Chemical Probes Research Articles

A multiplexed high throughput screening assay using flow cytometry identifies glycolytic molecular probes in bloodstream form Trypanosoma brucei

Kinetoplastid organisms, including Trypanosoma brucei, are a significant health burden in many tropical and semitropical countries. Much of their metabolism is poorly understood. To better study kinetoplastid metabolism, chemical probes that inhibit kinetoplastid enzymes are needed. To discover chemical probes, we have developed a high-throughput flow cytometry screening assay that simultaneously measures multiple glycolysis-relevant metabolites in live T. brucei bloodstream form parasites. We transfected parasites with biosensors that measure glucose, ATP, or glycosomal pH. The glucose and ATP sensors were FRET biosensors, while the pH sensor was a GFP-based biosensor. The pH sensor exhibited a different fluorescent profile from the FRET sensors, allowing us to simultaneously measure pH and either glucose or ATP. Cell viability was measured in tandem with the biosensors using thiazole red. We pooled sensor cell lines, loaded them onto plates containing a compound library, and then analyzed them by flow cytometry. The library was analyzed twice, once with the pooled pH and glucose sensor cell lines and once with the pH and ATP sensor cell lines. Multiplexing sensors provided some internal validation of active compounds and gave potential clues for each compound's target(s). We demonstrated this using the glycolytic inhibitor 2-deoxyglucose and the alternative oxidase inhibitor salicylhydroxamic acid. Individual biosensor-based assays exhibited a Z′-factor value acceptable for high-throughput screening, including when multiplexed. We tested assay performance in a pilot screen of 14,976 compounds from the Life Chemicals Compound Library. We obtained hit rates from 0.2 to 0.4% depending on the biosensor, with many compounds impacting multiple sensors. We rescreened 44 hits, and 28 (64%) showed repeatable activity for one or more sensors. One compound exhibited EC50 values in the low micromolar range against two sensors. We expect this method will enable the discovery of glycolytic chemical probes to improve metabolic studies in kinetoplastid parasites.

Development of a Standardized Protocol for the Classification of Column Sets in Comprehensive Two-Dimensional Gas Chromatography

One-dimensional gas chromatography (1D-GC) stationary phases are generally classified according to their relative polarity into non-polar, semi-polar, and polar columns. In comprehensive two-dimensional gas chromatography (GC×GC), it is the polarity difference between the two tandem-assembled stationary phases that determines the selectivity of the column ensemble. This polarity difference is called orthogonality, and GC×GC column sets can be broadly categorized into four groups based on the direction of the serial coupling between the primary and secondary columns. A significant portion of the GC×GC column sets in use today are operated in forward-orthogonality mode, which means that the secondary column is more polar than the primary column. A growing number of reported GC×GC applications operate in reversed-orthogonality configurations, where the secondary column is less polar than the primary column. Very few examples exist of non-orthogonal column sets because of the fact that there is limited additional selectivity that the secondary column can offer over the separation that has already been achieved in the primary column when the two phases are either identical or close in polarity. The fourth group of GC×GC column sets, called hybrid orthogonality, involves the coupling of stationary phases with peculiar selectivity differences that manifest themselves in the bi-dimensional separation plots. In this work, we are presenting a normalized approach to GC×GC column set characterization that is based on the use of a reference mixture of standards called the Century Mix. The Century Mix contains 100 chemical probes of different functionalities that span a reasonable range of volatilities and polarities to capture the selectivity profile of any GC×GC column set. The Century Mix also contains important chemical probes that are used for 1D-GC column characterization (such as the Grob mix and the Rohrschneider/McReynolds compounds) to make some connections between the 1D-GC building block columns and the GC×GC column sets. We finally also outline some other important metrics of comparison that should be taken into consideration to assess the overall performance of a GC×GC system.

