scholarly journals Electrophilic PROTACs that degrade nuclear proteins by engaging DCAF16

2018 ◽  
Author(s):  
Xiaoyu Zhang ◽  
Vincent M. Crowley ◽  
Thomas G. Wucherpfennig ◽  
Melissa M. Dix ◽  
Benjamin F. Cravatt
Keyword(s):  
Protein Degradation ◽  
Protein Content ◽  
Substrate Recognition ◽  
Ubiquitin Ligases ◽  
Nuclear Proteins ◽  
E3 Ubiquitin Ligases ◽  
E3 Ligases ◽  
Dependent Protein

Ligand-dependent protein degradation has emerged as a compelling strategy to pharmacologically control the protein content of cells. So far, only a limited number of E3 ligases have been found to support this process. Here, we use a chemical proteomic strategy to discover that DCAF16 – a poorly characterized substrate recognition component of CUL4-DDB1 E3 ubiquitin ligases – promotes nuclear-restricted protein degradation upon modification by cysteine-directed heterobifunctional electrophilic compounds.

scholarly journals HaloTag-Targeted Sirtuin Rearranging Ligand (SirReal) for the Development of Proteolysis Targeting Chimeras (PROTACs) Against the Lysine Deacetylase Sirtuin 2 (Sirt2)

2020 ◽  
Author(s):  
Matthias Schiedel ◽  
Attila Lehotzky ◽  
Sándor Szunyogh ◽  
Judit Oláh ◽  
Sören Hammelmann ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Small Molecule ◽  
Ubiquitin Ligase ◽  
E3 Ubiquitin Ligase ◽  
E3 Ligase ◽  
Ubiquitin Ligases ◽  
E3 Ubiquitin Ligases ◽  
Selective Inhibitors ◽  
E3 Ligases ◽  
Lysine Deacetylase

We have discovered the sirtuin rearranging ligands (SirReals) as a novel class of highly potent and selective inhibitors of the NAD+-dependent lysine deacetylase sirtuin 2 (Sirt2). In previous studies, conjugation of a SirReal with a ligand for the E3 ubiquitin ligase cereblon to form a so-called proteolysis targeting chimera (PROTAC), enabled small molecule-induced degradation of Sirt2. Here, we report the structure-based development of a chloroalkylated SirReal that induces the degradation of Sirt2 mediated by Halo-tagged E3 ubiquitin ligases. Using this orthogonal approach for Sirt2 degradation, we show that also other E3 ligases than cereblon, such as the E3 ubiquitin ligase parkin, can be harnessed for small molecule-induced Sirt2 degradation, thereby emphasizing the great potential of parkin to be utilized as an E3 ligase for new PROTACs approaches. Thus, our study provides new insights into targeted protein degradation in general and Sirt2 degradation in particular.

scholarly journals HaloTag-Targeted Sirtuin Rearranging Ligand (SirReal) for the Development of Proteolysis Targeting Chimeras (PROTACs) Against the Lysine Deacetylase Sirtuin 2 (Sirt2)

2020 ◽  
Author(s):  
Matthias Schiedel ◽  
Attila Lehotzky ◽  
Sándor Szunyogh ◽  
Judit Oláh ◽  
Sören Hammelmann ◽  
...  
Keyword(s):  
Protein Degradation ◽  
Small Molecule ◽  
Ubiquitin Ligase ◽  
E3 Ubiquitin Ligase ◽  
E3 Ligase ◽  
Ubiquitin Ligases ◽  
E3 Ubiquitin Ligases ◽  
Selective Inhibitors ◽  
E3 Ligases ◽  
Lysine Deacetylase

We have discovered the sirtuin rearranging ligands (SirReals) as a novel class of highly potent and selective inhibitors of the NAD+-dependent lysine deacetylase sirtuin 2 (Sirt2). In previous studies, conjugation of a SirReal with a ligand for the E3 ubiquitin ligase cereblon to form a so-called proteolysis targeting chimera (PROTAC), enabled small molecule-induced degradation of Sirt2. Here, we report the structure-based development of a chloroalkylated SirReal that induces the degradation of Sirt2 mediated by Halo-tagged E3 ubiquitin ligases. Using this orthogonal approach for Sirt2 degradation, we show that also other E3 ligases than cereblon, such as the E3 ubiquitin ligase parkin, can be harnessed for small molecule-induced Sirt2 degradation, thereby emphasizing the great potential of parkin to be utilized as an E3 ligase for new PROTACs approaches. Thus, our study provides new insights into targeted protein degradation in general and Sirt2 degradation in particular.

