Bioinformatics and Biology Insights最新文献

{"title":"Machine Learning Techniques in Chronic Kidney Diseases: A Comparative Study of Classification Model Performance.","authors":"Nguyen Dong Phuong, Nguyen Trung Tuyen, Vu Thi Thai Linh, Nghi N Nguyen, Thanh Q Nguyen","doi":"10.1177/11779322251356563","DOIUrl":"https://doi.org/10.1177/11779322251356563","url":null,"abstract":"<p><p>The kidneys are vital organs responsible for filtering and eliminating toxins from the body. Chronic kidney disease (CKD) is becoming increasingly prevalent, affecting not only older adults but also younger populations. To minimize kidney damage for those at risk, an accurate assessment and monitoring of CKD are crucial. Machine learning models can assist physicians in this task by providing fast and accurate detection. As a result, many health care systems have adopted machine learning, especially for disease diagnosis. In this study, we developed a system to support the diagnosis of CKD. The data were collected from the UCL machine learning database, with missing values filled using the \"mean/mode\" and the \"random sampling method.\" After data processing, we applied the polynomial technique to generate additional features, allowing the models to be better generalized. Then, we utilized feature-based stratified splitting with K-means and implemented 6 machine learning algorithms (Random Forest, Support Vector Machine [SVM], Naive Bayes, Logistic Regression, K-Nearest Neighbor [KNN], and XGBoost) to compare their performance based on accuracy. Among them, Random Forest, XGBoost, SVM, and logistic regression achieved the highest accuracy of 100%, followed by Naive Bayes (97%) and KNN (93%).</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251356563"},"PeriodicalIF":2.4,"publicationDate":"2025-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12304504/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144741153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trans-Cannabitriol as a Dual Inhibition of MPOX Adhesion Receptors L1R and E8L: An In Silico Perspective.","authors":"Hanane Abbou, Razana Zegrari, Zainab Gaouzi, Lahcen Belyamani, Ilhame Bourais, Rachid Eljaoudi","doi":"10.1177/11779322251355315","DOIUrl":"10.1177/11779322251355315","url":null,"abstract":"<p><p>The re-emergence of monkeypox virus (MPXV) as a global public health concern highlights the urgent need for novel therapeutic strategies targeting viral proteins essential for infection. This study investigates the inhibitory potential of Trans-Cannabitriol (trans-CBT), a minor cannabinoid, against MPXV proteins L1R, H3L, and E8L using an integrative in silico framework. Homology modeling was employed to generate 3D structures of these proteins, followed by molecular docking and 1 µs molecular dynamics (MD) simulations. The trans-CBT demonstrated strong binding affinities for L1R (-10.76 kcal/mol) and E8L (-8.531 kcal/mol), with weaker interactions observed for H3L (-5.739 kcal/mol). Four MD simulations of 1 µs revealed that trans-CBT stabilizes L1R by reducing its flexibility and solvent exposure, potentially inhibiting viral entry into host cells. In contrast, trans-CBT increased the flexibility and conformational changes of E8L, possibly impairing its function in viral attachment and pathogenesis. ADMET and target prediction analyses further supported its drug-likeness and safety, with the absence of strong CB1/CB2 binding suggesting that trans-CBT may exert its antiviral effects independently of classical cannabinoid pathways. These findings provide insights into the diverse mechanisms of action of trans-CBT on MPXV proteins and underscore its potential as a broad-spectrum antiviral agent. While promising, further experimental validation and optimization are necessary to assess the real-world applicability of trans-CBT in combating MPXV infections. This work contributes to the expanding field of cannabinoid-derived antivirals and highlights the importance of exploring under-investigated phytochemicals for therapeutic applications.