Nuclear envelope and chromatin choreography direct cellular differentiation

The nuclear envelope plays an indispensable role in the spatiotemporal organization of chromatin and transcriptional regulation during the intricate process of cell differentiation. This review outlines the distinct regulatory networks between nuclear envelope proteins, transcription factors and epigenetic modifications in controlling the expression of cell lineage-specific genes during differentiation. Nuclear lamina with its associated nuclear envelope proteins organize heterochromatin via Lamina-Associated Domains (LADs), proximal to the nuclear periphery. Since nuclear lamina is mechanosensitive, we critically examine the impact of extracellular forces on differentiation outcomes. The nuclear envelope is spanned by nuclear pore complexes which, in addition to their central role in transport, are associated with chromatin organization. Furthermore, mutations in the nuclear envelope proteins disrupt differentiation, resulting in developmental disorders. Investigating the underlying nuclear envelope controlled regulatory mechanisms of chromatin remodelling during lineage commitment will accelerate our fundamental understanding of developmental biology and regenerative medicine.

Evolution of the RNA alternative decay cis element into a high-affinity target for the immunomodulatory protein Roquin

RNA cis elements play pivotal roles in regulatory processes, e.g. in transcriptional and translational regulation. Two stem-looped cis elements, the constitutive and alternative decay elements (CDE and ADE, respectively) are shape-specifically recognized in mRNA 3' untranslated regions (UTRs) by the immune-regulatory protein Roquin. Roquin initiates mRNA decay and contributes to balanced transcript levels required for immune homoeostasis. While the interaction of Roquin with several CDEs is described, our knowledge about ADE complex formation is limited to the mRNA of Ox40, a gene encoding a T-cell costimulatory receptor. The Ox40 3'UTR comprises both a CDE and ADE, each sufficient for Roquin-mediated control. Opposed to highly conserved and abundant CDE structures, ADEs are rarer, but predicted to exhibit a greater structural heterogeneity. This raises the question of how and when two structurally distinct cis elements evolved as equal target motifs for Roquin. Using an interdisciplinary approach, we here monitor the evolution of sequence and structure features of the Ox40 ADE across species. We designed RNA variants to probe en-detail determinants steering Roquin-RNA complex formation. Specifically, those reveal the contribution of a second RNA-binding interface of Roquin for recognition of the ADE basal stem region. In sum, our study sheds light on how the conserved Roquin protein selected ADE-specific structural features to evolve a second high-affinity mRNA target cis element relevant for adaptive immune regulation. As our findings also allow expanding the RNA target spectrum of Roquin, the approach can serve a paradigm for understanding RNA-protein specificity through back-tracing the evolution of the RNA element.

Long-term impact of molecular epidemiology shifts of methicillin-resistant Staphylococcus aureus on severity and mortality of bloodstream infection

A 2019 nationwide study in Japan revealed the predominant methicillin-resistant Staphylococcus aureus (MRSA) types in bloodstream infections (BSIs) to be sequence type (ST)8-carrying SCCmec type IV (ST8-MRSA-IV) and clonal complex 1-carrying SCCmec type IV (CC1-MRSA-IV). However, detailed patient characteristics and how these MRSA types evolve over time remain largely unknown. In this long-term single-center study, MRSA strains isolated from blood cultures at Nagasaki University Hospital from 2012 to 2019 were sequenced and analyzed. Additionally, we compared the SCCmec types and patient characteristics identified in this study with previous data from our hospital spanning 2003-2007 and 2008-2011. Over this 16-year period, SCCmec type II decreased significantly from 79.2% to 15.5%, while type IV increased from 18.2% to 65.5%. This shift in SCCmec types was associated with notable changes in severity and outcomes; the sequential organ failure assessment (SOFA) score decreased from 5.8 to 3.1; in-hospital mortality declined from 39.8% to 15.5%. In contrast, no significant changes in patient demographics, such as age, sex, or underlying diseases, were observed. Between 2012 and 2019, the major combinations of SCCmec type and sequence type were ST8-MRSA-IV, ST8-MRSA-I, CC1-MRSA-IV, and ST5-MRSA-II. Additionally, ST8-MRSA-IV was divided into CA-MRSA/J, t5071-ST8-MRSA-IV, and USA300-like clone based on the results of molecular analysis. These major combinations showed similar drug resistance patterns, molecular characteristics, and phylogenetic features to those identified in nationwide surveillance. This study highlights the evolving nature of MRSA types in bloodstream infections, correlating with improved patient outcomes over time.

Structural comparison of substrate-binding pockets of serine β-lactamases in classes A, C, and D

β-lactams have been the most successful antibiotics, but the rise of multi-drug resistant (MDR) bacteria threatens their effectiveness. Serine β-lactamases (SBLs), among the most common causes of resistance, are classified as A, C, and D, with numerous variants complicating structural and substrate spectrum comparisons. This study compares representative SBLs of these classes, focusing on the substrate-binding pocket (SBP). SBP is kidney bean-shaped on the indented surface, formed mainly by loops L1, L2, and L3, and an additional loop Lc in class C. β-lactams bind in a conserved orientation, with the β-lactam ring towards L2 and additional rings towards the space between L1 and L3. Structural comparison shows each class has distinct SBP structures, but subclasses share a conserved scaffold. The SBP structure, accommodating complimentary β-lactams, determines the substrate spectrum of SBLs. The systematic comparison of SBLs, including structural compatibility between β-lactams and SBPs, will help understand their substrate spectrum.

Phages adapt to recognize an O-antigen polysaccharide site by mutating the "backup" tail protein ORF59, enabling reinfection of phage-resistant Klebsiella pneumoniae

Phages demonstrate remarkable promise as antimicrobial agents against antibiotic-resistant bacteria. However, the emergence of phage-resistant strains poses challenges to their effective application. In this paper, we presented the isolation of a phage adaptive mutant that demonstrated enhanced and sustained antibacterial efficacy through the co-evolution of Klebsiella pneumoniae (K. pneumoniae) 111-2 and phage ZX1Δint in vitro. Our experiments revealed that phage ZX1Δint successfully completed the adsorption phase by binding to the host surface, specifically targeting the capsular polysaccharide (CPS) receptor via the primary receptor-binding protein (RBP) ORF60 and the auxiliary RBP ORF59. Upon exposure to phage predation, mutations in genes wbaP, wbaZ or wzc, which encode the synthesis of the CPS, conferred resistance by reducing phage adsorption. In response to these host defense mechanisms, the adaptive mutant phages have evolved to utilize an alternative binding site located on an O-antigen site of lipopolysaccharide (LPS) through a mutation in the backup RBP ORF59. This evolutionary change enabled the phages to reinfect previously phage-resistant strains. Notably, the adaptive mutant phage PR2 carrying the ORF59 mutation Q777R, demonstrated the capacity to infect both wild-type and resistant strains, exhibiting prolonged antimicrobial activity against the wild strains. In conclusion, our findings elucidated a complex phage-host adsorption-antagonism mechanism characterized by mutation-driven alterations in phage receptor recognition. This work contributes to a deeper understanding of phage adaptability and highlights the potential for phages to combat phage-resistant bacteria through an in vitro evolutionary approach.

Exploring covalent inhibitors of SARS-CoV-2 main protease: from peptidomimetics to novel scaffolds

Peptidomimetic inhibitors mimic natural peptide substrates, employing electrophilic warheads to covalently interact with the catalytic Cys145 of Mpro. Examples include aldehydes, α-ketoamides, and aza-peptides, with discussions on their mechanisms of action, potency, and structural insights. Non-peptidomimetic inhibitors utilise diverse scaffolds and mechanisms, achieving covalent modification of Mpro.

Quantifying antibody binding: techniques and therapeutic implications

The binding kinetics of an antibody for its target antigen represent key determinants of its biological function and success as a novel biotherapeutic. Defining these interactions and kinetics is critical for understanding the pharmacological and pharmacodynamic profiles of antibodies in therapeutic applications, with line of sight to clinical translation. In this review, we discuss the latest developments in approaches to measure and modulate antibody-antigen interactions, including antibody engineering, novel antibody formats, current, and emerging technologies for measuring antibody-antigen binding interactions, and emerging perspectives within the field. We also explore how emerging computational methods are set to become powerful tools for modeling antibody-binding interactions under physiologically relevant conditions. Finally, we consider the therapeutic implications of modulating target engagement in terms of pharmacodynamics and pharmacokinetics.

