Illuminating G-Protein-Coupling Selectivity of GPCRs.

Heterotrimetic G proteins consist of four subfamilies (Gs, Gi/o, Gq/11, and G12/13) that mediate signaling via G-protein-coupled receptors (GPCRs), principally by receptors binding Gα C termini. G-protein-coupling profiles govern GPCR-induced cellular responses, yet receptor sequence selectivity determinants remain elusive. Here, we systematically quantified ligand-induced interactions between 148 GPCRs and all 11 unique Gα subunit C termini. For each receptor, we probed chimeric Gα subunit activation via a transforming growth factor-α (TGF-α) shedding response in HEK293 cells lacking endogenous Gq/11 and G12/13 proteins, and complemented G-protein-coupling profiles through a NanoBiT-G-protein dissociation assay. Interrogation of the dataset identified sequence-based coupling specificity features, inside and outside the transmembrane domain, which we used to develop a coupling predictor that outperforms previous methods. We used the predictor to engineer designer GPCRs selectively coupled to G12. This dataset of fine-tuned signaling mechanisms for diverse GPCRs is a valuable resource for research in GPCR signaling.

Electrochemistry-Enabled C-Heteroatom Bond Formation of Alkyl Germanes.

Because of their robustness and orthogonal reactivity features, alkyl germanes bear significant potential as functional handles for the construction of C(sp3)-rich scaffolds, especially in the context of modular synthetic approaches. However, to date, only radical-based reactivity has been accessible from these functional handles, which limits the types of possible decorations. Here, we describe the first general C(sp3)-heteroatom bond formation of alkyl germanes (-GeEt3) by leveraging electrochemistry to unlock polar reactivity. This approach allowed us to couple C(sp3)-GeEt3 with a variety of nucleophiles to construct ethers, esters, amines, amides, sulfonamides, sulfides, as well as C-P, C-F, and C-C bonds. The compatibility of the electrochemical approach with a modular synthetic strategy of a C1 motif was also showcased, involving the sequential functionalization of Cl, Bpin, and ultimately GeEt3 via electrochemistry.

A flexible repertoire of transcription factor binding sites and a diversity threshold determines enhancer activity in embryonic stem cells.

Transcriptional enhancers are critical for development and phenotype evolution and are often mutated in disease contexts; however, even in well-studied cell types, the sequence code conferring enhancer activity remains unknown. To examine the enhancer regulatory code for pluripotent stem cells, we identified genomic regions with conserved binding of multiple transcription factors in mouse and human embryonic stem cells (ESCs). Examination of these regions revealed that they contain on average 12.6 conserved transcription factor binding site (TFBS) sequences. Enriched TFBSs are a diverse repertoire of 70 different sequences representing the binding sequences of both known and novel ESC regulators. Using a diverse set of TFBSs from this repertoire was sufficient to construct short synthetic enhancers with activity comparable to native enhancers. Site-directed mutagenesis of conserved TFBSs in endogenous enhancers or TFBS deletion from synthetic sequences revealed a requirement for 10 or more different TFBSs. Furthermore, specific TFBSs, including the POU5F1:SOX2 comotif, are dispensable, despite cobinding the POU5F1 (also known as OCT4), SOX2, and NANOG master regulators of pluripotency. These findings reveal that a TFBS sequence diversity threshold overrides the need for optimized regulatory grammar and individual TFBSs that recruit specific master regulators.

Hybrid Versus Conventional Colorectal Endoscopic Submucosal Dissection: A Multicenter Randomized Controlled Trial (Short-Endoscopic Submucosal Dissection).