A benchmark quantum chemical probe into the structural stability of various anchoring groups to form graphene oxides

Graphene and graphene oxides (GO) are among the intriguing materials of this era, being widely used in many modern technologies. Many properties of GOs are owing to its more reactivity as compared with graphene. It is interesting to study the changes in chemical properties while changing graphene to GOs. There are commonly known three ways to change a graphene to GO by adding epoxy, hydroxyl and carboxyl groups. We used quantum chemical methods to systematically attach epoxy, hydroxyl and carboxyl groups on graphene surface. We designed GOs as hydroxyl (OH-GO), epoxy (O-GO), carboxyl (COOH-GO) derivatives of graphene and one derivative with all functional groups collectively (HEC-GO). In the current work, we have employed DFT method by using B3LYP functional along with 6-31G* basis set to calculate electronic properties computationally. The calculated band gap for GOs are less than pristine graphene (1.680 eV). Minimum band gap of 1.565 eV is shown by O-GO, while compound HEC-GO with collective functional groups shows 1.539 eV. Frontier molecular orbitals, molecular electrostatic potential maps and density of state analysis has been performed. Localized orbital locator (LOL) are drawn to check the charge transfer via topology visualization. Binding energy has been calculated using basis set superposition error (BSSE) correction. COOH-GO shows binding energy of −302.90 kcal/mol which is seen better than OH-GO and O-GO systems. NPA analysis showed that there is more ICT as functional groups are attached to the pristine graphene molecule because of the strong electron withdrawing nature of attached groups. TD-DFT with TD-B3LYP/6-31G* is employed to check the absorption properties of entitled compounds. Graphene shows maximum absorption at 341 nm, while GOs shows red shift, e.g., COOH-GO at 371 nm, OH-GO at 386 nm, HEC-GO at 409 nm and O-GO at 462 nm. The current investigation highlighted the molecular level insights about the stability and relative role of epoxy, hydroxyl and carboxyl groups on graphene surface during formation of GOs.

Development of a Novel Amplifiable System to Quantify Hydrogen Peroxide in Living Cells.

Although many redox signaling molecules are present at low concentrations, typically ranging from micromolar to submicromolar levels, they often play essential roles in a wide range of biological pathways and disease mechanisms. However, accurately measuring low-abundant analytes has been a significant challenge due to the lack of sensitivity and quantitative capability of existing measurement methods. In this study, we introduced a novel chemically induced amplifiable system for quantifying low-abundance redox signaling molecules in living cells. We utilized H2O2 as a proof-of-concept analyte and developed a probe that quantifies cellular peroxide levels by combining the NanoBiT system with androgen receptor dimerization as a reporting mechanism. Our system demonstrated a highly sensitive response to cellular peroxide changes induced both endogenously and exogenously. Furthermore, the system can be adapted for the quantification of other signaling molecules if provided with suitable probing chemistry.

Fast quantitative MRI: Spiral Acquisition Matching-Based Algorithm (SAMBA) for Robust T1 and T2 Mapping

Conventional diagnostic images from Magnetic Resonance Imaging (MRI) are typically qualitative and require subjective interpretation. Alternatively, quantitative MRI (qMRI) methods have become more prevalent in recent years with multiple clinical and preclinical imaging applications. Quantitative MRI studies on preclinical MRI scanners are being used to objectively assess tissues and pathologies in animal models and to evaluate new molecular MRI contrast agents. Low-field preclinical MRI scanners (≤3.0T) are particularly important in terms of evaluating these new MRI contrast agents at human MRI field strengths. Unfortunately, these low-field preclinical qMRI methods are challenged by long acquisition times, intrinsically low MRI signal levels, and susceptibility to motion artifacts. In this study, we present a new rapid qMRI method for a preclinical 3.0T MRI scanner that combines a Spiral Acquisition with a Matching-Based Algorithm (SAMBA) to rapidly and quantitatively evaluate MRI contrast agents. In this initial development, we compared SAMBA with gold-standard Spin Echo MRI methods using Least Squares Fitting (SELSF) in vitro phantoms and demonstrated shorter scan times without compromising measurement accuracy or repeatability. These initial results will pave the way for future in vivo qMRI studies using state-of-the-art chemical probes.

Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA.

RNA molecules perform a diversity of essential functions for which their linear sequences must fold into higher-order structures. Techniques including crystallography and cryogenic electron microscopy have revealed 3D structures of ribosomal, transfer, and other well-structured RNAs; while chemical probing with sequencing facilitates secondary structure modeling of any RNAs of interest, even within cells. Ongoing efforts continue increasing the accuracy, resolution, and ability to distinguish coexisting alternative structures. However, no method can discover and quantify alternative structures with base pairs spanning arbitrarily long distances - an obstacle for studying viral, messenger, and long noncoding RNAs, which may form long-range base pairs. Here, we introduce the method of Structure Ensemble Ablation by Reverse Complement Hybridization with Mutational Profiling (SEARCH-MaP) and software for Structure Ensemble Inference by Sequencing, Mutation Identification, and Clustering of RNA (SEISMIC-RNA). We use SEARCH-MaP and SEISMIC-RNA to discover that the frameshift stimulating element of SARS coronavirus 2 base-pairs with another element 1 kilobase downstream in nearly half of RNA molecules, and that this structure competes with a pseudoknot that stimulates ribosomal frameshifting. Moreover, we identify long-range base pairs involving the frameshift stimulating element in other coronaviruses including SARS coronavirus 1 and transmissible gastroenteritis virus, and model the full genomic secondary structure of the latter. These findings suggest that long-range base pairs are common in coronaviruses and may regulate ribosomal frameshifting, which is essential for viral RNA synthesis. We anticipate that SEARCH-MaP will enable solving many RNA structure ensembles that have eluded characterization, thereby enhancing our general understanding of RNA structures and their functions. SEISMIC-RNA, software for analyzing mutational profiling data at any scale, could power future studies on RNA structure and is available on GitHub and the Python Package Index.

In vivo -Active Soluble Epoxide Hydrolase-targeting PROTACs with Improved Potency and Stability.

Soluble epoxide hydrolase (sEH) is a bifunctional enzyme involved in fatty acid metabolism and promising drug target. We previously reported first-generation sEH proteolysis-targeting chimeras (PROTACs) with limited degradation potency and low aqueous and metabolic stability. Herein, we report the development of next-generation sEH PROTAC molecules with improved stability and degradation potency. One of the most potent molecules (compound 8 ) exhibits a half-maximal degradation concentration in the sub-nM range, is stable in vivo , and effectively degrades sEH in mouse livers and brown adipose tissues. Given the role played by sEH in many metabolic and nonmetabolic diseases, the presented molecules provide useful chemical probes for the study of sEH biology. They also hold potential for therapeutic development against a range of disease conditions, including diabetes, inflammation, and metabolic disorders.

Discovery of Potent and Selective G9a Degraders for the Treatment of Pancreatic Cancer.

G9a, which was initially identified as a histone H3 Lys9 (H3K9) methyltransferase, is potentially an attractive therapeutic target for human cancers. Despite its importance, there is no available selective G9a chemical probe because its homologous protein GLP shares approximately 80% of its sequence with G9a. The development of G9a chemical probes with high selectivity for G9a over GLP is a big challenge but is extremely valuable for understanding G9a-related biology. Herein, we developed a first-in-class selective G9a degrader G9D-4, which induced a dose- and time-dependent G9a degradation without degradation of GLP. G9D-4 exhibited effective antiproliferative activities in a panel of pancreatic cancer cell lines and was able to sensitize KRASG12D mutant pancreatic cancer cells to KRASG12D inhibitor MRTX1133. These data clearly demonstrated the practicality and importance of a selective G9a degrader as a preliminary chemical probe suitable for understanding G9a-related biology and a promising strategy for the treatment of pancreatic cancer.

