Protein Binding Research Articles

CCT6A regulates cervical cancer cell glycolysis and proliferation under hypoxic conditions via the TCAB1/TERT.

Cervical cancer is one of the most common female malignancies worldwide, a hypoxic microenvironment usually causes enhanced viability and glycolytic capacity of cervical cancer cells. The aim of this study was to investigate the association between chaperonin containing t-complex polypeptide 1 subunit 6A (CCT6A) and cell proliferation as well as hypoxic glycolysis. Bioinformatics analysis was conducted to explore the association between cervical cancer and its partner protein under hypoxic conditions, namely CCT6A. Subsequently, the expression of CCT6A was silenced, and the effects of CCT6A silencing on cervical cancer cell proliferation, cell cycle, glycolysis-related proteins, and telomerase activity were examined. Bioinformatics analysis was performed to investigate the expression of CCT6A in cervical cancer under hypoxic conditions. The expression of CCT6A was silenced in cervical cancer cells, Hela and Siha, to study its effects on cell proliferation and hypoxic glycolysis. The localization of telomerase activity-related proteins, TCAB1 and TERT, was detected using immunofluorescence, and their interaction was assessed using immunoprecipitation. A cellular hypoxia model was established, and the products of the glycolysis reaction were detected. A nude mouse tumor model was constructed, and the changes in glycolysis-related proteins in tumor tissues were examined using western blot, while Ki67 expression in tumor tissues was evaluated by immunohistochemistry. Telomerase activity was found to be enhanced in CCT6A-silenced cervical cancer cells, along with an increase in telomerase cajal body protein 1 (TCAB1) and telomerase reverse tranase (TERT) protein binding associated with telomerase activity. Additionally, the proportion of cells in the Gap 2/mitosis (G2/M) stage and the 5-ethynyl-2'-deoxyuridine (EdU) positivity rate were decreased in CCT6A-silenced cells, indicating a reduction in cell proliferation. The expression of cell cycle-related proteins, including Cyclin E, CCNA2 and cyclin-dependent kinase 2 (CDK2), was suppressed. Furthermore, under a hypoxic environment, silencing CCT6A led to a significant reduction in cell viability and downregulation of glycolysis-related proteins, such as lactate dehydrogenase A (LDHA) and hexokinase 2 (HK2). Mechanistically, silencing CCT6A may reduce telomerase activity by inhibiting the TCAB1/TERT interaction. Additionally, TERT was found to activate the promoter region of the HK2 gene, and inhibition of TERT activity reduced the transcriptional level of HK2. The study primarily explored the involvement of CCT6A in cervical cancer, yet it did not account for the myriad of other elements potentially influencing cell proliferation and glycolysis. It's essential to recognize that cervical cancer's etiology is multifaceted, shaped by an array of genetic variations, environmental influences, and protein interactions. Silencing CCT6A could effectively attenuate the upregulation of cell proliferation and glycolytic function mediated by TCAB1/TERT in cervical cancer cells.

Improved analysis of grape seed extract by liquid chromatography–high resolution mass spectrometry (LC-HRMS) reveals that proanthocyanidin-protein interaction mechanisms in cream depend on degree of polymerization

This study aimed to comprehensively characterize chemical profiles of proanthocyanidins (PACs) from grape seed extract (GSE), examine their interactions with proteins in a cream system, and define the mechanisms mediating PAC-protein interactions. GSE PACs were fractionated and characterized by thiolysis followed by liquid chromatography–high resolution mass spectrometry (LC-HRMS) analysis. New PACs with a degree of polymerization (DP) up to 16 were identified by improved HRMS data processing methods. In the model cream system, high-DP PACs exhibited greater precipitation capacity and protein binding than low-DP PACs. Low-DP PACs primarily engaged in hydrogen bonding, while high-DP PACs predominantly utilized multiple hydrophobic interaction sites to form cream protein aggregates. Furthermore, particle size and viscosity measurement of cream revealed a progressively DP-dependent increase in aggregated fat globules and cream viscosity. These findings enhanced our understanding of PACs’ structural intricacies and highlighted their functional role as PAC-rich natural ingredients in creating structured cream systems.