scholarly journals Ubiquitination, Biotech Startups, and the Future of TRIM Family Proteins: A TRIM-Endous Opportunity

Cells ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 1015
Author(s):  
Utsa Bhaduri ◽  
Giuseppe Merla
Keyword(s):  
Drug Discovery ◽  
Protein Degradation ◽  
Ubiquitin Ligase ◽  
Genetic Disorders ◽  
E3 Ubiquitin Ligase ◽  
Ubiquitin Ligases ◽  
E3 Ubiquitin Ligases ◽  
Post Translational Modification ◽  
Disease Biology ◽  
The Future

Ubiquitination is a post-translational modification that has pivotal roles in protein degradation and diversified cellular processes, and for more than two decades it has been a subject of interest in the biotech or biopharmaceutical industry. Tripartite motif (TRIM) family proteins are known to have proven E3 ubiquitin ligase activities and are involved in a multitude of cellular and physiological events and pathophysiological conditions ranging from cancers to rare genetic disorders. Although in recent years many kinds of E3 ubiquitin ligases have emerged as the preferred choices of big pharma and biotech startups in the context of protein degradation and disease biology, from a surface overview it appears that TRIM E3 ubiquitin ligases are not very well recognized yet in the realm of drug discovery. This article will review some of the blockbuster scientific discoveries and technological innovations from the world of ubiquitination and E3 ubiquitin ligases that have impacted the biopharma community, from biotech colossuses to startups, and will attempt to evaluate the future of TRIM family proteins in the province of E3 ubiquitin ligase-based drug discovery.

scholarly journals Comprehensive database of human E3 ubiquitin ligases: application to aquaporin-2 regulation

2016 ◽  
Vol 48 (7) ◽  
pp. 502-512 ◽  
Author(s):  
Barbara Medvar ◽  
Viswanathan Raghuram ◽  
Trairak Pisitkun ◽  
Abhijit Sarkar ◽  
Mark A. Knepper
Keyword(s):  
Human Genome ◽  
Large Scale ◽  
E3 Ligase ◽  
Ubiquitin Ligases ◽  
Bayes Rule ◽  
E3 Ubiquitin Ligases ◽  
E3 Ligases ◽  
Aquaporin 2 ◽  
Large Scale Data ◽  
Level Data

Aquaporin-2 (AQP2) is regulated in part via vasopressin-mediated changes in protein half-life that are in turn dependent on AQP2 ubiquitination. Here we addressed the question, “What E3 ubiquitin ligase is most likely to be responsible for AQP2 ubiquitination?” using large-scale data integration based on Bayes' rule. The first step was to bioinformatically identify all E3 ligase genes coded by the human genome. The 377 E3 ubiquitin ligases identified in the human genome, consisting predominant of HECT, RING, and U-box proteins, have been used to create a publically accessible and downloadable online database ( https://hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases/ ). We also curated a second database of E3 ligase accessory proteins that included BTB domain proteins, cullins, SOCS-box proteins, and F-box proteins. Using Bayes' theorem to integrate information from multiple large-scale proteomic and transcriptomic datasets, we ranked these 377 E3 ligases with respect to their probability of interaction with AQP2. Application of Bayes' rule identified the E3 ligases most likely to interact with AQP2 as (in order of probability): NEDD4 and NEDD4L (tied for first), AMFR, STUB1, ITCH, ZFPL1. Significantly, the two E3 ligases tied for top rank have also been studied extensively in the reductionist literature as regulatory proteins in renal tubule epithelia. The concordance of conclusions from reductionist and systems-level data provides strong motivation for further studies of the roles of NEDD4 and NEDD4L in the regulation of AQP2 protein turnover.

scholarly journals Comprehensive Analysis of E3 Ubiquitin Ligases Reveals Ring Finger Protein 223 as a Novel Oncogene Activated by KLF4 in Pancreatic Cancer

2021 ◽  
Vol 9 ◽  
Author(s):  
Lei Feng ◽  
Jieqing Wang ◽  
Jianmin Zhang ◽  
Jingfang Diao ◽  
Longguang He ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Transcriptional Activation ◽  
Prognostic Significance ◽  
Ring Finger ◽  
Ubiquitin Ligases ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
E3 Ubiquitin Ligases ◽  
E3 Ligases ◽  
Elevated Expression

