a highly modularized and convenient TPD method with good potential for both fundamental researches and clinical usage.Graphic abstract

Author(s):  
Kalyn M Rambacher ◽  
Matthew F Calabrese ◽  
Masaya Yamaguchi

Targeted protein degradation is a broad and expanding field aimed at the modulation of protein homeostasis. A focus of this field has been directed toward molecules that hijack the ubiquitin proteasome system with heterobifunctional ligands that recruit a target protein to an E3 ligase to facilitate polyubiquitination and subsequent degradation by the 26S proteasome. Despite the success of these chimeras toward a number of clinically relevant targets, the ultimate breadth and scope of this approach remains uncertain. Here we highlight recent advances in assays and tools available to evaluate targeted protein degradation, including and beyond the study of E3-targeted chimeric ligands. We note several challenges associated with degrader development and discuss various approaches to expanding the protein homeostasis toolbox.


2021 ◽  
pp. 247255522110175
Author(s):  
Peter Stacey ◽  
Hannah Lithgow ◽  
Xiao Lewell ◽  
Agnieszka Konopacka ◽  
Stephen Besley ◽  
...  

Targeted protein degradation is an emerging new strategy for the modulation of intracellular protein levels with applications in chemical biology and drug discovery. One approach to enable this strategy is to redirect the ubiquitin–proteasome system to mark and degrade target proteins of interest (POIs) through the use of proteolysis targeting chimeras (PROTACs). Although great progress has been made in enabling PROTACs as a platform, there are still a limited number of E3 ligases that have been employed for PROTAC design. Herein we report a novel phenotypic screening approach for the identification of E3 ligase binders. The key concept underlying this approach is the high-throughput modification of screening compounds with a chloroalkane moiety to generate HaloPROTACs in situ, which were then evaluated for their ability to degrade a GFP-HaloTag fusion protein in a cellular context. As proof of concept, we demonstrated that we could generate and detect functional HaloPROTACs in situ, using a validated Von Hippel–Lindau (VHL) binder that successfully degraded the GFP-HaloTag fusion protein in living cells. We then used this method to prepare and screen a library of approximately 2000 prospective E3 ligase-recruiting molecules.


2021 ◽  
Author(s):  
Alessio Ciulli ◽  
Nicole Trainor

Those with a keen interest in targeting proteins, from chemical biologists to drug hunters alike, cannot help but take notice that a new type of molecule is making waves across this research space. Proteolysis Targeting Chimeras (or PROTACs) are protein degraders, which utilize the cell’s own waste disposal machinery to eliminate instead of inhibit a target protein. The key to PROTACs is their bifunctionality: they simultaneously bind a target protein and an E3 ligase protein, which then ubiquitylates the target, marking it for proteasomal degradation. This concept originated in the late 1990s and the first PROTAC was reported in 2001 by the laboratories of Craig Crews and Raymond Deshaies. However, interest in PROTACs did not pick up until 2015 when improved molecules were developed by the laboratories of Jay Bradner, Alessio Ciulli and Craig Crews. Ever since, PROTACs and the wider field of targeted protein degradation have expanded exponentially, with many groups around the world developing degraders as chemical tools to study proteins and as drug candidates for the treatment of diseases.


2020 ◽  
Vol 6 (8) ◽  
pp. eaay5154 ◽  
Author(s):  
Jing Liu ◽  
He Chen ◽  
Leina Ma ◽  
Zhixiang He ◽  
Dong Wang ◽  
...  

By hijacking endogenous E3 ligase to degrade protein targets via the ubiquitin-proteasome system, PROTACs (PRoteolysis TArgeting Chimeras) provide a new strategy to inhibit protein targets that were regarded as undruggable before. However, the catalytic nature of PROTAC potentially leads to uncontrolled degradation that causes systemic toxicity issues, limiting the application of PROTAC in the clinic. Here, we introduce a light-inducible switch on PROTACs, thereafter termed as opto-PROTAC, to enable the degradation of protein targets in a spatiotemporal manner. By adding a photolabile caging group on pomalidomide as a parental compound and two additional PROTACs, dBET1 and dALK, we demonstrated light-inducible protein degradation. These opto-PROTACs display no activities in the dark, while the restricted degradation can be induced at a specific time and rate by ultraviolet A irradiation. Our approach provides a generalizable platform for the development of light-controlled PROTACs and enables PROTAC to be a precision medicine.


Author(s):  
Swarupananda Mukherjee ◽  
Saumyakanti Giri ◽  
Sohini Bera ◽  
Sharanya Mukherjee ◽  
Shankha Dey ◽  
...  

The protein degradation is a well-controlled, highly selective mechanism for intracellular protein degradation and its turnover. There are several proteins in our body but among them some goes for degradation at a time. Proteins which are going to be degraded are identified by a 76 amino acid polypeptide known as ubiquitin and the process is known as ubiquitination. Ubiquitation means the attachment of many ubiquitin molecules to the target protein molecule that need to be broken down. During the ubiquitination procedure iso peptide bonds are formed. And these iso peptide bonds are formed between the nitrogen molecule of the lysine residue from the target protein and the carbon molecule of the ubiquitin molecule. Through this endogenous ubiquitin-proteasome machinery, disease responsible proteins can be permanently removed. Energy is required for this process and that’s why ATP is employed in this process. This targeted protein degradation plays a very crucial role for cancer and other diseases. Through this review we just enlighten the significant points if the targeted protein degradation and its significance.


2019 ◽  
Vol 11 (20) ◽  
pp. 2715-2734 ◽  
Author(s):  
Wenhai Huang ◽  
Beibei Wang ◽  
Zhimin Zhang ◽  
Chixiao Zhang ◽  
Shenxin Zeng ◽  
...  