Effect of Photoperiod Duration on Flower Bud Differentiation and Related Gene Expression in Bougainvillea glabra 'Sao Paulo'.

Environmental conditions, such as photoperiod, affect the developmental response of plants; thus, plants have evolved molecular mechanisms to adapt to changes in photoperiod. In Bougainvillea spp., the mechanism of flower formation underlying flowering control techniques remains poorly understood, and the physiological changes that occur during flower bud formation and the expression of related genes are not yet fully understood. In this study, we induced flowering of potted Bougainvillea glabra 'Sao Paulo' plants under light-control treatments and analyzed their effects on flowering time, number of flower buds, flowering quality, as well as quality of flower formation, which was analyzed using transcriptome sequencing. Light-control treatment effectively induced the rapid formation of flower buds and early flowering in B. glabra 'Sao Paulo', with the time of flower bud formation being 119 days earlier and the flowering period extended six days longer than those of the control plants. The light-control treatment caused the bracts to become smaller and lighter in color, while the number of flowers increased, and the neatness of flowering improved. Transcriptome sequencing of the apical buds identified 1235 differentially expressed genes (DEGs) related to the pathways of environmental adaptation, biosynthesis of other secondary metabolites, glycan biosynthesis and metabolism, and energy metabolism. DEGs related to gibberellin metabolism were analyzed, wherein five DEGs were identified between the control and treatment groups. Transcriptomic analysis revealed that the gibberellin regulatory pathway is linked to flowering. Specifically, GA and GID1 levels increased during this process, enhancing DELLA protein degradation. However, decreasing this protein's binding to CO did not halt FT upregulation, thereby advancing the flowering of B. glabra 'Sao Paulo'. The findings of our study have implications for future research on photoperiod and its role in controlling flowering timing of Bougainvillea spp.

Phospho-Chitooligosaccharides below 1 kDa Inhibit HIV-1 Entry In Vitro.

Despite present antiviral agents that can effectively work against HIV-1 replication, side effects and drug resistance have pushed researchers toward novel approaches. In this context, there is a continued focus on discovering new and more effective antiviral compounds, particularly those that have a natural origin. Polysaccharides are known for their numerous bioactivities, including inhibiting HIV-1 infection and replication. In the present study, phosphorylated chitosan oligosaccharides (PCOSs) were evaluated for their anti-HIV-1 potential in vitro. Treatment with PCOSs effectively protected cells from HIV-1-induced lytic effects and suppressed the production of HIV-1 p24 protein. In addition, results show that PCOSs lost their protective effect upon post-infection treatment. According to the results of ELISA, PCOSs notably disrupted the binding of HIV-1 gp120 protein to T cell surface receptor CD4, which is required for HIV-1 entry. Overall, the results point out that PCOSs might prevent HIV-1 infection at the entry stage, possibly via blocking the viral entry through disruption of virus-cell fusion. Nevertheless, the current results only present the potential of PCOSs, and further studies to elucidate its action mechanism in detail are needed to employ phosphorylation of COSs as a method to develop novel antiviral agents.

Interactions of proteins with heparan sulfate.