Antibodies to watch in 2025

The commercial development of antibody therapeutics is a global enterprise involving thousands of biopharmaceutical firms and supporting service organizations. To date, their combined efforts have resulted in over 200 marketed antibody therapeutics and a pipeline of nearly 1,400 investigational product candidates that are undergoing evaluation in clinical studies as treatments for a wide variety of diseases. Here, we discuss key events in antibody therapeutics development that occurred during 2024 and forecast key events related to the late-stage clinical pipeline that may occur in 2025. In particular, we report on 21 antibody therapeutics granted a first approval in at least one country or region during 2024, including bispecific antibodies tarlatamab (IMDELLTRA®), zanidatamab (Ziihera®), zenocutuzumab (BIZENGRI®), odronextamab (Ordspono®), ivonescimab (®), and antibody-drug conjugate (ADC) sacituzumab tirumotecan (®). We also discuss 30 investigational antibody therapeutics for which marketing applications were undergoing review by at least one regulatory agency, as of our last update on December 9, 2024, including ADCs datopotamab deruxtecan, telisotuzumab vedotin, patritumab deruxtecan, trastuzumab botidotin, becotatug vedotin, and trastuzumab rezetecan. Of 178 antibody therapeutics we include in the late-stage pipeline, we summarize key data for 18 for which marketing applications may be submitted by the end of 2025, such as bi- or multispecific antibodies denecimig, sonelokimab, erfonrilimab, and anbenitamab. Key trends in the development and approval of antibody formats such as bispecifics and ADCs, as well as clinical-phase transition and global approval success rates for these antibody formats, are reported.

Virulence factors and therapeutic methods of Trueperella pyogenes: A review

Trueperella pyogenes is a prevalent opportunistic pathogen responsible for a wide range of infections in livestock and wildlife, such as in cattle, pigs, European bison and forest musk deer. Much of the successful infection of T. pyogenes relies on its virulence factors, including pyolysin as well as adhesion factors. The swift rise of bacterial resistance has highlighted the urgent need for developing new therapeutic strategies. Currently, virulence factor-mediated vaccine development and other therapeutic approaches are widely regarded as the primary interventions for addressing diseases associated with this pathogen. This review examines the broader virulence potential of T. pyogenes, focusing on haemolysin, host cell adhesion proteins, the prevalence of antibiotic resistance, and the development of vaccines mediated by virulence factors. Additionally, it discusses current and future approaches aimed at improving therapeutic interventions.

Biparatopic binding of ISB 1442 to CD38 in trans enables increased cell antibody density and increased avidity

ISB 1442 is a bispecific biparatopic antibody in clinical development to treat hematological malignancies. It consists of two adjacent anti-CD38 arms targeting non-overlapping epitopes that preferentially drive binding to tumor cells and a low-affinity anti-CD47 arm to enable avidity-induced blocking of proximal CD47 receptors. We previously reported the pharmacology of ISB 1442, designed to reestablish synthetic immunity in CD38+ hematological malignancies. Here, we describe the discovery, optimization and characterization of the ISB 1442 antigen binding fragment (Fab) arms, their assembly to 2 + 1 format, and present the high-resolution co-crystal structures of the two anti-CD38 Fabs, in complex with CD38. This, with biophysical and functional assays, elucidated the underlying mechanism of action of ISB 1442. In solution phase, ISB 1442 forms a 2:2 complex with CD38 as determined by size-exclusion chromatography with multi-angle light scattering and electron microscopy. The predicted antibody-antigen stoichiometries at different CD38 surface densities were experimentally validated by surface plasmon resonance and cell binding assays. The specific design and structural features of ISB 1442 enable: 1) enhanced trans binding to adjacent CD38 molecules to increase Fc density at the cancer cell surface; 2) prevention of avid cis binding to monomeric CD38 to minimize blockade by soluble shed CD38; and 3) greater binding avidity, with a slower off-rate at high CD38 density, for increased specificity. The superior CD38 targeting of ISB 1442, at both high and low receptor densities, by its biparatopic design, will enhance proximal CD47 blockade and thus counteract a major tumor escape mechanism in multiple myeloma patients.

Copper-instigated modulatory cell mortality mechanisms and progress in kidney diseases

Copper is a vital cofactor in various enzymes, plays a pivotal role in maintaining cell homeostasis. When copper metabolism is disordered and mitochondrial dysfunction is impaired, programmed cell death such as apoptosis, paraptosis, pyroptosis, ferroptosis, cuproptosis, autophagy and necroptosis can be induced. In this review, we focus on the metabolic mechanisms of copper. In addition, we discuss the mechanism by which copper induces various programmed cell deaths. Finally, this review examines copper's involvement in prevalent kidney diseases such as acute kidney injury and chronic kidney disease. The findings indicate that the use of copper chelators or plant extracts can mitigate kidney damage by reducing copper accumulation, offering novel insights into the pathogenesis and treatment strategies for kidney diseases.

New aspects of a small GTPase RAB35 in brain development and function

In eukaryotic cells, organelles in the secretory, lysosomal, and endocytic pathways actively exchange biological materials with each other through intracellular membrane trafficking, which is the process of transporting the cargo of proteins, lipids, and other molecules to appropriate compartments via transport vesicles or intermediates. These processes are strictly regulated by various small GTPases such as the RAS-like in rat brain (RAB) protein family, which is the largest subfamily of the RAS superfamily. Dysfunction of membrane trafficking affects tissue homeostasis and leads to a wide range of diseases, including neurological disorders and neurodegenerative diseases. Therefore, it is important to understand the physiological and pathological roles of RAB proteins in brain function. RAB35, a member of the RAB family, is an evolutionarily conserved protein in metazoans. A wide range of studies using cultured mammalian cells and model organisms have revealed that RAB35 mediates various processes such as cytokinesis, endocytic recycling, actin bundling, and cell migration. RAB35 is also involved in neurite outgrowth and turnover of synaptic vesicles. We generated brain-specific Rab35 knockout mice to study the physiological roles of RAB35 in brain development and function. These mice exhibited defects in anxiety-related behaviors and spatial memory. Strikingly, RAB35 is required for the precise positioning of pyramidal neurons during hippocampal development, and thereby for normal hippocampal lamination. In contrast, layer formation in the cerebral cortex occurred superficially, even in the absence of RAB35, suggesting a predominant role for RAB35 in hippocampal development rather than in cerebral cortex development. Recent studies have suggested an association between RAB35 and neurodegenerative diseases, including Parkinson's disease and Alzheimer's disease. In this review, we provide an overview of the current understanding of subcellular functions of RAB35. We also provide insights into the physiological role of RAB35 in mammalian brain development and function, and discuss the involvement of RAB35 dysfunction in neurodegenerative diseases.

AI-based quality assessment methods for protein structure models from cryo-EM

Cryogenic electron microscopy (cryo-EM) has revolutionized structural biology, with an increasing number of structures being determined by cryo-EM each year, many at higher resolutions. However, challenges remain in accurately interpreting cryo-EM maps. Inaccuracies can arise in regions of locally low resolution, where manual model building is more prone to errors. Validation scores for structure models have been developed to assess both the compatibility between map density and the structure, as well as the geometric and stereochemical properties of protein models. Recent advancements have introduced artificial intelligence (AI) into this field. These emerging AI-driven tools offer unique capabilities in the validation and refinement of cryo-EM-derived protein atomic models, potentially leading to more accurate protein structures and deeper insights into complex biological systems.

Resolution of complex mixtures of duplex and antiparallel triplex DNA structures by capillary electrophoresis and multivariate analysis

Triplex DNA structures, which are formed by the addition of an extra strand to a target B-DNA duplex, have attracted increasing interest due to their analytical and therapeutic applications. These structures are classified into parallel and antiparallel, depending on the orientation of the Triplex-Forming Oligonucleotide (TFO) relative to the B-DNA duplex. Whereas the formation of parallel triplexes is easily detected by monitoring spectral changes in the UV region, the formation of antiparallel triplexes produces small or even no spectral variations, which makes their detection difficult and uncertain. In this study, we propose the use of capillary electrophoresis with ultraviolet absorption spectrophotometric (CE-UV) detection combined with the multivariate curve resolution-alternating least squares (MCR-ALS) chemometric method to analyse mixtures of DNA sequences capable of forming mixtures of B-DNA duplex and triplex antiparallel structures. Rapid and reproducible CE-UV analysis in hydroxypropylcellulose (HPC)-coated capillaries are done in a pH 7.4 buffer containing Mg(II) for the stabilization of the intermolecular species. Spectra measured from 220 to 300 nm along the CE-UV analysis of individual DNA strands and of their mixtures at different ratios are merged into an augmented data matrix. This is later analyzed with MCR-ALS to deconvolute characteristic pure spectra and electropherograms for each one of the CE-UV analysis considered. This procedure has allowed the resolution and detection of DNA species present in mixtures of DNA strands capable of forming duplexes, as well as antiparallel triplex structures.

