Annotation of biologically relevant ligands in UniProtKB using ChEBI

Leveraging protein language models for robust antimicrobial peptide detection

Antimicrobial peptides (AMPs) are promising candidates for addressing the global challenge of antibiotic resistance due to their broad-spectrum antimicrobial properties. Traditional AMP identification methods, while effective, are labor-intensive and time-consuming. Recent advancements in deep learning and large language models (LLMs), especially protein language models (PLMs) present a transformative approach for AMP prediction. In this study, we propose PLAPD, a novel framework leveraging a pre-trained ESM2 protein language model for AMP classification. Besides, PLAPD combines local feature extraction via convolutional layers and global feature extraction with a residual Transformer module. We benchmarked PLAPD against state-of-the-art AMP prediction models using a dataset comprising 8,268 peptide sequences, achieving superior performance in Accuracy (0.87), Precision (0.9359), Specificity (0.9456), MCC (0.7486), and AUC (0.9225). The results highlight the potential of PLAPD as a high-throughput and accurate tool for AMP discovery.

Oxidation of α-hydroxy acids by D-2-hydroxyglutarate dehydrogenase enzymes

α-Hydroxy acids are naturally occurring organic molecules with various medical and industrial applications. However, some α-hydroxy acids, like D-2-hydroxyglutarate (D2HG), have been implicated in cancers and neurometabolic disorders such as D2HG aciduria. Several studies on the D2HG oxidizing enzyme D-2-hydroxyglutarate dehydrogenase (D2HGDH) from various eukaryotic and prokaryotic sources focus on the use and application of the enzyme as biosensors for detecting D2HG. A recent gene knockout study on the bacterial D2HGDH homologs from Pseudomonas stutzeri and Pseudomonas aeruginosa identified the D2HGDH to be essential for bacterial survival by driving l-serine biosynthesis. Thus, D2HGDH is a good candidate for a therapeutic target against the multidrug-resistant P. aeruginosa. However, there is no consensus on the D2HGDH catalytic mechanism, and several D2HGDH homologs have not been characterized in their structural properties, which are two crucial features for therapeutic design. P. aeruginosa D2HGDH, the most extensively studied D2HGDH homolog, is emerging as a paradigm for D2HGDH and flavoproteins with metal ions in their active site. In this review, we have explored the structures of all published D2HGDH homologs from 12 species using AlphaFold 3 and highlighted the fully conserved structure and active site topologies of all D2HGDH homologs. Additionally, evolutionary and functional studies coupled with analyses of enzymatic activities reveal that prokaryotic and eukaryotic D2HGDH homologs, diverging from two distinct ancestors, may have differentially evolved to specialize in their α-hydroxy acid catalysis. Additionally, this review identifies all D2HGDH homologs as metal and FAD-dependent enzymes that employ a metal-triggered FAD reduction in their catalysis. Elucidation of the D2HGDH mechanism will allow designing antibiotics that target these enzymes as potential therapeutics against pathogenic bacteria like P. aeruginosa in addition to the application of D2HGDH homologs as biosensors.

Immunoinformatics-driven design of a multi-epitope vaccine against nipah virus: A promising approach for global health protection

This study focuses on developing a multi-epitope vaccine against the highly pathogenic Nipah virus using immunoinformatics. It aims to design a vaccine targeting the viral nucleoprotein to elicit robust immune responses. The approach integrates epitope prediction, vaccine construction, and validation through computational tools to address the lack of effective vaccines and mitigate global health threats posed by Nipah virus outbreaks. Immunoinformatics approaches have been utilized for epitope prediction, focusing on B-cell and T-cell epitopes of the Nipah virus nucleoprotein. The multi-epitope vaccine was constructed using linkers and adjuvants to enhance immunogenicity. Structural refinement, molecular docking with human ephrin B2 receptor, and immune simulations were performed to validate the vaccine's stability, binding efficiency, and immune response potential. The designed multi-epitope vaccine exhibited high antigenicity (0.56), non-allergenicity, and non-toxicity. Docking analysis showed a strong binding affinity with the ephrin B2 receptor (binding energy: -920 kcal/mol). Immune simulations indicated significant immune responses with high IgG and IgM levels and memory B-cell activation. Population coverage analysis revealed a global coverage of 88.3 %, supporting its potential for broad immunization. The designed vaccine against the Nipah virus demonstrates promising antigenicity, stability, and strong binding with the ephrin B2 receptor. With global population coverage and a robust immune response, it holds potential for clinical development. Further experimental validation and in vitro studies are recommended to confirm its efficacy as a viable vaccine candidate for the Nipah virus.

Targeting Mycobacterium tuberculosis: identification of potential phytochemicals from traditional plants against glucosyl-3-phosphoglycerate phosphatase (GpgP)

Tuberculosis (TB) is a transmissible disease that causes severe infections in adults as well as in infants, as they have immature immune systems. Lungs are the main site for pulmonary TB infection, although TB can affect other parts like lymph nodes, bone, joints, etc., which is known as extrapulmonary TB. M. tuberculosis is becoming one of the world's most severe pathogens due to growing multidrug resistance (MDR) and extensively drug resistance (XDR), rendering treatment medications useless. GpgP was chosen as the promising drug target protein in this study because it is primarily involved in the catalysis of the second step in the production of Methylglucose lipopolysaccharides (MGLPs), which regulate the synthesis of mycolic acids, which are an essential component for building the mycobacterial cell envelope. The cell envelope of M. tuberculosis is unique and is responsible for the bacteria's flexibility and pathogenicity. An in-house library of phytochemicals was utilized for screening in AutoDock Vina, and then the ligands were docked using AutoDock with the drug target protein for further validation. Then, four ligands were filtered out using SwissADME that were further studied by performing molecular dynamic simulations. After a thorough analysis, CID_446611 and CID_5282146 ligands were identified as potential inhibitors of GpgP.

Cell division protein CdpA organises and anchors the midcell ring in haloarchaea

Many archaea appear to divide through the coordinated activities of two FtsZ homologues (FtsZ1 and FtsZ2) and another bacterial cell division homologue (SepF), which are part of the midcell division ring. Here, we identify an additional protein (HVO_0739, renamed CdpA) that is involved in cell division in Haloferax volcanii, with homologues in other Haloarchaea. CdpA localises at the midcell division ring, and this requires the presence of the ring-assembly protein FtsZ1. The division constriction protein FtsZ2 also influences the proper midcell assembly and structure of CdpA. In the absence of CdpA, cells frequently fail to divide properly, and FtsZ1 formed poorly condensed pseudo-helical structures spanning across a broad region of the cell, whereas FtsZ2 showed mispositioned foci, nano-rings, and filaments. The rate of directional movement of FtsZ1 and FtsZ2 structures around the division ring appears minimally affected by loss of CdpA, which resulted in continual repositioning of the aberrant FtsZ structures in the cells. In contrast to the FtsZ proteins, CdpA formed relatively immobile foci around the ring. Protein domain function studies, pull-down assays, and multimer structure predictions suggest that CdpA is part of a membrane complex that tethers FtsZ2 and other division proteins to the midcell membrane. Our discovery of an archaeal FtsZ organisation and midcell anchor protein offers new insights into cell division mechanisms that are similar across the tree of life.

Exploration of the mechanism of Polyphyllin I against hepatocellular carcinoma based on network pharmacology, molecular docking and experimental validation

PURPOSE

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. Targeted therapies hold promise for HCC treatment, and understanding the molecular mechanisms of action is crucial for developing novel therapeutic strategies. Polyphyllin I, a natural compound with known antitumor activity, represents a potential therapeutic candidate.

METHODS

This study employed a network pharmacology approach to investigate the anti-HCC effects of Polyphyllin I and its underlying mechanisms. Drug and disease related targets were identified and intersected to construct Components-Gene Symbols-Disease and Protein-Protein Interaction networks. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. Molecular docking simulations were conducted to explore the interactions between Polyphyllin I and key pathway proteins (VEGF-C and β-catenin). Finally, in vitro and in vivo experiments validated the anti-HCC effects and underlying mechanisms of Polyphyllin I.

RESULTS

Network pharmacology analysis revealed that Polyphyllin I targets multiple genes and pathways implicated in HCC development and progression. GO and KEGG analyses identified significant enrichment of pathways related to cell proliferation, apoptosis and angiogenesis, including VEGF and the Wnt/β-catenin signaling pathways. Molecular docking simulations demonstrated strong binding affinities between Polyphyllin I and VEGF-C and β-catenin. In vitro and in vivo experiments confirmed that Polyphyllin I effectively inhibits HCC cell proliferation, induces apoptosis, and suppresses angiogenesis, potentially by modulating the VEGF-C and Wnt/β-catenin signaling pathways.

CONCLUSIONS

The study provides compelling evidence for the antitumor activity of Polyphyllin I in HCC and elucidates its possible molecular mechanisms, suggesting that Polyphyllin I holds great potential as a therapeutic agent for HCC.

In Silico and In Vivo Pharmacological Study of Acmella paniculata Flowers for Anti-Inflammatory and Antiarthritic Potential

Acmella paniculata has been traditionally used in folklore medicine to alleviate pain and manage articular rheumatism. This study explores its potential anti-inflammatory and antiarthritic effects through in silico and in vivo approaches. A. paniculata bioactives' antiarthritic mechanisms were elucidated using computational techniques, namely, gene set enrichment analysis, network pharmacology, molecular docking, and molecular dynamics (MD) simulations using KEGG pathway analysis, PyRx, Discovery Studio, and GROMACS tools. A. paniculata hydroalcoholic extract (APE) and the ethyl acetate fraction (APF) were analyzed via LC‒MS for phytochemical profiling. In vivo studies assessed anti-inflammatory and antiarthritic potential in carrageenan-induced paw edema and complete Freund's adjuvant (CFA)-induced arthritis models in Wistar rats. Ferulic acid, isoferulic acid, and acetyl aleuritolic acid were identified as bioactives that targeted RELA, a key NF-κB component. Stable interactions were confirmed through docking and MD simulations. LC‒MS verified these compounds in APE and APF. In vivo study revealed significant reductions in paw volume, arthritis scores, and inflammatory markers (CRP, RF, IL-6, and TNF-α) and improved histopathological outcomes in the APE and APF-treated groups compared to the CFA. These findings highlight the anti-inflammatory and antiarthritic potential of A. paniculata via multi-protein modulation, particularly NF-κB signaling, and it can be utilized as a promising therapeutic for rheumatoid arthritis.