Heparan sulfate (HS) is a glycosaminoglycan, polysaccharides that are considered to have arisen in the last common unicellular ancestor of multicellular animals. In this light, the large interactome of HS and its myriad functions in relation to the regulation of cell communication are not surprising. The binding of proteins to HS determines their localisation and diffusion, essential for embryonic development and homeostasis. Following the biosynthesis of the initial heparosan polymer, the subsequent modifications comprise an established canonical pathway and a minor pathway. The more frequent former starts with N-deacetylation and N-sulfation of GlcNAc residues, the latter with C-5 epimerisation of a GlcA residue adjacent to a GlcNAc. The binding of proteins to HS is driven by ionic interactions. The multivalent effect arising from the many individual ionic bonds between a single protein and a polysaccharide chain results in a far stronger interaction than would be expected from an ion-exchange process. In many instances, upon binding, both parties undergo substantial conformational change, the resulting hydrogen and van der Waal bonds contributing significant free energy to the binding reaction. Nevertheless, ionic bonds dominate the protein-polysaccharide interaction kinetically. Together with the multivalent effect, this provides an explanation for the observed trapping of HS-binding proteins in extracellular matrix. Importantly, individual ionic bonds have been observed to be dynamic; breaking and reforming, while the protein remains bound to the polysaccharide. These considerations lead to a model for 1D diffusion of proteins in extracellular matrix on HS, involving mechanisms such as sliding, chain switching and rolling.

Effect of dual modifications with ultrasonication and succinylation on Cicer arietinum protein-iron complexes: Characterization, digestibility, in-vitro cellular mineral uptake and preparation of fortified smoothie

The research aimed to evaluate the effect of ultrasonication and succinylation on the functional, iron binding, physiochemical, and cellular mineral uptake efficacy of chickpea protein concentrate. Succinylation resulted in significant improvements in the water-holding capacity (WHC) (25.47 %), oil-holding capacity (OHC) (31.38 %), and solubility (5.80 %) of the chickpea protein-iron complex. Mineral bioavailability significantly increased by 4.41 %, and there was a significant increase in cellular mineral uptake (64.64 %), retention (36.68 %), and transport (27.96 %). The ferritin content of the succinylated chickpea protein-iron complex showed a substantial increase of 66.31%. Furthermore, the dual modification approach combining ultrasonication and succinylation reduced the particle size of the protein-iron complex with a substantial reduction of 83.25 %. It also resulted in a significant enhancement of 51.5 % in the SH (sulfhydryl) content and 48.92 % in the surface hydrophobicity. Mineral bioavailability and cellular mineral uptake, retention, and transport were further enhanced through dual modification. In terms of application, the addition of single and dual-modified chickpea protein-iron complex to a fruit-based smoothie demonstrated positive acceptance in sensory attributes. Overall, the combined approach of succinylation and ultrasonication to the chickpea protein-iron complex shows a promising strategy for enhancing the physiochemical and techno-functional characteristics, cellular mineral uptake, and the development of vegan food products.

Gold(Ⅰ) organometallics with alkynyl and N-heterocyclic carbene ligands and their medicinal and computational chemistry evaluation as prospective anticancer drugs

Gold(Ⅰ) organometallics of the type alkynylgold(Ⅰ)(NHC) (where NHC = N-heterocyclic carbene) 5a – 5f and 6a/b were prepared and evaluated as prospective anticancer agents by computational and medicinal chemistry methods. DFT calculations showed similar stability for the series, with differing dipole moments, depending on the substituents on the alkynyl and the NHC ligands. Studies in cancer cell lines indicated in general that the complexes with the largest dipole moments exhibited the highest antiproliferative activity in comparison with structurally closely related complexes. Thus, complexes 5f, (with 4-fluoroethynylbenzene as alkynyl precursor), and 6b, (with mestranol as alkynyl precursor) containing the same methoxy‑substituted NHC ligand showed in general the strongest biological activity. Protein binding studies confirmed a high affinity to albumin (around 90 %) and cellular uptake studies indicated an increased uptake of the most active complex 5f.