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251355315"},"PeriodicalIF":2.4,"publicationDate":"2025-07-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12290344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144727827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatic Analysis of WNT Family Proteins.","authors":"Konstantin Midlovets, Natalia Volkova, Mykyta Peka","doi":"10.1177/11779322251353347","DOIUrl":"10.1177/11779322251353347","url":null,"abstract":"<p><p>WNT proteins constitute a highly conserved family of signaling molecules that play an important role in regulating embryonic development and maintaining adult tissue homeostasis. Their diverse biological functions are mediated through multiple signaling pathways, including both canonical β-catenin-dependent and several non-canonical mechanisms. The regulatory activity of WNT proteins is closely linked to their unique structural organization, the presence of N-terminal signal peptides, and posttranslational modifications. In this study, <i>in silico</i> methods were used to analyze the structural features of WNT proteins. Specifically, the isoelectric points, GRAVY scores, aliphatic indices, and instability indices were determined, and correlation analysis was performed to examine relationships between the latter three parameters. In addition, the characteristics of N-terminal signal peptides in WNT family proteins were investigated, with a particular focus on the bioinformatic prediction of N-terminal peptide lengths in the WNT2B protein isoforms. Furthermore, <i>in silico</i> modeling and molecular dynamics simulations were employed to study the tertiary structure of WNT2B and to assess the significance of O-acylation at serine for the behavior of the mature protein in an aqueous environment. Thus, using computational approaches, new data were obtained on the structural features and dynamic properties of this group of regulatory proteins.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251353347"},"PeriodicalIF":2.3,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12264420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144648476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Uncovering the Anti-Herpetic Activity of Anionic Peptides Derived From the Cytoplasmic Domain of Nectin-1.","authors":"Rakesh Rahangdale, Sumit Birangal, Gautham Shenoy, Fayaz Shaik Mohammad, Mukesh Pasupuleti, Raghu Chandrashekar Hariharapura","doi":"10.1177/11779322251344130","DOIUrl":"10.1177/11779322251344130","url":null,"abstract":"<p><p>Nectin-1/herpes simplex virus glycoprotein D (HSV gD) interaction is crucial to drive herpes simplex virus (HSV) entry. Polyanions are known to show great potential as antivirals. Thus, we explored a peptide-based biotherapeutic approach and, for the first time, evaluated an anionic peptide derived from nectin-1 designed to bind HSV gD. Peptides enriched in acidic and basic residues were selected and computationally modeled using PEP-FOLD3, PROCHECK, ClusPro 2.0, and Desmond. Their antiviral efficacy was tested through virucidal, cell pretreatment, attachment inhibition, entry inhibition, and cytopathic effect (CPE) inhibition assays using a 10 TCID₅₀ (Tissue Culture Infectious Dose 50%) viral dose. Among 4 designed peptides, C1 and C2 showed strong binding to HSV-1 and HSV-2 gD in molecular dynamic (MD) simulations. Peptide C1 exhibited significant virucidal activity (HSV-1: 64.92%, HSV-2: 67.16%), attachment inhibition (HSV-1: 62.03%, HSV-2: 59.38%), and host cell-entry inhibition (HSV-1: 71.37%, HSV-2: 76.28%) at 250 µg/mL concentration. Combination treatment with peptides C1 and C2 at a final concentration of 250 µg/mL (125 µg/mL each) exhibited an additive effect against HSV-1 (68.57%) and HSV-2 (73.37%) infections when tested by CPE inhibition assay. This highlights the potential of HSV gD-targeted anionic peptides for future anti-HSV therapeutics.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251344130"},"PeriodicalIF":2.3,"publicationDate":"2025-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12182627/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144474008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immunoinformatics-Aided Design of a Multiepitope Vaccine Against <i>Eimeria Tenella</i>-Associated Chicken Coccidiosis.","authors":"Adeyinka I Fadahunsi, Adewale J Atansuyi, Abayomi I Adebayo, Clifford A Chineke","doi":"10.1177/11779322251348307","DOIUrl":"10.1177/11779322251348307","url":null,"abstract":"<p><p>Avian coccidiosis, caused by Eimeria protozoa, presents a significant threat to poultry, with <i>Eimeria tenella</i> being particularly harmful due to its impact on the chicken cecum. Growing resistance to current treatments necessitates alternative therapeutic approaches. Consequently, this