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Search Results (18)
  • Open Access


    Deciphering key genes involved in cisplatin resistance in kidney renal clear cell carcinoma through a combined in silico and in vitro approach


    Oncology Research, Vol.31, No.6, pp. 899-916, 2023, DOI:10.32604/or.2023.030760

    Abstract The low survival rate of Kidney renal clear cell carcinoma (KIRC) patients is largely attributed to cisplatin resistance. Rather than focusing solely on individual proteins, exploring protein-protein interactions could offer greater insight into drug resistance. To this end, a series of in silico and in vitro experiments were conducted to identify hub genes in the intricate network of cisplatin resistance-related genes in KIRC chemotherapy. The genes involved in cisplatin resistance across KIRC were retrieved from the National Center for Biotechnology Information (NCBI) database using search terms as “Kidney renal clear cell carcinoma” and “Cisplatin resistance”. The genes… More >

  • Open Access


    Developing a Breast Cancer Resistance Protein Substrate Prediction System Using Deep Features and LDA

    Mehdi Hassan1,2, Safdar Ali3, Jin Young Kim2,*, Muhammad Sanaullah4, Hani Alquhayz5, Khushbakht Safdar6

    CMC-Computers, Materials & Continua, Vol.76, No.2, pp. 1643-1663, 2023, DOI:10.32604/cmc.2023.038578

    Abstract Breast cancer resistance protein (BCRP) is an important resistance protein that significantly impacts anticancer drug discovery, treatment, and rehabilitation. Early identification of BCRP substrates is quite a challenging task. This study aims to predict early substrate structure, which can help to optimize anticancer drug development and clinical diagnosis. For this study, a novel intelligent approach-based methodology is developed by modifying the ResNet101 model using transfer learning (TL) for automatic deep feature (DF) extraction followed by classification with linear discriminant analysis algorithm (TLRNDF-LDA). This study utilized structural fingerprints, which are exploited by DF contrary to conventional More >

  • Open Access


    In silico Prediction and Analysis of Potential Off-Targets and Off-Target Mutation Detection in StERF3-Gene Edited Potato Plants

    Hafiza Arooj Razzaq1, Siddra Ijaz1,*, Imran Ul Haq2, Faisal Saeed Awan1

    Phyton-International Journal of Experimental Botany, Vol.92, No.8, pp. 2451-2460, 2023, DOI:10.32604/phyton.2023.030501

    Abstract The imperative aspect of the CRISPR/Cas9 system is a short stretch of 20 nucleotides of gRNA that control the overall specificity. Due to the small size, the chance of its multiple occurrences in the genome increases; however, a few mismatches are tolerated by the Cas9 endonuclease activity. An accurate and careful in silico-based off-target prediction while target selection is preferred to address the issue. These predictions are based on a comprehensive set of selectable parameters. Therefore, we investigated the possible off-target prediction and their screening in StERF3 gene-edited potato plants while developing StERF3-loss-of-function mutants using CRISPR/Cas9 More >

  • Open Access


    Comparative studies on the binding site of anesthetics to GABA a receptors using in silico docking methods


    BIOCELL, Vol.47, No.7, pp. 1661-1673, 2023, DOI:10.32604/biocell.2023.027984

    Abstract Background: Although the GABAA receptor (GABAAR) has been proposed as the main action site for sevoflurane, isoflurane, halothane, enflurane, propofol, and benzodiazepines (BZDs), binding of these anesthetics with high-resolution structures of the GABAAR have been rarely examined by comparative docking analyses. Moreover, various combinations of ligands on more GABAARs with various subtypes need to be analyzed to understand the elaborate action mechanism of GABAARs better because some GABAA ligands showed specificity toward the distinct subtypes of the GABAAR. Methods: We performed in silico docking analysis to compare the binding modes of sevoflurane, isoflurane, halothane, enflurane, propofol,… More >

  • Open Access


    In Vitro and in Silico Insights on the Biological Activities, Phenolic Compounds Composition of Hypericum perforatum L. Hairy Root Cultures

    Oliver Tusevski1,*, Marija Todorovska1, Jasmina Petreska Stanoeva2, Marina Stefova2, Sonja Gadzovska Simic1

    Phyton-International Journal of Experimental Botany, Vol.92, No.3, pp. 921-941, 2023, DOI:10.32604/phyton.2023.024995

    Abstract Three Hypericum perforatum hairy root lines (HR B, HR F and HR H) along with non-transformed roots were analyzed for phenolic compounds composition and in vitro enzyme inhibitory properties. In silico molecular modeling was performed to predict the interactions of the most representative phenolic compounds in HR clones with enzymes related to depression, neurodegeneration and diabetes. Chromatographic analyses revealed that HR clones represent an efficient source of quinic acid and hydroxybenzoic acids, epicatechin and procyanidin derivatives, quercetin and kaempferol glycosides, as well numerous xanthones. In vitro antidepressant activity of HR extracts through monoamine oxidase A (MAO-A) inhibition was attributed… More >