Pharmacokinetic/pharmacodynamic evaluation of gamithromycin against rabbit pasteurellosis

BackgroundGamithromycin is an effective therapy for bovine and swine respiratory diseases but not utilized for rabbits. Given its potent activity against respiratory pathogens, we sought to determine the pharmacokinetic profiles, antimicrobial activity and target pharmacokinetic/pharmacodynamic (PK/PD) exposures associated with therapeutic effect of gamithromycin against Pasteurella multocida in rabbits.ResultsGamithromycin showed favorable PK properties in rabbits, including high subcutaneous bioavailability (86.7 ± 10.7%) and low plasma protein binding (18.5–31.9%). PK analysis identified a mean plasma peak concentration (Cmax) of 1.64 ± 0.86 mg/L and terminal half-life (T1/2) of 31.5 ± 5.74 h after subcutaneous injection. For P. multocida, short post-antibiotic effects (PAE) (1.1–5.3 h) and post-antibiotic sub-inhibitory concentration effects (PA-SME) (6.6–9.1 h) were observed after exposure to gamithromycin at 1 to 4× minimal inhibitory concentration (MIC). Gamithromycin demonstrated concentration-dependent bactericidal activity and the PK/PD index area under the concentration-time curve over 24 h (AUC24h)/MIC correlated well with efficacy (R2 > 0.99). The plasma AUC24h/MIC ratios of gamithromycin associated with the bacteriostatic, bactericidal and bacterial eradication against P. multocida were 15.4, 24.9 and 27.8 h in rabbits, respectively.ConclusionsSubcutaneous administration of 6 mg/kg gamithromycin reached therapeutic concentrations in rabbit plasma against P. multocida. The PK/PD ratios determined herein in combination with ex vivo activity and favorable rabbit PK indicate that gamithromycin may be used for the treatment of rabbit pasteurellosis.

High expression of CASP1 induces atherosclerosis.

Atherosclerosis is a chronic, progressive vascular disease. The relationship between CASP1 gene expression and atherosclerosis remains unclear. The atherosclerosis dataset GSE132651 and GSE202625 profiles were downloaded from gene expression omnibus. Differentially expressed genes (DEGs) were screened. The construction and analysis of protein-protein interaction network, functional enrichment analysis, gene set enrichment analysis, and Comparative Toxicogenomics Database analysis were performed. Gene expression heatmap was drawn. TargetScan was used to screen miRNAs that regulate central DEG. 47 DEGs were identified. According to gene ontology analysis, they were mainly enriched in the regulation of stimulus response, response to organic matter, extracellular region, extracellular region, and the same protein binding. Kyoto Encyclopedia of Gene and Genome analysis results showed that the target cells were mainly enriched in the PI3K-Akt signaling pathway, Ras signaling pathway, and PPAR signaling pathway. In the enrichment project of Metascape, vascular development, regulation of body fluid levels, and positive regulation of cell motility can be seen in the gene ontology enrichment project. Eleven core genes (CASP1, NLRP3, MRC1, IRS1, PPARG, APOE, IL13, FGF2, CCR2, ICAM1, HIF1A) were obtained. IRS1, PPARG, APOE, FGF2, CCR2, and HIF1A genes are identified as core genes. Gene expression heatmap showed that CASP1 was highly expressed in atherosclerosis samples and low expressed in normal samples. NLRP3, MRC1, IRS1, PPARG, APOE, IL13, FGF2, CCR2, ICAM1, HIF1A were low expressed in atherosclerosis samples. CTD analysis showed that 5 genes (CASP1, NLRP3, CCR2, ICAM1, HIF1A) were found to be associated with pneumonia, inflammation, cardiac enlargement, and tumor invasiveness. CASP1 gene is highly expressed in atherosclerosis. The higher the CASP1 gene, the worse the prognosis.

Multiphosphorylation-Dependent Recognition of Anti-pS2 Antibodies against RNA Polymerase II C-Terminal Domain Revealed by Chemical Synthesis.

