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 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 Photocontrollable PROTAC molecules: Structure and mechanism of action

2021 ◽  
Vol 71 (3) ◽  
pp. 161-176
Author(s):  
Mladen Koravović ◽  
Gordana Tasić ◽  
Milena Rmandić ◽  
Bojan Marković
Keyword(s):  
Protein Degradation ◽  
Ubiquitin Ligase ◽  
Binding Sites ◽  
E3 Ubiquitin Ligase ◽  
Drug Binding ◽  
Post Translational Modification ◽  
Protein Activity ◽  
Target Drug ◽  
Traditional Drug

Traditional drug discovery strategies are usually focused on occupancy of binding sites that directly affect functions of proteins. Hence, proteins that lack such binding sites are generally considered pharmacologically intractable. Modulators of protein activity, especially inhibitors, must be applied in appropriate dosage regimens that often lead to high systemic drug exposures in order to maintain sufficient protein inhibition in vivo. Consequently, there is a risk of undesirable off-target drug binding and side effects. Recently, PROteolysis TArgeting Chimera (PROTAC) technology has emerged as a new pharmacological modality that exploits PROTAC molecules for induced protein degradation. PROTAC molecule is a heterobifunctional structure consisting of a ligand that binds a protein of interest (POI), a ligand for recruiting an E3 ubiquitin ligase (an enzyme involved in the POI ubiquitination) and a linker that connects these two. After POI-PROTAC-E3 ubiquitin ligase ternary complex formation, the POI undergoes ubiquitination (an enzymatic post-translational modification in which ubiquitin is attached to the POI) and degradation. By merging the principles of photopharmacology and PROTAC technology, photocontrollable PROTACs for spatiotemporal control of induced protein degradation have recently emerged. The main advantage of photocontrollable over conventional PROTACs is the possible prevention of off-target toxicity thanks to local photoactivation.

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.

scholarly journals Expression Patterns and Functional Analysis of E3 Ubiquitin Ligase Genes in Rice

2021 ◽  
Author(s):  
huijuan zhang ◽  
Dewei Zheng ◽  
Fengming Song ◽  
Ming Jiang
Keyword(s):  
Ubiquitin Ligase ◽  
Abiotic Stresses ◽  
Magnaporthe Grisea ◽  
Function Analysis ◽  
Expression Patterns ◽  
E3 Ubiquitin Ligase ◽  
Ubiquitin Ligases ◽  
E3 Ubiquitin Ligases ◽  
Biotic And Abiotic Stresses ◽  
Genes Expression

Abstract Background: E3 ubiquitin ligases involve in many processes, containing the response to biotic and abiotic stresses. However, the functions of E3 ubiquitin ligases in rice were rarely studied.Results: In this research, 11 E3 ubiquitin ligase genes were selected and the function analysis was done in rice. These 11 E3 ubiquitin ligase genes showed different expression patterns under different treatments. The BMV:Os06g13870- infiltrated seedlings showed decreased resistance to Magnaporthe grisea (M. grisea) when compared with BMV:00-infiltrated seedlings, while BMV:Os04g34030- and BMV:Os02g33590-infiltrated seedlings showed increased resistance. They involved in the resistance against M. grisea maybe by regulating the accumulation of reactive oxygen species (ROS) and expression levels of defense-related genes. The BMV:Os06g34390-infiltrated seedlings showed decreased tolerance to drought stress while BMV:Os02g33590-infiltraed seedlings showed increased tolerance, maybe through regulating proline content, sugar content and drought-responsive genes’ expression. BMV:Os05g01940-infiltrated seedlings showed decreased tolerance to cold stress by regulating malondial dehyde (MDA) content and cold-responsive genes’ expression.Conclusion: These results showed that E3 ubiquitin ligases involved in the resistance to biotic and abiotic stresses in rice.

scholarly journals The Molecular and Pathophysiological Functions of Members of the LNX/PDZRN E3 Ubiquitin Ligase Family

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5938
Author(s):  
Jeongkwan Hong ◽  
Minho Won ◽  
Hyunju Ro
Keyword(s):  
Ubiquitin Ligase ◽  
E3 Ubiquitin Ligase ◽  
Ubiquitin Ligases ◽  
Ubiquitin Proteasome System ◽  
E3 Ubiquitin Ligases ◽  
Intercellular Signaling ◽  
Cellular Functions ◽  
Ring Type ◽  
Ubiquitin Ligase Activity ◽  
Ubiquitin Proteasome

