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In Silico Research in Biomedicine
ISSN 3050-7871 · Elsevier · 208 artikel di indeks
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Artikel Jurnal
Insights from comparative analysis of Nipah virus strains and identifying key host-pathogen interactions and their potential inhibitors
Nipah virus (NiV), a World Health Organization priority pathogen, was analyzed at the genome, gene, and protein levels. The Human-Nipah protein-protein interaction network enabled functional enrichment analysis of the host-pathogen interactome. Molecular docking and dynamics simulations…
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miR-466 as a central miRNA with tumor-suppressive potential in the regulatory network of adrenocortical carcinoma
Adrenocortical carcinoma (ACC) is a rare and aggressive malignancy with limited prognostic markers and therapeutic options. This study presents a systems-level analysis of microRNA-centered regulatory alterations in ACC, focusing on miR‑466. Comparative network reconstruction revealed substantial…
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In silico assessment of cyanobacterial alkaloids as probable medications against SARS-CoV-2
The COVID-19 a devastating global pandemic of this century, has taken massive tolls in terms of morbidity and mortality due to high transmissibility and most severe post-recovery consequences. This pandemic continues to pose major global health challenges, driven by rapid viral evolution and…
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Combining molecular docking and molecular dynamics simulation to explore Quercetin's affinity and interactions with wild-type and mutated phosphatase and tensin homolog (PTEN)
This study investigates the interaction of Quercetin with wild-type and mutant PTEN, a key tumor suppressor inactivated in many cancers. Using molecular docking and MD simulations, we found Quercetin has a significantly higher binding affinity for mutant PTEN, with docking energies of –6.44…
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The role of mitochondrial DNA-copy number in infectious disease: A bidirectional two-sample Mendelian randomization study
Background: The causal relationship between blood cellular mitochondrial DNA copy number (mtDNA-CN) and infectious diseases remains to be elucidated. Methods: We conducted a bidirectional two-sample MR study using the summary statistics of blood cellular mtDNA-CN correlations from a meta-analysis…
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Computational identification of potential dengue RdRp inhibitors through docking, ADMET, and molecular dynamics
Dengue fever, caused by the dengue virus (DENV), remains a significant global health threat due to the lack of specific antiviral treatments or vaccines. Currently, no approved antivirals target DENV RNA-dependent RNA polymerase (RdRp), a crucial enzyme for viral replication. This study explores…
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Biomolecular interactions of Cyperus articulatus essential oil metabolites with Staphylococcus aureus Sortase A: Molecular dynamics simulation and pharmacokinetic studies
The essential oil of Cyperus articulatus has been extensively studied for its antibacterial activities against a wide range of pathogenic bacteria. The present work aimed to examine the molecular interactions of the central Cyperus articulatus rhizome essential oil metabolites with the target…
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Molecular docking and dynamics reveal potential galactagogue mechanism of Breynia patens via D2R, OXTR, and TRβ modulation
Objective: This study investigates the in-silico interactions of 17 active components from Breynia patens extract with lactation-related proteins. Methods: The compounds were first screened via rigid docking using AutoDock Vina against three target receptors: dopamine receptor D2R, oxytocin…
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Novel TRPA1 antagonist lead compound and its therapeutic potential in organophosphate poisoning
Organophosphate toxicity mediated by the TRPA1 ion channel presents a significant challenge in neurotoxicology. This study computationally explores a novel, potential inhibitory site within the TRPA1 channel pore, centered on the Serine 1039 residue. Using a comprehensive computational pipeline…
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Deep learning framework reveals drug combinations involving dipeptidyl peptidase-4 inhibitors for treatment of polycystic ovarian syndrome on a heterogeneous network
Polycystic Ovarian Syndrome (PCOS) is associated with infertility, cancer, diabetes and mental disorders. Still, there is no accepted solution for treatment. The crisis pertains to gastrointestinal issues and toxicity of existent Metformin-based drug combinations. Also, there is lack of synergistic…