Phosphorylation is a major constituent of the CTD code, which describes the set of post-translational modifications on 52 repeats of a YSPTSPS consensus heptad that orchestrates the binding of regulatory proteins to the C-terminal domain (CTD) of RNA polymerase II. Phospho-specific antibodies are used to detect CTD phosphorylation patterns. However, their recognition repertoire is underexplored due to limitations in the synthesis of long multiphosphorylated peptides. Herein, we describe the development of a synthesis strategy that provides access to multiphosphorylated CTD peptides in high purity without HPLC purification for immobilization onto microtiter plates. Native chemical ligation was used to assemble 12 heptad repeats in various phosphoforms. The synthesis of >60 CTD peptides, 48-90 amino acids in length and containing up to 6 phosphosites, enabled a detailed and rapid analysis of the binding characteristics of different anti-pSer2 antibodies. The three antibodies tested showed positional selectivity with marked differences in the affinity of the antibodies for pSer2-containing peptides. Furthermore, the length of the phosphopeptides allowed a systematic analysis of the multivalent chelate-type interactions. The absence of multivalency-induced binding enhancements is probably due to the high flexibility of the CTD scaffold. The effect of clustered phosphorylation proved to be more complex. Recognition of pSer2 by anti-pSer2-antibodies can be prevented and, perhaps surprisingly, enhanced by the phosphorylation of "bystander" amino acids in the vicinity. The results have relevance for functional analysis of the CTD in cell biological experiments.

Mechanism insights into hydrothermal-activated tannic acid (TA) for simultaneously sewage sludge deep dewatering and antibiotics removal

Tannic acid (TA) aided hydrothermal treatment (HT) can decrease effective HT temperatures for sludge deep dewatering by chelator protein, but faces notable and economic challenges including the failure to remove antibiotics and the limited protein binding capacity. Herein, hydrothermally activated TA (in situ TA + HT) was conducted to simultaneously improve sludge dewaterability and antibiotic (tetracycline (TC), oxytetracycline (OTC), norfloxacin (NOR), ofloxacin (OFL)) removal. Compared to traditional HT and HT + TA treatment, the in-situ TA + HT process could further strengthen the TA-aided HT efficacy in enhancing sludge and reducing the protein content in the filtrate simultaneously; in which the optimal HT temperature for the dewatering of the sludge was reduced from 180 °C to 140 °C. Furthermore, the total removal efficiency of target antibiotics was achieved at more than 71.0–94.7% for TC and OTC, and 72.0–84.8% for NOR and OFL. The highly reactive species (·OH) generation and the electron transfer efficiency from the hydrothermal-activated TA process were responsible for the elimination of antibiotics and promoted the hydrolyzation and mineralization of HMW protein in sludge during the HT process. Meanwhile, the degradation of HMW proteins and the destruction of the secondary structure of these proteins resulted in improved hydrophobicity and dewaterability of sludge. Hydrothermally activated TA induces covalent binding with the protein. As a result, hydrothermal-activated TA could promote the removal of antibiotics and proteinaceous compounds from the sludge samples, improving the hydrophobicity of sludge and releasing bound water from the sludge flocs during HT. Finally, the cost of hydrothermal-activated TA was 66.51% lower than that of thermal drying treatment. This study not only proposed an effective method to improve traditional HT for sludge thermal dry-free treatment, but also provided new information on the catalysis roles of polyphenols in the hydrothermal conversion of sludge.

Dual-responsive nanocarriers for efficient cytosolic protein delivery and CRISPR-Cas9 gene therapy of inflammatory skin disorders.

Developing protein drugs that can target intracellular sites remains a challenge due to their inadequate membrane permeability. Efficient carriers for cytosolic protein delivery are required for protein-based drugs, cancer vaccines, and CRISPR-Cas9 gene therapies. Here, we report a screening process to identify highly efficient materials for cytosolic protein delivery from a library of dual-functionalized polymers bearing both boronate and lipoic acid moieties. Both ligands were found to be crucial for protein binding, endosomal escape, and intracellular protein release. Polymers with higher grafting ratios exhibit remarkable efficacies in cytosolic protein delivery including enzymes, monoclonal antibodies, and Cas9 ribonucleoprotein while preserving their activity. Optimal polymer successfully delivered Cas9 ribonucleoprotein targeting NLRP3 to disrupt NLRP3 inflammasomes in vivo and ameliorate inflammation in a mouse model of psoriasis. Our study presents a promising option for the discovery of highly efficient materials tailored for cytosolic delivery of specific proteins and complexes such as Cas9 ribonucleoprotein.