An approach to predict and inhibit Amyloid Beta dimerization pattern in Alzheimer's disease

Alzheimer's Disease (AD) is one of the leading neurodegenerative diseases that affect the human population. Several hypotheses are in the pipeline to establish the commencement of this disease; however, the amyloid hypothesis is one of the most widely accepted ones. Amyloid plaques are rich in Amyloid Beta (Aβ) proteins, which are found in the brains of Alzheimer's patients. They are the spliced product of a transmembrane protein called Amyloid Precursor Protein (APP); when they enter into the amylogenic pathway, they get cleaved simultaneously by Beta and Gamma Secretase and produce Aβ protein. Appearances of Amyloid plaques are the significant clinical hallmarks of this disease. AD is mainly present in two genetically distinct forms; sporadic and familial AD. Sporadic Alzheimer's Disease (sAD) is marked by a later clinical onset of the disease, whereas, familial Alzheimer's Disease (fAD) is an early onset of the disease with mendelian inheritance. Several mutations have been clinically reported in the last decades that have shown a direct link with fAD. Many of those mutations are reported to be present in the APP. In this study, we selected a few significant mutations present in the Aβ stretch of the APP and tried to differentiate the wild-type Aβ dimers formed in sAD and the mutant dimers formed in fAD through molecular modelling as there are no structures available from wet-lab studies till date. We analysed the binding interactions leading to formations of the dimers. Our next aim was to come up with a solution to treat AD using the method of drug repurposing. For that we used virtual screening and molecular docking simulations of the already existing anti-inflammatory drugs and studied their potency in resisting the formation of Aβ dimers. This is the first such report of drug repurposing for the treatment of AD, which might pave new pathways in therapy.

Protein identification using Cryo-EM and artificial intelligence guides improved sample purification

Protein purification is essential in protein biochemistry, structural biology, and protein design, enabling the determination of protein structures, the study of biological mechanisms, and the characterization of both natural and de novo designed proteins. However, standard purification strategies often encounter challenges, such as unintended co-purification of contaminants alongside the target protein. This issue is particularly problematic for self-assembling protein nanomaterials, where unexpected geometries may reflect novel assembly states, cross-contamination, or native proteins originating from the expression host. Here, we used an automated structure-to-sequence pipeline to first identify an unknown co-purifying protein found in several purified designed protein samples. By integrating cryo-electron microscopy (Cryo-EM), ModelAngelo's sequence-agnostic model-building, and Protein BLAST, we identified the contaminant as dihydrolipoamide succinyltransferase (DLST). This identification was validated through comparisons with DLST structures in the Protein Data Bank, AlphaFold 3 predictions based on the DLST sequence from our E. coli expression vector, and traditional biochemical methods. The identification informed subsequent modifications to our purification protocol, which successfully excluded DLST from future preparations. To explore the potential broader utility of this approach, we benchmarked four computational methods for DLST identification across varying resolution ranges. This study demonstrates the successful application of a structure-to-sequence protein identification workflow, integrating Cryo-EM, ModelAngelo, Protein BLAST, and AlphaFold 3 predictions, to identify and ultimately help guide the removal of DLST from sample purification efforts. It highlights the potential of combining Cryo-EM with AI-driven tools for accurate protein identification and addressing purification challenges across diverse contexts in protein science.

Efficient method of synthesizing sn-2 eicosapentaenoic acid (EPA) monoacylglycerols using circular ethanolysis and glycerolysis

The sn-2 monoacylglycerol (MAG) of eicosapentaenoic acid (EPA) can be used as a health-promoting ingredient in functional foods. However, the lack of a good recovery method to prepare high-purity 2-EPA MAGs has limited their application. In this study, circular ethanolysis and glycerolysis were repeated three times to synthesize 2-EPA MAGs and obtain a high recovery of EPA in them. Ethanolysis was carried out using 12 % of Lipozyme 435 and an ethanol-to-triacylglycerol (TAG) ratio of 60, which led to a TAG conversion rate of 97.3 %. Glycerolysis was then carried out using 16 % of CL "Amano" IM and a substrate-to-glycerol ratio of 9 (under vacuum), which led to a conversion rate of ethyl ester to TAGs of 96.8 %. After three ethanolysis-glycerolysis cycles, a relatively high recovery of EPA in the 2-MAG (72.1 %) was obtained. After purification, a high purity 2-EPA MAG product (EPA: 92.2 ± 1.8 %; 2-MAG: 91.50 ± 0.14 %) was obtained.

Interfacial structure and protein incorporation in sparsely tethered phospholipid membranes

Tethered bilayer lipid membranes (tBLMs) are a robust model system for studying the biophysics of cell membranes, including protein-lipid interactions and membrane dynamics. In this study we describe the structural properties of a novel tBLM platform based on self-assembled monolayers (SAMs) on gold presenting sparsely distributed linear tethers. The interfacial architecture of tBLMs built on two types of alkane tether arrangements, homogeneously distributed short tethers and nanoclustered long tethers, were resolved using neutron reflectometry (NR). A series of tBLM systems was prepared and structurally characterized, with variations in membrane phase (gel and fluid lipids), substrate attachment type (floating and tethered), and electrostatic properties (zwitterionic and negatively charged lipids). Furthermore, the versatility of the tBLM platform was demonstrated by incorporating transmembrane proteins, specifically the outer membrane protein F (OmpF), into the tethered bilayer. Quantitative analyses using NR and quartz crystal microbalance with dissipation monitoring (QCM-D) confirmed successful protein incorporation, with an estimated OmpF volume fraction ∼ 18 % within the tBLM. The tBLMs exhibited excellent stability and maintained structural integrity under continuous flow conditions during up to 16-hour NR experiments. Our results highlight the adaptability of this sparse tethering system for creating physiologically relevant membrane models, facilitating precise investigations of membrane-associated processes and protein interactions. The study establishes the potential of this platform for advancing biophysical research on cell membranes and membrane proteins, as well as developing biomimetic systems for analytical and screening applications.

Synergistic insights into positive allosteric modulator and agonist using Gaussian accelerated and tau random acceleration simulations in the metabotropic glutamate receptor 2

Schizophrenia is a severe brain disorder that usually produces a lifetime of disability. Related research shows activating metabotropic glutamate receptors holds therapeutic potential. Agonist-positive allosteric modulations (ago-PAMs) not only activate metabotropic glutamate receptors but also enhance glutamate-induced responses, offering a promising treatment strategy. However, the molecular mechanisms by which ago-PAM enhances glutamate-induced responses remain unclear, as does the potential influence of glutamate on ago-PAM. In this study, Gaussian accelerated molecular dynamics and tau random acceleration molecular dynamics simulations were employed to investigate the molecular mechanism between ago-PAM and glutamate in full-length mGlu2. Results suggest that the ago-PAM JNJ-46281222 enhances the binding affinity and residence time of glutamates in the Venus flytrap (VFT) domains by initiating a variant reverse communication from the heptahelical transmembrane (7TM) domains to VFTs via the cysteine-rich domains. Meanwhile, glutamate facilitates the interaction between Trp676 and Glu701 to further induce the relaxation of TM5, promoting the opening of the PAM-binding pocket. Glutamate can also promote the upward rotation of the cyclopropylmethyl group of the JNJ-46281222 to bring the TM6-TM6 distance closer. Nevertheless, it remains uncertain how the binding between mGlu2 and G protein differs when induced by small molecules binding in allosteric sites, orthosteric sites, or both. In conclusion, this study shed new light on the positive coordination relationship between ago-PAM and glutamate in the full-length mGlu2 receptor, which could help develop novel and more effective ago-PAM to treat schizophrenia.