INTRODUCTION: Hybrid endoscopic submucosal dissection (H-ESD), which utilizes ESD knife along with snare-based resection, has been developed to overcome the technical complexity of conventional ESD (C-ESD). The aim of this study was to compare the therapeutic outcomes of H-ESD vs C-ESD for nonpedunculated colorectal lesions ≥20 mm in size. METHODS: We conducted a multicenter randomized controlled trial to compare H-ESD and C-ESD (Short-ESD trial). Patients with colorectal lesions between 20 and 50 mm in size were randomly assigned (1:1) to H-ESD or C-ESD. Primary outcome was procedure time/speed. Secondary outcomes were en bloc and complete (R0) resection rates and adverse event rates. RESULTS: A total of 89 patients (median age 63 years; 49.3% women) with the median polyp size of 30 mm underwent H-ESD (n = 40) and C-ESD (n = 49). The mean procedure time of H-ESD was significantly shorter than that of C-ESD (41.1 ± 16.3 vs 54.3 ± 28.2 minutes; P = 0.007). The en bloc and R0 resection rates trended lower in the H-ESD vs C-ESD groups (77.5% vs 87.8%; P = 0.26% and 72.5% vs 79.6%; P = 0.46) without reaching statistical significance. Adverse event rate was similar between H-ESD and C-ESD (10% vs 8.2%; P = 1.00). DISCUSSION: Both H-ESD and C-ESD were safe and effective for resection of large colorectal lesions. H-ESD was associated with a shorter procedure time. H-ESD may represent a viable alternative to C-ESD, with the main advantage being easy applicability of a snare-based technique for colorectal lesions. Future studies are needed to further define the most suitable lesions for H-ESD, as to optimize efficiency and safety without compromising resection outcomes. ClinicaTrials.gov NCT NCT05347446.

RANBP2 and USP9x regulate nuclear import of adenovirus minor coat protein IIIa.

As intracellular parasites, viruses exploit cellular proteins at every stage of infection. Adenovirus outbreaks are associated with severe acute respiratory illnesses and conjunctivitis, with no specific antiviral therapy available. An adenoviral vaccine based on human adenovirus species D (HAdV-D) is currently in use for COVID-19. Herein, we investigate host interactions of HAdV-D type 37 (HAdV-D37) protein IIIa (pIIIa), identified by affinity purification and mass spectrometry (AP-MS) screens. We demonstrate that viral pIIIa interacts with ubiquitin-specific protease 9x (USP9x) and Ran-binding protein 2 (RANBP2). USP9x binding did not invoke its signature deubiquitination function but rather deregulated pIIIa-RANBP2 interactions. In USP9x-knockout cells, viral genome replication and viral protein expression increased compared to wild type cells, supporting a host-favored mechanism for USP9x. Conversely, RANBP2-knock down reduced pIIIa transport to the nucleus, viral genome replication, and viral protein expression. Also, RANBP2-siRNA pretreated cells appeared to contain fewer mature viral particles. Transmission electron microscopy of USP9x-siRNA pretreated, virus-infected cells revealed larger than typical paracrystalline viral arrays. RANBP2-siRNA pretreatment led to the accumulation of defective assembly products at an early maturation stage. CRM1 nuclear export blockade by leptomycin B led to the retention of pIIIa within cell nuclei and hindered pIIIa-RANBP2 interactions. In-vitro binding analyses indicated that USP9x and RANBP2 bind to C-terminus of pIIIa amino acids 386-563 and 386-510, respectively. Surface plasmon resonance testing showed direct pIIIa interaction with recombinant USP9x and RANBP2 proteins, without competition. Using an alternative and genetically disparate adenovirus type (HAdV-C5), we show that the demonstrated pIIIa interaction is also important for a severe respiratory pathogen. Together, our results suggest that pIIIa hijacks RANBP2 for nuclear import and subsequent virion assembly. USP9x counteracts this interaction and negatively regulates virion synthesis. This analysis extends the scope of known adenovirus-host interactions and has potential implications in designing new antiviral therapeutics.

Facile Layer Diffusion Technique for Synthesis of Terbium-Based Metal Organic Framework for Fluorometric Sensing of Hydroquinone.

A photoluminescent terbium (III)-based Metal Organic Framework (MOF) was synthesized at room temperature by layer diffusion method utilizing mixed carboxylate linkers (4,4'-oxybis(benzoic acid) and benzene-1,3,5 tricarboxylic acid). Synthesized MOF has crystalline nature and rod-shaped morphology and is thermally stable up to 455 °C. The fluorescence emission spectra and theoretical results revealed that carboxylate linkers functioned as sensitizers for Tb(III) photoluminescence which resulted in four distinct emission peaks at 495, 547, 584, and 621 nm corresponding to the transitions 5D4 → 7F6, 5D4 → 7F5, 5D4 → 7F4, and 5D4 → 7F3. Using synthesized MOF as fluorescent probe, hydroquinone was detected in aqueous medium with a detection limit of 0.048 µM, remarkable recovery (95.6-101.1%), and relative standard deviation less than 2.25%. The quenching phenomenon may be ascribed to electron transfer from synthesized probe to oxidized hydroquinone via carboxylic groups on the surface of MOF, which is further supported by photo-induced electron transfer mechanism. This study introduces a cheaper, faster, and more accurate method for hydroquinone detection.