Pancreatic cancer is one of the major malignancies and causes of mortality worldwide. E3 ubiquitin–protein ligases transfer activated ubiquitin from ubiquitin-conjugating enzymes to protein substrates and confer substrate specificity in cancer. In this study, we first downloaded data from The Cancer Genome Atlas pancreatic adenocarcinoma dataset, acquired all 27 differentially expressed genes (DEGs), and identified genomic alterations. Then, the prognostic significance of DEGs was analyzed, and eight DEGs (MECOM, CBLC, MARCHF4, RNF166, TRIM46, LONRF3, RNF39, and RNF223) and two clinical parameters (pathological N stage and T stage) exhibited prognostic significance. RNF223 showed independent significance as an unfavorable prognostic marker and was chosen for subsequent analysis. Next, the function of RNF223 in the pancreatic cancer cell lines ASPC-1 and PANC-1 was investigated, and RNF223 silencing promoted pancreatic cancer growth and migration. To explore the potential targets and pathways of RNF223 in pancreatic cancer, quantitative proteomics was applied to analyze differentially expressed proteins, and metabolism-related pathways were primarily enriched. Finally, the reason for the elevated expression of RNF223 was analyzed, and KLF4 was shown to contribute to the increased expression of RNF233. In conclusion, this study comprehensively analyzed the clinical significance of E3 ligases. Functional assays revealed that RNF223 promotes cancer by regulating cell metabolism. Finally, the elevated expression of RNF223 was attributed to KLF4-mediated transcriptional activation. This study broadens our knowledge regarding E3 ubiquitin ligases and signal transduction and provides novel markers and therapeutic targets in pancreatic cancer.

scholarly journals Establishment of a Wheat Cell-Free Synthesized Protein Array Containing 250 Human and Mouse E3 Ubiquitin Ligases to Identify Novel Interaction between E3 Ligases and Substrate Proteins

PLoS ONE ◽  
2016 ◽  
Vol 11 (6) ◽  
pp. e0156718 ◽  
Author(s):  
Hirotaka Takahashi ◽  
Atsushi Uematsu ◽  
Satoshi Yamanaka ◽  
Mei Imamura ◽  
Tatsuro Nakajima ◽  
...  
Keyword(s):  
Ubiquitin Ligases ◽  
Protein Array ◽  
E3 Ubiquitin Ligases ◽  
E3 Ligases ◽  
Substrate Proteins ◽  
Human And Mouse

scholarly journals Potential of E3 Ubiquitin Ligases in Cancer Immunity: Opportunities and Challenges

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3309
Author(s):  
Peng Ye ◽  
Xiaoxia Chi ◽  
Jong-Ho Cha ◽  
Shahang Luo ◽  
Guanghui Yang ◽  
...  
Keyword(s):  
Checkpoint Inhibitors ◽  
Ubiquitin Ligases ◽  
Immune Checkpoints ◽  
E3 Ubiquitin Ligases ◽  
E3 Ligases ◽  
Beneficial Effects ◽  
Clinical Strategies ◽  
Immune Pathway ◽  
Future Direction ◽  
Cancer Immunotherapies

Cancer immunotherapies, including immune checkpoint inhibitors and immune pathway–targeted therapies, are promising clinical strategies for treating cancer. However, drug resistance and adverse reactions remain the main challenges for immunotherapy management. The future direction of immunotherapy is mainly to reduce side effects and improve the treatment response rate by finding new targets and new methods of combination therapy. Ubiquitination plays a crucial role in regulating the degradation of immune checkpoints and the activation of immune-related pathways. Some drugs that target E3 ubiquitin ligases have exhibited beneficial effects in preclinical and clinical antitumor treatments. In this review, we discuss mechanisms through which E3 ligases regulate tumor immune checkpoints and immune-related pathways as well as the opportunities and challenges for integrating E3 ligases targeting drugs into cancer immunotherapy.

scholarly journals Functional Significance of the E3 Ubiquitin Ligases in Disease and Therapeutics

2021 ◽  
Author(s):  
Julius Tieroyaare Dongdem ◽  
Cletus Adiyaga Wezena
Keyword(s):  
Therapeutic Potential ◽  
Protein Complexes ◽  
Ring Finger ◽  
Ubiquitin Ligases ◽  
E3 Ubiquitin Ligases ◽  
Phd Finger ◽  
E3 Ligases ◽  
Cellular Processes ◽  
Future Drug ◽  
Ubiquitin Conjugating Enzyme