Unveiling the potential of tankyrase I inhibitors for the treatment of type 2 diabetes mellitus: A hybrid approach using network pharmacology, 2D structural similarity, molecular docking, MD simulation and in-vitro studies

AIMS

This study explores the association between the Wnt signaling pathway and T2DM, emphasizing the role of Tankyrase1 (TNKS1) in metabolic regulation. Using network pharmacology and computational approaches, it aims to identify potential FDA-approved drugs for repurposing as Wnt inhibitors to improve insulin sensitivity and reduce fat accumulation.

MATERIALS AND METHODS

Network pharmacology analysis was performed to explore the association between the Wnt pathway and T2DM, identifying Catenin Beta 1 (CTNBB1) as a key hub gene involved in disease progression. A 2D structural similarity search was conducted using reference tankyrase inhibitors (E7449 and XAV939). Potential drug candidates were subjected to molecular docking and 100 ns molecular dynamics (MD) simulations with the Tankyrase I (PDB ID: 4W6E) protein. The shortlisted compounds were further evaluated for Wnt inhibitory activity using the TCF/LEF reporter assay, while their anti-diabetic potential was assessed through a glucose uptake assay in L6 myoblast cells.

KEY FINDINGS

Niclosamide, Capmatinib, Esomeprazole, and Fenofibrate were identified as promising candidates with strong binding affinities and stable interactions with key amino acids (Gly1185, Ser1221, Tyr1224, Asp1198, Tyr1213, and His1201). Experimental validation through in-vitro Wnt inhibition and glucose uptake assays confirmed that drugs Fenofibrate and Conivaptan exhibited significant Wnt inhibitory activity, suggesting their potential role in modulating T2DM-related pathways.

SIGNIFICANCE

This study highlights the role of the Wnt signaling pathway in T2DM pathogenesis and identifies potential drug candidates for repurposing as Tankyrase1/Wnt inhibitors. The findings provide a foundation for further in-vivo investigations into the anti-diabetic potential of the identified drugs, paving the way for novel therapeutic strategies in T2DM management.

In silico identification of archaeal DNA-binding proteins

MOTIVATION

The rapid advancement of next-generation sequencing technologies has generated an immense volume of genetic data. However, these data are unevenly distributed, with well-studied organisms being disproportionately represented, while other organisms, such as from archaea, remain significantly underexplored. The study of archaea is particularly challenging due to the extreme environments they inhabit and the difficulties associated with culturing them in the laboratory. Despite these challenges, archaea likely represent a crucial evolutionary link between eukaryotic and prokaryotic organisms, and their investigation could shed light on the early stages of life on Earth. Yet, a significant portion of archaeal proteins are annotated with limited or inaccurate information. Among the various classes of archaeal proteins, DNA-binding proteins are of particular importance. While they represent a large portion of every known proteome, their identification in archaea is complicated by the substantial evolutionary divergence between archaeal and the other better studied organisms.

RESULTS

To address the challenges of identifying DNA-binding proteins in archaea, we developed Xenusia, a neural network-based tool capable of screening entire archaeal proteomes to identify DNA-binding proteins. Xenusia has proven effective across diverse datasets, including metagenomics data, successfully identifying novel DNA-binding proteins, with experimental validation of its predictions.

AVAILABILITY AND IMPLEMENTATION

Xenusia is available as a PyPI package, with source code accessible at https://github.com/grogdrinker/xenusia, and as a Google Colab web server application at xenusia.ipynb.

Expression and immunological role of FUNDC2 in pan-cancer

FUNDC2 is a novel mitochondrial protein and is highly involved in various cancers. However, expression pattern and possible role and mechanism of FUNDC2 in pan-cancer remain to be investigated. TIMER 2.0 was used to investigate the expression patterns and immune infiltration of FUNDC2. GEPIA was applied to study the relationship between level of FUNDC2 and prognosis of the patients with pan-cancer. STRING was employed to analyze the potential interacting proteins of FUNDC2. The phosphorylation sites were predicted by cBioPortal and PhosphoNet. Furthermore, variations of FUNDC2 in cancers were investigated by cBioPortal. Finally, AlphaFold was used to predict the structure of FUNDC2. The data show that there were significant differences in the expression levels of FUNDC2 between cancer tissues and controls. Specifically, the levels of FUNDC2 in 8 cancers were significantly lower than the respective controls. The survival time of the cancer patients with higher levels of FUNDC2 was longer than that of lower FUNDC2 in most different types of cancers. The pattern of FUNDC2 was significantly related to immune infiltration of B cells of cancer patients. STRING analysis revealed that FUNDC2 can interact with FUNDC1, et al. Fifteen phosphorylation sites were predicted by PhosphoNet and cBioPortal, of which the S167 also overlapped with the mutation sites of FUNDC2. These data collectively show that the mitochondrial protein FUNDC2 may serve as a possible prognostic biomarker across various cancers and the mechanism may include immune infiltration.

Indium-111-Labeled Single-Domain Antibody for In Vivo CXCR4 Imaging Using Single-Photon Emission Computed Tomography

C-X-C chemokine receptor type 4 (CXCR4) is highly expressed in a range of pathologies, including cancers like multiple myeloma and non-Hodgkin lymphoma, inflammatory diseases such as rheumatoid arthritis, and viral infections like HIV. Currently, the most advanced radiotracer for CXCR4 imaging in clinics is [68Ga]PentixaFor. However, its structure is prone to modifications, complicating the development of a specific CXCR4 fluorine-18-labeled tracer with good pharmacokinetic properties. This study aimed to screen multiple CXCR4-targeting variable domains of heavy-chain-only antibody (VHH or single-domain antibody (sdAb)) constructs to identify the most promising sdAb as a vector molecule for the future development of a CXCR4 fluorine-18 tracer. We have generated five CXCR4-specific sdAb constructs with a cysteine-containing C-terminal tag (C-Direct tag) (VUN400-C-Direct, VUN401-C-Direct, VUN410-C-Direct, VUN411-C-Direct, and VUN415-C-Direct) and one probe (VUN400-C) without. The reduced sdAbs were coupled to maleimide-DOTAGA for 111In-labeling. Their binding affinity against human CXCR4 (hCXCR4) was assessed by using a previously described BRET-based displacement assay. The in vivo profile was assessed using naive mice. Based on the plasma stability (60 min post injection (p.i.)), we selected VUN400-C-Direct and its derivative VUN400-C for further evaluation. These compounds ([111In]In-DOTAGA-VUN400-C-Direct and [111In]In-DOTAGA-VUN400-C) were tested in mice bearing xenografts derived from U87.CD4, U87.CXCR4, and U87.CD4.CXCR4 cells through ex vivo biodistribution studies and SPECT/CT imaging. The six sdAb constructs were labeled with a high radiochemical conversion (75-97%) and purity (>95%). In radioactive binding assays using U87.CD4.CXCR4 cells, [111In]In-DOTAGA-VUN400-C-Direct and [111In]In-DOTAGA-VUN401-C-Direct displayed the highest cellular uptake, achieving 10.4 ± 1.6% and 11.5 ± 1.1%, respectively. In naive mice, [111In]In-DOTAGA-VUN400-C-Direct showed the most favorable biodistribution profile, with low uptake across all organs except the kidneys (Standardized Uptake Value (SUV) > 50, n = 3, 60 min p.i.), but average plasma stability (40.6 ± 9.4%, n = 3, 60 min p.i.). In a xenografted tumor model, [111In]In-DOTAGA-VUN400-C-Direct showed only minor uptake (SUVU87.CXCR4 0.71 ± 0.002, n = 3, 60 min p.i.). [111In]In-DOTAGA-VUN400-C demonstrated nearly identical plasma stability (41.08 ± 5.45%, n = 4) but showed high and specific uptake in the CXCR4-expressing xenografted tumor (SUVU87.CD4.CXCR4 3.75 ± 1.08 vs SUVU87.CD4 = 0.64 ± 0.19, n = 5, 60 min p.i.), which could be blocked by coinjection of AMD3100 (5 mg/kg) (SUVU87.CD4.CXCR4 0.55 ± 0.32 vs SUVU87.CD4 = 0.39 ± 0.07, n = 2, 60 min p.i.). In conclusion, all six sdAbs exhibited high in vitro affinity against hCXCR4. Among these, [111In]In-DOTAGA-VUN400-C showed high CXCR4-specific tumor uptake and favorable pharmacokinetic properties, indicating VUN400-C's potential as a promising vector for future CXCR4 PET imaging applications with fluorine-18.

Exploring bioactive natural products for treating neurodegenerative diseases: a computational network medicine approach targeting the estrogen signaling pathway in amyotrophic lateral sclerosis and Parkinson's disease

Amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) share overlapping molecular mechanisms, including estrogen signaling dysregulation, oxidative stress, and neuroinflammation. Standard treatments often lead to adverse effects due to unintended cross-talk with the estrogen signaling pathway. Identifying key regulatory genes and bioactive plant-derived compounds that modulate estrogen signaling without interfering with standard therapies offers a promising neuroprotective strategy. A network medicine and systems biology approach was used, beginning with the screening of 29 medicinal plants for ALS and 49 for PD, identifying 12 shared plants with neuroprotective potential. Bioactive compounds were screened for gene, protein, and pathway interactions, leading to target prediction (846 ALS-related and 690 PD-related targets) and disease association mining, which identified 93 overlapping genes (OGs). Protein-protein interaction (PPI) network analysis and MCODE clustering revealed ESR1, EGFR, and SRC as key hub-bottleneck (HB) genes, further validated via differential gene expression analysis. Gene ontology (GO) and pathway enrichment analyses revealed significant enrichment in estrogen signaling confirming the involvement of HB genes in neurodegenerative disease progression. Differential expression analysis confirmed ESR1 upregulation in ALS but downregulation in PD, suggesting a converse disease-specific regulatory pattern. Gene regulatory network (GRN) analysis identified hsa-miR-145-5p (ALS) and hsa-miR-181a-5p (PD) as key regulators, while FOXC1, GATA2, and TP53 emerged as crucial transcription factors (TFs) influencing disease progression. Molecular docking and MD simulations validated strong and stable interactions of Eupalitin (CYP19A1, -9.0 kcal/mol), Hesperetin (ESR1, -8.1 kcal/mol), and Sumatrol (PIK3CA, -8.9 kcal/mol). These phytochemicals, derived from Rosmarinus officinalis, Artemisia scoparia, Ocimum tenuiflorum, and Indigofera tinctoria, maintained stable hydrogen bonding and hydrophobic interactions for over 30% of a 25 ns simulation, supporting their therapeutic potential. The identification of ESR1, EGFR, and SRC as key targets, alongside estrogen signaling involvement, highlights the need for targeted nutraceutical interventions. These findings pave the way for safer, plant-based therapies that mitigate neurodegeneration while preserving estrogen signaling integrity, offering a promising adjuvant strategy alongside existing treatments.