The ligand of Numb protein-X (LNX) family, also known as the PDZRN family, is composed of four discrete RING-type E3 ubiquitin ligases (LNX1, LNX2, LNX3, and LNX4), and LNX5 which may not act as an E3 ubiquitin ligase owing to the lack of the RING domain. As the name implies, LNX1 and LNX2 were initially studied for exerting E3 ubiquitin ligase activity on their substrate Numb protein, whose stability was negatively regulated by LNX1 and LNX2 via the ubiquitin-proteasome pathway. LNX proteins may have versatile molecular, cellular, and developmental functions, considering the fact that besides these proteins, none of the E3 ubiquitin ligases have multiple PDZ (PSD95, DLGA, ZO-1) domains, which are regarded as important protein-interacting modules. Thus far, various proteins have been isolated as LNX-interacting proteins. Evidence from studies performed over the last two decades have suggested that members of the LNX family play various pathophysiological roles primarily by modulating the function of substrate proteins involved in several different intracellular or intercellular signaling cascades. As the binding partners of RING-type E3s, a large number of substrates of LNX proteins undergo degradation through ubiquitin-proteasome system (UPS) dependent or lysosomal pathways, potentially altering key signaling pathways. In this review, we highlight recent and relevant findings on the molecular and cellular functions of the members of the LNX family and discuss the role of the erroneous regulation of these proteins in disease progression.

scholarly journals New Discoveries on the Roles of “Other” HECT E3 Ubiquitin Ligases in Disease Development

2020 ◽  
Author(s):  
Emma I. Kane ◽  
Donald E. Spratt
Keyword(s):  
Ubiquitin Ligase ◽  
Developmental Disorders ◽  
E3 Ubiquitin Ligase ◽  
Ubiquitin Ligases ◽  
Disease Development ◽  
E3 Ubiquitin Ligases ◽  
Gene Encoding ◽  
Family Function ◽  
Substrate Proteins ◽  
Comprehensive Discussion

HECT E3 ubiquitin ligases selectively recognize, bind, and ubiquitylate their substrate proteins to target them for 26S proteasomal degradation. There is increasing evidence that HECT E3 ubiquitin ligase dysfunction due to misfolding and/or the gene encoding the protein being mutated is responsible for the development of different diseases. Apart from the more prominent and well-characterized E6AP and members of the NEDD4 family, new studies have begun to reveal how other members of the HECT E3 ubiquitin ligase family function as well as their links to disease and developmental disorders. This chapter provides a comprehensive discussion on the more mysterious members of the HECT E3 ubiquitin ligase family and how they control intracellular processes. Specifically, AREL1, HACE1, HECTD1, HECTD4, G2E3, and TRIP12 will be examined as these enzymes have recently been identified as contributors to disease development.

scholarly journals A Decoy Library Uncovers U-box E3 Ubiquitin Ligases that Regulate Flowering Time in Arabidopsis

2020 ◽  
Author(s):  
Ann M. Feke ◽  
Jing Hong ◽  
Wei Liu ◽  
Joshua M. Gendron
Keyword(s):  
Flowering Time ◽  
Ubiquitin Ligase ◽  
Floral Development ◽  
E3 Ubiquitin Ligase ◽  
Development Program ◽  
Ubiquitin Ligases ◽  
Biological Processes ◽  
E3 Ubiquitin Ligases ◽  
Developmental Transitions ◽  
Bona Fide

ABSTRACTTargeted degradation of proteins is mediated by E3 ubiquitin ligases and is important for the execution of many biological processes. Previously, we created and employed a large library of E3 ubiquitin ligase decoys to identify regulators of the circadian clock (Feke et al., 2019). In tandem with the screen for circadian regulators, we performed a flowering time screen using our U-box-type E3 ubiquitin ligase decoy transgenic library. We identified five U-box decoy transgenic populations that have defects in flowering time or the floral development program. We used additional genetic and biochemical studies to validate PLANT U-BOX 14 (PUB14), MOS4-ASSOCIATED COMPLEX 3A (MAC3A), and MAC3B as bona fide regulators of flowering time. This work reinforces the utility of the decoy library in identifying regulators of important developmental transitions in plants and expands the scope of the technique beyond our previous studies.