In silico characterization of the gating and selectivity mechanism of the human TPC2 cation channel

Two-pore channels (TPCs) are twofold symmetric endolysosomal cation channels forming important drug targets, especially for antiviral drugs. They are activated by calcium, ligand binding, and membrane voltage, and to date, they are the only ion channels shown to alter their ion selectivity depending on the type of bound ligand. However, despite their importance, ligand activation of TPCs and the molecular mechanisms underlying their ion selectivity are still poorly understood. Here, we set out to elucidate the mechanistic basis for the ion selectivity of human TPC2 (hTPC2) and the molecular mechanism of ligand-induced channel activation by the lipid PI(3,5)P2. We performed all-atom in silico electrophysiology simulations to study Na+ and Ca2+ permeation across full-length hTPC2 on the timescale of ion conduction and investigated the conformational changes induced by the presence or absence of bound PI(3,5)P2. Our findings reveal that hTPC2 adopts distinct conformations depending on the presence of PI(3,5)P2 and elucidate the allosteric transition pathways between these structures. Additionally, we examined the permeation mechanism, solvation states, and binding sites of ions during ion permeation through the pore. The results of our simulations explain the experimental observation that hTPC2 is more selective for Na+ over Ca2+ ions in the presence of PI(3,5)P2via a multilayer selectivity mechanism. Importantly, mutations in the selectivity filter region of hTPC2 maintain cation conduction but change the ion selectivity of hTPC2 drastically.

Identification of acetylcholinesterase inhibitors and stability analysis of THC@HP-β-CD inclusion complex: A comprehensive computational study

Complexing medications with cyclodextrins can enhance their solubility and stability. In this study, we investigated the host-guest complexation between Tetrahydrocurcumin (THC) and Hydroxypropyl-β-Cyclodextrin (HP-β-CD) using density functional theory (DFT) at the B3LYP-D3/TPZ level of theory in two possible orientations. To determine the reactive sites in both complexes for electrophilic and nucleophilic attacks, we calculated and interpreted the binding energy, HOMO and LUMO orbitals, global chemical reactivity descriptors, natural bond orbital (NBO) analysis, and Fukui indices. The results indicate that Orientation A is energetically more favorable than Orientation B. Non-covalent interactions (NCI) were analyzed using reduced density gradient (RDG) approaches, providing detailed insights into host-guest interactions, including hydrogen bonding and van der Waals forces. To further assess stability, we conducted 1000 ns molecular dynamics (MD) simulations and analyzed the root mean square deviations (RMSD) for systems containing 1, 2, and 10 complexes. The RMSD analysis confirmed the stability of the systems, with average RMSD values of 2.01, 3.21, and 4.29 Å, respectively. In the second part of this study, we examined the interaction between THC and the target protein Acetylcholinesterase (E.C. 3.1.1.7) with PDB ID 1QTI. Molecular docking was performed to identify the binding modes and interaction energies of the THC-protein complex. Subsequently, 1000 ns MD simulations were conducted to assess the stability and dynamic behavior of the THC-protein complex over an extended period. The analysis provided valuable insights into the binding interactions and stability of THC with the target protein, further confirming its potential as a therapeutic agent.

Elucidating the impact of S-adenosylmethionine and histamine binding on N-methyltransferase conformational dynamics: Insights from an in silico study

S-adenosylmethionine (SAM)-dependent histamine N-methyltransferase (HNMT) is a crucial enzyme involved in histamine methylation, playing an important role in the epigenetic modification of biology. It entails the addition of methyl groups to histamine molecules, thereby regulating gene expression, cellular signal transduction, and other biological processes. Therefore, gaining a profound understanding of the detailed mechanism underlying HNMT-mediated methylation reactions is instrumental in elucidating the role of histamine methylation in biology. This study employed molecular dynamics (MD) simulations to assess the mechanism of cooperative catalytic reaction between the substrate-binding domain (S domain) and the cofactor-binding domain (C domain) of HNMT. The results indicated that the interplay between the cofactor (SAM) and the C domain was mostly unaltered by substrate Histamine (HSM) binding. Nevertheless, SAM binding could induce conformational changes in the S domain, thus creating a favorable environment for substrate recognition and catalysis. Additionally, key amino acid residues that significantly contributed to substrate binding were identified based on molecular mechanics-generalized Born surface area (MM/GBSA) calculations. These findings could serve as a theoretical basis for the design of potential inhibitors and modulators targeting HNMT.

Preparation and characterization of LGR5 LOOP region-specific nanobodies

Leucine-rich repeat-containing G-protein-coupled receptor 5 (LGR5), also known as G-protein-coupled receptor 49 (GPR49), is a class A G-protein-coupled receptor (GPCR) that plays a pivotal role in embryonic development and functions as a marker for adult stem cells in various tissues and organs. LGR5 possesses a large extracellular domain (ecto-domain) enriched with leucine-rich repeats (LRR), primarily responsible for binding to ligands such as R-spondins. The C-terminal LRR extracellular LOOP region of LGR5 refers to the loop structure connecting the C-terminus of LGR5 to the first transmembrane helix. As the LOOP region is located extracellularly, it is readily accessible to exogenous molecules such as antibodies, nanobodies, or small-molecule drugs. In this study, we successfully expressed and purified the LGR5 LOOP region protein in a prokaryotic expression system. The purified protein was subsequently used as an antigen to immunize camels, leading to the generation of nanobodies. These nanobodies are composed solely of the variable domain of the heavy-chain antibody (VHH), with a molecular weight of approximately 15 kDa. Using the purified LGR5 LOOP region protein as an antigen, we isolated nanobodies that specifically bind to it. Subsequent assays demonstrated that the selected nanobody, NB 4C4 and NB 3E8, specifically targeted the LGR5 LOOP region, exhibited an inhibitory effect on β-catenin-mediated Wnt signaling to a certain extent. This study provides insights for the development of LGR5-targeted diagnostic reagents and antibody-based therapeutic strategies.

Expression and biochemical characterization of a novel NAD+-dependent xylitol dehydrogenase from the plant endophytic fungus Trichodermagamsii

Xylitol dehydrogenase (XDH; EC 1.1.1.9), encoded by the XYL2 gene, is a key enzyme in the fungal xylose metabolic pathway. In this work, a putative XDH from the plant endophytic fungus Trichoderma gamsii (TgXDH) was hetero-expressed in Escherichia coli BL21(DE3), purified to the homogeneity, and biochemically characterized. Sequence analysis revealed that TgXDH is 363 amino acids long and belongs to the zinc-containing medium-chain alcohol dehydrogenase superfamily. The size-exclusion chromatography analysis and SDS-PAGE showed that the purified recombinant TgXDH had a native molecular mass of ∼155 kDa and was composed of four identical subunits of molecular mass of ∼39 kDa. The optimum temperature and pH of this enzyme were 25 °C and pH 9.5, respectively. Kinetic analysis showed that it is an NAD+-dependent enzyme that has a polyol substrate preference (based on kcat/Km) in the order xylitol > ribitol ≈ d-sorbitol. The Km values for NAD+ with these three polyols ranged from 0.23 to 0.70 mM. Moreover, TgXDH showed high substrate affinities as compared to most of its homologs. The Km values for xylitol, ribitol, and d-sorbitol were 5.23 ± 0.68 mM, 8.01 ± 1.22 mM, and 12.34 ± 1.37 mM, respectively. Collectively, the results will contribute to understanding the biochemical properties of a novel XDH from the filamentous fungi and provide a promising XDH for industrial production of ethanol.

Differentially labeled flaviviral protease-cofactor complex for NMR spectroscopic applications

Flaviviruses such as Dengue, Zika and West-Nile viruses have a positive strand RNA genome which is translated to a polyprotein inside the host cell. The viral polypeptide is matured to its constituents by the enzymatic action of NS2B-NS3 protease-cofactor complex. The flaviviral protease-cofactor complex attracted a lot of interest recently because of its potential for therapeutic intervention and the unique nature of catalysis where the peptide cofactor regulates the enzymatic activity. Obtaining the enzyme and cofactor differentially labeled with naturally abundant nuclei and NMR active nuclei respectively will be helpful in reducing the spectral complexity by making the enzyme invisible in a multidimensional NMR spectrum while only showing peaks from the cofactor. This will enable one to study the properties of the cofactor in isolation using NMR spectroscopy. Here, I have used a strategy for selectively labeling the cofactor within the complex with NMR active nuclei while peaks from the enzyme were rendered invisible. The protocol used here takes advantage of an 'on-column unfolding' step during the initial Ni-NTA chromatography to separate the enzyme and cofactor in unfolded conditions. The labeled cofactor was then allowed to fold in the presence of an unlabeled enzyme to obtain a differently labeled complex. We compared the 1H-15N HSQC spectrum of the differently labeled, wild type and free cofactor to ensure that the cofactor attained the desired fold within the complex. The protocol is scalable, inexpensive and can be applied to other two-component enzyme systems where a peptide cofactor is essential for the folding of an enzyme.