Molecular docking and dynamics simulations revealed the potential inhibitory activity of honey-iQfood ingredients against GSK-3β and CDK5 protein targets for brain health

Honey-iQfood is an herbal supplement made of a mixture of polyherbal extracts and wild honey. The mixture is traditionally claimed to improve various conditions related to brain cells and functions including dementia and Alzheimer's disease. Glycogen synthase kinase-3 beta (GSK-3β) and cyclin-dependent kinase 5 (CDK5) have been identified as being involved in the pathological hyperphosphorylation of tau proteins, which leads to the formation of neurofibrillary tangles and causes Alzheimer's disease. Therefore, this study was conducted to confirm the traditional claims by detection of active compounds, namely curcumin, gallic acid, catechin, rosmarinic acid, and andrographolide in the raw materials of Honey-iQfood through HPLC analysis, molecular docking, and dynamic simulations. Two potential compounds, andrographolide, and rosmarinic acid, produced the best binding affinities following the molecular docking of the active compounds against the GSK-3β and CDK5 targets. Andrographolide binds with GSK-3β at -8.2 kcal/mol, whereas rosmarinic acid binds to CDK5 targets at -8.6 kcal/mol. Molecular dynamics was further carried out to confirm the docking results and clarify their dynamic properties such as RMSD, RMSF, rGyr, SASA, PSA, and binding free energy. CDK5-andrographolide complexes had the best MM-GBSA score (-83.63 kcal/mol) compared to other complexes, indicating the better interaction profile and stability of the complex. These findings warrant further research into andrographolide and rosmarinic acid as efficient inhibitors of tau protein hyperphosphorylation to verify their therapeutic potential in brain-related illnesses.

FOXO6: A unique transcription factor in disease regulation and therapeutic potential

FOXO6, a unique member of the Forkhead box O (FOXO) transcription factor family, has emerged as a pivotal regulator in various physiological and pathological processes, including apoptosis, oxidative stress, autophagy, cell cycle control, and inflammation. Unlike other FOXO proteins, FOXO6 exhibits distinct regulatory mechanisms, particularly its inability to undergo classical nucleocytoplasmic shuttling. These unique properties suggest that FOXO6 may function through alternative pathways, positioning it as a novel research target. This review provides the first comprehensive review of FOXO6's biological functions and its roles in the progression of multiple diseases, such as cancer, metabolic disorders, neurodegenerative conditions, and cardiovascular dysfunction. We highlight FOXO6's interaction with critical signaling pathways, including PI3K/Akt, PPARγ, and TXNIP, and discuss its contributions to tumor progression, glucose and lipid metabolism, oxidative stress, and neuronal degeneration. Moreover, FOXO6's potential as a therapeutic target is explored, with particular emphasis on its ability to modulate drug resistance and its implications for disease treatment. Despite its promising therapeutic potential, the development of FOXO6-targeted therapies remains challenging due to overlapping functions within the FOXO family and the context-dependent nature of FOXO6's regulatory roles. This review underscores the need for further experimental and clinical studies to elucidate the molecular mechanisms underlying FOXO6's functions and to validate its application in disease prevention and treatment. By systematically analyzing current research, this review aims to provide a foundational reference for future studies on FOXO6, paving the way for novel therapeutic strategies targeting this unique transcription factor.

Selective PET imaging of CXCR4 using the Al18F-labeled antagonist LY2510924

BACKGROUND

[68Ga]PentixaFor detects C-X-C chemokine receptor type 4 (CXCR4) overexpression in various malignancies, such as multiple myeloma and non-Hodgkin lymphomas, as well as in endocrine and inflammatory disorders. This study aimed to develop an Al18F-labeled radiotracer derived from LY2510924 for CXCR4-targeted imaging, leveraging the physical and logistical advantages of fluorine-18.

METHODS

We designed a CXCR4-specific radioprobe, [18F]AlF-NOTA-SC, based on LY2510924 by incorporating a triglutamate linker and NOTA chelator to enable Al18F-labeling. The in vitro CXCR4 affinity was assessed using cell-based binding assays. Subsequently, in vivo pharmacokinetics and tumor uptake of [18F]AlF-NOTA-SC were assessed in naïve mice and mice with xenografts derived from U87.CD4/U87.CD4.CXCR4 and MM.1 S cells. Finally, biodistribution was determined in a non-human primate using PET-MR.

RESULTS

Compared to Ga-PentixaFor, AlF-NOTA-SC demonstrated similar in vitro affinity for human CXCR4. [18F]AlF-NOTA-SC was produced with a decay-corrected radiochemical yield of 21.0 ± 7.1% and an apparent molar activity of 16.4 ± 3.6 GBq/µmol. In [18F]AlF-NOTA-SC binding assays on U87.CD4.CXCR4 cells, the total bound fraction was 7.1 ± 0.5% (58% blocking by AMD3100). In naïve mice, the radiotracer did not accumulate in any organs; however, it showed a significant CXCR4-specific uptake in xenografted tumors (SUVmeanU87.CD4 = 0.04 ± 0.00 (n = 3); SUVmeanU87.CD4.CXCR4 = 3.04 ± 0.65 (n = 3); SUVmeanMM.1 S = 1.95 ± 0.11 (n = 3)). In a non-human primate, [18F]AlF-NOTA-SC accumulated in CXCR4 expressing organs, such as the spleen and bone marrow.

CONCLUSION

[18F]AlF-NOTA-SC exhibited CXCR4-specific uptake in vitro and in vivo, with fast and persistent tumor accumulation, making it a strong candidate for clinical translation as an 18F-alternative to [68Ga]PentixaFor.

Identification of Active Ingredients in Ginseng Volatile Oil: A Strategy Combining Computer Virtual Screening With Experimental Validation

BACKGROUND

Ginseng volatile oil (GVO) is a valuable active ingredient in ginseng (Panax ginseng C. A. Mey.) with high research potential. Drying procedures alter the real composition of the fresh material, for example, the evaporation of compounds with low boiling point. In this study, the composition of volatile oil in fresh ginseng (FG), sun-dried ginseng (SDG), and red ginseng (RD) was systematically analyzed to clarify the dominant components of FG and their potential pharmacological effects, which provides a basis for application and development of FG.

METHODOLOGY

GVO was obtained through water vapor distillation and analyzed using GC-MS. Pattern recognition analysis was employed to differentiate components in three processed types of ginseng. Based on this analysis, the active ingredients and key targets were screened. The binding mode and affinity were verified using molecular docking technology. Finally, the anticancer activity of GVO was verified by cell experiments.

RESULTS

A total of 53 components were identified in three processed types of ginseng by GC-MS. Among them, 32 differential components were screened by pattern recognition analysis. Ultimately, 6 active ingredients (panaxydol, nerolidyl acetate, falcarinol, cis-β-farnesene, γ-elemene, and β-elemene) and 15 key targets were determined by network pharmacology analysis. Molecular docking results revealed that β-elemene exhibited a higher affinity with EGFR, ESR1, and ERK2. Cell experiments indicated that GVO promotes apoptosis in cancer cells.

CONCLUSION

This research proposed a strategy that integrated "component detection-virtual multitarget screening-active component prediction-experimental verification" to expedite the identification of active ingredients, providing insights for application of FG and the development of functional products.

From Genes to Molecules: The Fusarium PKS16 Gene Cluster Facilitates the Biosynthesis of Proliferapyrones

Ascomycete fungi of the genus Fusarium are found in manifold ecological niches and thus pursue several lifestyles. On average, individual Fusarium species have the genetic capability to produce 50 natural products (NPs), which are in general thought to improve the fungus's fitness in defined environments. This also includes NPs with toxic potential (mycotoxins) contaminating food and feed sources. Recent research has shown that the production of NPs is tightly regulated on the transcriptional level and depends on the delicate balance between the deposition and removal of histone marks. Within this study, we show that the expression of the prior cryptic Fusarium PKS16 biosynthetic gene cluster (BGC) greatly depends on modifications at histone H3 lysine 27 (H3K27). By combining molecular-, chemical-, and bioinformatic analyses we show that the PKS16 BGC from F. fujikuroi B14 (FfB14) consists of nine genes, including a positively acting pathway-specific transcription factor, which although absent in some fusaria, functions in activating other PKS16 cluster genes. Moreover, we linked the PKS16 BGC to the biosynthesis of proliferapyrone (PRO) E, an isomer of the recently isolated PRO A.

Characterization and therapeutic potential of newly isolated bacteriophages targeting the most common Salmonella serovars in Europe

Despite meticulous monitoring of Salmonella spp. throughout the food chain to ensure safer animal food products for consumers, the number of salmonellosis cases in humans continues to rise annually in Europe. Phage therapy emerges as a promising tool for controlling and eradicating Salmonella in primary production. This study aimed to fully characterize new phage therapy candidates isolated from animal sources. To achieve this, a phenotypic and genetic characterization of five phage isolates was conducted. The five phages demonstrated physical stability across a wide range of temperatures and pH levels, effectively lysing 12 different Salmonella serovars, including the most prevalent ones in the European Union in recent years, as well as multidrug-resistant strains isolated from the field. Additionally, four of the phages exhibited depolymerase production in the host range, with genomic analysis confirming that all five possessed sequences encoding for this activity, suggesting their potential as surface-disinfecting agents. Genetic analysis further revealed that the phages belong to distinct genera: Felixounavirus, Cornellvirus, Skatevirus, Agtevirus and Berlinvirus. Notably, none of the phages contained harmful sequences that could compromise their future application, such as virulence factors, antibiotic resistance genes or temperate markers. Overall, these five phages show promise as suitable candidates for phage therapy applications or phage-based Salmonella eradication strategies, where their integration in the existing biocontrol measures may enhance both food safety and public health.