Regulation of reactive species during ionizing radiation by peroxydisulfate for enhanced degradation of typical pollutants in coking wastewater

This study focused on exploring the effect of peroxydisulfate (PDS) on the regulation of reactive species during water radiolysis process and its potential application for degrading organic pollutants. The results indicated that PDS was successfully activated by ionizing radiation for efficient removal of three typical phenolic compounds over a wide pH range (3.0∼12.0) at absorbed dose of 5 kGy. Chemical probe methods provided the evidence that the addition of PDS could introduce the sulfate radicals (SO4•−) and enhance the production of hydroxyl radicals (•OH). According to the quenching tests, •OH and SO4•− were the dominant reactive species responsible for the degradation of 4-NP, while hydrated electron (eaq−) played a minor role. The regulatory effect of PDS on active species in the ionizing radiation process could divided by (i) PDS could be directly activated by ionizing radiation to produce •OH and SO4•− via energy transfer pathway; (ii) PDS could boost the conversion of eaq− to SO4•− via electron transfer pathway. Furthermore, we assessed the applicability of the IR and IR/PDS systems in treating mixed solutions containing various pollutants and actual coking wastewater.

Small-molecule probe for IBD risk variant GPR65 I231L alters cytokine signaling networks through positive allosteric modulation.

The proton-sensing heterotrimeric guanine nucleotide-binding protein-coupled receptor GPR65 is expressed in immune cells and regulates tissue homeostasis in response to decreased extracellular pH, which occurs in the context of inflammation and tumorigenesis. Genome-wide association studies linked GPR65 to several autoimmune and inflammatory diseases such as multiple sclerosis and inflammatory bowel disease (IBD). The loss-of-function GPR65 I231L IBD risk variant alters cellular metabolism, impairs protective tissue functions, and increases proinflammatory cytokine production. Hypothesizing that a small molecule designed to potentiate GPR65 at subphysiological pH could decrease inflammatory responses, we found positive allosteric modulators of GPR65 that engage and activate both human and mouse orthologs of the receptor. We observed that the chemical probe BRD5075 alters cytokine and chemokine programs in dendritic cells, establishing that immune signaling can be modulated by targeting GPR65. Our investigation offers improved chemical probes to further interrogate the biology of human GPR65 and its clinically relevant genetic variants.

Identification of Potent ADCK3 Inhibitors through Structure-Based Virtual Screening.

ADCK3 is a member of the UbiB family of atypical protein kinases in humans, with homologues in archaea, bacteria, and eukaryotes. In lieu of protein kinase activity, ADCK3 plays a role in the biosynthesis of coenzyme Q10 (CoQ10), and inactivating mutations can cause a CoQ10 deficiency and ataxia. However, the exact functions of ADCK3 are still unclear, and small-molecule inhibitors could be useful as chemical probes to elucidate its molecular mechanisms. In this study, we applied structure-based virtual screening (VS) to discover a novel chemical series of ADCK3 inhibitors. Through extensive structural analysis of the active-site residues, we developed a pharmacophore model and applied it to a large-scale VS. Out of ∼170,000 compounds virtually screened, 800 top-ranking candidate compounds were selected and tested in both ADCK3 and p38 biochemical assays for hit validation. In total, 129 compounds were confirmed as ADCK3 inhibitors, and among them, 114 compounds are selective against p38, which was used as a counter-target. Molecular dynamics (MD) simulations were then conducted to predict the binding modes of the most potent compounds within the ADCK3 active site. Through metadynamics analysis, we successfully detected the key amino acid residues that govern intermolecular interactions. The findings provided in this study can serve as a promising starting point for drug development.

Discovery of Two Highly Selective Structurally Orthogonal Chemical Probes for Activin Receptor-like Kinases 1 and 2.