Pure and Antimony-doped Tin Oxide Nanoparticles for Fluorescence Sensing and Dye Degradation Applications.

Luminescent antimony doped tin oxide nanoparticles have drawn tremendous attention from researchers due to its low cost, chemical inertness and stability. Herein, a quick, facile and economic hydrothermal/solvothermal method was utilized for the preparation of antimony doped (1%, 3%, 5%, 7% and 10%) tin oxide nanoparticles. The antimony doping in a reasonable range can change the properties of SnO2. As such, a lattice distortion increases with increase in doping, which is evidenced through crystallographic studies. It was found that the highest photocatalytic degradation efficiency of malachite green (MG) dye of about 80.86% was achieved with 10% Sb-doped SnO2 in aqueous media due to small particle size. Moreover, 10% Sb-doped SnO2 also showed the highest fluorescence quenching efficiency of about 27% for Cd2+ of concentration 0.11 µg/ml in the drinking water. The limit of detection (LOD) comes out as 0.0152 µg/ml. This sample selectively detected the cadmium ion even in the presence of other heavy metal ions. Notably, 10% Sb-doped SnO2 could appeared as a promising sensor for fast analysis of Cd2+ ions in real samples.

PRECOGx: exploring GPCR signaling mechanisms with deep protein representations.

In this study we show that protein language models can encode structural and functional information of GPCR sequences that can be used to predict their signaling and functional repertoire. We used the ESM1b protein embeddings as features and the binding information known from publicly available studies to develop PRECOGx, a machine learning predictor to explore GPCR interactions with G protein and ß-arrestin, which we made available through a new webserver (https://precogx.bioinfolab.sns.it/). PRECOGx outperformed its predecessor (e.g. PRECOG) in predicting GPCR-transducer couplings, being also able to consider all GPCR classes. The webserver also provides new functionalities, such as the projection of input sequences on a low-dimensional space describing essential features of the human GPCRome, which is used as a reference to track GPCR variants. Additionally, it allows inspection of the sequence and structural determinants responsible for coupling via the analysis of the most important attention maps used by the models as well as through predicted intramolecular contacts. We demonstrate applications of PRECOGx by predicting the impact of disease variants (ClinVar) and alternative splice forms from healthy tissues (GTEX) of human GPCRs, revealing the power to dissect system biasing mechanisms in both health and disease.

Triply Selective & Sequential Diversification at Csp 3: Expansion of Alkyl Germane Reactivity for C-C & C-Heteroatom Bond Formation.

We report the triply selective and sequential diversification of a single Csp 3 carbon carrying Cl, Bpin and GeEt3 for the modular and programmable construction of sp3-rich molecules. Various functionalizations of Csp 3-Cl and Csp 3-BPin (e.g. alkylation, arylation, homologation, amination, hydroxylation) were tolerated by the Csp 3-GeEt3 group. Moreover, the methodological repertoire of alkyl germane functionalization was significantly expanded beyond the hitherto known Giese addition and arylation to alkynylation, alkenylation, cyanation, halogenation, azidation, C-S bond formation as well as the first demonstration of stereo-selective functionalization of a Csp 3-[Ge] bond.

Construction of heterocycle-fused tetrahydrocarbazoles through a formal [3 + 3]-annulation of 2-indolylmethanols with para-quinone methides.

A metal-free approach for the synthesis of tetrahydroindolo[2,3-b]carbazoles has been developed through an acid-mediated one-pot [3 + 3]-annulation of 2-indolylmethanols and 3-indolyl-substituted para-quinone methides. This operationally simple protocol allowed us to prepare many unsymmetrical tetrahydroindolo[2,3-b]carbazoles in good to excellent yields with a broad substrate scope. This concept was also elaborated to the synthesis of tetrahydrothieno[2,3-b]carbazoles and tetrahydrothieno[3,2-b]carbazoles.

