Biology subjects

Won, S. J.

Publications and source records attributed to Won, S. J..

11 recordsLinked to original sources

bioRxiv2025

Transcriptional and neuroprotective effects of hexokinase-2 inhibitors administered afterstroke

The inflammatory response induced by stroke can exacerbate injury to peri-infarct tissue. Microglia and other immune cells that mediate this response require increased glycolytic flux during pro-inflammatory activation. These cells, unlike neurons and most other cell types, utilize hexokinase-2 (HK2) rather than hexokinase-1 for glycolysis, such that HK2 inhibitors may selectively target them to suppress post-ischemic inflammation. Here we compared the effects of the non-selective hexokinase inhibitor 2-deoxyglucose to the HK2-selective inhibitors lonidamine and 3-bromopyruvate on secondary injury after stroke. A spatial transcriptomic assessment was performed in parallel to compare effects of the inhibitors on microglial gene expression and microglia - neuron interactions and to screen for off-target effects. Each of the inhibitors suppressed pro-inflammatory gene upregulation in peri-infarct microglia and attenuated the upregulation of cell stress functional pathways in the neighboring neurons, but had minimal effect on neuronal gene expression in uninjured cortex. The HK2-selective inhibitors were more effective than 2-deoxyglucose in suppressing morphological microglial changes, neuronal oxidative stress, and neurite loss. 3-bromopyruvate administered after stroke produced long-term improvements in functional outcome. Selective HK2 inhibitors may thus provide a clinically applicable means to suppress microglial activation and thereby improve outcomes after stroke without endangering neuronal energy metabolism.

neuroscience↗

bioRxiv2024

Stress hyperglycemia exacerbates inflammatory brain injury after stroke

Post-stroke hyperglycemia occurs in 30% - 60% of ischemic stroke patients as part of the systemic stress response, but neither clinical evidence nor pre-clinical studies indicate whether post-stroke hyperglycemia affects stroke outcome. Here we investigated this issue using a mouse model of permanent ischemia. Mice were maintained either normoglycemic or hyperglycemic during the interval of 17 - 48 hours after ischemia onset. Post-stroke hyperglycemia was found to increase infarct volume, blood-brain barrier disruption, and hemorrhage formation, and to impair motor recovery. Post-stroke hyperglycemia also increased superoxide formation by peri-infarct microglia/macrophages. In contrast, post-stroke hyperglycemia did not increase superoxide formation or exacerbate motor impairment in p47phox-/- mice, which cannot form an active superoxide-producing NADPH oxidase-2 complex. These results suggest that hyperglycemia occurring hours-to-days after ischemia can increase oxidative stress in peri-infarct tissues by fueling NADPH oxidase activity in reactive microglia/macrophages, and by this mechanism contribute to worsened functional outcome.

neuroscience↗

bioRxiv2024

Redirecting the pioneering function of FOXA1 with covalent small molecules

Pioneer transcription factors (TFs) exhibit a specialized ability to bind to and open closed chromatin, facilitating engagement by other regulatory factors involved in gene activation or repression. Chemical probes are lacking for pioneer TFs, which has hindered their mechanistic investigation in cells. Here, we report the chemical proteomic discovery of electrophilic small molecules that stereoselectively and site-specifically bind the pioneer TF, FOXA1, at a cysteine (C258) within the forkhead DNA-binding domain. We show that these covalent ligands react with FOXA1 in a DNA-dependent manner and rapidly remodel its pioneer activity in prostate cancer cells reflected in redistribution of FOXA1 binding across the genome and directionally correlated changes in chromatin accessibility. Motif analysis supports a mechanism where the covalent ligands relax the canonical DNA binding preference of FOXA1 by strengthening interactions with suboptimal ancillary sequences in predicted proximity to C258. Our findings reveal a striking plasticity underpinning the pioneering function of FOXA1 that can be controlled by small molecules.

biochemistry↗

bioRxiv2024

Unlocking the Potential of High-Quality Dopamine Transporter Pharmacological Data: Advancing Robust Machine Learning-Based QSAR Modeling

