Chemical Tools Research Articles

A Direct Chemical Repair of Etheno-Type RNA Damages.

Etheno damages in RNA represent a unique class of structural alterations that arise from exposure to various environmental stressors or endogenous processes. They significantly distort the RNA structure and affect crucial biological functions, including RNA-protein interactions, ribosome function, and translation fidelity. However, repair mechanisms for those etheno damages in RNA are still being elucidated. Here, a synthetic flavin derivative PS9 has been identified as the first example of chemical repair approach for this type of RNA damages. It efficiently managed the removal of etheno-type εA and εC damages in nucleosides, oligonucleotides in vitro, and in E. coli RNA in vivo under blue light irradiation. The capacity of the chemical approach relies on a unique cycloaddition activation of the etheno-bridge with singlet oxygen, which is distinct from traditional epoxidation of the C=C double bonds by proteins from the AlkB family. The understanding and effective manipulation of etheno damages in RNA with chemical tools hold implications for deciphering their role in mutagenesis and RNA biology, potentially opening avenues for targeted therapeutic interventions and biomarker development.

A Direct Chemical Repair of Etheno‐Type RNA Damages

Etheno damages in RNA represent a unique class of structural alterations that arise from exposure to various environmental stressors or endogenous processes. They significantly distort the RNA structure and affect crucial biological functions, including RNA‐protein interactions, ribosome function, and translation fidelity. However, repair mechanisms for those etheno damages in RNA are still being elucidated. Here, a synthetic flavin derivative PS9 has been identified as the first example of chemical repair approach for this type of RNA damages. It efficiently managed the removal of etheno‐type εA and εC damages in nucleosides, oligonucleotides in vitro, and in E. coli RNA in vivo under blue light irradiation. The capacity of the chemical approach relies on a unique cycloaddition activation of the etheno‐bridge with singlet oxygen, which is distinct from traditional epoxidation of the C=C double bonds by proteins from the AlkB family. The understanding and effective manipulation of etheno damages in RNA with chemical tools hold implications for deciphering their role in mutagenesis and RNA biology, potentially opening avenues for targeted therapeutic interventions and biomarker development.

Inhibitory DNA Aptamer Tools against SOCS3-gp130 Interactions.

The Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway plays a crucial role in transmembrane signal transduction, enabling cells to communicate with the extracellular environment, which requires precise regulation to prevent abnormal signaling outcomes. Within this complex pathway, suppressor of cytokine signaling 3 (SOCS3) acts as a pivotal negative regulator via binding to cytokine receptors. However, our understanding of the regulatory mechanisms governing SOCS3 interactions has been limited by the lack of suitable chemical probes. Aptamers, a notable category of chemical tools, have emerged as a viable avenue for the development of chemical inhibitors. In this study, we successfully identified specific inhibitory aptamers that bind to SOCS3 and effectively disrupt the interaction between SOCS3 and glycoprotein 130, a common cytokine receptor for interleukin-6 and leukemia inhibitory factor, which regulates the survival of normal human endometrial stromal cells. These aptamers not only provide a valuable chemical tool to advance our understanding of the regulatory dynamics of the JAK/STAT signaling pathway by SOCS3 but also hold great promise for the future development of therapeutic interventions.

Management of Fusarium Wilt of Lettuce

Abstract In recent years, Fusarium wilt, caused by Fusarium oxysporum f. sp. lactucae, has become the most important lettuce disease throughout the world. Since the pathogen is seed-transmitted, the disease spreads through infected seeds, favoured by the global commerce. We describe the biology and epidemiology of the pathogen, as well as the differentiation of four physiological races, with their distribution in different geographical areas. The reaction of the lettuce types and varieties to the pathogen are also described, as well as the diagnostic tools available for an appropriate detection of the pathogen, including the races. Like other soil-borne diseases, Fusarium wilt of lettuce is difficult to manage with a single product and/or with a single approach. At present, minimizing crop losses due to Fusarium wilt on lettuce entails the deployment of all available existing disease control tools within an integrated management programme. The first preventative strategy is the use of healthy seeds. Stock seeds should be produced in the areas associated with the lowest disease risk and subjected to standardized health analysis. Furthermore, seeds should be treated with chemical/physical or biological treatments. Among chemical tools, soil disinfestation is becoming very difficult due to the loss of registered fumigants. A careful monitoring of the race situation in the field would be useful for efficient use of genetic means of control. The seed industry is investing in the search of new varieties resistant to Fusarium wilt. Looking forward, the development of commercially acceptable cultivars of desired types of lettuce with high levels of resistance to Fusarium wilt as well as refinement of existing or development of new cultural, chemical and biofungicide tools should lead to more efficient and effective disease management. Information © The Authors 2024