Acid-catalysed intramolecular Friedel-Crafts annulation of hetero-atom-functionalized para-quinone methides: access to O-, S- and N-based heterocycles.

We describe here an acid-mediated one-pot approach to access substituted xanthene and thioxanthane derivatives from ortho-heteroaryl phenyl-substituted para-quinone methides via 1,6 intramolecular arylation. The scope of this work was further elaborated to the synthesis of 10H-indolo[1,2-a]indole-based heterocyclic systems using indole based para-quinone methides.

Efficient Turn-On Zr Based Metal Organic Framework Fluorescent Sensor for Ultrafast Detection of Danofloxacin in Milk Samples.

Metal organic framework, UiO-67 was synthesized by coordinating Zr(IV) with 4,4'-biphenyldicarboxylic acid (BPDC) ligand. Morphology and crystallinity of MOF was confirmed with FE-SEM and PXRD procedure. Danofloxacin (DANO), a veterinary fluoroquinolone antibiotic, was detected in milk by employing UiO-67 as "turn-on" fluorescent sensor. Original photoluminescent (PL) efficiency of UiO-67 sensor was enhanced on its electronic interaction with DANO molecule. Significant PL efficiency enhancement, lower detection limit 0.49 ng/mL (1.37 nM), swift detection (time < 1 min), and excellent linear correlation (R2 = 0.9988) indicated extraordinary sensitivity of developed UiO-67 sensor for DANO. Selectivity and performance of sensor was unaltered in presence of interfering species and detection results were obtained under permissible variation limits. Method applied successfully for ultra-trace detection of DANO residues in milk samples.

Lyophilized mixed micelles of exemestane: A novel paradigm to improve its absorption and anticancer activity.

The objective of the present investigation was to prepare and optimize lyophilized mixed micelles (Lyp-EXE-MMs) of exemestane (EXE) with improved solubility, bioavailability, in vivo anticancer activity, and physical stability, by using various cryoprotectants. The prepared lyophilized mixed micelles were characterized by various techniques, including dynamic light scattering, zeta potential, powdered X-ray diffraction, differential scanning calorimetry (DSC), nuclear magnetic resonance (1 H NMR), transmission electron microscopy (TEM), and so on. Thereafter, the lyophilized micelles were evaluated for ex vivo permeation, in vitro drug release and gene/protein expression (RT-PCR and Western blot analysis) in MCF-7 breast cancer cells. The developed formulation was also investigated for its in vivo anticancer study in BALB/c mice with induced breast cancer. The use of trehalose (10% w/w) was proven to be a suitable cryoprotectant for these micelles. Lyp-EXE-MMs were spherical, with a particle size of 42.9 ± 3.8 nm and a polydispersity index of 0.307 ± 0.122. Furthermore, % drug loading and % entrapment efficiency were found to be 5.8 ± 1.4 and 89.1 ± 1.1, respectively. Lyp-EXE-MMs showed sustained release behavior as compared to EXE-suspensions in SGF/SIF (pH 1.2 and 6.8) and phosphate buffer saline (pH 7.4). The micelles induced apoptosis through the regulation of BAX, BCL2, Caspase-3, p53, and CYP19A1 in MCF-7 cells, which was correlated to enhanced ex vivo drug permeation. Animals receiving EXE micelle formulations showed reduced tumor volume and improved survivability and pharmacokinetic parameters as compared to pure EXE. Lyp-EXE-MMs were found to withstand simulated harsh conditions of SGF/SIF during stability studies. The fabricated EXE micellar preparations hold a promising approach for breast cancer treatment.

Construction of Oxygen- and Nitrogen-based Heterocycles from p-Quinone Methides.