The dopamine transporter (DAT) plays a critical role in the central nervous system and has been implicated in numerous psychiatric disorders. The ligand-based approaches are instrumental to decipher the structure-activity relationship (SAR) of DAT ligands, especially the quantitative SAR (QSAR) modeling. By gathering and analyzing data from literature and databases, we systematically assemble a diverse range of ligands binding to DAT, aiming to discern the general features of DAT ligands and uncover the chemical space for potential novel DAT ligand scaffolds. The aggregation of DAT pharmacological activity data, particularly from databases like ChEMBL, provides a foundation for constructing robust QSAR models. The compilation and meticulous filtering of these data, establishing high-quality training datasets with specific divisions of pharmacological assays and data types, along with the application of QSAR modeling, prove to be a promising strategy for navigating the pertinent chemical space. Through a systematic comparison of DAT QSAR models using training datasets from various ChEMBL releases, we underscore the positive impact of enhanced data set quality and increased data set size on the predictive power of DAT QSAR models.

bioinformatics↗

bioRxiv2024

Chemical tools to expand the ligandable proteome: diversity-oriented synthesis-based photoreactive stereoprobes

Chemical proteomics enables the global assessment of small molecule-protein interactions in native biological systems and has emerged as a versatile approach for ligand discovery. The range of small molecules explored by chemical proteomics has, however, been limited. Here, we describe a diversity-oriented synthesis (DOS)-inspired library of stereochemically-defined compounds bearing diazirine and alkyne units for UV light-induced covalent modification and click chemistry enrichment of interacting proteins, respectively. We find that these photo-stereoprobes interact in a stereoselective manner with hundreds of proteins from various structural and functional classes in human cells and demonstrate that these interactions can form the basis for high-throughput screening-compatible nanoBRET assays. Integrated phenotypic analysis and chemical proteomics identified photo-stereoprobes that modulate autophagy by engaging the mitochondrial serine protease CLPP. Our findings show the utility of photo-stereoprobes for expanding the ligandable proteome, furnishing target engagement assays, and discovering and characterizing bioactive small molecules by cell-based screening.

biochemistry↗

bioRxiv2024

Superoxide enters neurons via LRRC8A-containing volume-regulated anion channels

Superoxide (O2-) is both an intercellular signaling molecule and a cause of neuronal oxidative stress. Superoxide entry into neurons is thought to be indirect, requiring its dismutation to nonpolar hydrogen peroxide. Here we show instead that superoxide enters neurons directly, via LRRC8A-containing volume-sensitive organic anion channels. In primary cultures, neuronal oxidative stress induced either by NMDA receptor stimulation or exposure to authentic superoxide was blocked by the anion channel blockers DIDS and DCPIB and by LRRC8A gene disruption. In mouse cortex, neuronal oxidative stress induced by either NMDA injection or transient ischemia was likewise blocked by both DCPIB and LRRC8A gene disruption. These findings identify a role for LRRC8A-containing volume-sensitive organic anion channels in neuronal oxidative signaling, stress, and glutamate excitotoxicity.

neuroscience↗

bioRxiv2024

Expanding the ligandable proteome by paralog hopping with covalent probes

More than half of the [~]20,000 protein-encoding human genes have at least one paralog. Chemical proteomics has uncovered many electrophile-sensitive cysteines that are exclusive to a subset of paralogous proteins. Here, we explore whether such covalent compound-cysteine interactions can be used to discover ligandable pockets in paralogs that lack the cysteine. Leveraging the covalent ligandability of C109 in the cyclin CCNE2, we mutated the corresponding residue in paralog CCNE1 to cysteine (N112C) and found through activity-based protein profiling (ABPP) that this mutant reacts stereoselectively and site-specifically with tryptoline acrylamides. We then converted the tryptoline acrylamide-N112C-CCNE1 interaction into a NanoBRET-ABPP assay capable of identifying compounds that reversibly inhibit both N112C- and WT-CCNE1:CDK2 complexes. X-ray crystallography revealed a cryptic allosteric pocket at the CCNE1:CDK2 interface adjacent to N112 that binds the reversible inhibitors. Our findings thus provide a roadmap for leveraging electrophile-cysteine interactions to extend the ligandability of the proteome beyond covalent chemistry.

biochemistry↗

bioRxiv2022

Proteomic discovery of chemical probes that perturb protein complexes in human cells

Most human proteins lack chemical probes, and several large-scale and generalizable small-molecule binding assays have been introduced to address this problem. How compounds discovered in such "binding-first" assays affect protein function, nonetheless, often remains unclear. Here, we describe a "function-first" proteomic strategy that uses size exclusion chromatography (SEC) to assess the global impact of electrophilic compounds on protein complexes in human cells. Integrating the SEC data with cysteine-directed activity-based protein profiling identifies changes in protein-protein interactions that are caused by site-specific liganding events, including the stereoselective engagement of cysteines in PSME1 and SF3B1 that disrupt the PA28 proteasome regulatory complex and stabilize a dynamic state of the spliceosome, respectively. Our findings thus show how multidimensional proteomic analysis of focused libraries of electrophilic compounds can expedite the discovery of chemical probes with site-specific functional effects on protein complexes in human cells.

