Translational protein RpsE as an alternative target for novel nucleoside analogues to treat MDR Enterobacter cloacae ATCC 13047: network analysis and molecular dynamics study

World Journal of Microbiology and Biotechnology, Journal Year: 2023, Volume and Issue: 39(7)

Published: May 8, 2023

Language: Английский

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Potential Signature Therapeutic Biomarkers TOP2A, MAD2L1, and CDK1 in Colorectal Cancer: A Systems Biomedicine-Based Approach

Biochemical Genetics, Journal Year: 2023, Volume and Issue: 62(3), P. 2166 - 2194

Published: Oct. 26, 2023

Language: Английский

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Molecular mechanisms and clinical significance of perineural invasion in malignancies: the pivotal role of tumor-associated Schwann cells in cancer progression and metastasis

Medical Oncology, Journal Year: 2025, Volume and Issue: 42(5)

Published: April 21, 2025

Language: Английский

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Computational advancements to facilitate therapeutic application of phytochemicals: Where do we stand?

Deleted Journal, Journal Year: 2025, Volume and Issue: 7(5)

Published: May 14, 2025

Abstract The bioactivity of phytochemicals has been widely reported in the literature, however, abundance phytochemical resources and their potent activities require laborious screening methods for feasible applications. Owing to lack pharmacologically safe therapeutic options tackle emerging infections drug resistance, there is an increasing interest diverse potential bioactive phytochemicals. However, consolidated reports on same are very limited. present article provides overview exemplary studies from last decade application silico that have guided fast efficient domain pertains functional aspects phytochemicals, such as antibacterial, antiviral, antiparasitic, antifungal, antioxidant, anti-inflammatory, anticancer effects. Based reviewed computational approaches, a common popularly adopted pipeline was illustrated utility A list databases provided help researchers identify phytocompounds research. prospect generating high volume research data can facilitate machine learning artificial intelligence-based future predictions during healthcare emergencies disease outbreaks.

Language: Английский

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Doxorubicin downregulates cell cycle regulatory hub genes in breast cancer cells

Medical Oncology, Journal Year: 2024, Volume and Issue: 41(9)

Published: Aug. 8, 2024

Language: Английский

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Comprehensive analysis on the diagnostic role of circulatory exosome‐based miR‐92a‐3p for osteoblastic metastases in prostate adenocarcinoma

Journal of Molecular Recognition, Journal Year: 2023, Volume and Issue: 36(8)

Published: May 31, 2023

Abstract Prostate adenocarcinoma (PRAD) is the second leading cause of death in men and key factor that attributes to severity higher mortality rates tumor's ability promote osteoblastic metastases (OM). Currently, no blood‐based biomarkers are present bridges crosstalk between PRAD OM progression. Conversely, circulatory microRNAs (miRNAs) gaining interest among scientific community for its potential as markers cancer detection. Using computational pipeline, this study screened exosome‐based miRNA functionally regulating PRAD. We retrieved expression profile miRNA, mRNA from microarray, RNA‐Seq samples deposited global repositories identified differentially expressed miRNAs (DEMs) genes. Thereafter, average was extracellular vesicle specifically exosomes. Survival analysis clinical profiling significant miR‐92a‐3p be a OM. This further examined by interactions with various noncoding RNA elements, transcription factors, oncogenes, tumor suppressor genes, protein kinases regulated miR‐92a‐3p. Identifying pattern, nodal metastasis, Gleason score, hazard ratio deciphered critical role targets Further, binding association analyzed through energy, seed match accessibility showed miRNA‐targets involved cytokine, TGF‐β, Wnt signaling having close regulatory promoting Our findings highlight potent diagnostic biomarker The comprehensive insights our can elemental designing

Language: Английский

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Cancer pharmacoinformatics: Databases and analytical tools

Functional & Integrative Genomics, Journal Year: 2024, Volume and Issue: 24(5)