In the last few years, there has been an explosive growth in the area of para-quinone methide (p-QM) chemistry. This boom is actually due to the unique reactivity pattern of p-QMs, and also their remarkable synthetic applications. In fact, p-QMs serve as synthons for unsymmetrical diaryl- and triarylmethanes, and also for the construction of diverse range of carbocycles and heterocycles. In the last few years, a wide range of structurally complex heterocyclic frameworks could be accessed through the synthetic transformations of structurally modified stable p-QMs. Therefore, the main focus of this review article is to cover the recent advancements in the transition-metal, Lewis acid and base-catalyzed/mediated synthetic transformations of the stable p-quinone methides (p-QMs) to oxygen- and nitrogen-containing heterocycles.

Recent advances in the organocatalytic applications of cyclopropene- and cyclopropenium-based small molecules.

The development of novel small molecule-based catalysts for organic transformations has increased noticeably in the last two decades. A very recent addition to this particular research area is cyclopropene- and cyclopropenium-based catalysts. At one point in time, particularly in the mid-20th century, much attention was focused on the structural aspects and physical properties of cyclopropene-based compounds. However, a paradigm shift was observed in the late 20th century, and the focus shifted to the synthetic utility of these compounds. In fact, a wide range of cyclopropene derivatives have been found serving as valuable synthons for the construction of carbocycles, heterocycles and other useful organic compounds. In the last few years, the catalytic applications of cyclopropene/cyclopropenium-based compounds have been uncovered and many synthetic protocols have been developed using cyclopropene-based compounds as organocatalysts. Therefore, the main objective of this review is to highlight recent developments in the catalytic applications of cyclopropene-based small molecules in different areas of organocatalysis such as phase-transfer catalysis (PTC), Brønsted base catalysis, hydrogen-bond donor catalysis, nucleophilic carbene catalysis, and electrophotocatalysis developed within the past two decades.

PRECOG: PREdicting COupling probabilities of G-protein coupled receptors.

G-protein coupled receptors (GPCRs) control multiple physiological states by transducing a multitude of extracellular stimuli into the cell via coupling to intra-cellular heterotrimeric G-proteins. Deciphering which G-proteins couple to each of the hundreds of GPCRs present in a typical eukaryotic organism is therefore critical to understand signalling. Here, we present PRECOG (precog.russelllab.org): a web-server for predicting GPCR coupling, which allows users to: (i) predict coupling probabilities for GPCRs to individual G-proteins instead of subfamilies; (ii) visually inspect the protein sequence and structural features that are responsible for a particular coupling; (iii) suggest mutations to rationally design artificial GPCRs with new coupling properties based on predetermined coupling features.

Pollution evaluation, human health effect and tracing source of trace elements on road dust of Dhanbad, a highly polluted industrial coal belt of India.

Dust samples were collected from roads of five distinct types of land use zones (National Highway, residential areas, sensitive areas, mining areas, and busy traffic areas) of Dhanbad to determine the pollution characteristics, health risk, and identifying the source of trace elements. The dust samples were segregated into ≤ 60 µm and trace elements like Cd, Cr, Cu, Fe, Mn, Ni, Pb, and Zn were analysed. Concentrations of Cd, Cr, Cu, Fe, and Mn were observed highest in the mining areas, whereas Ni, Pb, and Zn presented higher concentration values at National Highway and busy traffic zones. Cd showed highest geo-accumulation index (Igeo), contamination factor (Cf), and ecological risk (ER) among all the trace elements. The health risk assessment model was performed to assess the health effects of carcinogenic and non-carcinogenic pollutants caused due to multi-elemental exposure on adults and children. The significantly higher HQ (Hazard Quotient) and HI (Hazard Index) values posed by Cr, Fe, and Mn indicated potential non-carcinogenic risks to the people of Dhanbad. Similarly, values of CR (Cancer Risk) for Cd, Cr and Ni were within the range of 10-6-10-4, which indicated to cause carcinogenic risk to the population by the exposure of road dust. Principal Component Analysis (PCA) and Pearson correlation showed that coal mining activities in Jharia coalfield, coal-based industries like coke-oven plants, coal washeries and heavy vehicular load in the roads of Dhanbad were the major causes of emission of these trace elements.

pH-Independent Dissolution and Enhanced Oral Bioavailability of Aripiprazole-Loaded Solid Self-microemulsifying Drug Delivery System.