  • Open Access


    Experimental and In Silico Analysis of Cordycepin and its Derivatives as Endometrial Cancer Treatment

    Pedro Fong*1, Cheng N. Ao*†1, Kai I. Tou*, Ka M. Huang*, Chi C. Cheong*, Li R. Meng*

    Oncology Research, Vol.27, No.2, pp. 237-251, 2019, DOI:10.3727/096504018X15235274183790

    Abstract The aim of this study was to investigate the inhibition effects of cordycepin and its derivatives on endometrial cancer cell growth. Cytotoxicity MTT assays, clonogenic assays, and flow cytometry were used to observe the effects on apoptosis and regulation of the cell cycle of Ishikawa cells under various concentrations of cordycepin, cisplatin, and combinations of the two. Validated in silico docking simulations were performed on 31 cordycepin derivatives against adenosine deaminase (ADA) to predict their binding affinities and hence their potential tendency to be metabolized by ADA. Cordycepin has a significant dose-dependent inhibitory effect on More >

  • Open Access


    A Combined Chemical, Computational, and In Vitro Approach Identifies SBL-105 as Novel DHODH Inhibitor in Acute Myeloid Leukemia Cells

    Hossam Kamli*, Gaffar S. Zaman*, Ahmad Shaikh*, Abdullah A. Mobarki, Prasanna Rajagopalan*‡

    Oncology Research, Vol.28, No.9, pp. 899-911, 2020, DOI:10.3727/096504021X16281573507558

    Abstract Inhibition of the dihydroorotate dehydrogenase (DHODH) has been successful at the preclinical level in controlling myeloid leukemia. However, poor clinical trials warrant the search for new potent DHODH inhibitors. Herein we present a novel DHODH inhibitor SBL-105 effective against myeloid leukemia. Chemical characteristics were identified by 1 H NMR, 13C NMR, and mass spectroscopy. Virtual docking and molecular dynamic simulation analysis were performed using the automated protocol with AutoDock-VINA, GROMACS program. Human-recombinant (rh) DHODH was used for enzyme inhibition study. THP-1, TF-1, HL-60, and SKM-1 cell lines were used. MTT assay was used to assess cell… More >

  • Open Access


    Nuclear Stress-Strain State over Micropillars: A Mechanical In silico Study

    Rachele Allena1,*, Denis Aubry2

    Molecular & Cellular Biomechanics, Vol.19, No.1, pp. 1-16, 2022, DOI:10.32604/mcb.2022.018958

    Abstract Cells adapt to their environment and stimuli of different origin. During confined migration through sub-cellular and sub-nuclear pores, they can undergo large strains and the nucleus, the most voluminous and the stiffest organelle, plays a critical role. Recently, patterned microfluidic devices have been employed to analyze the cell mechanical behavior and the nucleus self-deformations. In this paper, we present an in silico model to simulate the interactions between the cell and the underneath microstructured substrate under the effect of the sole gravity. The model lays on mechanical features only and it has the potential to assess… More >

  • Open Access


    Potential genomic biomarkers of obesity and its comorbidities for phthalates and bisphenol A mixture: In silico toxicogenomic approach


    BIOCELL, Vol.46, No.2, pp. 519-533, 2022, DOI:10.32604/biocell.2022.018271

    Abstract This in silico toxicogenomic study aims to explore the relationship between phthalates and bisphenol A (BPA) co-exposure and obesity, as well as its comorbid conditions, in order to construct a possible set of genomic biomarkers. The Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org) was used as the main data mining tool, along with GeneMania (https://genemania.org), ToppGene Suite (https://toppgene.cchmc.org) and DisGeNET (http://www.disgenet.org). Among the phthalates, bis(2-ethylhexyl) phthalate (DEHP) and dibutyl phthalate (DBP) were chosen as the most frequently curated phthalates in CTD, which also share similar mechanisms of toxicity. DEHP, DBP and BPA interacted with 84, 90 and 194… More >

  • Open Access


    In Silico analysis and linking of metabolism-related genes with the immune landscape in head and neck squamous cell carcinoma

    JIAYU ZHANG1,2,3,#, RUOYAN CAO1,2,3,#, JIANMIN PENG1,2,3, QINCHAO HU1,2,3, JUAN XIA1,2,3,*, BIN CHENG1,2,3,*

    BIOCELL, Vol.46, No.1, pp. 111-125, 2022, DOI:10.32604/biocell.2022.016612

    Abstract Metabolic reprogramming and immunologic suppression are two critical characteristics promoting the progression of head and neck squamous cell carcinoma (HNSCC). The integrative analysis of all the metabolism-related genes (MRGs) in HNSCC is lacking and the interaction between the metabolism and the immune characteristics also requires more exploration to uncover the potential mechanisms. Therefore, this study was designed to establish a prognostic signature based on all the MRGs in HNSCC. Genes of HNSCC samples were available from the TCGA and GEO databases while the MRGs were retrieved from a previous study. Ultimately 4 prognostic MRGs were… More >

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