Published: Sept. 19, 2024

Language: Английский

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Transcriptomic, mutational and structural bioinformatics approaches to explore the therapeutic role of FAP in predominant cancer types

Discover Oncology, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 23, 2024

Abstract Fibroblast activating protein (FAP) is a cell surface marker of cancer-associated fibroblasts with distinct pro-tumorigenic role. The present study analyzed the pan-cancer expression; and clinical mutational profiles FAP coding gene. Molecular dynamics simulation (MDS) deciphered backbone energetics FAP. Virtual screening subsequent pharmacokinetic-profiling (PK) filtered lead molecules, which were subjected to molecular docking. MDS projected stable trajectory for protein, as evidenced by low residue-level fluctuations, dynamics, energetics. Around five stabilization deleterious mutations in catalytic domain identified. binding energy (BE) from docking studies screened top molecules site-specific intermolecular interaction studies. Lead-16 (ZINC000245289699) exhibited significant BE inhibition constant −6.87 kcal/mol 12.27 μM, respectively, across its mutants. Interestingly, docked complexes interacted triad residues (S624, D702, H734). showed lower average root-mean-square fluctuations compared unbound suggesting ligand–protein complex. tumor-specific expression critical overall survival suggest inhibitors potential cancer therapeutic intervention hindering tumor microenvironment-driven progression.

Language: Английский

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Exploring the prognostic significance of PKCε variants in cervical cancer

BMC Cancer, Journal Year: 2023, Volume and Issue: 23(1)

Published: Sept. 4, 2023

Protein Kinase C-epsilon (PKCε) is a member of the novel subfamily PKCs (nPKCs) that plays role in cancer development. Studies have revealed its elevated expression levels are associated with cervical cancer. Previously, we identified pathogenic variations different domains through various bioinformatics tools and molecular dynamic simulation. In present study, aim was to find association variants rs1553369874 rs1345511001 determine influence these on protein-protein interactions PKCε, which can lead towards development poor survival rates.The clinicopathological features determined genotyping analysis. Odds ratio relative risk along Fisher exact test were calculated evaluate significance disease risk. Protein-protein docking performed docked complexes subjected dynamics simulation gauge impact PKCε's interactions.This study genetic Smad3 interacts PKCε this interaction promotes angiogenesis; therefore, selected for docking. The analysis promoted aberrant might activation oncogenic pathways. data obtained from suggested prognostic PRKCE gene rs1345511001.Through further vitro vivo validation, be used at clinical level as markers therapeutic targets against

Language: Английский

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An explainable machine learning data analytics method using TIGIT-linked genes for identifying biomarker signatures to clinical outcomes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Dec. 7, 2023

ABSTRACT In the last decade, immunotherapies targeting immune checkpoint inhibitors have been extremely effective in eliminating subsets of some cancers patients. Multi-modal and non-immune factors that contribute to clinical outcomes utilized for predicting response therapies developing diagnostics. However, these data analytic methods involve a combination complex mathematical analytics, even-more biological mechanistic pathways. order develop method analytics transcriptomics sets, we an explainable machine learning (ML) model investigate genes involved signaling pathway T-cell-immunoreceptor with immunoglobulin ITIM domain (TIGIT). TIGIT is receptor on T, NK, T-regulatory cells, has classified as inhibitor due its ability inhibit innate adaptive responses. We extracted gene whole genome sequencing 1029 early breast cancer patient tumors, adjacent normal tissues from TCGA UCSC Xena Data Hub public databases. followed workflow which following steps: i) acquisition, processing, visualization by ii) developed predictive prognostic using input (gene expression data) output (survival time) parameters iii) interpretation was performed calculating SHAP (Shapely-Additive-exPlanations); iv) application Cox-regression model, trained L-2 regularization optimization 5 fold cross validation. The identified signatures associated predicted survival outcome test set score 0.601. summary, this case study TIGIT-mediated pathways roadmap biologists harness ML effectively.

Language: Английский

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