Activin receptor-like kinases 1-7 (ALK1-7) regulate a complex network of SMAD-independent as well as SMAD-dependent signaling pathways. One of the widely used inhibitors for functional investigations of these processes, in particular for bone morphogenetic protein (BMP) signaling, is LDN-193189. However, LDN-193189 has insufficient kinome-wide selectivity complicating its use in cellular target validation assays. Herein, we report the identification and comprehensive characterization of two chemically distinct highly selective inhibitors of ALK1 and ALK2, M4K2234 and MU1700, along with their negative controls. We show that both MU1700 and M4K2234 efficiently block the BMP pathway via selective in cellulo inhibition of ALK1/2 kinases and exhibit favorable in vivo profiles in mice. MU1700 is highly brain penetrant and shows remarkably high accumulation in the brain. These high-quality orthogonal chemical probes offer the selectivity required to become widely used tools for in vitro and in vivo investigation of BMP signaling.

Proteome-wide Ligand and Target Discovery by Using Strain-Enabled Cyclopropane Electrophiles.

The evolving use of covalent ligands as chemical probes and therapeutic agents could greatly benefit from an expanded array of cysteine-reactive electrophiles for efficient and versatile proteome profiling. Herein, to expand the current repertoire of cysteine-reactive electrophiles, we developed a new class of strain-enabled electrophiles based on cyclopropanes. Proteome profiling has unveiled that C163 of lactate dehydrogenase A (LDHA) and C88 of adhesion regulating molecule 1 (ADRM1) are ligandable residues to modulate the protein functions. Moreover, fragment-based ligand discovery (FBLD) has revealed that one fragment (Y-35) shows strong reactivity toward C66 of thioredoxin domain-containing protein 12 (TXD12), and its covalent binding has been demonstrated to impact its downstream signal pathways. TXD12 plays a pivotal role in enabling Y-35 to exhibit its antisurvival and antiproliferative effects. Finally, dicarbonitrile-cyclopropane has been demonstrated to be an electrophilic warhead in the development of GSTO1-involved dual covalent inhibitors, which is promising to alleviate drug resistance.

Enhanced Point-of-Care SARS-CoV-2 Detection: Integrating RT-LAMP with Microscanning.

The COVID-19 pandemic has highlighted the urgent need for rapid and accurate diagnostic methods for various infectious diseases, including SARS-CoV-2. Traditional RT-PCR methods, while highly sensitive and specific, require complex equipment and skilled personnel. In response, we developed an integrated RT-LAMP-MS assay, which combines rapid reverse transcription loop-mediated isothermal amplification (RT-LAMP) with microscanning (MS) technology for detecting SARS-CoV-2. The assay uses magnesium pyrophosphate formed during LAMP amplification as a visual marker, allowing direct observation via microscopy without the need for additional chemical indicators or probes. For the SARS-CoV-2/IC RT-LAMP-MS assay, the sample-LAMP reagent mixture was added to a microchip with SARS-CoV-2 primers and internal controls, then incubated at 62 °C for 30 min in a heat block, followed by amplification analysis using a microscanner. In clinical tests, the RT-LAMP-MS assay showed 99% sensitivity and 100% specificity, which is identical to the RT-LAMP results and comparable to the commercial AllplexTM SARS-CoV-2 assay results. Additionally, the limit of detection (LOD) was determined to be 10-1 PFU mL-1 (dynamic range: 103~10-1 PFU mL-1). The assay delivers results in 30 min, uses low-cost equipment, and demonstrates 100% reproducibility in repeated tests, making it suitable for point-of-care use in resource-limited settings.

Primed for Interactions: Investigating the Primed Substrate Channel of the Proteasome for Improved Molecular Engagement.

Protein homeostasis is a tightly conserved process that is regulated through the ubiquitin proteasome system (UPS) in a ubiquitin-independent or ubiquitin-dependent manner. Over the past two decades, the proteasome has become an excellent therapeutic target through inhibition of the catalytic core particle, inhibition of subunits responsible for recognizing and binding ubiquitinated proteins, and more recently, through targeted protein degradation using proteolysis targeting chimeras (PROTACs). The majority of the developed inhibitors of the proteasome's core particle rely on gaining selectivity through binding interactions within the unprimed substrate channel. Although this has allowed for selective inhibitors and chemical probes to be generated for the different proteasome isoforms, much remains unknown about the interactions that could be harnessed within the primed substrate channel to increase potency or selectivity. Herein, we discuss small molecules that interact with the primed substrate pocket and how their differences may give rise to altered activity. Taking advantage of additional interactions with the primed substrate pocket of the proteasome could allow for the generation of improved chemical tools for perturbing or monitoring proteasome activity.