study employed an immunoinformatics approach to design a multiepitope vaccine targeting <i>E tenella</i>. Key proteins, including the sporulated oocyst TA4 antigen, alkylglycerone-phosphate synthase, and apical membrane antigen-1, were analysed for epitope prediction. Further comprehensive downstream analysis identified 13 MHC class I, 6 MHC class II, and 7 B-cell epitopes, which were linked with suitable linkers. Also, cholera toxin subunit B was incorporated as an adjuvant, creating a 531-amino-acid construct. The vaccine demonstrated favourable predicted antigenicity, non-allergenicity, and stability properties. Molecular docking predicted interaction with toll-like receptor 15, while immune response simulation showed potential induction of various immunocytes, including helper and cytotoxic T-cells, natural killer cells, and immunoglobulins. The vaccine was predicted to promote antigen clearance after the second dose, suggesting strong memory response potential. These findings indicate the designed vaccine could stimulate a potent protective immune response against <i>E tenella</i> infection. However, further in vitro and in vivo validation studies are necessary to confirm the vaccine's efficacy before clinical application in poultry immunization programmes.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251348307"},"PeriodicalIF":2.3,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174798/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Shared Genetic Characteristics of Coronary Artery Disease and Peripheral artery Disease: Insights From Integrated Bioinformatics Analysis of RNA-Sequencing Data.","authors":"Abdul Qadir Nawabi, Lijuan Chen","doi":"10.1177/11779322251344123","DOIUrl":"10.1177/11779322251344123","url":null,"abstract":"<p><p>Coronary artery disease (CAD) and peripheral artery disease have serious effects on quality of life. Recent studies have shown that peripheral arterial disorders increase a person's risk of developing CAD. The clinical symptoms of these conditions include palpitations, fatigue, confusion, shortness of breath, and, in severe cases, heart failure or stroke. Despite these similarities, many diseases have no known treatments, which raises grave concerns for world health. The study aims to identify common differentially expressed genes (DEGs) between CAD and peripheral arterial disease (PAD) patients and investigate biological pathways, network-based analysis, immune and inflammatory profiling, biomarker identification, and multi-omics integration. This helps in early detection and targeted treatment strategies. The results revealed 48 upregulated DEGs that were shared among CAD and peripheral arterial disorders. Functional enrichment analysis revealed mainly myofibril assembly and actomyosin organization, highlighting muscle development and cellular structure, and KEGG pathway analysis revealed amino acid metabolism pathways. A network of protein-protein interactions (PPIs) was built via the STRING and visualized by Cytoscape plugin, CytoHubba, and MCODE, which led to the identification of 10 hub genes, ie, <i>GLS, CCND2, RBL2, ITGB1, IL6ST, THRB, MBNL1, PDE5A, PROS1</i>, and <i>CACNA2D3</i>. Most of these genes involved in key functions, such as voltage-gated calcium channel trafficking, cGMP degradation, RNA splicing, thyroid hormone receptor beta, IL6ST, and cytokine signaling, play crucial roles. Within this subnetwork, we identified 10 crucial seed nodes that are integral to the network's structure and function. The seed nodes highlight significant regulatory connections, providing insights into the underlying biological mechanisms involved. The transcription factor regulatory network of the hub genes revealed this phenomenon. Finding the important seed nodes in this regulatory network makes their role in maintaining the network's integrity and functionality even more clear. This could lead to new targeted therapies and better ways of managing CAD and peripheral blood disorders.