Bioinformatics analysis of the in silico engineered protein vaccine with and without Escherichia coli heat labile enterotoxin adjuvant on the model of Klebsiella pneumoniae

Klebsiella pneumoniae (K. pneumoniae) has been identified as a major cause of nosocomial infections with multidrug-resistant phenotypes. Vaccination is one of the most effective methods to prevent infectious diseases. We aim to design a vaccine candidate based on the epitope-rich domains of the OmpA, OMPK17, and fimb proteins of K. pneumoniae that could protect against this infection. A vaccine structure was constructed by selecting five epitope-rich domains from three proteins. We decided to add the heat-labile toxin (LT) of Escherichia coli as an adjuvant to the designed protein structure. The evaluation of the vaccine candidates' interaction with the immune system's receptors showed an appropriate interaction of the specially adjuvated protein with TLR2 and TLR4. The stability of the interactions was also studied by molecular dynamics (MD) for to 100 ns. All parameters showed that the structure of the candidate proteins alone and in complex with TLR2 and TLR4 are stable, especially the adjuvanted protein. Immune response simulations showed that both candidates induce acceptable protective immune responses. Overall, the LT-adjuvanted design protein may have the potential to induce more favorable protective immune responses. However, further in vitro and in vivo studies are required to obtain more definitive results.

Genomic evidence on the distribution and ecological function of Pseudomonas in hadal zone

The hadal zone is the deepest region on Earth. It serves as a depositional zone for the sinking matter from surface ocean and continental margin, aided by its unique V-shaped structure. Due to extreme depth (over 6000 m), normally only organic matter with low degradability typically reaches the bottom of the trench. Concurrently, reports have indicated highly active carbon turnover and dense bacterial cells in the Mariana Trench. There remains a cognitive gap in understanding the connection between this phenomenon and the microbial taxa along with their metabolic activities. Here, we surveyed the Pseudomonas, one of the most widely distributed bacterial genera on Earth. The result revealed widespread distribution of Pseudomonas in the hadal zones. We obtained 21 metagenome-assembled genomes (MAGs) from seawater and sediment samples of the Mariana Trench, including three novel species. Comparative genomic analysis showed that hadal Pseudomonas possess more unique ortholog groups of genes related to energy generation and substances transport, distinct from those in other marine zones. These bacteria exhibit the ability to utilize diverse electron acceptors and accumulate compatible solutes, indicating two key strategies for adaptation for high hydrostatic pressure conditions. Furthermore, predicted genomic capabilities suggest that Pseudomonas could decompose various components of organic matter, particularly aromatics, as supported by metatranscriptomic datasets. These findings significantly enhance our understanding of Pseudomonas diversity and metabolic potential, providing valuable insights into the carbon and nitrogen cycles in hadal trench ecosystems.

Astrocytic EphA4 signaling is important for the elimination of excitatory synapses in Alzheimer's disease

Cell surface receptors, including erythropoietin-producing hepatocellular A4 (EphA4), are important in regulating hippocampal synapse loss, which is the key driver of memory decline in Alzheimer's disease (AD). However, the cell-specific roles and mechanisms of EphA4 are unclear. Here, we show that EphA4 expression is elevated in hippocampal CA1 astrocytes in AD conditions. Specific knockout of astrocytic EphA4 ameliorates excitatory synapse loss in the hippocampus in AD transgenic mouse models. Single-nucleus RNA sequencing analysis revealed that EphA4 inhibition specifically decreases a reactive astrocyte subpopulation with enriched complement signaling, which is associated with synapse elimination by astrocytes in AD. Importantly, astrocytic EphA4 knockout in an AD transgenic mouse model decreases complement tagging on excitatory synapses and excitatory synapses within astrocytes. These findings suggest an important role of EphA4 in the astrocyte-mediated elimination of excitatory synapses in AD and highlight the crucial role of astrocytes in hippocampal synapse maintenance in AD.

In Silico Analysis and Transcriptional Profiling of A Putative Metalloprotease ADAMTSL as A Potential Tick Antigen against Rhipicephalus microplus

The cattle tick, Rhipicephalus microplus, is the most significant ectoparasite in the cattle industry. The application of acaricides constitutes the main control method. However, inadequate treatments have serious drawbacks, including the appearance of multi-resistant ticks. Tick vaccines offer a safe and economically sustainable alternative for controlling R. microplus. Nevertheless, the efficacy of existing vaccines has been limited by polymorphisms in target antigens among strains from different geographical regions. In this study, we characterized a putative Metalloprotease from the ADAMTSL family. We analyzed three regions to evaluate their transcriptional profiling in different R. microplus tick tissues, using two constitutive genes (β-tubulin and Elfa-1) as references. The expression levels showed that ADAMTSL-R1 was upregulated 39.37-fold (p ≤ 0.05) in salivary glands. The ADAMTSL-R2 showed the highest expression, rising 7.69-fold (p ≤ 0.05) in ovaries and up to 59.39-fold (p ≤ 0.05) in egg mass. Furthermore, this region showed the highest level of conservation among Rhipicephalus isolates. The ADAMTSL-R3 was upregulated only in the egg mass. The results of this study provide a basis for future research focused on elucidating the role of these protein variants in tick biology, including their feeding mechanisms and potential implications in pathogen transmission. Understanding these factors may aid in developing an effective tick vaccine.

Engineering cellular dephosphorylation boosts (+)-borneol production in yeast

(+)-Borneol, the main component of "Natural Borneol" in the Chinese Pharmacopoeia, is a high-end spice and precious medicine. Plant extraction cannot meet the increasing demand for (+)-borneol, while microbial biosynthesis offers a sustainable supply route. However, its production was extremely low compared with other monoterpenes, even with extensively optimizing the mevalonate pathway. We found that the key challenge is the complex and unusual dephosphorylation reaction of bornyl diphosphate (BPP), which suffers the side-reaction and the competition from the cellular dephosphorylation process, especially lipid metabolism, thus limiting (+)-borneol synthesis. Here, we systematically optimized the dephosphorylation process by identifying, characterizing phosphatases, and balancing cellular dephosphorylation metabolism. For the first time, we identified two endogenous phosphatases and seven heterologous phosphatases, which significantly increased (+)-borneol production by up to 152%. By engineering BPP dephosphorylation and optimizing the MVA pathway, the production of (+)-borneol was increased by 33.8-fold, which enabled the production of 753 mg/L under fed-batch fermentation in shake flasks, so far the highest reported in the literature. This study showed that rewiring dephosphorylation metabolism was essential for high-level production of (+)-borneol in Saccharomyces cerevisiae, and balancing cellular dephosphorylation is also helpful for efficient biosynthesis of other terpenoids since all whose biosynthesis involves the dephosphorylation procedure.

Shigella infection is facilitated by interaction of human enteric α-defensin 5 with colonic epithelial receptor P2Y11

Human enteric α-defensin 5 (HD5) is an immune system peptide that acts as an important antimicrobial factor but is also known to promote pathogen infections by enhancing adhesion of the pathogens. The mechanistic basis of these conflicting functions is unknown. Here we show that HD5 induces abundant filopodial extensions in epithelial cells that capture Shigella, a major human enteroinvasive pathogen that is able to exploit these filopodia for invasion, revealing a mechanism for HD5-augmented bacterial invasion. Using multi-omics screening and in vitro, organoid, dynamic gut-on-chip and in vivo models, we identify the HD5 receptor as P2Y11, a purinergic receptor distributed apically on the luminal surface of the human colonic epithelium. Inhibitor screening identified cAMP-PKA signalling as the main pathway mediating the cytoskeleton-regulating activity of HD5. In illuminating this mechanism of Shigella invasion, our findings raise the possibility of alternative intervention strategies against HD5-augmented infections.

An improved chromosome-level genome assembly and annotation of Hong Kong catfish (Clarias fuscus)

Clarias fuscus, renowned for its resilience and nutritional value, is a significant aquaculture species in China. To facilitate further genetic research and breeding programs in this species, we generated an improved high-quality chromosome-level genome assembly of a female C. fuscus using MGI, PacBio, and Hi-C sequencing technologies. The final genome assembly spans 982.84 Mb, with contig and scaffold N50 values of 36.16 Mb and 37.66 Mb, respectively, and successfully anchors 99.60% of the sequences to 28 pseudochromosomes. We also predicted 24,849 protein-coding genes, with 97.3% of them functionally annotated. BUSCO analysis indicates a completeness of 97.03% for the assembly and 96.6% for the annotation. This study significantly advances the genomic resources available for C. fuscus and supports future molecular breeding and functional genomics research.

(R)evolution of Viruses: Introduction to biothermodynamics of viruses

As of 26 April 2024, the International Committee on Taxonomy of Viruses has registered 14690 virus species. Of these, only several dozen have been chemically and thermodynamically characterized. Every virus species is characterized by a specific empirical formula and thermodynamic properties - enthalpy, entropy and Gibbs energy. These physical properties are used in a mechanistic model of virus-host interactions at the cell membrane and in the cytoplasm. This review article presents empirical formulas and Gibbs energies for all major variants of SARS-CoV-2. This article also reports and suggests a mechanistic model of evolutionary changes, with the example of time evolution of SARS-CoV-2 from 2019 to 2024.