Unveiling Nano-Resveratrol induced by oil-in-water binding to human haemoglobin in the presence of holo-transferrin as binary and ternary systems: Spectroscopy, molecular dynamic and hemoglobin oxygenation approaches

Resveratrol (RES) is a member of polyphenols compounds capable of performing antioxidant activities and exhibiting anti-inflammatory and anticancer properties. This study attempted to increase the bioavailability and solubility of RES through an O/W nano-emulsion process. The performance of synthesized Nano-RES with hemoglobin (Hb) and human holo transferrin (HTF) as the binary and ternary systems was investigated by the means of various spectroscopic techniques and cancer cell experiments. Fluorescence quenching measurement configured the static quenching mechanism of Hb-Nano-RES and (Hb-HTF) interaction with Nano-RES complexes. According to the results, the measurements for binding constant of Hb-Nano-RES and (Hb-HTF) Nano-RES complexes were observed to be (6.62 ± 0.08) × 104 and (6.37 ± 0.09) × 104 M−1 at 298 K respectively. Thermodynamic parameters revealed the participation of electrostatic forces throughout the binding of ligands and proteins. Furthermore, the resonance light scattering signal of Hb and Hb-HTF in the presence of Nano-RES displayed the formation and production of complexes in larger sizes. According to the data of far-UV CD and UV/vis, the secondary structure of proteins was altered by the interaction of Nano-RES with both proteins. The results of melting point assessment confirmed the impact of Nano-RES on increasing the thermal stability of Hb-HTF complex as a ternary system. As the different behavior of Hb and Hb-HTF in the presence of Nano-RES concentrations was approved by the conductivity analysis, the distances between donor and acceptor was determined by fluorescence resonance energy transfer measurements (FRET) to be 1.68 nm and 1.77 nm for Hb-Nano-RES and (Hb-HTF) Nano-RES complexes, respectively. Molecular dynamic study was carried out to investigate the binding interactions of RES to Hb and Hb-HTF complex and was followed by MD simulation under the calculation of 100 ns. Lastly, we evaluated the cytotoxicity of Nano-RES in different concentrations on A549 and BEAS-2B cells, which increased the rate of apoptosis in A549 cells.

A molecular biology approach to identify Francisella tularensis proteins that interact with Band 3 of human erythrocytes.

Francisella tularensis is a pathogenic gram-negative bacterium that causes the zoonotic disease Tularemia. In addition, F. tularensis is classified as a Class A Bioterrorism agent by the CDC due to the ease of aerosolization and the ability of this bacterium to cause fatal infection in low doses. Previous studies suggest that invasion of mammalian erythrocytes by F. tularensis helps to increase colonization of ticks, an arthropod vector of this pathogen. Our laboratory previously found that the erythrocyte membrane glycoprotein, Band 3 is required by F. tularensis for invasion of red blood cells. Therefore, we predict that bacterial proteins interact with Band 3 to facilitate invasion. To identify these proteins, we will express codon-optimized Band 3 linked to a Glutathione-S transferase tag in F. tularensis LVS. Subsequent pull-down assays may reveal F. tularensis protein binding partners to Band 3 responsible for facilitating erythrocyte invasion.

Graph-based algorithms to dissect long-distance water-mediated H-bond networks for conformational couplings in GPCRs.

Changes in structure and dynamics elicited by agonist ligand binding at the extracellular side of G protein coupled receptors (GPCRs) must be relayed to the cytoplasmic G protein binding side of the receptors. To decipher the role of water-mediated hydrogen-bond networks in this relay mechanism, we have developed graph-based algorithms and analysis methodologies applicable to datasets of static structures of distinct GPCRs. For a reference dataset of static structures of bovine rhodopsin solved at the same resolution, we show that graph analyses capture the internal protein-water hydrogen-bond network. The extended analyses of static structures of rhodopsins and opioid receptors suggest a relay mechanism whereby inactive receptors have in place much of the internal core hydrogen-bond network required for long-distance relay of structural change, with extensive local H-bond clusters observed in structures solved at high resolution and with internal water molecules.