scholarly journals Decoys provide a scalable platform for the genetic analysis of plant E3 ubiquitin ligases that regulate circadian clock function

2018 ◽  
Author(s):  
Ann Feke ◽  
Wei Liu ◽  
Jing Hong ◽  
Man-Wah Li ◽  
Chin-Mei Lee ◽  
...  
Keyword(s):  
Circadian Clock ◽  
Ubiquitin Ligase ◽  
E3 Ubiquitin Ligase ◽  
Ubiquitin Ligases ◽  
Gene Families ◽  
Dominant Negative ◽  
E3 Ubiquitin Ligases ◽  
Genetic Redundancy ◽  
Clock Period ◽  
Knock Out

ABSTRACTThe circadian clock in all eukaryotes relies on the regulated degradation of clock proteins to maintain 24-hour rhythmicity. Despite this knowledge, we know very few of the components that mediate degradation of proteins to control clock function. This is likely due to high levels of gene duplication and functional redundancy within plant E3 ubiquitin ligase gene families. In order to overcome this issue and discover E3 ubiquitin ligases that control circadian clock function, we generated a library of transgenic Arabidopsis lines expressing dominant-negative “decoy” E3 ubiquitin ligases. We determined their effects on the plant circadian clock and identified dozens of new potential regulators of circadian clock function. To demonstrate the potency of the decoy screening methodology to overcome genetic redundancy and identify bona fide clock regulators, we performed follow-up studies on PUB59 and PUB60. Using knock-out studies, we show that they redundantly control circadian clock period by regulating gene splicing. Furthermore, we confirm that they are part of a conserved protein complex that mediates splicing in eukaryotes. This work demonstrates the viability of E3 ubiquitin ligase decoys as a scalable screening platform to overcome traditional genetic challenges and discover E3 ubiquitin ligases that regulate plant developmental processes.

scholarly journals The Ubiquitin E3 Ligase MaLUL2 Is Involved in High Temperature-Induced Green Ripening in Banana Fruit

2020 ◽  
Vol 21 (24) ◽  
pp. 9386
Author(s):  
Wei Wei ◽  
Jian-ye Chen ◽  
Ze-xiang Zeng ◽  
Jian-fei Kuang ◽  
Wang-jin Lu ◽  
...  
Keyword(s):  
High Temperature ◽  
Ubiquitin Ligase ◽  
E3 Ubiquitin Ligase ◽  
Ubiquitin Ligases ◽  
Negative Regulator ◽  
Banana Fruit ◽  
E3 Ubiquitin Ligases ◽  
Stay Green ◽  
E3 Ligases ◽  
Ring Type

Harvested banana fruit ripened under warm temperatures above 24 °C remain green peel, leading to severe economic loss. E3 ubiquitin-ligases, as the major components in the ubiquitination pathway, have been implicated to play important roles in temperature-stress responses. However, the molecular mechanism underlying high temperature-triggered stay-green ripening bananas in association with E3 ubiquitin-ligases, remains largely unknown. In this study, a RING-type E3 ubiquitin ligase termed MaLUL2, was isolated and characterized from banana fruit. The MaLUL2 gene contains 1095 nucleotides and encodes a protein with 365 amino acids. The MaLUL2 protein contains a domain associated with RING2 (DAR2) and a RING domain, which are the typical characteristics of RING-type E3 ligases. MaLUL2 expression was up-regulated during high temperature-induced green ripening. Subcellular localization showed that MaLUL2 localized in the nucleus, cytoplasm, and plasma membrane. MaLUL2 displayed E3 ubiquitin ligase activity in vitro. More importantly, transient overexpression of MaLUL2 in banana fruit peel increased the level of ubiquitination in vivo and led to a stay-green phenotype, accompanying with decreased expression of chlorophyll catabolic genes. Collectively, these findings suggest that MaLUL2 might act as a negative regulator of chlorophyll degradation and provide novel insights into the regulatory mechanism of high temperature-induced green ripening bananas.

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