Computational analysis of the alpha-2 domain of apolipoprotein B - 100, a potential triggering factor in LDL aggregation

Atherosclerosis, the major underlying cause of cardiovascular disease, is believed to arise from the accumulation of low-density lipoprotein (LDL) in the arterial subendothelial space, ultimately leading to plaque formation. It is proposed that the accumulation of LDL is linked to its intrinsic aggregation propensity. Although the native LDL is not prone to aggregation, LDL(-), an electronegative LDL characterized in the plasma, has been shown to prime LDL aggregation in a domino-like behavior similar to amyloidogenic proteins. LDL(-) has also been observed to have a misfolded apolipoprotein B-100 (apo B-100), a huge protein consisting of 4563 amino acid residues. As misfolding of proteins is commonly associated with amyloid formation, apo B-100 is therefore being considered as the possible triggering factor in LDL aggregation. Previous computational studies have implicated the α2 domain to be the aggregation-prone region of apo B-100. In this study, the amyloidogenic properties of the α2 domain of apo B-100 were interrogated using both in silico and in vitro techniques. Since the crystal structure of the 570-amino acid α2 domain of apo B-100 is yet to be solved, we used several secondary structure prediction tools to model putative helical regions that make up the α2 domain. The stability of each of the 17 helices thus identified was further probed using molecular dynamics (MD), with the least stable of the helices considered as potentially amyloidogenic. In a 100 ns simulation window, helices k (YFEKLVGFIDDAVK), m (YHQFVDETNDKIREVTQRLNGEIQA), and p (QQELQRYLSLVGQVYS) were the least stable and appeared to transition to β-structures, the hallmark of amyloidogenesis. When the simulation was extended to longer times, only helices k and p formed stable β-sheets that persisted. Analysis of the data indicates that the final β-sheet conformation was stabilized by the π-π stacking interactions between the aromatic rings of Tyr-1 and Phe-8 for helix k and likely π-π stacking contacts between Arg-6 guanidino group and Tyr-15 ring for helix p. Based on the in silico work, we proceeded to synthesize and spectroscopically characterize helices k, m17-25 (QRLNGEIQA), and p. As expected, k and p formed detectable amyloids, with the latter appearing to be substantially more amyloidogenic based on kinetic aggregation assays. Amyloid fibrils formed by p were confirmed using circular dichroism spectroscopy and transmission electron microscopy. Data obtained could be exploited to further investigate the roles of peptides derived from the α2 domain helices of apo B-100 in triggering LDL aggregation. Based on preliminary data, one of the peptides designed based on this work reduced the aggregation of LDL.

Synthesis and Characterization of Schiff Bases and Their Ag(I) Complexes Containing 2,5,6-Trisubstituted Imidazothiadiazole Derivatives: Molecular Docking and In Vitro Cytotoxic Effects Against Nonsmall Lung Cancer Cell Line

In this study, four novels 2,5,6-trisubstituted imidazothiadiazole derivative ligands and their Ag(I) complexes were synthesized and characterized using various spectroscopic analysis techniques. First, imidazo[2,1-b][1,3,4]thiadiazole derivative (3) was obtained from the reaction of 5-amino-1,3,4-thiadiazole-2-thiol with benzyl bromide in the presence of KOH in an ethanolic medium. In the next step, the resultant compound reacted sequentially with four substituted phenacyl bromide derivatives (4a-4d) under refluxed ethanol for 24 h to obtain substituted 2-(benzylthio)-6-phenylimidazo[2,1-b][1,3,4]thiadiazole derivatives (5-8). Compounds (9-12) were obtained by attaching a carbonyl group to carbon number 5 of the imidazothiadiazole group in these compounds with the help of Vilsmeier-Haack reagent. The resultant compounds were reacted in an ethanolic medium to synthesize the novel (13-16) ligands by adding ethylenediamine in a 1:2 molar ratio. The Ag(I) complexes of the resultant ligands were synthesized by mixing silver acetate with the ligands in a dimethyl sulfoxide medium to obtain (17-20) complexes. All the synthesized compounds were analyzed using FTIR, 1H NMR, 13C NMR, mass spectroscopy, magnetic susceptibility, ICP-OES, and thermogravimetric analysis techniques. The study also investigates the in vitro cytotoxic effect of the ligands and complexes on A549 (nonsmall cell lung cancer) cells using the MTT assay and shows that the 13, 15, and 16 ligands, together with their complexes, exhibit potent cytotoxicity. In addition, in silico molecular docking simulations were conducted both to support the in vitro cytotoxicity experiments and to ascertain the active binding sites and interactions of the ligands and complexes on the EGFR receptor. The result indicates that ligands and complexes may serve as promising candidates for further investigation as anticancer agents.

Exposure to Group B Streptococcus-induced chorioamnionitis alters the proteome of placental extracellular vesicles

INTRODUCTION

Group B Streptococcus (GBS) is an opportunistic pathogen that can induce chorioamnionitis (CA), increasing the risk of neurodevelopmental disorders (NDDs) in the offspring. The placenta facilitates maternal-fetal communication through the release of extracellular vesicles (EVs), which may carry inflammatory molecules such as interleukin (IL)-1. Although the role of EVs in immune modulation is well established, their specific characterization in the context of GBS-induced CA has not yet been investigated. Understanding placental-derived EVs could further define how IL-1 and other inflammatory factors contribute to NDDs.

METHODS

We used an established rat model of GBS-induced CA. EVs from control and GBS infected dams were isolated from placentas and characterized using nanoparticle tracking analysis and transmission electron microscopy. The protein content was assessed via mass spectrometry, followed by subsequent pathway analysis. ELISA was used to quantify cytokine levels.

RESULTS

GBS-infected placentas exhibited calcification and increased weight, while fetal weight decreased. Analysis of the proteome from control versus GBS placental EVs revealed distinct profiles, with many proteins involved in the innate immune response, including alarmins (S100A8/9), complement pathways, and cytokine signaling pathways. Pathway analysis highlighted IL-1α and IL-1β identified as key upstream regulators. Notably, EVs from GBS-infected males showed a 44-fold increase in intracellular IL-1β compared to controls.

DISCUSSION

These findings indicate that GBS-induced CA alters the protein content of EVs from placental cells. Our findings of increased IL-1β-associated EVs highlight the need for further investigation into the role of these cytokines from GBS-exposed placentas and their role in brain injuries leading to NDDs.

Genome wide identification of MATE and ALMT gene family in lentil (Lens culinaris Medikus) and expression profiling under Al stress condition

BACKGROUND

The membrane transporters viz. multidrug and toxic compound extrusion (MATE) and aluminum-activated malate transporter (ALMT) are associated with aluminum (Al) tolerance by accelerating secretion of organic acids, which can influence nutrient availability and stress response. However, such transporter families have not yet been reported in lentil under Al stress condition.

METHOD AND RESULTS

In this study, 90 MATE and 14 ALMT genes were identified and clustered into four (MATE) and five (ALMT) subfamilies/clades with smaller subgroups. All the MATE and ALMT genes were unevenly dispersed across lentil chromosomes. Duplication analysis suggested that LcMATE gene family has expanded primarily through tandem duplication event. Collinearity of lentil with soybean suggested a close relationship between the MATE genes. The MATE promoter regions harboured many stress responsive as well as Al resistance transcription factor 1 related cis-regulatory elements. Predicted 3D (three-dimensional) structure and molecular docking revealed that 5 LcMATE proteins could bind citrate and contain amino acids related to its secretion via citrate exuding motif and other neighbouring sites. Expression analyses of LcMATE and LcALMT genes were performed using quantitative real-time polymerase chain reaction (qRT-PCR). Six genes namely, LcM1, LcM42, LcM46, LcM47, LcALMT8 and LcALMT14 responded to Al stress with varying levels of expression patterns at different time points (3, 6, 12 and 24 h).

CONCLUSION

Our findings offer thorough details on the MATE and ALMT transporters in lentils and will aid in valuable understanding for future functional studies of these transporters in generating Al tolerant cultivars.

Covalent targeting of splicing in T cells

Despite significant interest in therapeutic targeting of splicing, few chemical probes are available for the proteins involved in splicing. Here, we show that elaborated stereoisomeric acrylamide EV96 and its analogues lead to a selective T cell state-dependent loss of interleukin 2-inducible T cell kinase (ITK) by targeting one of the core splicing factors SF3B1. Mechanistic investigations suggest that the state-dependency stems from a combination of differential protein turnover rates and extensive ITK mRNA alternative splicing. We further introduce the most comprehensive list to date of proteins involved in splicing and leverage cysteine- and protein-directed activity-based protein profiling with electrophilic scout fragments to demonstrate covalent ligandability for many classes of splicing factors and splicing regulators in T cells. Taken together, our findings show how chemical perturbation of splicing can lead to immune state-dependent changes in protein expression and provide evidence for the broad potential to target splicing factors with covalent chemistry.

EvaluationMaster: A GUI Tool for Structure-Based Virtual Screening Evaluation Analysis and Decision-Making Support

Structure-based virtual screening (SBVS) plays an indispensable role in the early phases of drug discovery, utilizing computational docking techniques to predict interactions between molecules and biological targets. During the SBVS process, selecting appropriate target structures and screening algorithms is crucial, as these choices significantly shape the outcomes. Typically, such selections require researchers to be proficient with multiple algorithms and familiar with evaluation and analysis processes, complicating their tasks. These algorithms' lack of graphical user interfaces (GUIs) further complicates it. To address these challenges, we introduced EvaluationMaster, the first GUI tool designed specifically to streamline and standardize the evaluation and decision-making processes in SBVS. It supports four docking algorithms' evaluation under multiple target structures and offers a comprehensive platform that manages the entire workflow─including the downloading of molecules, construction of decoy datasets, prediction of protein pockets, batch docking, and extensive data analysis. By automating complex evaluation tasks and providing clear visualizations of analysis results, EvaluationMaster significantly reduces the learning curve for researchers and boosts the efficiency of evaluations, potentially improving SBVS hit rates and accelerating the discovery and development of new therapeutic agents.