Unanticipated mechanisms of covalent inhibitor and synthetic ligand cobinding to PPARγ

Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor transcription factor that regulates gene expression programs in response to ligand binding. Endogenous and synthetic ligands, including covalent antagonist inhibitors GW9662 and T0070907, are thought to compete for the orthosteric pocket in the ligand-binding domain (LBD). However, we previously showed that synthetic PPARγ ligands can cooperatively cobind with and reposition a bound endogenous orthosteric ligand to an alternate site, synergistically regulating PPARγ structure and function (Shang et al., 2018). Here, we reveal the structural mechanism of cobinding between a synthetic covalent antagonist inhibitor with other synthetic ligands. Biochemical and NMR data show that covalent inhibitors weaken—but do not prevent—the binding of other ligands via an allosteric mechanism, rather than direct ligand clashing, by shifting the LBD ensemble toward a transcriptionally repressive conformation, which structurally clashes with orthosteric ligand binding. Crystal structures reveal different cobinding mechanisms including alternate site binding to unexpectedly adopting an orthosteric binding mode by altering the covalent inhibitor binding pose. Our findings highlight the significant flexibility of the PPARγ orthosteric pocket, its ability to accommodate multiple ligands, and demonstrate that GW9662 and T0070907 should not be used as chemical tools to inhibit ligand binding to PPARγ.

A Phenotypic High-Throughput Screen Identifies Small Molecule Modulators of Endogenous RGS10 in BV-2 Cells.

Chronic dysregulation of microglial phenotypic balance contributes to prolonged neuroinflammation and neurotoxicity, which is a hallmark of neurodegenerative diseases. Thus, targeting microglial inflammatory signaling represents a promising therapeutic strategy for neurodegenerative diseases. Regulator of G protein Signaling 10 (RGS10) is highly expressed in microglia, where it suppresses pro-inflammatory signaling. However, RGS10 is silenced following microglial activation, augmenting inflammatory responses. While modulating RGS10 expression is a promising strategy to suppress pro-inflammatory microglial activation, no chemical tools with this ability exist. We developed a phenotypic high-throughput assay to screen for compounds with the ability to reverse interferon-γ (IFNγ)-induced RGS10 silencing in BV-2 cells. Identified hits had no effect on RGS10 expression in the absence of stimulus or in response to lipopolysaccharide (LPS). Furthermore, the hits reversed some of the inflammatory gene expression induced by IFNγ. This is the first demonstration of the potential for small molecule intervention to modulate the RGS10 expression in microglia.

Visual and Quantitative Analysis of Dietary Fiber-Microbiota Interactions via Metabolic Labeling In Vivo.

Dietary fiber (DF)-based interventions are crucial in establishing a health-promoting gut microbiota. However, directly investigating DFs' in vivo interactions with intestinal bacteria remains challenging due to the lack of suitable tools. Here, we develop an in vivo metabolic labeling-based strategy, which enables not only imaging and identifying the bacteria that bind with specific DF in the intestines, but also quantifying DF's impact on their metabolic status. Four DFs, including galactan, rhamnogalacturonan and two inulins, are fluorescently derivatized and used for in vivo labeling to visually record DFs' interactions with gut bacteria. The subsequent cell-sorting, 16S rDNA sequencing, and fluorescence in situ hybridization identify the taxa that bind each DF. We then select a DF-binding species newly identified herein and verify its DF-catabolizing capability in vitro. Furthermore, we find that the indigenous metabolic status of Gram-positive bacteria, whether inulin-binders or not, is significantly enhanced by the inulin supplement. This trend isn't observed in Gram-negative microbiota, even for the inulin-binders, demonstrating the ability of our methods in differentiating the primary, secondary DF-degraders from cross-feeders, a question that is difficult to answer by using other methods. Our strategy provides a novel chemical biology tool for deciphering the complex DF-bacteria interactions in the gut.