Effect of irradiated nonionic surfactant on drug-protein binding

In this work, the effect of γ-irradiated surfactants on drug–protein binding has been assessed. Irradiated aqueous solutions of Pluronic F-127, Pluronic L-35, Tween 20, and Tween 80 surfactants were used. Gamma irradiation was carried out for three different doses, to these four surfactants viz., 6, 30, and 36 kGy. Two drugs, Ornidazole (ONZ) and Telmisartan (TMS) were used for the binding study. The effect of four irradiated surfactants in the presence of drug – Bovine serum albumin (BSA) protein was analyzed. The drug solutions in methanol-aqueous media were combined with BSA in the initial step. In the next two succeeding steps, drug–BSA interaction in the presence of unirradiated and irradiated surfactants were carried out. The results of drug-BSA due to addition of irradiated and unirradiated surfactants were compared. The interaction processes were assessed through UV Spectroscopy, DLS, zeta potential, turbidity, and docking studies. Improved binding was observed for both the drugs and four surfactants for irradiated surfactants as determined from the binding constant values using UV spectroscopic studies. The DLS measurements demonstrated no general trend of increase or decrease in micellar size with absorbed dose. The binding and change in the size of micelles were observed to be highly drug and surfactant-specific. Among the four surfactants, irradiated Pluronic F-127 showed higher binding affinity. To the best of our knowledge, this is the first report on the effect of γ-irradiated surfactant on drug–BSA interaction. This can be applied to other drug–protein systems to tune their interaction to the required level. Communicated by Ramaswamy H. Sarma

Biological Activities, DFT and Molecular Docking Studies of Novel Schiff Bases Derived from Sulfamethoxypyridazine

AbstractThe present study reported the synthesis and biological activities of sulfamethoxypyridazine (SMPR) Schiff bases (SBs) with different aromatic aldehydes. The antimicrobial potential of SBs against various pathogenic strains (S. epidermidis, E. coli, S. agalactiae, S. aureus, S. typhi, K. pneumoniae, C. albicans, and C. tropicalis) was explored by disc diffusion method. The antidiabetic potential was monitored by inhibition of α‐amylase, α‐glucosidase, and anti‐inflammatory activity was studied by protein denaturation assay. The binding of protein with SBs was determined by MOE docking. The synthesized SBs reveal significant antimicrobial potential against all strains (p values<0.0001) better than the parent drug SMPR but less than amoxicillin. The synthesized SBs exhibited reasonable inhibition potential against α‐glucosidase, α‐amylase, and anti‐inflammatory activity. The derivative 10 a depicted antioxidant (IC50 value 12.18 μg/mL) and anti‐inflammatory (IC50 value 49.37 μg/mL) even better than standard ascorbic acid and diclofenac sodium (IC50 values 49.92 and 123.81 μg/mL), respectively. Molecular docking results revealed that synthesized SBs have good binding affinities towards different receptor proteins and results support our experimental results. The electronic properties have been calculated using density function theory (DFT) to determine the chemical reactivity of studied compounds. The low energy gap between Frontier Molecular Orbitals (FMOs) revealed the significant chemical reactivity of compounds 8 a and 10 a, among other compounds.

FRET Assays for the Identification of C. albicans HSP90-Sba1 and Human HSP90α-p23 Binding Inhibitors.