Proteolysis-targeting chimeras (PROTACs) have received much attention for their promising therapeutic intervention in recent years. These molecules, with the mechanism of simultaneous recruitment of target protein and an E3 ligase, can trigger the cellular ubiquitin–proteasome system to degrade the target proteins. This article systematically introduces the mechanism of small-molecule PROTACs, and summarized the research progress of small-molecule PROTACs. The prospect for further application and the problems to be solved are also discussed.


Author(s):  
Liang Li ◽  
Dazhao Mi ◽  
Haixiang Pei ◽  
Qiuhui Duan ◽  
Xinyue Wang ◽  
...  

Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2646-2646
Author(s):  
Dijiong Wu ◽  
Keding Shao ◽  
Qihao Zhou ◽  
Jie Sun ◽  
Ziqi Wang ◽  
...  

Abstract The major feature that distinguishes acute promyelocytic leukemia (APL) cells from other malignant hematopoietic cells is the expression of promyelocytic leukemia-retinoicacid receptor α (PML-RARα) fusion protein, which contributes to the inhibition of RARα-regulated hematopoietic cellular differentiation. The complete remission rate of APL exceeded 90% with the application of all-trans retinoic acid (ATRA), arsenic trioxide (ATO), and anthracycline-based chemotherapy. However, the 7-year cumulative incidence of relapses was reported as 28.6% in APL maintenance with ATRA and daunorubicin and even reached 33% in the ATRA maintenance treatment group. The relapse/refractory patients showed resistance to ATRA and/or ATO, which has been identified as a clinically significant problem. Currently, no effective drugs are available to reverse the ATRA resistance. Matrine (MAT) is the main active component of Sophora flavescens. It has been used to treat chronic hepatitis for several years in China. Recently, the molecule has been proven to exhibit an anti-leukemic effect. Previous studies have revealed that MAT can reverse the ATRA resistance of NB4-LR1 cells when coupled with ATRA. The treatment with 0.1mmol/L MAT and 1μmol/L ATRA can restore the ability of NB4-LR1 cells to differentiate, which might be related to the increased level of cyclic adenosine monophosphate and protein kinase A activity in NB4-LR1 cells, reduced telomerase activity and downregulated expression of topoisomerase II beta (TopoIIβ) (Wu, et al. Planta Med 2014). Subsequently, this study aimed to investigate the mechanism underlying the degradation of the PML/RARα fusion protein in the presence of MAT and ATRA in NB4 and NB4-LR1 cell lines. ATRA-sensitive (NB4) and ATRA-resistant (NB4-LR1) cell lines were used. Nitroblue tetrazolium reduction assay and flow cytometry were used to detect the differentiation ability. The activity of ubiquitin-proteasome and autophagy-mediated pathways in both cells treated with ATRA with or without MAT were compared in protein and mRNA level (Western blot analysis, qRT-PCR), the Fluorescent substrate Suc-LLVY-AMC detection was used to detect the activity of proteasome, and electron microscope for observing autophagosome. MG 132(proteasome inhibitor), rapamycin (autophagy activator, RAPA), hydroxychloroquine (lysosomal inhibitor, HCQ) and STI571 [retinoic acid receptor alpha (RARα) ubiquitin stabilizer] were used as positive controls. The effect of MAT was observed in vivo using xenografts. Results showed that MAT improved the sensitivity of NB4-LR1cells to ATRA treatment, which was consistent with the expression of PML-RARα fusion protein (Fig.A-C).The ubiquitin proteasome pathway plays a crucial role in protein degradation. MAT promoted the ubiquitylation level in NB4-LR1 by stabilized the 20S protein expression and enhanced the activity of the proteasome (Fig.D). ATRA inhibited the expression of RARα in NB4-LR1 cells, which was contradictory to that in NB4 cells. MAT can stabilize the expression of RARα in NB4-LR1 cells, whereas MG132 downregulated the expression of RARα in both cell lines, which hampered the differentiation of NB4 cells (Fig.E-G). In addition to UPP, the autophagy pathway also had a significant role in arsenious acid- or ATRA-mediated PML-RARα fusion protein degradation. MAT could promoted the autophagy in NB4-LR1 cells, with an increase in microtubule-associated protein 1 light chain3 (LC3)-II and LC3-II/LC3-I ratio and exhaustion of P62 (Fig.H-K). A similar phenomenon was observed in mouse xenografts (Fig.L-N). In summary, the present study revealed the difference in the chain reaction of sensitive and resistant APL cell lines (NB4 and NB4-LR1, respectively) to the treatment of ATRA, explaining the mechanism underlying the resistance to ATRA. ATRA decrease the level of 20S core subunit and the RARα in NB4-LR1 cells, but could not activate the autophagy process. These effects were reversed by the combination of MAT. The proteasome inhibitor might hamper the RARα stabilization and hence was not advantageous for the differentiation of cells. It also induced autophagy in NB4-LR1 cells. MAT induced the activation of UPP and mediated the autophagic degradation process, which synergistically induced the degradation of PML-RARα fusion protein and promote the differentiation of NB4-LR1 cells. Figure. Figure. Disclosures No relevant conflicts of interest to declare.


Author(s):  
Cyrille Kounde ◽  
Maria M. Shchepinova ◽  
Edward Tate

A caging group has been appended to a widely used Von Hippel Lindau (VHL) E3 ligase ligand for targeted protein degradation with PROTACs. Proteolysis is triggered only after a short irradiation time allowing spatiotemporal control of the protein’s fate.


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