Going Beyond Woodward and Hoffmann's Electrocyclizations and Cycloadditions: Sigmatropic Rearrangements.

On June 1, 1965, R. B. Woodward and Roald Hoffmann published their third communication in the Journal of the American Chemical Society in which they applied orbital symmetry control to explain the mechanism of a wide variety of valence isomerizations that they termed "sigmatropic reactions." This publication reveals the research trajectory taken by Hoffmann from which this portion of the no-mechanism problem was solved. Hoffmann used five different quantum chemical tools, all based on either extended Hückel theoretical calculations or frontier molecular orbital theory, in his research. Hoffmann's laboratory notebooks and his three draft manuscripts along with Woodward's four subsequent drafts have survived the past 59 years and provide an excellent window into the thinking and manuscript-writing processes used by these Nobel laureates in February-April 1965.

Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays.

In response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to approximate compound-dependent changes in thermal stability, the proteome-wide thermal shift assay has emerged as a powerful tool in this arsenal. The most recent iterations have drastically improved the overall efficiency of these assays, providing an opportunity to screen compounds at a previously unprecedented rate. Taking advantage of this advance, we quantified more than one million thermal stability measurements in response to multiple classes of therapeutic and tool compounds (96 compounds in living cells and 70 compounds in lysates). When interrogating the dataset as a whole, approximately 80% of compounds (with quantifiable targets) caused a significant change in the thermal stability of an annotated target. There was also a wealth of evidence portending off-target engagement despite the extensive use of the compounds in the laboratory and/or clinic. Finally, the combined application of cell- and lysate-based assays, aided in the classification of primary (direct ligand binding) and secondary (indirect) changes in thermal stability. Overall, this study highlights the value of these assays in the drug development process by affording an unbiased and reliable assessment of compound mechanism of action.

Large-scale characterization of drug mechanism of action using proteome-wide thermal shift assays

In response to an ever-increasing demand of new small molecules therapeutics, numerous chemical and genetic tools have been developed to interrogate compound mechanism of action. Owing to its ability to approximate compound-dependent changes in thermal stability, the proteome-wide thermal shift assay has emerged as a powerful tool in this arsenal. The most recent iterations have drastically improved the overall efficiency of these assays, providing an opportunity to screen compounds at a previously unprecedented rate. Taking advantage of this advance, we quantified more than one million thermal stability measurements in response to multiple classes of therapeutic and tool compounds (96 compounds in living cells and 70 compounds in lysates). When interrogating the dataset as a whole, approximately 80% of compounds (with quantifiable targets) caused a significant change in the thermal stability of an annotated target. There was also a wealth of evidence portending off-target engagement despite the extensive use of the compounds in the laboratory and/or clinic. Finally, the combined application of cell- and lysate-based assays, aided in the classification of primary (direct ligand binding) and secondary (indirect) changes in thermal stability. Overall, this study highlights the value of these assays in the drug development process by affording an unbiased and reliable assessment of compound mechanism of action.

Synthesis of SulfoCy5‐ and SulfoCy7‐αGalCer Probes as Chemical Tools for Investigating the Uptake of Liposomal αGalCer Conjugates by Antigen Presenting Cells

Abstractα‐Galactosylceramide (αGalCer) is a synthetic glycolipid that, when loaded into the CD1d receptor of antigen presenting cells, activates iNKT cells to coordinate the generation of both innate and adaptive immune responses. In vaccines, the αGalCer adjuvant is generally delivered in liposomes, but interestingly, little is known about the intracellular fate of αGalCer‐antigen conjugates resulting in the absence of clear “design rules” for this type of compounds and their formulations. To unravel the uptake mechanism of liposomal αGalCer conjugates and understand the fate of its components, we synthesized sulfoCy7‐αGalCer 1 and sulfoCy5‐αGalCer 2. The fluorescent probes were obtained from a linker‐functionalized αGalCer, which was then modified with sulfoCy7/sulfoCy5. After formulation in liposomes, the cellular presentation was studied in a murine dendritic cell line using fluorescence imaging and flow cytometry. Imaging indicates that liposomes loaded with sulfoCy5‐αGalCer are taken up by DC2.4 cells in a heterogeneous and concentration‐dependent manner. Additionally, fluorescence antibody staining confirms that αGalCer is ultimately presented by CD1d receptors, but importantly is cleaved from sulfoCy5 before reaching the cell surface. These results validate our synthetic probes as useful in mechanistic studies of the uptake of αGalCer‐antigen conjugates as shown here for DC2.4 cells.

