Small-molecule inhibitors targeting small ubiquitin-like modifier pathway for the treatment of cancers and other diseases

Custom affinity probes reveal DNA-damage-induced, ssDNA-independent chromatin SUMOylation in budding yeast

The small ubiquitin-related modifier SUMO regulates cellular processes in eukaryotes either by modulating individual protein-protein interactions or with relaxed substrate selectivity by group modification. Here, we report the isolation and characterization of designed ankyrin repeat protein (DARPin)-based affinity probes directed against budding yeast SUMO (Smt3). We validate selected DARPins as compartment-specific inhibitors or neutral detection agents. Structural characterization reveals a recognition mode distinct from that of natural SUMO interactors. In vivo application pinpoints Smt3's essential function to the nucleus and demonstrates DARPin-mediated sensitization toward various stress conditions. A subset of selected clones is validated as SUMOylation reporters in cells. In this manner, we identify a DNA-damage-induced nuclear SUMOylation response that-in contrast to previously reported chromatin group SUMOylation-is independent of single-stranded DNA and the SUMO-E3 Siz2 but depends on Mms21 and likely reflects late intermediates of homologous recombination. Thus, Smt3-specific DARPins can provide insight into the dynamics of SUMOylation in defined subcellular structures.

SUMO-LMNet: Lossless mapping network for predicting SUMOylation sites in SUMO1 and SUMO2 using high-dimensional features

Accurate SUMOylation site prediction is crucial for deciphering gene regulation and disease mechanisms. However, distinguishing SUMO1 and SUMO2 modifications remains a major challenge due to their structural similarities. Conventional prediction models often struggle to differentiate between these paralogues, limiting their applicability in biological research. To address this, we introduce SUMO-LMNet, a deep learning-based framework for the precise prediction of SUMO1 and SUMO2 sites. Unlike previous models, SUMO-LMNet integrates a lossless mapping strategy and deep learning architectures to enhance both prediction accuracy and interpretability. Our model extracts high-dimensional features from sequences and transforms them into two-dimensional feature maps, enabling convolutional neural networks (CNNs) to effectively capture both local and global dependencies within the data. By leveraging a Lossless Mapping Network (LM-Net), this approach preserves the original feature space, ensuring that feature integrity is retained without loss of spatial information. While Grad-CAM highlights key features in individual predictions, it lacks consistency across samples and does not provide a dataset-wide evaluation of feature importance. To address this, we introduce Combined Heatmap Feature Analysis (CHFA), which systematically aggregates feature importance across multiple samples, providing a more reliable and interpretable dataset-wide assessment. Experimental results reveal distinct feature dependencies between SUMO1 and SUMO2, underscoring the necessity of paralogue-specific predictive models. Through a systematic comparison of multiple neural network architectures, we demonstrate that our model achieves over 80 % accuracy in distinguishing SUMO1 and SUMO2 modification sites. By prioritizing candidate sites for further study, our model aids experimental design and accelerates the discovery of biologically relevant SUMOylation targets. SUMO-LMNet is publicly available at https://predictor.isu.edu.tw/sumo-lmnet.

Recent Advances on the Regulations of Organic Anion Transporters

The organic anion transporter (OAT) family of over 10 members within the solute carrier (SLC) superfamily of membrane proteins plays critical roles in facilitating the flux of negatively charged molecules in and out of cell membranes. These anionic molecules include various endogenous and exogenous compounds such as signaling molecules, nutrients, metabolites, toxins, and drugs. Therefore, OATs actively contribute to the systemic homeostasis and efficacy of therapeutics. This article provides a brief overview on recent advances in the understanding of the regulatory mechanisms that control the expression and activity of OATs in both health and diseases.

Topotecan and Ginkgolic Acid Inhibit the Expression and Transport Activity of Human Organic Anion Transporter 3 by Suppressing SUMOylation of the Transporter

Organic anion transporter 3 (OAT3), expressed at the basolateral membrane of kidney proximal tubule cells, facilitates the elimination of numerous metabolites, environmental toxins, and clinically important drugs. An earlier investigation from our laboratory revealed that OAT3 expression and transport activity can be upregulated by SUMOylation, a post-translational modification that covalently conjugates SUMO molecules to substrate proteins. Topotecan is a semi-synthetic derivative of the herbal extract camptothecin, approved by the FDA to treat several types of cancer. Ginkgolic acid (GA) is one of the major components in the extract of Ginkgo biloba leaves that has long been used in food supplements for preventing dementia, high blood pressure, and supporting stroke recovery. Both topotecan and GA have been shown to affect protein SUMOylation. In the current study, we tested our hypothesis that topotecan and GA may regulate OAT3 SUMOylation, expression, and transport function. Our data show that the treatment of OAT3-expressing cells with topotecan or GA significantly decreases the SUMOylation of OAT3 by 50% and 75%, respectively. The same treatment also led to substantial reductions in OAT3 expression and the OAT3-mediated transport of estrone sulfate, a prototypical substrate. Such reductions in cell surface expression of OAT3 correlated well with an increased rate of OAT3 degradation. Mechanistically, we discovered that topotecan enhanced the association between OAT3 and the SUMO-specific protease SENP2, a deSUMOylation enzyme, which contributed to the significant decrease in OAT3 SUMOylation. In conclusion, this study unveiled a novel role of topotecan and GA in inhibiting OAT3 expression and transport activity and accelerating OAT3 degradation by suppressing OAT3 SUMOylation. During comorbidity therapies, the use of topotecan or Ginkgo biloba extract could potentially decrease the transport activity of OAT3 in the kidneys, which will in turn affect the therapeutic efficacy and toxicity of many other drugs that are substrates for the transporter.

Discovery of a Dual SENP1 and SENP2 Inhibitor

SUMOylation is a reversible post–translational modification (PTM) involving covalent attachment of small ubiquitin-related modifier (SUMO) proteins to substrate proteins. Dysregulation of SUMOylation and deSUMOylation results in cellular malfunction and is linked to various diseases, such as cancer. Sentrin-specific proteases (SENPs) were identified for the maturation of SUMOs and the deconjugation of SUMOs from their substrate proteins. Hence, this is a promising target tackling the dysregulation of the SUMOylation process. Herein, we report the discovery of a novel protein-protein interaction (PPI) inhibitor for SENP1-SUMO1 by virtual screening and subsequent medicinal chemistry optimization of the hit molecule. The optimized inhibitor ZHAWOC8697 showed IC₅₀ values of 8.6 μM against SENP1 and 2.3 μM against SENP2. With a photo affinity probe the SENP target was validated. This novel SENP inhibitor represents a new valuable tool for the study of SUMOylation processes and the SENP-associated development of small molecule-based treatment options.

Post-Translational Modifications of STING: A Potential Therapeutic Target

Stimulator of interferon genes (STING) is an endoplasmic-reticulum resident protein, playing essential roles in immune responses against microbial infections. However, over-activation of STING is accompanied by excessive inflammation and results in various diseases, including autoinflammatory diseases and cancers. Therefore, precise regulation of STING activities is critical for adequate immune protection while limiting abnormal tissue damage. Numerous mechanisms regulate STING to maintain homeostasis, including protein-protein interaction and molecular modification. Among these, post-translational modifications (PTMs) are key to accurately orchestrating the activation and degradation of STING by temporarily changing the structure of STING. In this review, we focus on the emerging roles of PTMs that regulate activation and inhibition of STING, and provide insights into the roles of the PTMs of STING in disease pathogenesis and as potential targeted therapy.