OligoTRAFTACs: A generalizable method for transcription factor degradation

Targeted transcription factor degradation using oligonucleotide-based transcription factor targeting chimeras (TRAFTACs).

Identification and Quantification of Glutathionylated Cysteines under Ischemic Stress

Ischemia reperfusion injury contributes to adverse cardiovascular diseases in part by producing a burst of reactive oxygen species that induce oxidations of many muscular proteins. Glutathionylation is one of the major protein cysteine oxidations that often serve as molecular mechanisms behind the pathophysiology associated with ischemic stress. Despite the biological significance of glutathionylation in ischemia reperfusion, identification of specific glutathionylated cysteines under ischemic stress has been limited. In this report, we have analyzed glutathionylation under oxygen-glucose deprivation (OGD) or repletion of nutrients after OGD (OGD/R) by using a clickable glutathione approach that specifically detects glutathionylated proteins. Our data find that palmitate availability induces a global level of glutathionylation and decreases cell viability during OGD/R. We have then applied a clickable glutathione-based proteomic quantification strategy, which enabled the identification and quantification of 249 glutathionylated cysteines in response to palmitate during OGD/R in the HL-1 cardiomyocyte cell line. The subsequent bioinformatic analysis found 18 glutathionylated cysteines whose genetic variants are associated with muscular disorders. Overall, our data report glutathionylated cysteines under ischemic stress that may contribute to adverse outcomes or muscular disorders.

Targeted protein degradation: A promise for undruggable proteins

Protein homeostasis, or "proteostasis," is indispensable for a balanced, healthy environment within the cell. However, when natural proteostasis mechanisms are overwhelmed from excessive loads of dysregulated proteins, their accumulation can lead to disease initiation and progression. Recently, the induced degradation of such disease-causing proteins by heterobifunctional molecules, i.e., PROteolysis TArgeting Chimeras (PROTACs), is emerging as a potential therapeutic modality. In the 2 decades since the PROTAC concept was proposed, several additional Targeted Protein Degradation (TPD) strategies have also been explored to target previously undruggable proteins, such as transcription factors. In this review, we discuss the progress and evolution of the TPD field, the breadth of the proteins targeted by PROTACs and the biological effects of their degradation.

Targeted degradation of transcription factors by TRAFTACs: TRAnscription Factor TArgeting Chimeras

Many diseases, including cancer, stem from aberrant activation or overexpression of oncoproteins that are associated with multiple signaling pathways. Although proteins with catalytic activity can be successfully drugged, the majority of other protein families, such as transcription factors, remain intractable due to their lack of ligandable sites. In this study, we report the development of TRAnscription Factor TArgeting Chimeras (TRAFTACs) as a generalizable strategy for targeted transcription factor degradation. We show that TRAFTACs, which consist of a chimeric oligonucleotide that simultaneously binds to the transcription factor of interest (TOI) and to HaloTag-fused dCas9 protein, can induce degradation of the former via the proteasomal pathway. Application of TRAFTACs to two oncogenic TOIs, NF-κB and brachyury, suggests that TRAFTACs can be successfully employed for the targeted degradation of other DNA-binding proteins. Thus, TRAFTAC technology is potentially a generalizable strategy to induce degradation of other transcription factors both in vitro and in vivo.

Mutant-selective degradation by BRAF-targeting PROTACs

Over 300 BRAF missense mutations have been identified in patients, yet currently approved drugs target V600 mutants alone. Moreover, acquired resistance inevitably emerges, primarily due to RAF lesions that prevent inhibition of BRAF V600 with current treatments. Therefore, there is a need for new therapies that target other mechanisms of activated BRAF. In this study, we use the Proteolysis Targeting Chimera (PROTAC) technology, which promotes ubiquitination and degradation of neo-substrates, to address the limitations of BRAF inhibitor-based therapies. Using vemurafenib-based PROTACs, we achieve low  nanomolar degradation of all classes of BRAF mutants, but spare degradation of WT RAF family members. Our lead PROTAC outperforms vemurafenib in inhibiting cancer cell growth and shows in vivo efficacy in a Class 2 BRAF xenograft model. Mechanistic studies reveal that BRAF^WT is spared due to weak ternary complex formation in cells owing to its quiescent inactivated conformation, and activation of BRAF^WT sensitizes it to degradation. This study highlights the degree of selectivity achievable with degradation-based approaches by targeting mutant BRAF-driven cancers while sparing BRAF^WT, providing an anti-tumor drug modality that expands the therapeutic window.

Hundreds of BRAF mutations have been identified in patients with cancer but currently approved drugs only target BRAF V600 mutants. Here, the authors develop a vemurafenib-based PROTAC that induces degradation of all classes of BRAF mutants without affecting wild-type RAF proteins.

Double-Barreled CRISPR Technology as a Novel Treatment Strategy For COVID-19

Coronavirus is one of the causative agents for multiple human respiratory illnesses. A novel coronavirus, similar to the one that caused severe acute respiratory syndrome (SARS) in 2003, was identified as the cause of the current pandemic of coronavirus disease (COVID-19), which was first reported in late December 2019 in Wuhan, China. Since then, this novel coronavirus has spread across the globe, with most identified COVID-19 cases and fatalities occurring in the United States. In this Perspective, we discuss coronavirus pathogenicity, conventional antiviral therapies, prophylactic strategies, and novel treatment strategies for COVID-19. We highlight the application of CRISPR technology as an emerging pan-antiviral therapy. We also discuss the challenges of in vivo delivery of CRISPR components and propose novel approaches to achieve selective delivery exclusively into SARS-CoV-2-infected cells with high efficiency by hijacking the surface proteins of SARS-CoV-2.