Discovery of KW0113 as a First and Effective PROTAC Degrader of DNMT1 Protein.

DNA methyltransferase 1 (DNMT1) is an attractive therapeutic target for acute myelocytic leukemia (AML) and other malignancies. It has been reported that the genetic depletion of DNMT1 inhibited AML cell proliferation through reversing DNA methylation abnormalities. However, no DNMT1-targeted PROTAC degraders have been reported yet. Herein, a series of proteolysis-targeting chimera (PROTAC) degrader of DNMT1 based on dicyanopyridine scaffold and VHL E3 ubiquitin ligase ligand was developed. Among them, KW0113 (DC50=643/899 nM in MV4-11/MOLM-13 cells) exhibited optimal DNMT1 degradation. KW0113 induced DNMT1-selective degradation in a dose- and time-dependent manner through VHL engagement. Moreover, KW0113 inhibited AML cell growth by reversing promoter DNA hypermethylation and tumor-suppressor genes silencing. In conclusion, these findings proved the capability of PROTAC strategy for inducing DNMT1 degradation, demonstrated the therapeutic potential of DNMT1-targeted PROTACs. This work also provided a convenient chemical knockdown tool for DNMT1-related studies.

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

Chemical proteomics enables the global analysis 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, remained 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 screening and chemical proteomics identified photo-stereoprobes that modulate autophagy by engaging the mitochondrial serine protease CLPP. Our findings show the utility of DOS-inspired photo-stereoprobes for expanding the ligandable proteome, furnishing target engagement assays, and facilitating the discovery and characterization of bioactive compounds in phenotypic screens.

Chemical Tools for Probing the Ub/Ubl Conjugation Cascades.

Conjugation of ubiquitin (Ub) and structurally related ubiquitin-like proteins (Ubls), essential for many cellular processes, employs multi-step reactions orchestrated by specific E1, E2 and E3 enzymes. The E1 enzyme activates the Ub/Ubl C-terminus in an ATP-dependent process that results in the formation of a thioester linkage with the E1 active site cysteine. The thioester-activated Ub/Ubl is transferred to the active site of an E2 enzyme which then interacts with an E3 enzyme to promote conjugation to the target substrate. The E1-E2-E3 enzymatic cascades utilize labile intermediates, extensive conformational changes, and vast combinatorial diversity of short-lived protein-protein complexes to conjugate Ub/Ubl to various substrates in a regulated manner. In this review, we discuss various chemical tools and methods used to study the consecutive steps of Ub/Ubl activation and conjugation, which are often too elusive for direct studies. We focus on methods developed to probe enzymatic activities and capture and characterize stable mimics of the transient intermediates and transition states, thereby providing insights into fundamental mechanisms in the Ub/Ubl conjugation pathways.

A Target Class Ligandability Evaluation of WD40 Repeat-Containing Proteins.

Target class-focused drug discovery has a strong track record in pharmaceutical research, yet public domain data indicate that many members of protein families remain unliganded. Here we present a systematic approach to scale up the discovery and characterization of small molecule ligands for the WD40 repeat (WDR) protein family. We developed a comprehensive suite of protocols for protein production, crystallography, and biophysical, biochemical, and cellular assays. A pilot hit-finding campaign using DNA-encoded chemical library selection followed by machine learning (DEL-ML) to predict ligands from virtual libraries yielded first-in-class, drug-like ligands for 7 of the 16 WDR domains screened, thus demonstrating the broader ligandability of WDRs. This study establishes a template for evaluation of protein family wide ligandability and provides an extensive resource of WDR protein biochemical and chemical tools, knowledge, and protocols to discover potential therapeutics for this highly disease-relevant, but underexplored target class.

Expanding the Repertoire of ceDAF-12 Ligands for Modulation of the Steroid Endocrine System in C. Elegans.