Purification and expression of a novel bacteriocin, JUQZ-1, against Pseudomonas syringae pv. Actinidiae (PSA), secreted by Brevibacillus laterosporus Wq-1, isolated from the rhizosphere soil of healthy kiwifruit

Kiwifruit canker, caused by Pseudomonas syringae pv. actinidiae (PSA), has led to significant losses in the kiwifruit industry each year. Due to the drug resistance feature of PSA, biological control is currently the most promising method. Developing biocontrol bacteria against PSA could help solve the issue of drug resistance generated during the chemical control of PSA to a certain extent. In this research, a Wq-1 strain that demonstrated excellent inhibitory activity against PSA was isolated from the rhizosphere soil of healthy kiwifruit. Based on the morphological characteristics and phylogenetic analysis of the 16S rRNA gene sequence, the isolated strain was identified as Brevibacillus laterosporus Wq-1. Bacteriostatic proteins were isolated from the cell-free culture filtrate of strain Wq-1 and were found to have a molecular weight of approximately 12 kDa, as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Liquid chromatography-tandem mass spectrometry (LC-MS/MS) detection revealed that there were several peptides in the target band that were consistent with protein 01021 in the genome. The gene of the 01021 protein was cloned into the plasmid pPICZa, and the recombinant bacteriocin was successfully expressed using the Pichia pastoris X33 expression system. The recombinant protein 01021 effectively inhibited the growth of PSA. This is the first report of the protein's antimicrobial activity, distinguishing it from previously identified bacteriocins. Therefore, we named this bacteriocin JUQZ-1. In addition, our results showed that the protein JUQZ-1 not only exhibited a broad bacteriostatic spectrum but also high thermal and pH stability suitable for harsh environmental conditions., JUQZ-1, a protein with antimicrobial properties and strong environmental tolerance, may serve as a promising alternative to antibiotics.

Exploring the antifungal potential of Cannabis sativa-derived stilbenoids and cannabinoids against novel targets through in silico protein interaction profiling

Cannabinoid and stilbenoid compounds derived from Cannabis sativa were screened against eight specific fungal protein targets to identify potential antifungal agents. The proteins investigated included Glycosylphosphatidylinositol (GPI), Enolase, Mannitol-2-dehydrogenase, GMP synthase, Dihydroorotate dehydrogenase (DHODH), Heat shock protein 90 homolog (Hsp90), Chitin Synthase 2 (CaChs2), and Mannitol-1-phosphate 5-dehydrogenase (M1P5DH), all of which play crucial roles in fungal survival and pathogenicity. This research evaluates the binding affinities and interaction profiles of selected cannabinoids and stilbenoids with these eight proteins using molecular docking and molecular dynamics simulations. The ligands with the highest binding affinities were identified, and their pharmacokinetic profiles were analyzed using ADMET analysis. The results indicate that GMP synthase exhibited the highest binding affinity with Cannabistilbene I (-9.1 kcal/mol), suggesting hydrophobic solid interactions and multiple hydrogen bonds. Similarly, Chitin Synthase 2 demonstrated significant binding with Cannabistilbene I (-9.1 kcal/mol). In contrast, ligands such as Cannabinolic acid and 8-hydroxycannabinolic acid exhibited moderate binding affinities, underscoring the variability in interaction strengths among different proteins. Despite promising in silico results, experimental validation is necessary to confirm therapeutic potential. This research lays a crucial foundation for future studies, emphasizing the importance of evaluating binding affinities, pharmacokinetic properties, and multi-target interactions to identify promising antifungal agents.

In vivo, In vitro, and In silico Studies of Umbelliferone and Irinotecan on MDA-MB-231 Breast Cancer Cell Line and Drosophila melanogaster Larvae

AIMS

Deaths from cancer are still very common all over the world and continue to be the focus of scientific research. Chemotherapy is one of the primary treatments used to prevent deaths from cancer. Side effects of chemotherapeutic drugs and resistance of cells to drugs are essential problems that limit the treatment process. Drug combination therapy is regarded as a significant application that inhibits the growth of tumors and is anticipated to provide a solution for the issues encountered. The combination therapy aims at a synergistic effect that will limit drug resistance and cytotoxic effects with appropriate drug combinations. In this context, we aim to investigate the In vitro, In vivo, and In silico effects of single and combined doses of umbelliferone and irinotecan, known for their anticarcinogenic and curative effects, on MDA-MB-231 breast cancer cell lines and the model organism Drosophila melanogaster. Background: Irinotecan is currently used as an anticarcinogenic drug. Anticarcinogenic effects of umbelliferone have also been detected. The in vivo, in vitro, and in silico impacts of single and combined doses use of these two agents are not yet available in the literature.

OBJECTIVE

This study aims to determine the anticarcinogenic effects of single and combined use of umbelliferone and irinotecan at the molecular level. It also attempts to determine the binding energies of chemicals to cancerrelated proteins through docking and molecular dynamic studies.

METHODS

The cytotoxic effects of individual and combinational doses of umbelliferone and irinotecan on the MDAMB- 231 cell line and D. melanogaster were calculated by XTT and probit analyses. IC50 values for the cancer cells, LC50, and LC99 values for D. melanogaster were found. Gene expression analysis was performed to determine the effects of chemical agents on miR-7, miR-11, and miR-14, and their expression levels were found. The sequences of miRNAs not found in the literature were determined, and their molecular imaging was performed. In addition, the binding energies of irinotecan and umbelliferone to Bcl-2, Bad, and Akt1 proteins, which are known to have apoptotic effects, were found by the molecular docking method. Molecular dynamics studies of Bad proteins and chemicals were also performed. The drug potential of chemicals was determined by ADME/T analysis.

RESULTS

The cytotoxic effect on cells was calculated, and the IC50 value of umbelliferone was calculated as 158 μM, the IC50 value of irinotecan was calculated as 48,3 μM and the IC50 value was calculated as 20 μM. In the probit analysis performed to calculate the cytotoxic effects of drugs on D. melanogaster, the LC50 value of umbelliferone was 2,5 μM, and the LC99 value was 13,4 μM. The LC50 value of irinotecan was found to be 0,1 μM, and the LC99 value was 0,28 μM. It was concluded that single and combined doses of chemicals in the invasion experiment significantly affected the spread of cells. As a result of expression analysis, a significant increase in HsamiR- 7 (Homo sapiens miRNA-7), Hsa-miR-14 (Homo sapiens miRNA-14), and Hsa-miR-11(Homo sapiens miRNA-11) expression was observed in cells treated with umbelliferone irinotecan compared to the control groups.

CONCLUSION

In our study, it can be concluded that the cytotoxic effects of individual and combination doses of umbelliferone and irinotecan on MDA-MB-231 cells and D. melanogaster larvae are significant. In addition, the effects of umbelliferone and irinotecan on the expression level of miR-7, which is a common D. melanogaster and human miRNA, should be widely investigated. Expression analyses and docking studies of Hsa-miR-11 and Hsa-miR-14, which have been newly studied and are not in data repositories, are important for cancer research. In particular, the expression and binding energy of these miRNAs in new drug combinations and the expression level in different cancer cell lines are important for future studies. Another crucial point is that in vivo tests using different model species validate the usage of drugs at both single and mixed dosages. Other: As a result of this study, the In vivo, In vitro, and In silico effects of single and combined doses of umbelliferone and irinotecan were determined. In future studies, it would be useful to determine the binding energies of umbelliferone and irinotecan to other cancer-related proteins and to find their interactions with different miRNAs. Additionally, studies on different model organisms are also important.

Synthetic Retinoid Sulfarotene Selectively Inhibits Tumor-Repopulating Cells of Intrahepatic Cholangiocarcinoma via Disrupting Cytoskeleton by P-Selectin/PSGL1 N-Glycosylation Blockage

Intrahepatic cholangiocarcinoma (ICC) is a highly lethal malignancy that currently lacks effective clinical treatments. Eliminating stem cell-like cancer cells is an extremely promising but challenging strategy for treating ICC. A recently developed synthetic retinoid, sulfarotene, abrogates proliferation, and induces apoptosis of tumor-repopulating cells (TRCs) that exhibit stem cell-like properties, yet its effect and underlying mechanisms remain elusive in ICC. It is found that although 5-fluorouracil, cisplatin, pemigatinib, and gemcitabine all inhibit ICC-TRCs, sulfarotene demonstrates superior efficacy. Sulfarotene induces retinoic acid receptor alpha (RARɑ) translocation from the cytoplasm to the nucleus, suppressing P-selectin expression at the transcriptional level. Moreover, it directly interacts with fucosyltransferase 8 (FUT8), inhibiting the core fucosylation of P-selectin glycoprotein ligand 1 (PSGL1). These actions collectively inhibit ICC-TRCs via destroying PSGL1-regulated cytoskeleton. The findings provide a strategy of inhibiting P-selectin/PSGL1 interaction and altering PSGL1 glycosylation pattern to compromise the cytoskeletal integrity and eliminate ICC-TRCs.

SG-ML-PLAP: A structure-guided machine learning-based scoring function for protein-ligand binding affinity prediction

Computational methods to predict binding affinity of protein-ligand complex have been used extensively to design inhibitors for proteins selected as drug targets. In recent years machine learning (ML) is being increasingly used for design of drugs/inhibitors. However, ranking compounds as per their experimental binding affinity has remained a major challenge. Therefore, it is necessary to develop ML-based scoring function (MLSF) for predicting the binding affinity of protein-ligand complexes. In this work, protein-ligand interaction features, namely, extended connectivity interaction fingerprints (ECIF), derived from the PDBbind dataset have been used to build ML models for binding affinity prediction. The benchmarking has been done on the Comparative Assessment of Scoring Functions (CASF) dataset and also by predicting the binding affinity of unseen protein-ligand complexes which have structural features different from those present in the training dataset. Furthermore, an improvement in the performance of MLSF on the redocked CASF complexes generated by AutoDock Vina software was seen when the training set consisting of crystal structures was supplemented with redocked protein-ligand complexes. The MLSF trained on crystal structures alone using a combination of ECIF and VINA features also predicted binding affinities of crystal as well as docked complexes with high accuracy. Overall, the MLSF developed in this work shows improved performance compared to conventional SFs and several other MLSFs. It will be a valuable resource for identifying novel inhibitors by structure-based virtual screening protocols. The proposed MLSF SG-ML-PLAP (Structure-Guided Machine-Learning-based Protein-Ligand Affinity Predictor) is freely accessible as a webserver, http://www.nii.ac.in/sg-ml-plap.html.