The multifaceted role of post-translational modifications of LSD1 in cellular processes and disease pathogenesis

Post-translational modifications (PTMs) of proteins play a crucial role in living organisms, altering the properties and functions of proteins. There are over 450 known PTMs involved in various life activities. LSD1 (lysine-specific demethylase 1) is the first identified histone demethylase that can remove monomethylation or dimethylation modifications from histone H3 lysine K4 (H3K4) and histone H3 lysine K9 (H3K9). This ability of LSD1 allows it to inhibit or activate transcription. LSD1 has been found to abnormally express at the protein level in various tumors, making it relevant to multiple diseases. As a PTM enzyme, LSD1 itself undergoes various PTMs, including phosphorylation, acetylation, ubiquitination, methylation, SUMOylation, and S-nitrosylation, influencing its activity and function. Dysregulation of these PTMs has been implicated in a wide range of diseases, including cancer, metabolic disorders, neurological disorders, cardiovascular diseases, and bone diseases. Understanding the species of PTMs and functions regulated by various PTMs of LSD1 provides insights into its involvement in diverse physiological and pathological processes. In this review, we discuss the structural characteristics of LSD1 and amino acid residues that affect its enzyme activity. We also summarize the potential PTMs that occur on LSD1 and their involvement in cellular processes. Furthermore, we describe human diseases associated with abnormal expression of LSD1. This comprehensive analysis sheds light on the intricate interplay between PTMs and the functions of LSD1, highlighting their significance in health and diseases.

Understanding the molecular mechanism of fumonisin esterases by kinetic and structural studies

Fumonisins are sphingolipid-like mycotoxins that cause serious damage by contaminating food and feed. The tricarballylic acid (TCA) units of fumonisin B1 (FB1; accounting for 70 % of fumonisin contamination) can be removed by fumonisin B1 esterase (FE, EC 3.1.1.87) providing a biotechnological FB1 detoxification possibility. Here, we report the regioselective cleavage of the TCA ester at C6 in the first step of FB1 hydrolysis and kinetic characterization for two FEs. The low KM values (4.76-44.3 μM) are comparable to concentrations of environmental contaminations, and the high catalytic efficiencies are promising for practical applications. The X-ray structure of one of the FEs enabled the understanding of the FB1 hydrolysis at molecular level and revealed an arginine pocket key for substrate binding, and the catalytic role of the glutamate preceding the catalytic serine. Computations showed that this FE is likely capable of detoxifying any fumonisin indicating its potential applicability in food and feed products.

Computer-aided drug design approaches for the identification of potent inhibitors targeting elongation factor G of Mycobacterium tuberculosis

Elongation factor G (EF-G) is essential for protein synthesis in Mycobacterium tuberculosis (Mtb), positioning it as a promising target for anti-tubercular drug development. This study employs Structure-Based Drug Design (SBDD) to identify potential small molecule inhibitors that specifically target EF-G. Initially, binding hotspots on EF-G were pinpointed, and the binding modes of various compounds were analyzed. Through protein-protein interaction studies, several promising candidates were validated. Virtual screening and molecular docking techniques were utilized to evaluate the binding affinities and interactions of 20 candidate molecules with Mtb EF-G. Additionally, toxicity profiles of these compounds were assessed using predictive models, which indicated non-carcinogenic properties. To further refine the selection process, Support Vector Machine (SVM) and Random Forest models were applied to predict cell wall permeability. Notably, Asinex (8853) and Asinex (102619) emerged as top candidates, boasting high probability scores for effective permeability. Molecular docking and molecular dynamics (MD) simulations revealed that Asinex (8853), Asinex (102619), and Otava (79226) exhibited strong binding affinities and favorable conformations within the active site of Mtb EF-G. These findings suggest that these compounds have significant potential as inhibitors, warranting further investigation into their efficacy as novel anti-tubercular agents. Overall, this study emphasizes the value of Structure-Based Drug Design in identifying promising therapeutic candidates against tuberculosis by targeting essential bacterial factors like EF-G.

Computational study of interaction of calixarene with ebola virus structural proteins and its potential therapeutic implications

Ebola virus (EBOV) is a negative-strand RNA virus that causes hemorrhagic fever and fatal illness in humans. According to WHO, the Ebola virus caused 28,646 fatal cases and 11,323 deaths in West Africa due to hemorrhagic fever and deadly disease in humans between 2013 and 2016. Between 1976 and 2022, approximately 15,409 fatalities caused by EBOV took place worldwide. Unfortunately, no effective vaccine or drugs are available to prevent this deadly disease. In the present study, State-of-the-art tools based on in-silico methods were used to elucidate the interaction pattern of calixarene (CAL) with seven EBOV structural proteins, i.e., GP1,2, nucleoprotein (NP), polymerase cofactor (VP35), (VP40), transcription activator (VP30), VP24, and RNA-dependent RNA polymerase (L). CAL is a cage-like compound with supramolecular features. The molecular docking lead analysis using AutoDock tool has been performed to find out the binding pattern of CAL with EBOV proteins. Obtained results revealed efficient inhibitory properties of calixarene (CAL) against seven Ebola virus structural proteins i.e., GP1,2, nucleoprotein (NP), polymerase cofactor (VP35), (VP40), transcription activator (VP30), VP24, and RNA-dependent RNA polymerase (L). Molecular docking analysis shows that the interaction of CAL with VP24 was highest with the total binding energy -12.47 kcal/mol and 26.90 nM inhibitions constant. Molecular Dynamics study has also quantified the efficiency of CAL against VP24. In conclusion, the present study suggests that CAL and its derivatives could be used as inhibitors to counter EBOV infection. Furthermore, in vitro and in vivo laboratory experimentation is required to establish CAL and its derivatives as a potential inhibitor against EBOV.

Leveraging molecular dynamics, physicochemical, and structural analysis to explore OMP33-36 protein as a drug target in Acinetobacter baumannii: An approach against nosocomial infection

The Acinetobacter baumannii is a member of the "ESKAPE" bacteria responsible for many serious multidrug-resistant (MDR) illnesses. This bacteria swiftly adapts to environmental cues leading to the emergence of multidrug-resistant variants, particularly in hospital/medical settings. In this work, we have demonstrated the outer membrane protein 33-36 (Omp33-36) porin as a potential therapeutic target in A. baumannii and the regulatory potential of phytocompounds using an in-silico drug screening approach. Omp33-36 protein receptor was retrieved from the protein data bank and characterized as a receptor protein. The possible compounds (ligands) from three plants namely Andrographis paniculata, Cascabela thevetia, and Prosopis cineraria, were evaluated for their potential against bacterial infections based on prior investigations and selected for further analysis. Initially, seventy potential phytocompounds were identified and retrieved from IMPPAT database, followed by Physio-chemical characterizations and toxicity assessment using swissADME and ProTox server respectively. 15 compounds have shown significant drug-likeliness and were implemented for their interaction analysis with Omp33-36 using Autodock Vina. The docking study presented seven compounds with the best binding affinities, ranging from -7.2 kcal/mol to -7.9 kcal/mol and further, based on the potential of these compounds, 4 phytocompounds were introduced for molecular dynamic simulation for 200ns. During MD simulation, compounds Prosogerin, Quercitin and Tamarixetin have shown a substantial affinity for the Omp33-36 protein and binding energy ranging from -18 to -33 kcal/mol. Overall, the analysis depicted the two compounds, Quercitin and Tamarixetin, with the most consistent interactions and indicated promise as drug leads in regulating A. baumannii infection. However, in-vitro and in-vivo experimental validation are required to propose the selected phytomolecules as a therapeutic lead against A. baumannii.

Total proteome and calcium-binding proteins from human breast milk: Exploring the impact of tobacco smoke exposure and environmental factors

This study integrates proteome analysis of human breast milk (HBM) from a homogeneous group of mothers who are of similar age and live in the same geographical area, along with an analysis of essential and potentially toxic elements in HBM in relation to lifestyle and environmental factors. This preliminary proteomic study, which examined 11 samples of HBM from lactating women, identified a total of 1619 proteins across all samples, revealing significant differences in proteomes influenced by lactation stages, parity, and exposure to tobacco smoke. The pilot study aimed to explore the feasibility of correlating certain proteins with several elements, considered as indicators of tobacco smoke and environmental influences on HBM. Notably, a clear and significant correlation was found between altered calcium content in HBM and the proteome fraction associated with calcium-binding proteins. The findings suggest that all analyzed factors impact the HBM proteome and the activity of certain enzymes.