Steroid hormones are essential for the biological processes of eukaryotic organisms. The steroid endocrine system of C. elegans, which includes dafachronic acids (DA) and the nuclear receptor ceDAF-12, provides a simple model for exploring the role of steroid hormone signaling pathways in animals. In this study, we show for the first time the feasibility of designing synthetic steroids that can modulate different physiological processes, such as development, reproduction and ageing, in relation to ceDAF-12. Our results not only confirm the conclusions derived from genetic studies linking these processes but also provide new chemical tools to selectively manipulate them, as we found that different compounds produce different phenotypic results. The structures of these compounds are much more diverse than those of endogenous hormones and analogues previously described by other researchers, allowing further development of the chemical modulation of the steroid endocrine system in C. elegans and related nematodes.

A Perspective On A Promising Role For Caffeine In Modulating The Casr In Pancreatic Β-Cells

The extracellular calcium-sensing receptor (CaSR) is a G-protein-coupled receptor (GPCR) that plays a crucial role in the parathyroid glands and kidneys in maintaining calcium (Ca2+) homeostasis. The extracellular CaSR is present in various cell types not implicated in controlling plasma Ca2+ levels. There is accumulating evidence that CaSR plays a significant role in regulating the function of β-cells in the pancreas. Divalent cations and insulin are released together during exocytosis, and their concentration in the restricted intercellular compartments of the pancreatic islet increases to activate CaSR in neighboring cells. Subsequently, the activated CaSR stimulates insulin vesicle release in the adjacent cells, and by repeating these steps, the signal is amplified in the whole islet. Recent work developed a photoaffinity-tagged glutathione derivative (DAZ-G) as a chemical tool. The study demonstrated that DAZ-G can identify and analyze CaSR ligands. The use of DAZ-G identified caffeine as a positive allosteric modulator of the CaSR, suggesting that the physiological effects of caffeine are partly attributed to its stimulation of the CaSR. Future work may utilize caffeine to activate the CaSR in pancreatic β-cells to improve their secretory function

Chemical approaches targeting the hurdles of hepatocyte transplantation: mechanisms, applications, and advances.

Hepatocyte transplantation (HTx) has been a novel cell-based therapy for severe liver diseases, as the donor livers for orthotopic liver transplantation are of great shortage. However, HTx has been confronted with two main hurdles: limited high-quality hepatocyte sources and low cell engraftment and repopulation rate. To cope with, researchers have investigated on various strategies, including small molecule drugs with unique advantages. Small molecules are promising chemical tools to modulate cell fate and function for generating high quality hepatocyte sources. In addition, endothelial barrier, immune responses, and low proliferative efficiency of donor hepatocytes mainly contributes to low cell engraftment and repopulation rate. Interfering these biological processes with small molecules is beneficial for improving cell engraftment and repopulation. In this review, we will discuss the applications and advances of small molecules in modulating cell differentiation and reprogramming for hepatocyte resources and in improving cell engraftment and repopulation as well as its underlying mechanisms.

Chemical Tools for Monitoring and Targeting Collagen Cross-linking.

The formation of collagen, the most abundant protein in mammals, is vital for the integrity of skin, tendons, and tissue in essentially any organ. Excessive collagen formation is, however, characteristic of fibrotic and malignant diseases, which include major global health issues. The diagnosis of abnormal collagen production and deposition is, therefore, critical for disease prognosis and helps guide treatment decisions. Here, we summarize our research on the development of tailored tools for monitoring and targeting excessive collagen crosslinking. We anticipate these tools will provide a deep understanding at the molecular level of collagen formation in normal and disease conditions with applications in imaging and disease treatment.

Profiling Cysteine Proteases Activities in Neuroinflammatory Cells.

A new activity-based probe (ABP) of cysteine proteases (FGA139) has been designed and synthesized. The design of the ABP has been done based upon the chemical structure of an irreversible inhibitor of cysteine proteases by attaching a bodipy fluorophore at the N-terminus of the peptide backbone. The synthetic route of the probe has a metathesis and a "click" reaction as key steps. Although some studies have been reported about the role played by cysteine proteases in neurodegenerative diseases, there are not definitive conclusions. The obtained ABP has been employed as a chemical tool to profile activities of cysteine proteases cathepsins B, L, and calpain in neurodegenerative cell models through confocal imaging. Colocalization of the probe to specific antibodies of the proteases and competitive experiments with non-fluorescent inhibitors confirm the specificity of the ABP. From a theranostic perspective, our findings strongly suggest that FGA139 exhibits a protective role in various cell lines against oxidative stress or pro-inflammatory toxicity and it effectively attenuates macrophage activation triggered by LPS.