Targeting MurG enzyme in Klebsiella pneumoniae: An in silico approach to novel antimicrobial discovery

Antibiotic resistance poses a global crisis fuelled by widespread antibiotic use, particularly against Gram-negative bacteria like Klebsiella pneumoniae, a leading cause of hospital-acquired infections with high mortality rates. Urgent identification of effective drug targets is imperative, with a focus on metabolic pathways to inhibit bacterial growth. Targeting the crucial metabolic pathways of K. pneumoniae would be a more efficient way to prevent its growth and the diseases that it causes. The present study focused on inhibiting the UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (MurG) enzyme, which is a key enzyme in peptidoglycan biosynthesis pathway. A high throughput virtual screening was used to find possible lead molecules from Enamine -High-Throughput Screening Center library. The resulting high binding affinity ligands were further assessed for their drug-likeness and other pharmacokinetic properties. Based on these analyses, the three ligands Z95813755_1, Z324718246_1 and Z324718246_2 were selected for further molecular dynamic simulation studies. The molecular dynamic simulation results and MM/PBSA analysis predicted that both Z95813755_1 and Z324718246_2, molecules show higher binding affinity towards MurG. For the first time we are reporting potential candidate inhibitors against MurG from K. pneumoniae, providing new insights in management of multi drug resistant K. pneumoniae infections.

In silico design and assessment of a multi-epitope peptide vaccine against multidrug-resistant Acinetobacter baumannii

Acinetobacter baumannii, an opportunistic and notorious nosocomial pathogen, is responsible for many infections affecting soft tissues, skin, lungs, bloodstream, and urinary tract, accounting for more than 722,000 cases annually. Despite the numerous advancements in therapeutic options, no approved vaccine is currently available for this particular bacterium. Consequently, this study focused on creating a rational vaccine design using bioinformatics tools. Three outer membrane proteins with immunogenic potential and properties of good vaccine candidates were used to select epitopes based on good antigenic properties, non-allergenicity, high binding scores, and a low IC50 value. A multi-epitope peptide (MEP) construct was created by sequentially linking the epitopes using suitable linkers. ClusPro 2.0 and C-ImmSim web servers were used for docking analysis with TLR2/TLR4 and immune response respectively. The Ramachandran plot showed an accurate model of the MEP with 100% residue in the most favored and allowed regions. The construct was highly antigenic, stable, non-allergenic, non-toxic, and soluble, and showed maximum population coverage. Additionally, molecular docking demonstrated strong binding between the designed MEP vaccine and TLR2/TLR4. In silico immunological simulations showed significant increases in T-cell and B-cell populations. Finally, codon optimization and in silico cloning were conducted using the pET-28a (+) plasmid vector to evaluate the efficiency of the expression of vaccine peptide in the host organism (Escherichia coli). This designed MEP vaccine would support and accelerate the laboratory work to develop a potent vaccine targeting MDR Acinetobacter baumannii.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00292-3.

Mycobacterium tuberculosis Mce3R TetR-like Repressor Forms an Asymmetric Four-Helix Bundle and Binds a Nonpalindrome Sequence†

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, is a major global health concern. TetR family repressors (TFRs) are important for Mtb's adaptation to the human host environment. Our study focuses on one notable Mtb repressor, Mce3R, composed of an unusual double TFR motif. Mce3R-regulated genes encode enzymes implicated in cholesterol metabolism, resistance against reactive oxygen species, and lipid transport activities important for Mtb survival and persistence in the host and for the cellular activity of a 6-azasteroid derivative. Here, we present the structure of Mce3R bound to its DNA operator, unveiling a unique asymmetric assembly previously unreported. We obtained a candidate DNA-binding motif through MEME motif analysis, comparing intergenic regions of mce3R orthologues and identifying nonpalindromic regions conserved between orthologues. Using an electrophoretic mobility shift assay (EMSA), we confirmed that Mce3R binds to a 123-bp sequence that includes the predicted motif. Using scrambled DNA and DNA oligonucleotides of varying lengths with sequences from the upstream region of the yrbE3A (mce3) operon, we elucidated the operator region to be composed of two Mce3R binding sites, each a 25-bp asymmetric sequence separated by 53 bp. Mce3R binds with a higher affinity to the downstream site with a Kd of 2.4 ± 0.7 nM. The cryo-EM structure of Mce3R bound to the 123-bp sequence was refined to a resolution of 2.51 Å. Each Mce3R monomer comprises 21 α-helices (α1-α21) folded into an asymmetric TFR-like structure with a core asymmetric four-helix bundle. This complex has two nonidentical HTH motifs and a single ligand-binding domain. The two nonidentical HTHs from each TFR bind within the high-affinity, nonpalindromic operator motif, with Arg53 and Lys262 inserted into the major groove. Site-directed mutagenesis of Arg53 to alanine abrogated DNA binding, validating the Mce3R/DNA structure obtained. Among 811,645 particles, 63% were Mce3R homodimer bound to two duplex oligonucleotides. Mce3R homodimerizes primarily through α15, and each monomer binds to an identical site in the DNA duplex oligonucleotide.

Investigating cognitive impairments and hippocampal proteome alterations in aged male rats with TAA-Induced minimal hepatic encephalopathy

The aging population faces a gradual decline in physical and mental capacities, with an increased risk of liver cirrhosis and chronic liver diseases leading to hepatic encephalopathy (HE). The intertwining of physiological manifestations of aging with the pathophysiology of HE significantly impairs cognitive ability, reduces quality of life, and increases mortality. Hence, effective therapeutic intervention is imperative. The present study investigated the impact of minimal HE (MHE) on cognitive impairment in an aged rat population by analyzing hippocampal proteome dynamics. For this purpose, an old MHE rat model was induced via thioacetamide. The label-free LC‒MS/MS method was employed to explore hippocampal proteomic changes and associated dysregulated biological pathways. A total of 1533 proteins were identified, and among these, 30 proteins were significantly differentially expressed (18 upregulated, and 12 downregulated). Three upregulated proteins, namely, fetuin-A, p23, and intersectin-1 were selected and validated for their increased expression via western blotting and immunofluorescence analysis, which confirmed the mass spectrometry results. These proteins have not been reported previously in MHE cases. We also identified the possible dysregulated biological pathways associated with the differentially expressed proteins via Metascape, a network analysis tool. We found that the differentially expressed proteins may be involved in the generation of precursor metabolites and energy, the neurotransmitter release cycle, positive regulation of dendritic spine development, chaperone-mediated protein folding and protein stabilization. This study highlights the potential mechanisms underlying neurological dysfunction in the aged population with MHE and identifies novel therapeutic targets for improved disease management.

De novo assembly of a near-complete genome of aquatic vegetable Zizania latifolia in the Yangtze River Basin

The cultivated Zizania latifolia, an aquatic vegetable prevalent in the Yangtze River Basin, represents a unique plant-fungus complex whose domestication is associated with host-parasite co-evolution. In this study, we present a high-quality, chromosome-scale genome assembly of cultivated Z. latifolia. We employed PacBio long-read sequencing and Hi-C technology to generate ~578.42 Mb genome assembly, which contains 47.59% repeat sequences with a contig N50 of ~33.75 Mb. The contigs were successfully clustered into 17 chromosomal-sized scaffolds with a GC content of 43.26%, showing 98.39% completeness in BUSCO analysis. In total, we predicted 39,934 protein-coding genes, 88.79% of which could be functionally annotated. This genome assembly provides a valuable resource for unraveling Z. latifolia's domestication process, and advances our understanding of the evolutionary history and agricultural potential of Z. latifolia.

In-silico identification of putatively functional intergenic small open reading frames in the cucumber genome and their predicted response to biotic and abiotic stresses

The availability of high-throughput sequencing technologies increased our understanding of different genomes. However, the genomes of all living organisms still have many unidentified coding sequences. The increased number of missing small open reading frames (sORFs) is due to the length threshold used in most gene identification tools, which is true in the genic and, more importantly and surprisingly, in the intergenic regions. Scanning the cucumber genome intergenic regions revealed 420 723 sORF. We excluded 3850 sORF with similarities to annotated cucumber proteins. To propose the functionality of the remaining 416 873 sORF, we calculated their codon adaptation index (CAI). We found 398 937 novel sORF (nsORF) with CAI ≥ 0.7 that were further used for downstream analysis. Searching against the Rfam database revealed 109 nsORFs similar to multiple RNA families. Using SignalP-5.0 and NLS, identified 11 592 signal peptides. Five predicted proteins interacting with Meloidogyne incognita and Powdery mildew proteins were selected using published transcriptome data of host-pathogen interactions. Gene ontology enrichment interpreted the function of those proteins, illustrating that nsORFs' expression could contribute to the cucumber's response to biotic and abiotic stresses. This research highlights the importance of previously overlooked nsORFs in the cucumber genome and provides novel insights into their potential functions.

Application of immunoinformatics to develop a novel and effective multiepitope chimeric vaccine against Variovorax durovernensis

Bloodstream infections pose a significant public health challenge caused by resistant bacteria such as Variovorax durovernensis, a recently reported Gram-negative bacterium, worsening the burden on healthcare systems. The design of a vaccine using chimeric peptides derived from a representative V. durovernensis strain holds significant promise for preventing disease onset. The current study aimed to employ reverse vaccinology (RV) approaches such as the retrieval of V. durovernensis proteomics data, removal of redundant proteins by CD-HIT, filtering of non-homologous proteins to humans and essential proteins, identification of outer membrane (OM) proteins by CELLO and PSORTb. Following these steps immunoinformatic approaches were applied, such as epitope prediction by IEDB, vaccine design using linkers and adjuvant and analysis of antigenicity, allergenicity, safety and stability. Among the 4208 nonredundant proteins, an OmpA family protein (A0A940EKP4) was designated a potential candidate for the development of a multiepitope vaccine construct. Upon analysis of OM protein, six immunodominant (B cell) epitopes were found on the basis of the chimeric construct following the prediction of CTL stands cytotoxic T lymphocyte and HTL stands helper T lymphocyte epitopes. To ensure comprehensive population coverage globally, the CTL and HTL coverage rates were 58.18 % and 46.56 %, respectively, and 77.23 % overall. By utilizing EAAAK, GPGPG, and AAY linkers, Cholera toxin B subunit adjuvants, and appropriate epitopes were smoothly incorporated into a chimeric vaccine effectively triggering both adaptive and innate immune responses. For example, the administered antigen showed a peak in counts on the fifthday post injection and then gradually declined until the fifteenth day. Elevated levels of several antibodies (IgG + IgM > 700,000; IgM > 600,000; IgG1 + IgG2; IgG1 > 500,000) were observed as decreased in the antigen concentration. Molecular dynamics simulations carried out via iMODS revealed strong correlations between residue pairs, highlighting the stability of the docked complex. The designed vaccine has promising potential in eliciting specific immunogenic responses, thereby facilitating future research for vaccine development against V. durovernensis.