Substitutions at the C-8 position of quinazolin-4-ones improve the potency of nicotinamide site binding tankyrase inhibitors

Human diphtheria toxin-like ADP-ribosyltransferases, PARPs and tankyrases, transfer ADP-ribosyl groups to other macromolecules, thereby controlling various signaling events in cells. They are considered promising drug targets, especially in oncology, and a vast number of inhibitors have already been successfully developed. These inhibitors typically occupy the nicotinamide binding site and extend along the NAD+ binding groove of the catalytic domain. Quinazolin-4-ones have been explored as compelling scaffolds for such inhibitors and we have identified a new position within the catalytic domain that has not been extensively studied yet. In this study, we investigate larger substituents at the C-8 position and, using X-ray crystallography, we demonstrate that nitro- and diol-substituents engage in new interactions with TNKS2, improving both affinity and selectivity. Both diol- and nitro-substituents exhibit intriguing inhibition of TNKS2, with the diol-based compound EXQ-1e displaying a pIC50 of 7.19, while the nitro-based compound EXQ-2d's pIC50 value is 7.86. Both analogues impact and attenuate the tankyrase-controlled WNT/β-catenin signaling with sub-micromolar IC50. When tested against a wider panel of enzymes, the nitro-based compound EXQ-2d displayed high selectivity towards tankyrases, whereas the diol-based compound EXQ-1e also inhibited other PARPs. Compound EXQ-2d displays in vitro cell growth inhibition of the colon cancer cell line COLO 320DM, while compound EXQ-1e displays nonspecific cell toxicity. Collectively, the results offer new insights for inhibitor development targeting tankyrases and PARPs by focusing on the subsite between a mobile active site loop and the canonical nicotinamide binding site.

An S-acylated N-terminus and a conserved loop regulate the activity of the ABHD17 deacylase

The dynamic addition and removal of long-chain fatty acids modulate protein function and localization. The α/β hydrolase domain-containing (ABHD) 17 enzymes remove acyl chains from membrane-localized proteins such as the oncoprotein NRas, but how the ABHD17 proteins are regulated is unknown. Here, we used cell-based studies and molecular dynamics simulations to show that ABHD17 activity is controlled by two mobile elements-an S-acylated N-terminal helix and a loop-that flank the putative substrate-binding pocket. Multiple S-acylation events anchor the N-terminal helix in the membrane, enabling hydrophobic residues in the loop to engage with the bilayer. This stabilizes the conformation of both helix and loop, alters the conformation of the binding pocket, and optimally positions the enzyme for substrate engagement. S-acylation may be a general feature of acyl-protein thioesterases. By providing a mechanistic understanding of how the lipid modification of a lipid-removing enzyme promotes its enzymatic activity, this work contributes to our understanding of cellular S-acylation cycles.

NuMA is a mitotic adaptor protein that activates dynein and connects it to microtubule minus ends

Nuclear mitotic apparatus protein (NuMA) is indispensable for the mitotic functions of the major microtubule minus-end directed motor cytoplasmic dynein 1. NuMA and dynein are both essential for correct spindle pole organization. How these proteins cooperate to gather microtubule minus ends at spindle poles remains unclear. Here, we use microscopy-based in vitro reconstitutions to demonstrate that NuMA is a dynein adaptor, activating processive dynein motility together with dynein's cofactors dynactin and Lissencephaly-1 (Lis1). Additionally, we find that NuMA binds and stabilizes microtubule minus ends, allowing dynein/dynactin/NuMA to transport microtubule minus ends as cargo to other minus ends. We further show that the microtubule-nucleating γ-tubulin ring complex (γTuRC) hinders NuMA binding and that NuMA only caps minus ends of γTuRC-nucleated microtubules after γTuRC release. These results provide new mechanistic insight into how dynein, dynactin, NuMA, and Lis1 together with γTuRC and uncapping proteins cooperate to organize spindle poles in cells.

Advancing Src kinase inhibition: From structural design to therapeutic innovation - A comprehensive review

Src kinase, a non-receptor tyrosine kinase implicated in cellular signaling networks, plays a pivotal role in tumor progression and therapeutic resistance. Despite intensive research efforts spanning decades, no Src-selective kinase inhibitors have yet entered clinical use, highlighting the challenges in developing targeted therapeutics. Here we review recent advances in small-molecule Src inhibitor development, focusing on structural design strategies, binding mechanisms, and therapeutic applications. We analyze emerging approaches including fragment-based drug design, allosteric targeting, and substrate-competitive inhibition that have yielded promising new scaffold classes. Special attention is given to innovations in achieving isozyme selectivity, particularly through exploitation of non-ATP binding pockets and covalent inhibition strategies. Integration of artificial intelligence, living organoid platforms, and targeted protein degradation technologies is accelerating inhibitor optimization. We discuss key challenges in Src inhibitor development, including the need for enhanced selectivity, reduced off-target effects, and improved resistance profiles. Our analysis reveals promising directions for future therapeutic development, emphasizing the importance of rational design principles guided by structural insights and emerging technologies. These findings provide a framework for developing next-generation Src inhibitors with improved clinical potential.

Different chemical scaffolds bind to L-phe site in Mycobacterium tuberculosis Phe-tRNA synthetase

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mt), is one of the deadliest infectious diseases. The rise of multidrug-resistant strains represents a major public health threat, requiring new therapeutic options. Bacterial aminoacyl-tRNA synthetases (aaRS) have been shown to be highly promising drug targets, including for TB treatment. These enzymes play an essential role in translating the DNA gene code into protein sequence by attaching specific amino acid to their cognate tRNAs. They have multiple binding sites that can be targeted for inhibitor discovery: amino acid binding pocket, ATP binding pocket, tRNA binding site and an editing domain. Recently we reported several high-resolution structures of M. tuberculosis phenylalanyl-tRNA synthetase (MtPheRS) complexed with tRNAPhe and either L-Phe or a nonhydrolyzable phenylalanine adenylate analog. Here, using Nucleic Magnetic Resonance (NMR) and Surface Plasmon Resonance (SPR) we identified fragments that bind to MtPheRS and we determined crystal structures of their complexes with MtPheRS/tRNAPhe. All the binders interact with the L-Phe amino acid binding site. The analysis of interactions of the new compounds combined with adenylate analog structure provides insights for the rational design of anti-tuberculosis drugs. The 3' arm of the tRNAPhe in all the structures was disordered with exception of one complex with D-735 compound. In this structure the 3' CCA end of the acceptor stem is observed in the editing domain of MtPheRS providing insights regarding the post-transfer editing activity of class II aaRS.

Foot-and-mouth disease vaccine quality: A universal test for intact viral capsids based on detection of VP4

Foot-and-mouth disease virus (FMDV) causes an economically devastating disease of livestock that is controlled in endemic areas by vaccines containing intact inactivated FMDV particles. In this study, a novel monoclonal antibody named 5B6 has been identified and characterised, that permits the detection of all serotypes of FMDV via a conserved epitope near the N-terminus of the VP4 capsid protein. The antibody recognises intact virus particles known as 146S (the protective antigen) which contain VP4 and not dissociated capsids known as 12S (poorly protective antigen) which lack VP4. This allowed the development of a universal assay to specifically detect the protective antigen in vaccine samples using a simple ELISA. Such a test could be used to assess the quality of formulated vaccine following manufacture or prior to administration, or to assess unformulated vaccine antigen, and would be of great utility to enhance the effectiveness of FMD vaccination programmes.