Reversible Spatiotemporal Control of Induced Protein Degradation by Bistable PhotoPROTACs

Off-tissue effects are persistent issues of modern inhibition-based therapies. By merging the strategies of photopharmacology and small-molecule degraders, we introduce a novel concept for persistent spatiotemporal control of induced protein degradation that potentially prevents off-tissue toxicity. Building on the successful principle of bifunctional all-small-molecule Proteolysis Targeting Chimeras (PROTACs), we designed photoswitchable PROTACs (photoPROTACs) by including ortho-F4-azobenzene linkers between both warhead ligands. This highly bistable yet photoswitchable structural component leads to reversible control over the topological distance between both ligands. The azo-cis-isomer is observed to be inactive because the distance defined by the linker is prohibitively short to permit complex formation between the protein binding partners. By contrast, the azo-trans-isomer is active since it can engage both protein partners to form the necessary and productive ternary complex. Importantly, due to the bistable nature of the ortho-F4-azobenzene moiety employed, the photostationary state of the photoPROTAC is persistent, with no need for continuous irradiation. This technique offers reversible on/off switching of protein degradation that is compatible with an intracellular environment and, therefore, could be useful in experimental exploration of biological signaling pathways-such as those crucial for oncogenic signal transduction. Additionally, this strategy may be suitable for therapeutic intervention to address a variety of diseases. By enabling reversible activation and deactivation of protein degradation, photoPROTACs offer advantages over conventional photocaging strategies that irreversibly release active agents.

SMYD2 glutathionylation contributes to degradation of sarcomeric proteins

Reactive oxygen species (ROS) contribute to the etiology of multiple muscle-related diseases. There is emerging evidence that cellular stress can lead to destabilization of sarcomeres, the contractile unit of muscle. However, it is incompletely understood how cellular stress induces structural destabilization of sarcomeres. Here we report that glutathionylation of SMYD2 contributes to a loss of myofibril integrity and degradation of sarcomeric proteins mediated by MMP-2 and calpain 1. We used a clickable glutathione approach in a cardiomyocyte cell line and found selective glutathionylation of SMYD2 at Cys13. Biochemical analysis demonstrated that SMYD2 upon oxidation or glutathionylation at Cys13 loses its interaction with Hsp90 and N2A, a domain of titin. Upon dissociation from SMYD2, N2A or titin is degraded by activated MMP-2, suggesting a protective role of SMYD2 in sarcomere stability. Taken together, our results support that SMYD2 glutathionylation is a novel molecular mechanism by which ROS contribute to sarcomere destabilization.

Clickable glutathione using tetrazine-alkene bioorthogonal chemistry for detecting protein glutathionylation

Protein glutathionylation is one of the major cysteine oxidative modifications in response to reactive oxygen species (ROS). We recently developed a clickable glutathione approach for detecting glutathionylation by using a glutathione synthetase mutant (GS M4) that synthesizes azido-glutathione (γGlu-Cys-azido-Ala) in situ in cells. In order to demonstrate the versatility of clickable glutathione and to increase the chemical tools for detecting glutathionylation, we sought to develop clickable glutathione that uses tetrazine-alkene bioorthogonal chemistry. Here we report two alkene-containing glycine surrogates (allyl-Gly and allyl-Ser) for the biosynthesis of clickable glutathione and their use for detection, enrichment, and identification of glutathionylated proteins. Our results provide chemical tools (allyl-Gly and allyl-Ser for GS M4) for versatile characterization of protein glutathionylation. In addition, we show that the active site of GS can be tuned to introduce a small size chemical tag on glutathione for exploring glutathione function in cells.

Correction: Clickable glutathione using tetrazine-alkene bioorthogonal chemistry for detecting protein glutathionylation

Correction for ‘Clickable glutathione using tetrazine-alkene bioorthogonal chemistry for detecting protein glutathionylation’ by Dilini N. Kekulandara et al., Org. Biomol. Chem., 2016, 14, 10886–10893.

A clickable glutathione approach for identification of protein glutathionylation in response to glucose metabolism

Glucose metabolism and mitochondrial function are closely interconnected with cellular redox-homeostasis. Although glucose starvation, which mimics ischemic conditions or insufficient vascularization, is known to perturb redox-homeostasis, global and individual protein glutathionylation in response to glucose metabolism or mitochondrial activity remains largely unknown. In this report, we use our clickable glutathione approach, which forms clickable glutathione (azido-glutathione) by using a mutant of glutathione synthetase (GS M4), for detection and identification of protein glutathionylation in response to glucose starvation. We found that protein glutathionylation is readily induced in HEK293 cells in response to low glucose concentrations when mitochondrial reactive oxygen species (ROS) are elevated in cells, and glucose is the major determinant for inducing reversible glutathionylation. Proteomic and biochemical analysis identified over 1300 proteins, including SMYD2, PP2Cα, and catalase. We further showed that PP2Cα is glutathionylated at C314 in a C-terminal domain, and PP2Cα C314 glutathionylation disrupts the interaction with mGluR3, an important glutamate receptor associated with synaptic plasticity.