Sorafenib and SIAIS361034, a novel PROTAC degrader of BCL-xL, display synergistic antitumor effects on hepatocellular carcinoma with minimal hepatotoxicity

The overexpression of BCL-xL is closely associated with poor prognosis in hepatocellular carcinoma (HCC). While the strategy of combination of BCL-xL and MCL-1 for treating solid tumors has been reported, it presents significant hepatotoxicity. SIAIS361034, a novel proteolysis targeting chimera (PROTAC) agent, selectively induces the ubiquitination and subsequent proteasomal degradation of BCL-xL through the CRBN-E3 ubiquitin ligase. When combined with sorafenib, SIAIS361034 showed a potent synergistic effect in inhibiting hepatocellular carcinoma development both in vitro and in vivo. Since SIAIS361034 exhibits a high degree of selectivity for degrading BCL-xL in hepatocellular carcinoma, the hepatotoxicity typically associated with the combined inhibition of BCL-xL and MCL-1 is significantly reduced, thereby greatly enhancing safety. Mechanistically, BCL-xL and MCL-1 sequester the BH3-only protein BIM on mitochondria at baseline. Treatment with SIAIS361034 and sorafenib destabilizes BIM/BCL-xL and BIM/MCL1 association, resulting in the liberation of more BIM proteins to trigger apoptosis. Additionally, we discovered a novel compensatory regulation mechanism in hepatocellular carcinoma cells. BIM can rapidly respond to changes in the balance between BCL-xL and MCL-1 through their co-transcription factor MEF2C to maintain apoptosis resistance. In summary, the combination therapy of SIAIS361034 and sorafenib represents an effective and safe approach for inhibiting hepatocellular carcinoma progression. The novel balancing mechanism may also provide insights for combination and precision therapies in the treatment of hepatocellular carcinoma.

Integrating Network Pharmacology and In Silico Analysis to Explore the Bioactive Compounds Against Gastric Cancer Treatment

Gastric cancer (GC) has become a major challenge in oncology research, primarily due to its detection at advanced stages. In this study, we identified and validated the pharmacological mechanisms involved in treating gastric cancer using an integrated approach combining network pharmacology, molecular docking, and a dynamic approach. Gastric cancer-related genes were obtained from DisGeNET, Genecard, and Malacard databases, while potential targets of bioactive compounds were predicted using SwissTargetPrediction. Network pharmacology and gene ontology (GO) enrichment analyses were employed to understand the molecular mechanisms of action. This should further be investigated to isolate bioactive compounds that can be used to treat different ailments. Albumin (ALB), B-cell lymphoma 2 (BCL-2), nuclear factor kappa B subunit 1 (NFKB1), hypoxia-inducible factor 1 alpha (HIF1A), and interleukin 6 (IL-6) had a higher expression in gastric cancer than in normal conditions. Top genes were validated by using the GEPIA (Gene Expression Profiling Interactive Analysis) database. Furthermore, the lead compounds dehydroxy-isocalamendiol and spathulenol exhibited the highest binding affinity with NFKB1 and HIF1A (-6.3 and -6 kJ/mol) in the molecular docking study. Enrichment analysis indicated enrichment of these hub targets in the programmed cell death-ligand 1 (PD-L1) checkpoint, phosphatidylinositol 3-kinases/protein kinase B (PI3K-Akt), Ras, and hypoxia-inducible factor-1 (HIF-1) signalling pathways with significant cut-offs of FDR < 0.01 and p < 0.05. Therefore, network pharmacology and molecular docking analyses revealed that dehydroxy-isocalamendiol and spathulenol exert therapeutic efficacy on gastric cancer by multiple targets, NFKB1 and HIF1A, and pathways (MAPK, PD-L1 checkpoint, PI3K-Akt, Ras, and HIF-1 pathways).

Drug-target prediction through self supervised learning with dual task ensemble approach

Drug-Target interaction (DTI) prediction, a transformative approach in pharmaceutical research, seeks novel therapeutic applications for computational method based virtual screening, existing drugs to address untreated diseases and discovery of existing drugs side effects. The proposed model predict DTI through Heterogeneous biological network by combining drug, genes and disease related knowledge. For the purpose of embedding extraction Self-supervised learning (SSL) has been used which, trains models through pretext tasks, eliminating the need for manual annotations. The pretext tasks are related to either structural based information or similarity based information. To mitigate GNN vulnerability to non-robustness, ensemble learning can be incorporated into GNNs, harnessing multiple models to enhance robustness. This paper introduces a Graph neural network based architecture consisting of task based module and ensemble module for link prediction of DTI. The ensemble module of dual task combinations, both in cold start and warm start scenarios achieve very good performance as it provide 0.960 in cold start and 0.970 in warm start mean AUCROC score with less deviation.

Catalpol improved energy metabolism and inflammation through the SIRT5-mediated signaling pathway to ameliorate myocardial injury

BACKGROUND AND PURPOSE

Catalpol (CAT) has diverse pharmacological functions, including cellular homeostasis maintenance and anti-inflammatory effects. Sirtuin 5 (SIRT5) plays a considerable role in regulating cellular homeostasis in cardiac diseases. Our research explores the therapeutic potential of CAT against myocardial injury and its underlying mechanism.

METHODS

The H9c2 cells were pretreated with different CAT concentrations for 24 h, or CAT for 24 h followed by CoCl2 stimulation. Cell viability was determined with MTT assay. Biochemical assays, western blotting, and quantitative real-time PCR (qRT-PCR), combined with bioinformatic analysis, were used to examine the impact of CAT on CoCl2-induced myocardial injury in H9c2 cells and further explore its molecular mechanisms.

RESULTS

CAT ameliorated levels of myocardial enzymes, increased nicotinamide adenine dinucleotide (NAD+/NADH) ratio and adenosine triphosphate (ATP), while inhibited lactic acid (LD), tumor necrosis factor-alpha (TNF-α), interleukin (IL)-1β, and IL-6 in CoCl2-induced H9c2 cells. Mechanistically, SIRT5 knockdown inhibited Lin28a expression and negated the effects of CAT on ATP level, LD content, and the expression of inflammatory factors in cells. CAT likely exerted its protective effects on myocardial function through the SIRT5-mediated signaling pathway.

CONCLUSIONS

CAT regulates energy metabolism and inflammation via the SIRT5-mediated signaling pathway, exerting a protective effect in myocardial injury.

ProtGraph: a tool for the quick and comprehensive exploration and exploitation of the peptide search space derived from protein sequence databases using graphs

Due to computational resource limitations, in mass spectrometry based proteomics only a limited set of peptide sequences is used for the matching against measured spectra. We present an approach to represent proteins by graphs and allow not only the canonical sequences but also known isoforms and annotated amino acid variations, e.g. originating from genomic mutations, and further common protein sequence features contained in Uniprot KB or other protein databases. Our C++ and Python implementation enables a groundbreaking comprehensive characterization of the peptide search space, encompassing for the first time all available annotations in a protein database (in combination more than $10^{200}$ possibilities). Additionally, it can be used to quickly extract the relevant subset of the search space for peptide to spectrum matching, e.g. filtering by the peptide mass. We demonstrate the advantages and innovative findings of our implementation compared to previous workflows by re-analysing publicly available datasets.

Integrated systems pharmacology, molecular docking, and MD simulations investigation elucidating the therapeutic mechanisms of BHD in Alzheimer's disease treatment

Alzheimer's disease (AD) poses a longstanding health challenge, prompting a century-long exploration into its etiology and progression. Despite significant advancements in medical science, current AD treatments provide only symptomatic relief, urging a shift towards innovative paradigms. This study, departing from the amyloid hypothesis, integrates Systems Pharmacology, Molecular Docking and Molecular Dynamic Simulations to investigate a polyherbal phytoformulation (US 7,273,626 B2) rooted in Ayurveda for AD, consisting of Bacopa monnieri, Hippophae rhamnoides, and Dioscorea bulbifera (BHD). Diosgenin emerges as a crucial compound, aligning with previous studies, yet recognizing its limitations in explaining BHD's mechanism, this research delves into the intricate network of interactions. Protein-Protein Interaction (PPI) network analysis identifies hub genes (ALOX5, GSK3B, ACHE, SRC, AKT1, EGFR, PIK3R1, ESR1 and APP), suggesting a systems-level modulation of AD. Enrichment analyses unveil 370 AD-associated genes and key terms like "Cellular Response to Chemical Stimulus" and "Regulation of Biological Quality." KEGG pathway analysis underscores BHD's potential in Alzheimer's disease pathway (hsa05010), Endocrine resistance (hsa01522), and PI3K-Akt signaling (hsa04151). Molecular docking, carefully selecting compounds (Kaempferol, Quercetin, Myricetin, Isorhamnetin, Beta-Sitosterol, Stigmasterol, Emodin and Diosgenin) and top modulated targets, validates interactions with high dock scores, providing promising therapeutic avenues. Two core targets, Acetylcholinesterase (AChE) and Estrogen Receptor 1 (ESR1), were identified for further investigation due to their critical roles in Alzheimer's disease. To validate the molecular docking results, Molecular Dynamics (MD) simulations were performed on the AChE complexes with Myricetin, Beta-Sitosterol, and Stigmasterol, as well as the ESR1 complexes with Emodin, Diosgenin, and Beta-Sitosterol. These simulations were then compared to the interactions observed with the marketed drugs Donepezil and Estradiol, which are commonly used in Alzheimer's treatment. The MD simulations provided detailed insights into the stability and behavior of these complexes over time. The findings indicated that Myricetin and Emodin not only maintained stable interactions with AChE and ESR1 but also exhibited greater stability than Donepezil and Estradiol at specific time points and protein regions, as demonstrated by lower RMSD and RMSF values. These results suggest that natural compounds hold promise as potential therapeutic agents in the treatment of Alzheimer's disease, offering new avenues for drug development, while the formulation BHD shows potential as an adjuvant in integrative medicine alongside standard Alzheimer's treatments, effectively targeting related pathways and genes.