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Immunosuppression-associated lncRNAs as prognostic biomarkers and therapeutic targets in NSCLC: A retrospective study
Background: Non-small cell lung cancer (NSCLC) is influenced by the immune regulation mediated by lncRNAs. However, the understanding of immunosuppression-associated lncRNAs and their clinical significance in NSCLC is still limited. Methods: We utilized RNA-seq and clinical data from the TCGA…
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In silico vaccine design targeting BoaA (Burkholderia Oligomeric Coiled-Coil Adhesin A): A novel approach to combat Burkholderia pseudomallei adhesion and virulence
Background: Melioidosis, caused by the Gram-negative bacteria Burkholderia pseudomallei, is a life-threatening illness seen in tropical climates. The lack of a viable vaccination and rising antibiotic resistance underline the critical need for new preventative methods against this WHO-designated…
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Design, synthesis, and in silico analysis of fluorescein-sorbitol derivatives as potential inhibitors of SARS-CoV and SARS-CoV-2 proteases
Fluorescein-sorbitol derivatives were synthesized under mild conditions through acetal formation between sorbitol and aldehydes, yielding products with good efficiency. Their structural integrity was verified using various spectral techniques. In silico evaluations, including molecular docking were…
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In silico identification and validation of immunogenic epitopes for mRNA vaccine development against babanki virus using bioinformatics approach
The Babanki virus, classified within the Alphavirus genus of the family Togaviridae, poses notable health challenges due to its association with febrile illnesses and possible arthritic symptoms. In this investigation, a comprehensive immunoinformatics and bioinformatics framework was applied to…
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In silico screening and molecular dynamics simulation of Leucas aspera bioactive compounds: Computational identification of novel AMPKα2 inhibitors for cancer therapy
Cancer remains a leading cause of global mortality, necessitating novel therapeutic approaches targeting cellular energy metabolism pathways. This study investigated bioactive compounds from Leucas aspera as potential AMPKα2 inhibitors for cancer therapy through comprehensive in silico analysis…
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Spectroscopic, molecular docking and quantum computational studies of 2,4-dinitrophenyl hydrazine
Density functional theory (DFT) optimization studies show that the strong electronegativity difference between N and H leads to NH bond contraction to approximately 1.01–1.02 Å in 2,4-dinitrophenyl hydrazine (2,4-DNPH), closely matching experimental X-ray values. The gauge-independent atomic…
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In Silico identification of taxane analogs as potentially-safer, chemoresistance-evading candidates for breast cancer
Breast cancer (BC) remains a leading cause of cancer-related death in women, with challenges like chemoresistance and treatment-induced toxicity limiting the efficacy of current therapies. The development of new drugs is a costly and lengthy process. This study employed a multi-step computational…
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In-Silico characterisation of antiviral activities of marine fungal derivatives: Focusing on TMPRSS2 as a therapeutic target
Marine fungi represent an underexplored source of bioactive metabolites with significant antiviral potential. The enzyme TMPRSS2, which primes the SARS-CoV-2 spike protein, is a crucial target for preventing viral entry into cells. Natural TMPRSS2 inhibitors derived from marine fungi offer…
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Integrative machine learning and structural bioinformatics strategies for the identification of selective sterol 14A-demethylase inhibitors targeting Trypanosoma Cruzi
Background of study: Chagas disease, commonly known as American trypanosomiasis is a potentially life-threatening infection caused by Trypanosoma cruzi. The current chemotherapy of chagas disease involves benznidazole and nifurtimox, however, both have several drawbacks such as intolerable side…
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Exploring the growth hormone and growth hormone receptor gene families in rainbow trout (Oncorhynchus mykiss): A genome-wide perspective
The growth hormone (GH) and growth hormone receptor (GHR) system is a central regulator of growth and metabolism in vertebrates, with critical implications for aquaculture productivity and functional genomics research. Despite its importance, a comprehensive comparative genome-wide analysis across…