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251344123"},"PeriodicalIF":2.3,"publicationDate":"2025-06-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12174686/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A User-Friendly Machine Learning Pipeline for Automated Leaf Segmentation in <i>Atriplex lentiformis</i>.","authors":"Michelle Lynn Yung, Kamila Murawska-Wlodarczyk, Alicja Babst-Kostecka, Raina Margaret Maier, Nirav Merchant, Aikseng Ooi","doi":"10.1177/11779322251344033","DOIUrl":"10.1177/11779322251344033","url":null,"abstract":"<p><p>Automated leaf segmentation pipelines must balance accuracy, scalability, and usability to be readily adopted in plant research. We present an end-to-end deep learning pipeline designed for practical use in plant phenotyping, which we developed and evaluated during a real-world plant growth experiment using <i>Atriplex lentiformis</i>. The pipeline integrates a fine-tuned Mask Region-based Convolutional Neural Network (Mask R-CNN) segmentation model trained on 176 plant images and achieves high performance despite the small training data set (Dice coefficient = 0.781). We quantitatively compare the fine-tuned Mask R-CNN model to Meta AI's Segment Anything Model (SAM) and evaluate natural language prompts using Grounded SAM and the Leaf-Only SAM post-processing pipeline for refining segmentation outputs. Our findings highlight that transfer learning on a specialized data set can still outperform a large foundation model in domain-specific tasks. In addition, we integrate QR codes for automated sample identification and benchmark multiple QR code decoding libraries, evaluating their robustness under real-world imaging conditions like distortion and lighting variation. To ensure accessibility, we deploy the pipeline as a user-friendly Streamlit web application, allowing researchers to analyze images without deep learning expertise. By focusing on practical deployment in addition to model performance, this study provides an open-source, scalable framework for plant science applications and addresses real-world challenges in automation and usability by the end-researcher.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251344033"},"PeriodicalIF":2.3,"publicationDate":"2025-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12149614/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144265239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative Machine Learning Approach to Explore Glycosylation Signatures and Immune Landscape in Moyamoya Disease.","authors":"Cunxin Tan, Jing Wang, Yanru Wang, Shaoqi Xu, Zhenyu Zhou, Junze Zhang, Shihao He, Ran Duan","doi":"10.1177/11779322251342412","DOIUrl":"10.1177/11779322251342412","url":null,"abstract":"<p><p>Moyamoya disease (MMD) is a rare, chronic cerebrovascular disorder of uncertain etiology. Although abnormal glucose metabolism has been implicated, the contribution of glycosylation-related genes in MMD remains elusive. In this study, we analyzed 2 transcriptome data sets (GSE189993 and GSE131293) from the Gene Expression Omnibus (GEO) database to identify 723 differentially expressed genes (DEGs) between MMD patients and controls. Intersection genes with known glycosylation-related genes underwent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. We utilized machine learning to select key hub genes, followed by immune cell infiltration and correlation analyses. In-depth immune cell analysis indicated that both CFP and MGAT5B were closely tied to various immune components, suggesting potential crosstalk between glycosylation pathways and immune regulation. Notably, CFP was positively associated with pDCs, HLA, and CCR, whereas MGAT5B correlated with B-cells, check-points, and T helper cells but showed a negative relationship with Tregs, hinting at an immunoregulatory mechanism influencing MMD progression. Motif-TF annotation highlighted csibp_M2095 as the motif with the highest normalized enrichment score (NES: 6.57). Reverse microRNA (miRNA)-gene prediction identified 75 miRNAs regulating these focus genes, along with 126 miRNA-miRNA interconnections. Connectivity Map (Cmap) analysis revealed that Chenodeoxycholic acid, MRS-1220, Phenytoin, and Piceid were strongly negatively correlated with MMD expression profiles, suggesting potential therapeutic candidates. Enzyme-linked immunosorbent assays confirmed elevated CFP and MGAT5B and reduced PTPN11 in MMD, aligning with our bioinformatic findings. Moreover, PTPN11 knockdown in human brain microvascular endothelial cells (HBMECs) significantly enhanced tube formation, indicating a role in vascular remodeling. Collectively, these results emphasize the importance of glycosylation-related genes and immune dysregulation in MMD pathogenesis. These findings broaden our understanding of MMD's underlying mechanisms and underscore the necessity of continued research into glycosylation-driven pathways for improved disease management.