The present study pursued the systematic development of a stable solid self-emulsifying drug delivery system (SMEDDS) of an atypical antipsychotic drug, aripiprazole (APZ), which exhibits poor aqueous solubility and undergoes extensive p-glycoprotein efflux and hepatic metabolism. Liquid SMEDDS excipients were selected on the basis of solubility studies, and the optimum ratio of surfactant/co-surfactant was determined using pseudo-ternary phase diagrams. The prepared formulations were subjected to in vitro characterization studies to facilitate the selection of optimum liquid SMEDD formulation containing 30% Labrafil® M 1944 CS, 46.7% Cremophor® EL and 23.3% PEG 400 which were further subjected to solidification using maltodextrin as a hydrophilic carrier. The optimized solid SMEDDS was extensively evaluated for stability under accelerated conditions, dissolution at various pH and pharmacokinetic profile. Solid-state attributes of the optimized solid SMEDDS indicated a marked reduction in crystallinity of APZ and uniform adsorption of liquid SMEDDS. Stability study of the solid SMEDDS demonstrated that the developed formulation retained its stability during the accelerated storage conditions. Both the optimized liquid and solid SMEDDS exhibited enhanced dissolution rate which was furthermore independent of the pH of the dissolution medium. Oral bioavailability studies in Sprague-Dawley rats confirmed quicker and greater extent of absorption with solid SMEDDS as evident from the significant reduction in Tmax in case of solid SMEDDS (0.83 ± 0.12 h) as compared with commercial tablet (3.33 ± 0.94 h). The results of the present investigation indicated the development of a stable solid SMEDDS formulation of APZ with enhanced dissolution and absorption attributes.

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes.

Transcriptional enhancers are critical for maintaining cell-type-specific gene expression and driving cell fate changes during development. Highly transcribed genes are often associated with a cluster of individual enhancers such as those found in locus control regions. Recently, these have been termed stretch enhancers or super-enhancers, which have been predicted to regulate critical cell identity genes. We employed a CRISPR/Cas9-mediated deletion approach to study the function of several enhancer clusters (ECs) and isolated enhancers in mouse embryonic stem (ES) cells. Our results reveal that the effect of deleting ECs, also classified as ES cell super-enhancers, is highly variable, resulting in target gene expression reductions ranging from 12% to as much as 92%. Partial deletions of these ECs which removed only one enhancer or a subcluster of enhancers revealed partially redundant control of the regulated gene by multiple enhancers within the larger cluster. Many highly transcribed genes in ES cells are not associated with a super-enhancer; furthermore, super-enhancer predictions ignore 81% of the potentially active regulatory elements predicted by cobinding of five or more pluripotency-associated transcription factors. Deletion of these additional enhancer regions revealed their robust regulatory role in gene transcription. In addition, select super-enhancers and enhancers were identified that regulated clusters of paralogous genes. We conclude that, whereas robust transcriptional output can be achieved by an isolated enhancer, clusters of enhancers acting on a common target gene act in a partially redundant manner to fine tune transcriptional output of their target genes.

Variational infinite heterogeneous mixture model for semi-supervised clustering of heart enhancers.

MOTIVATION: Mammalian genomes can contain thousands of enhancers but only a subset are actively driving gene expression in a given cellular context. Integrated genomic datasets can be harnessed to predict active enhancers. One challenge in integration of large genomic datasets is the increasing heterogeneity: continuous, binary and discrete features may all be relevant. Coupled with the typically small numbers of training examples, semi-supervised approaches for heterogeneous data are needed; however, current enhancer prediction methods are not designed to handle heterogeneous data in the semi-supervised paradigm. RESULTS: We implemented a Dirichlet Process Heterogeneous Mixture model that infers Gaussian, Bernoulli and Poisson distributions over features. We derived a novel variational inference algorithm to handle semi-supervised learning tasks where certain observations are forced to cluster together. We applied this model to enhancer candidates in mouse heart tissues based on heterogeneous features. We constrained a small number of known active enhancers to appear in the same cluster, and 47 additional regions clustered with them. Many of these are located near heart-specific genes. The model also predicted 1176 active promoters, suggesting that it can discover new enhancers and promoters. AVAILABILITY AND IMPLEMENTATION: We created the 'dphmix' Python package: https://pypi.org/project/dphmix/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.