Studies on 2-((2, 4-dihydroxybenzylidene) amino)-3-phenylpropanoic acid include antimicrobial, antidiabetic, antioxidant, anticancer, hemolysis, and theoretical QSAR

Studies show that microorganisms resistant to numerous antibiotics spread infections, lengthen hospital stays, and increase fatalities. Amplification factors increase the demand for innovative drug-resistant disease-fighting chemicals. This research synthesised the chiral L-phenyl alanine condensed with a 2, 4-dihydroxy benzaldehyde Schiff base for biological efficacy investigations such as antimicrobial, antidiabetic, DPPH free radical, MTT assay against HeLa cells and hemolysis studies after the characterization. Derived Schiff base showed good inhibition against K. pneumoniae (G-ve), Staphylococcus aureus (G + ve), and Candida albicans (Fungus) at a 50 μg/mL concentration. Minimum inhibitory concentration report exists in between 35 ppm and 45 ppm. It also exhibited IC50 concentrations between 138 and 265 μg/mL in the remaining biological studies. This study uses molecular docking with the help of mcule, the CLC drug discovery work bench and visual studio applications to justify the derived compound biological activity and used work related proteins such as 1HSK, 1XCW, 3K0K, 3FDN and 3GEY for docking study. The compound showed a good binding affinity score against the targets with negative values. This study covers drug-likeness using Spartan-14 HOMO-LUMO energy levels and Swiss ADME to determine the molecular properties of the chemical structure. Theoretical outcomes are compared with commercial drugs and observed nearby results. Both theoretical outcomes supported the experimental biological activities and were good coincidence.

SPR is a fast and straightforward method to estimate the binding constants of cyclic dinucleotides to their binding partners, such as STING or poxin

The development of small molecule drugs that target protein binders is the central goal in medicinal chemistry. During the lead compound development process, hundreds or even thousands of compounds are synthesized, with the primary focus on their binding affinity to protein targets. Typically, IC50 or EC50 values are used to rank these compounds. While thermodynamic values, such as the dissociation constant (KD), would be more informative, they are experimentally less accessible. In this study, we compare isothermal calorimetry (ITC) with surface plasmon resonance (SPR) using human STING, a key protein of innate immunity, and several cyclic dinucleotides (CDNs) that serve as its ligands. We demonstrate that SPR, with recent technological advancements, provides KDs that are sufficiently accurate for drug development purposes. To illustrate the versatility of our approach, we also used SPR to estimate the KD of poxin binding to cyclic GMP-AMP (cGAMP) that serves as a second messenger in the innate immune system. In conclusion, SPR offers a high benefit-to-cost ratio, making it an effective tool in the drug design process.

Structural elucidation of the O-antigen polysaccharide from shigatoxin-producing E. coli O179 using genetic information, NMR spectroscopy and the CASPER program

The serological properties of the O-antigen polysaccharide region of the lipopolysaccharides are used to differentiate E. coli strains into serogroups. In this study, we report the structure elucidation of the O-specific chain of E. coli O179 using NMR data, the program CASPER and analysis of biosynthetic information available in the E. coli O-antigen Database (ECODAB). The presence of genes that encode enzymes involved in the biosynthesis of the GDP-Man and UDP-GlcA within the O-antigen gene cluster of the bacteria indicates that the corresponding residues could be present in the polysaccharide. Furthermore, the occurrence of four genes that encode for glycosyltransferases indicates that the polysaccharide is composed of pentasaccharide repeating units; a bioinformatics approach based on predictive glycosyltransferase functions present in ECODAB revealed that the β-d-Manp-(1→4)-β-d-Manp-(1→3)-d-GlcpNAc structural element could be present in the O-specific chain. NMR spectroscopy data obtained from homonuclear and heteronuclear 2D NMR spectra (1H,1H-TOCSY, 1H,13C-HSQC, 1H,13C-H2BC and 1H,13C-HMBC) were analyzed using the CASPER program, revealing the following arrangement of monosaccharide residues as the most probable structure: →4)-α-d-GlcpA-(1→3)-[β-d-Glcp-(1→2)]β-d-Manp-(1→4)-β-d-Manp-(1→3)-β-d-GlcpNAc-(1→, which was further confirmed using 2D homonuclear 1H,1H-COSY and 1H,1H-NOESY spectra. The functions of the α-gluconosyltransferase and the β-glucosyltransferase were predicted using structural alignment of AlphaFold-predicted 3D structures. This O-antigen polysaccharide shares structural similarities with those of E. coli O6 and O188, S. boydii type 16, and the capsular polysaccharide of E. coli K43, explaining the serological cross-reactivities observed with strains belonging these O- and K-antigen groups.

Design and synthesis of novel structures with anti-tumor effects: Targeting telomere G-quadruplex and hTERT

The telomeric G-quadruplex (G4) along with the telomerase catalytic subunit hTERT are crucial in the extension of telomeres. Tumor cells can establish replicative immortality by activating the telomere-maintenance mechanism (TMM).Small molecule ligands can limit cancer telomere lengthening by by targeting at G4 and hTERT. The 144 structures were designed by summarising the common structure-activity relationship of G4 stabilisers and hTERT inhibitors.Molecular docking and mtQSAR activity prediction experiments finally identified a16 and a35 as the optimal structures. Subsequently their derivative compounds b1-b6 were synthesised,with b4 exhibiting the most pronounced inhibitory effect on tumour cells. The ability of b4 to distinguish single-stranded DNA, double-stranded DNA and telomere G4 was verified by fluorescence experiment, and the stable combination of b4 and hTERT was verified by molecular dynamics simulation. This suggests that the structural design of targeting G4 and hTERT is reasonable and has anti-tumor potential.

Nitrite binding to myoglobin and hemoglobin: Reactivity and structural aspects

Nitrite (NO2-) interacts with myoglobin (Mb) and hemoglobin (Hb) behaving as a ligand of both the ferrous (i.e., Mb(II) and Hb(II)) and ferric (i.e., Mb(III) and Hb(III)) forms. However, while the binding to the Fe(III) species corresponds to the formation of a stable complex (i.e., Mb(III)-NO2- and Hb(III)-NO2-), in the case of the ferrous forms the reaction proceeds with a nitrite reductase redox process, leading to the oxidation of the heme-protein with the reduction of NO2- to NO. This event is of the utmost importance for the rapid production of NO in vivo in the blood stream and in striated muscles, being crucial for the regulation of the blood flow, and thus for O2 supply to poorly oxygenated tissues, such as the eye's retina. Further, NO2- interacts with Mb(II)-O2 and Hb(II)-O2, inducing their oxidation with a complex mechanism, which has been only partially elucidated. Mb and Hb form the complex with NO2- through the O-nitrito binding mode (i.e., Fe-ONO-), which is regulated by residues paving the heme distal side; thus, in a site-directed mutant, where HisE7 is substituted by Val, the interaction occurs in the N-nitro binding mode (i.e., Fe-N(O)O-), like in most other heme-proteins. The structure-function relationships of the interaction of NO2- with both ferric and ferrous forms of Mb and Hb are discussed here.

Ubiquitin-conjugating enzyme E2S decreases the sensitivity of glioblastoma cells to temozolomide by upregulating PGAM1 via the interaction with OTUB2

BACKGROUND

Glioblastoma (GBM) is an aggressive cancer with limited therapeutic options. Investigating the mechanisms underlying temozolomide (TMZ) resistance and enhancing its sensitivity remain critical for improving GBM treatment outcomes. Ubiquitin-conjugating enzyme E2S (UBE2S) has been implicated in various cancers; however, its role in TMZ resistance in GBM remains unclear.

METHODS

After UBE2S knockdown, cell viability, apoptosis, and DNA damage were measured in TMZ-treated GBM cells. Immunoprecipitation coupled with mass spectrometry was employed to identify a protein complex involving UBE2S and phosphoglycerate mutase 1 (PGAM1). Co-immunoprecipitation and ubiquitination assays were conducted to examine the interactions among UBE2S, PGAM1, and Otubain-2 (OTUB2). In vivo, a GBM mouse model was used to evaluate the impact of UBE2S knockdown on TMZ efficacy.

RESULTS

UBE2S was found to be overexpressed in GBM cells, where it interacts with PGAM1 and OTUB2 to inhibit PGAM1 degradation via K48-linked deubiquitylation. This interaction increased PGAM1 protein levels, promoting DNA repair and reducing apoptosis, thereby decreasing the sensitivity of GBM cells to TMZ.

CONCLUSION

UBE2S plays a critical role in TMZ resistance by stabilizing PGAM1 protein levels through its interaction with OTUB2. Targeting UBE2S represents a promising therapeutic strategy to enhance TMZ efficacy and overcome chemotherapy resistance in GBM.