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251342412"},"PeriodicalIF":2.3,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12103670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structural Insights Into centSIRT6: Bioinformatic Analysis of N308K and A313S Substitution Effects.","authors":"Francisco Alejandro Lagunas-Rangel","doi":"10.1177/11779322251339698","DOIUrl":"10.1177/11779322251339698","url":null,"abstract":"<p><p>Sirtuin 6 (SIRT6), a member of the class III histone deacetylase (HDAC) family, is crucial for the maintenance of general health and is associated with increased life expectancy and resistance to age-related diseases such as cancer and metabolic disorders. A comparative analysis of the SIRT6 gene in Ashkenazi Jewish (AJ) centenarians and noncentenarian controls found a distinct allele, centSIRT6, enriched in the centenarian group. This allele features 2 linked substitutions, N308K and A313S, and exhibits enhanced functions, including more efficient suppression of LINE1 retrotransposons, improved repair of DNA double-strand breaks, and increased efficiency in cancer cell killing. Notably, centSIRT6 shows lower deacetylase activity but higher mono-adenosine diphosphate (ADP) ribosyl transferase activity compared with the wild-type enzyme. This study used several bioinformatics tools to explore the structural changes caused by the N308K and A313S substitutions in centSIRT6 and to elucidate how these alterations contribute to changes in the enzymatic activities of SIRT6. The results indicate that these mutations reduce the structural flexibility of centSIRT6, thus weakening its interactions with acetyl-lysine but strengthening its interactions with ADP-ribose. This research provides useful information for future experimental studies to further investigate the molecular mechanisms of centSIRT6.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251339698"},"PeriodicalIF":2.3,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12099093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144141432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Reverse Vaccinology and Immunoinformatic Approach for the Designing of a Novel mRNA Vaccine Against Stomach Cancer Targeting the Potent Pathogenic Proteins of <i>Helicobacter pylori</i>.","authors":"Abanti Barua, Md Habib Ullah Masum, Ahmad Abdullah Mahdeen","doi":"10.1177/11779322251331104","DOIUrl":"https://doi.org/10.1177/11779322251331104","url":null,"abstract":"<p><p><i>Helicobacter pylori</i> infection of the stomach's epithelial cells is a significant risk factor for stomach cancer. Various <i>H pylori</i> proteins (CagA, GGT, NapA, PatA, urease, and VacA) were targeted to design 2 messenger RNA (mRNA) vaccines, V1 and V2, using bioinformatics tools. Physicochemical parameters, secondary and tertiary structure, molecular docking and dynamic simulation, codon optimization, and RNA structure prediction have also been estimated for these developed vaccines. Physicochemical analyses revealed that these developed vaccines are soluble (GRAVY < 0), basic (pI < 7), and stable (aliphatic index < 80). The secondary and tertiary structure of the vaccines demonstrated robustness. The docking with toll-like receptors (TLRs) revealed that the vaccines have a potential affinity for TLR-2 (V1: -1132.3 kJ/mol, V2: -1093.6 kJ/mol) and TLR-4 (V1: -1042.7 kJ/mol, V2: -1201.2 kJ/mol), and molecular dynamics simulations confirmed their dynamic stability. Structural analyses of V1 (-505.96 kcal/mol) and V2 (-634.92 kcal/mol) mRNA vaccines underscored their stability. In addition, the vaccine showed a considerable rise in the counts of B cells and extended activation of both T cells was also observed for the vaccines, suggesting the potential for long-lasting immunity, and offering enhanced protection against <i>H pylori</i>. These findings not only suggest potential long-lasting immunity against <i>H pylori</i> but also offer hope for the future of stomach cancer prevention. Notably, the study emphasizes the need for subsequent animal and human-based studies to confirm these promising results.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251331104"},"PeriodicalIF":2.3,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12033411/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}