E3 ubiquitin ligases of which there are >600 putative in humans, constitute a family of highly heterogeneous proteins and protein complexes that are the ultimate enzymes responsible for the recruitment of an ubiquitin loaded E2 ubiquitin-conjugating enzyme, recognise the appropriate protein substrate and directly or indirectly transfer the ubiquitin load onto the substrate. The aftermath of an E3 ligase activity is usually the formation of an isopeptide bond between the free carboxylate group of ubiquitin’s C-terminal Gly76 and an ε-amino group of the substrate’s Lys, even though non-canonical ubiquitylation on non-amine groups of target proteins have been observed. E3 ligases are grouped into four distinct families: HECT, RING-finger/U-box, RBR and PHD-finger. E3 ubiquitin ligases play critical roles in subcellular signalling cascades in eukaryotes. Dysfunctional E3 ubiquitin ligases therefore tend to inflict dramatic effects on human health and may result in the development of various diseases including Parkinson’s, Amyotrophic Lateral Sclerosis, Alzheimer’s, cancer, etc. Being regulators of numerous cellular processes, some E3 ubiquitin ligases have become potential targets for therapy. This chapter will present a comprehensive review of up-to-date findings in E3 ligases, their role in the pathology of disease and therapeutic potential for future drug development.

scholarly journals E3 ubiquitin ligases: styles, structures and functions

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Quan Yang ◽  
Jinyao Zhao ◽  
Dan Chen ◽  
Yang Wang
Keyword(s):  
Cancer Progression ◽  
Large Family ◽  
Ubiquitin Ligases ◽  
E3 Ubiquitin Ligases ◽  
Therapeutic Approaches ◽  
E3 Ligases ◽  
Promising Target ◽  
Stress Signal ◽  
Ubiquitin Conjugating Enzyme ◽  
Almost All

AbstractE3 ubiquitin ligases are a large family of enzymes that join in a three-enzyme ubiquitination cascade together with ubiquitin activating enzyme E1 and ubiquitin conjugating enzyme E2. E3 ubiquitin ligases play an essential role in catalyzing the ubiquitination process and transferring ubiquitin protein to attach the lysine site of targeted substrates. Importantly, ubiquitination modification is involved in almost all life activities of eukaryotes. Thus, E3 ligases might be involved in regulating various biological processes and cellular responses to stress signal associated with cancer development. Thanks to their multi-functions, E3 ligases can be a promising target of cancer therapy. A deeper understanding of the regulatory mechanisms of E3 ligases in tumorigenesis will help to find new prognostic markers and accelerate the growth of anticancer therapeutic approaches. In general, we mainly introduce the classifications of E3 ligases and their important roles in cancer progression and therapeutic functions.

scholarly journals Genome-wide analysis of HECT E3 ubiquitin ligase gene family in Solanum lycopersicum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bhaskar Sharma ◽  
Harshita Saxena ◽  
Harshita Negi
Keyword(s):  
Gene Family ◽  
Ubiquitin Ligase ◽  
Plant Development ◽  
Stress Responses ◽  
E3 Ubiquitin Ligase ◽  
Ubiquitin Ligases ◽  
E3 Ubiquitin Ligases ◽  
E3 Ligases ◽  
Genome Wide Analysis ◽  
Genome Wide

AbstractThe E3 ubiquitin ligases have been known to intrigue many researchers to date, due to their heterogenicity and substrate mediation for ubiquitin transfer to the protein. HECT (Homologous to the E6-AP Carboxyl Terminus) E3 ligases are spatially and temporally regulated for substrate specificity, E2 ubiquitin-conjugating enzyme interaction, and chain specificity during ubiquitylation. However, the role of the HECT E3 ubiquitin ligase in plant development and stress responses was rarely explored. We have conducted an in-silico genome-wide analysis to identify and predict the structural and functional aspects of HECT E3 ligase members in tomato. Fourteen members of HECT E3 ligases were identified and analyzed for the physicochemical parameters, phylogenetic relations, structural organizations, tissue-specific gene expression patterns, and protein interaction networks. Our comprehensive analysis revealed the HECT domain conservation throughout the gene family, close evolutionary relationship with different plant species, and active involvement of HECT E3 ubiquitin ligases in tomato plant development and stress responses. We speculate an indispensable biological significance of the HECT gene family through extensive participation in several plant cellular and molecular pathways.

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