biochemistry↗

bioRxiv2022

Assigning functionality to cysteines by base editing of cancer dependency genes

Chemical probes are lacking for most human proteins. Covalent chemistry represents an attractive strategy for expanding the ligandability of the proteome, and chemical proteomics has revealed numerous electrophile-reactive cysteines on diverse proteins. Determining which of these covalent binding events impact protein function, however, remains challenging. Here, we describe a base-editing strategy to infer the functionality of cysteines by quantifying the impact of their missense mutation on cell proliferation. We show that the resulting atlas, which covers >13,800 cysteines on >1,750 cancer dependency proteins, correctly predicts the essentiality of cysteines targeted by cancer therapeutics and, when integrated with chemical proteomic data, identifies essential, ligandable cysteines on >110 cancer dependency proteins. We further demonstrate how measurements of reactivity in native versus denatured proteomes can discriminate essential cysteines amenable to chemical modification from those buried in protein structures, providing a valuable resource to prioritize the pursuit of small-molecule probes with high function-perturbing potential.

systems biology↗

bioRxiv2019

α-synuclein aggregates induce c-Abl activation and neurodegeneration by a redox stress mechanism

ObjectiveRedox stress, c-Abl activation, and -synuclein aggregates each independently contribute to neurodegeneration in Parkinsons disease. Interactions between these factors may underlie convergent and feed-forward mechanisms of disease progression. Methods-synuclein aggregate formation was induced in neuronal cultures and mouse substantia nigra by exposure to pre-formed human -synuclein fibrils or by AAV-mediated over-expression of -synuclein. Aggregate formation, c-Abl activation, redox stress, and neurodegeneration were evaluated by immunohistochemistry and Western blots, and mouse motor function was evaluated using the rota-rod and pole tests. To suppress redox stress, cultures and mice were treated with N-acetyl cysteine, a thiol repletion agent that supports neuronal glutathione metabolism. ResultsIn primary neuron cultures, the formation of -synuclein aggregates led to redox stress and c-Abl activation. Redox stress alone, in the absence of -synuclein aggregates, was also sufficient to induced c-Abl activation. N-acetyl cysteine suppressed redox stress, and likewise suppressed both c-Abl activation and -synuclein aggregation. A similar pattern was observed in the two mouse models of Parkinsons disease. In both models, -synuclein aggregates in the substantia nigra were accompanied by redox stress, c-Abl activation, dopaminergic neurodegeneration and motor impairment, all of which were attenuated in mice treated with oral N-acetyl cysteine. InterpretationThese results indicate that -synuclein aggregates induce c-Abl activation by a redox stress mechanism. c-Abl in turn promotes -synuclein aggregation, and this potentially feed-forward process can be blocked by N-acetyl cysteine. The findings thus add mechanistic support for N-acetyl cysteine as a therapeutic for Parkinsons disease.

neuroscience↗

bioRxiv2018

Cofilin-actin rod formation in neuronal processes after brain ischemia

Functional impairment after brain ischemia results in part from loss of neuronal spines and dendrites, independent of neuronal death. Cofilin-actin rods are covalently linked aggregates of colfilin-1 and actin that form in neuronal processes (neurites) under conditions of ATP depletion and oxidative stress, and which cause neurite degeneration if not disassembled. ATP depletion and oxidative stress occur with differing severity, duration, and time course in different ischemic conditions. Here we evaluated four mouse models of brain ischemia to define the conditions that drive formation of cofilin-actin rods. Three of the models provide early reperfusion: transient middle cerebral artery occlusion (MCAo), transient bilateral common carotid occlusion (CCAo), and cardiac arrest / cardiopulmonary resuscitation (CA/CPR). Early reperfusion restores ATP generating capacity, but also induces oxidative stress. The fourth model, photothrombotic cortical infarction, does not provide reperfusion. Cofilin-actin rods were formed in each of these models, but with differing patterns. Where acute reperfusion occurred, rod formation was maximal within 4 hours after reperfusion. Where infarction occurred, rods continued to form for at least 24 hours after ischemic onset, and extended into the adjacent non-ischemic tissue. Interventions that limit cofilin-actin rod formation may help to preserve integrity of neuronal processes in permanent ischemia.

neuroscience↗