Heat shock protein 90 (HSP90) is a critical target for anticancer and anti-fungal-infection therapies due to its central role as a molecular chaperone involved in protein folding and activation. In this study, we developed in vitro Förster Resonance Energy Transfer (FRET) assays to characterize the binding of C. albicans HSP90 to its co-chaperone Sba1, as well as that of the homologous human HSP90α to p23. The assay for human HSP90α binding to p23 enables selectivity assessment for compounds aimed to inhibit the binding of C. albicans HSP90 to Sba1 without affecting the physiological activity of human HSP90α. The combination of the two assays is important for antifungal drug development, while the assay for human HSP90α can potentially be used on its own for anticancer drug discovery. Since ATP binding of HSP90 is a prerequisite for HSP90-Sba1/p23 binding, ATP-competitive inhibitors can be identified with the assays. The specificity of binding of fusion protein constructs-HSP90-mNeonGreen (donor) and Sba1-mScarlet-I (acceptor)-to each other in our assay was confirmed via competitive inhibition by both non-labeled Sba1 and known ATP-competitive inhibitors. We utilized the developed assays to characterize the stability of both HSP90-Sba1 and HSP90α-p23 affinity complexes quantitatively. Kd values were determined and assessed for their precision and accuracy using the 95.5% confidence level. For HSP90-Sba1, the precision confidence interval (PCI) was found to be 70-120 (100 ± 20) nM while the accuracy confidence interval (ACI) was 100-130 nM. For HSP90α-p23, PCI was 180-260 (220 ± 40) nM and ACI was 200-270 nM. The developed assays were used to screen a nucleoside-mimetics library of 320 compounds for inhibitory activity against both C. albicans HSP90-Sba1 and human HSP90α-p23 binding. No novel active compounds were identified. Overall, the developed assays exhibited low data variability and robust signal separation, achieving Z factors > 0.5.

Probabilistic association of differentially expressed genes with cis-regulatory elements.

Differential gene expression in response to perturbations is mediated at least in part by changes in binding of transcription factors (TFs) and other proteins at specific genomic regions. Association of these cis-regulatory elements (CREs) with their target genes is a challenging task that is essential to address many biological and mechanistic questions. Many current approaches rely on chromatin conformation capture techniques or single-cell correlational methods to establish CRE-to-gene associations. These methods can be effective but have limitations, including resolution, gaps in detectable association distances, and cost. As an alternative, we have developed DegCre, a nonparametric method that evaluates correlations between measurements of perturbation-induced differential gene expression and differential regulatory signal at CREs to score possible CRE-to-gene associations. It has several unique features, including the ability to use any type of CRE activity measurement, yield probabilistic scores for CRE-to-gene pairs, and assess CRE-to-gene pairings across a wide range of sequence distances. We apply DegCre to six data sets, each using different perturbations and containing a variety of regulatory signal measurements, including chromatin openness, histone modifications, and TF occupancy. To test their efficacy, we compare DegCre associations to Hi-C loop calls and CRISPR-validated CRE-to-gene associations, establishing good performance by DegCre that is comparable or superior to competing methods. DegCre is a novel approach to the association of CREs to genes from a perturbation-differential perspective, with strengths that are complementary to existing approaches and allow for new insights into gene regulation.

Dominant negative OTULIN-related autoinflammatory syndrome.

OTU deubiquitinase with linear linkage specificity (OTULIN) regulates inflammation and cell death by deubiquitinating linear ubiquitin chains generated by the linear ubiquitin chain assembly complex (LUBAC). Biallelic loss-of-function mutations causes OTULIN-related autoinflammatory syndrome (ORAS), while OTULIN haploinsuffiency has not been associated with spontaneous inflammation. However, herein, we identify two patients with the heterozygous mutation p.Cys129Ser in OTULIN. Consistent with ORAS, we observed accumulation of linear ubiquitin chains, increased sensitivity to TNF-induced death, and dysregulation of inflammatory signaling in patient cells. While the C129S mutation did not affect OTULIN protein stability or binding capacity to LUBAC and linear ubiquitin chains, it did ablate OTULIN deubiquitinase activity. Loss of activity facilitated the accumulation of autoubiquitin chains on LUBAC. Altered ubiquitination of LUBAC inhibits its recruitment to the TNF receptor signaling complex, promoting TNF-induced cell death and disease pathology. By reporting the first dominant negative mutation driving ORAS, this study expands our clinical understanding of OTULIN-associated pathology.