Isotoosendanin inhibits triple-negative breast cancer metastasis by reducing mitochondrial fission and lamellipodia formation regulated by the Smad2/3-GOT2-MYH9 signaling axis.

Triple-negative breast cancer (TNBC) is incurable and prone to widespread metastasis. Therefore, identification of key targets for TNBC progression is urgently needed. Our previous study revealed that isotoosendanin (ITSN) reduced TNBC metastasis by targeting TGFβR1. ITSN is currently used as an effective chemical probe to further discover the key molecules involved in TNBC metastasis downstream of TGFβR1. The results showed that GOT2 was the gene downstream of Smad2/3 and that ITSN decreased GOT2 expression by abrogating the activation of the TGF-β-Smad2/3 signaling pathway through directly binding to TGFβR1. GOT2 was highly expressed in TNBC, and its knockdown decreased TNBC metastasis. However, GOT2 overexpression reversed the inhibitory effect of ITSN on TNBC metastasis both in vitro and in vivo. GOT2 interacted with MYH9 and hindered its binding to the E3 ubiquitin ligase STUB1, thereby reducing MYH9 ubiquitination and degradation. Moreover, GOT2 also enhanced the translocation of MYH9 to mitochondria and thus induced DRP1 phosphorylation, thereby promoting mitochondrial fission and lamellipodia formation in TNBC cells. ITSN-mediated inhibition of mitochondrial fission and lamellipodia formation was associated with reduced GOT2 expression. In conclusion, ITSN prevented MYH9-regulated mitochondrial fission and lamellipodia formation in TNBC cells by enhancing MYH9 protein degradation through a reduction in GOT2 expression, thus contributing to its inhibition of TNBC metastasis.

Ultra-efficient peroxymonosulfate utilization and trichloroethylene degradation in heterogeneous catalytic system guided by sheet-like Cu2MnO4 nanoparticles: The role of Cu(III)–O species and free radicals

Synthesizing cubic spinel Cu2MnO4 with nanosheet structure (SCMO) aimed to construct a “non-radical-mediated radical-oxidative reaction”, for increasing PMS utilization efficiency, and solving the defects of SO4•− and •OH through indirect PMS activation by electron transfer process. Compared with box-like Cu2MnO4 (11.1%, 0.0035 min−1) and ordinary Cu2MnO4 nanoparticles (21.3%, 0.0070 min−1), SCMO/PMS showed excellent trichloroethylene removal (98.8%, 0.1577 min−1). The pivotal role of Cu(III) was determined based on EPR analysis, quenching experiments, chemical probe experiments, hydrogen temperature-programmed reduction and Raman spectroscopy analysis, in-situ FTIR and Raman analyses. In brief, the interaction between PMS and SCMO could produce surface-bonded reactive complexes and the subsequent breaking of O–O bond in the sub-stable structure allowed the conversion of Cu(II) to Cu(III), which in turn facilitates the generation of •OH and SO4•−. The density functional theory (DFT) calculations provided supporting evidence for the electron donor role of SCMO and the increase of the electron acceptance capacity of PMS. SCMO/PMS system showed good resistance and degradation efficiency to complex composition and combined pollutants in actually contaminated groundwater, respectively. However, the coexistence of high concentrations of arsenic could significantly affect SCMO performance due to their adsorption on –OH groups, which still need in-depth study.

Glutathione-Based Photoaffinity Probe Identifies Caffeine as a Positive Allosteric Modulator of the Calcium-Sensing Receptor.