2,3-Butanediol dehydrogenase is more efficient than acetoin reductase at metabolizing reserve carbon to improve carbon cycling pathways in Lactococcus lactis N8

Acetoin (AC) and 2,3-butanediol (2,3-BDO) are metabolites produced by lactic acid bacteria using glucose as a carbon source. These two metabolites act as carbon reserves and can be reutilised by the cells. In this study, we investigated the enzymatic characteristics of acetoin reductase (ButA) and 2,3-butanediol dehydrogenase (ButB). The performance of butA or/and butB knockout mutants of Lactococcus lactis N8 was evaluated. ButA and ButB were heterologously expressed in E. coli, and their enzymatic characteristics were measured in vitro under different pH, temperature, and metal ion conditions. Kinetic parameters of the two enzymes indicated that ButA exhibited better catalytic efficiency with AC, whereas ButB performed better with 2,3-BDO. The dehydrogenase activity of ΔbutA, ΔbutB, and ΔbutBA strains were detected in vitro with AC or 2,3-BDO added medium. The ΔbutA mutant was found to metabolize both AC and 2,3-BDO more efficiently than the ΔbutB mutant. This study provides a comprehensive insight about the metabolic carbon reserve pool and cyclic pathways involving AC and 2,3-BDO in L. lactis N8.

Cholesterol ensures ciliary polycystin-2 localization to prevent polycystic kidney disease

The plasma membrane covering the primary cilium has a diverse accumulation of receptors and channels. To ensure the sensor function of the cilia, the ciliary membrane has higher cholesterol content than other cell membrane regions. A peroxisomal biogenesis disorder, Zellweger syndrome, characterized by polycystic kidney, is associated with a reduced level of ciliary cholesterol in cells. However, the etiological mechanism by which ciliary cholesterol lowering causes polycystic kidney disease remains unclear. Here, we demonstrated that lowering ciliary cholesterol by either pharmacological treatment or genetic depletion of peroxisomes impairs the localization of a ciliary ion channel polycystin-2. We also generated cultured renal medullary cells and mice carrying a missense variant in the cholesterol-binding site of polycystin-2 detected in the patient database of autosomal dominant polycystic kidney disease. This missense protein showed normal channel activity but decreased localization to the ciliary membrane. The homozygous mice exhibited embryonic lethality and the ciliopathy spectrum conditions of situs inversus and polycystic kidney. Our results suggest that cholesterol controls the ciliary localization of polycystin-2 to prevent polycystic kidney disease.

Optimized isolation of enzymatically active ubiquitin E3 ligase E6AP/UBE3A from mammalian cells

E6AP/UBE3A is the founding member of the HECT (Homologous to the E6-AP Carboxyl Terminus) ubiquitin E3 ligase family, which add ubiquitin post-translationally to protein substrates. E6AP has been structurally defined in complex with human papillomavirus (HPV) oncoprotein E6 and its gain-of-function substrate tumor suppressor p53; however, there is currently no report of E6AP being expressed and purified from mammalian cells, as studies to date have isolated E6AP from E. coli or insect cells. Here, we report an optimized protocol for purifying E6AP from suspended Human Embryonic Kidney (HEK) cells. Biophysical characterization by Q-TOF confirmed sample purity while mass photometry indicated that purified E6AP forms a monomer-oligomer mixture. E6AP produced by this method is catalytically active and amenable to structural characterization by cryo-electron microscopy (cryo-EM), biochemical assays, and small molecule screening campaigns.

Conformational flexibility of human ribokinase captured in seven crystal structures

d-ribose is a critical sugar substrate involved in the biosynthesis of nucleotides, amino acids, and cofactors, with its phosphorylation to ribose-5-phosphate by ribokinase (RK) constituting the initial step in its metabolism. RK is conserved across all domains of life, and its activity is significantly enhanced by monovalent metal (M+) ions, particularly K+, although the precise mechanism of this activation remains unclear. In this study, we present several crystal structures of human RK in both unliganded and substrate-bound states, offering detailed insights into its substrate binding process, reaction mechanism, and conformational changes throughout the catalytic cycle. Notably, bound ATP exhibited significant conformational flexibility in its triphosphate moiety, a feature shared with other RK homologues, suggesting that achieving a catalytically productive triphosphate configuration plays a key role in regulating enzyme activity. We also identified a unique conformational change in the M+ ion binding loop of human RK, specifically the flipping of the Gly306-Thr307 peptide plane, likely influenced by the ionic radius of the bound ion. These findings provide new insights into the RK reaction mechanism and its activation by M+ ions, paving the way for future investigations into the allosteric regulation of human RK and related sugar kinase enzymes.

Comprehensive amino acid composition analysis of seed storage proteins of cereals and legumes: identification and understanding of intrinsically disordered and allergenic peptides

The seed storage proteins of cereal and legumes are the primary source of amino acids which are required for sustaining the nitrogen and carbon demands during germination and growth. Humans derive most of their dietary proteins from storage proteins in form of a wide variety of foods, for consumption. The amino acid content of most of these proteins is biased and the need for this biasness is not understood. The high abundance of proline, glutamine, and cysteine in cereals makes the gluten fraction viscoelastic. The cereal proteins have less charge and legume proteins have more charge on them. Their non-polar amino acid distribution has large variations. These characteristics are strongly responsible for the partial and complete unfolding of several domains of the storage proteins. Many of the storage proteins share a highly conserved structural feature within the cupin superfamily spread across all kingdoms of life. The intrinsically disordered viscoelastic proteins help in making dough which is vital for the quality of bread. Unfolded regions harbor more immunogenic sequences and cause food-related allergies and intolerance. We have discussed these properties in terms of comparison of cereal and legume storage protein sequences and allergy. Our study supports the findings that large disordered regions contain allergen-representative peptides. Interestingly, a high number of allergen-representative peptides were cleavable by digestive enzymes. Furthermore, unfolded storage proteins mimic microbial immunogens to induce a memory immune response. Results findings can be used to guide the understanding of immunological characteristics of storage proteins and may assist in treatment decisions for food allergy.

Insight Into Factors Influencing the Aggregation Process in Wild-Type and P66R Mutant SOD1: Computational and Spectroscopic Approaches

Disturbances in metal ion homeostasis associated with amyotrophic lateral sclerosis (ALS) have been described for several years, but the exact mechanism of involvement is not well understood. To elucidate the role of metalation in superoxide dismutase (SOD1) misfolding and aggregation, we comprehensively characterized the structural features (apo/holo forms) of WT-SOD1 and P66R mutant in loop IV. Using computational and experimental methodologies, we assessed the physicochemical properties of these variants and their correlation with protein aggregation at the molecular level. Modifications in apo-SOD1 compared to holo-SOD1 were more pronounced in flexibility, stability, hydrophobicity, and intramolecular interactions, as indicated by molecular dynamics simulations. The enzymatic activities of holo/apo-WT SOD1 were 1.30 and 1.88-fold of the holo/apo P66R mutant, respectively. Under amyloid-inducing conditions, decreased ANS fluorescence intensity in the apo-form relative to the holo-form suggested pre-fibrillar species and amyloid aggregate growth due to occluded hydrophobic pockets. FTIR spectroscopy revealed that apo-WT-SOD1 and apo-P66R exhibited a mixture of parallel and intermolecular β-sheet structures, indicative of aggregation propensity. Aggregate species were identified using TEM, Congo red staining, and ThT/ANS fluorescence spectroscopy. Thermodynamic analyses with GdnHCl demonstrated that metal deficit, mutation, and intramolecular disulfide bond reduction are essential for initiating SOD1 misfolding and aggregation. These disruptions destabilize the dimer-monomer equilibrium, promoting dimer dissociation into monomers and decreasing the thermodynamic stability of SOD1 variants, thus facilitating amyloid/amorphous aggregate formation. Our findings offer novel insights into protein aggregation mechanisms in disease pathology and highlight potential therapeutic strategies against toxic protein aggregation, including SOD1.

Investigating self-supervised image denoising with denaturation

Self-supervised learning for image denoising problems in the presence of denaturation for noisy data is a crucial approach in machine learning. However, theoretical understanding of the performance of the approach that uses denatured data is lacking. To provide better understanding of the approach, in this paper, we analyze a self-supervised denoising algorithm that uses denatured data in depth through theoretical analysis and numerical experiments. Through the theoretical analysis, we discuss that the algorithm finds desired solutions to the optimization problem with the population risk, while the guarantee for the empirical risk depends on the hardness of the denoising task in terms of denaturation levels. We also conduct several experiments to investigate the performance of an extended algorithm in practice. The results indicate that the algorithm training with denatured images works, and the empirical performance aligns with the theoretical results. These results suggest several insights for further improvement of self-supervised image denoising that uses denatured data in future directions.