The calcium-sensing receptor (CaSR), abundantly expressed in the parathyroid gland and kidney, plays a central role in calcium homeostasis. In addition, CaSR exerts multimodal roles, including inflammation, muscle contraction, and bone remodeling, in other organs and tissues. The diverse functions of CaSR are mediated by many endogenous and exogenous ligands, including calcium, amino acids, glutathione, cinacalcet, and etelcalcetide, that have distinct binding sites in CaSR. However, strategies to evaluate ligand interactions with CaSR remain limited. Here, we developed a glutathione-based photoaffinity probe, DAZ-G, that analyzes ligand binding to CaSR. We showed that DAZ-G binds to the amino acid binding site in CaSR and acts as a positive allosteric modulator of CaSR. Oxidized and reduced glutathione and phenylalanine effectively compete with DAZ-G conjugation to CaSR, while calcium, cinacalcet, and etelcalcetide have cooperative effects. An unexpected finding was that caffeine effectively competes with DAZ-G's conjugation to CaSR and acts as a positive allosteric modulator of CaSR. The effective concentration of caffeine for CaSR activation (<10 μM) is easily attainable in plasma by ordinary caffeine consumption. Our report demonstrates the utility of a new chemical probe for CaSR and discovers a new protein target of caffeine, suggesting that caffeine consumption can modulate the diverse functions of CaSR.

SHAPEwarp-web: sequence-agnostic search for structurally homologous RNA regions across databases of chemical probing data.

RNA molecules perform a variety of functions in cells, many of which rely on their secondary and tertiary structures. Chemical probing methods coupled with high-throughput sequencing have significantly accelerated the mapping of RNA structures, and increasingly large datasets of transcriptome-wide RNA chemical probing data are becoming available. Analogously to what has been done for decades in the protein world, this RNA structural information can be leveraged to aid the discovery of structural similarity to a known RNA (or RNA family), which, in turn, can inform about the function of transcripts. We have previously developed SHAPEwarp, a sequence-agnostic method for the search of structurally homologous RNA segments in a database of reactivity profiles derived from chemical probing experiments. In its original implementation, however, SHAPEwarp required substantial computational resources, even for moderately sized databases, as well as significant Linux command line know-how. To address these limitations, we introduce here SHAPEwarp-web, a user-friendly web interface to rapidly query large databases of RNA chemical probing data for structurally similar RNAs. Aside from featuring a completely rewritten core, which speeds up by orders of magnitude the search inside large databases, the web server hosts several high-quality chemical probing databases across multiple species. SHAPEwarp-web is available fromhttps://shapewarp.incarnatolab.com.

Visible light-induced photocatalytic degradation of tetrabromobisphenol A on platinized tungsten oxide

In this study, we investigated the degradation of the flame retardant tetrabromobisphenol A (TBBPA) using platinized tungsten oxide (Pt/WO3), synthesized via a simple photodeposition method, under visible light. The results of degradation experiments show a significant enhancement in TBBPA degradation upon surface platinization of WO3, with the degradation rate increasing by 13.4 times compared to bare WO3. The presence of Pt on the WO3 surface stores conduction band electrons, which facilitates the two-electron reduction of oxygen and enhances the production of valence band holes (hVB+) and hydroxyl radicals (●OH). Both hVB+ and ●OH are significantly involved in the degradation of TBBPA in the visible light-irradiated Pt/WO3 system. This was verified through fluorescence spectroscopy employing coumarin as a chemical probe and oxidizing species-quenching experiments. The analysis of degradation products and their toxicity assessment demonstrate that the toxicity of TBBPA-contaminated water is significantly reduced after Pt/WO3 photocatalysis. The degradation rate of TBBPA increased with increasing Pt/WO3 dosage, reached an optimum at a Pt content of 0.5 wt%, but decreased with increasing TBBPA concentration. The decrease in degradation efficiency of Pt/WO3 was minor, both in the presence of various anions and after repeated use. This study proposes that Pt/WO3 is a viable photocatalyst for the degradation of TBBPA in water under visible light.