Comprehensive bioinformatics study reveals targets and molecular mechanism of hesperetin in overcoming breast cancer chemoresistance

Hermawan, Adam; Putri, Herwandhani; Utomo, Rohmad Yudi

doi:10.1007/s11030-019-10003-2

Cited by 26 publications

(20 citation statements)

References 76 publications

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“…related to the progress of human breast cancer [26][27][28][29][30][31]. These data clearly provide useful information for the resistance development of breast cancer.…”

Section: Plos Onementioning

confidence: 73%

Genome-wide DNA methylation analysis of breast cancer MCF-7 / Taxol cells with MeDIP-Seq

Shi

Gong

et al. 2020

PLoS ONE

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Breast cancer (BC) is the most frequently diagnosed tumor in women worldwide. Although the combination of surgery and Taxol chemotherapy can achieve a certain therapeutic effect, patients often develop drug-resistance, resulting in a poor prognosis. Therefore, it is significative to seek the molecular mechanism of chemotherapy resistance. Recent studies have found that abnormal epigenetic regulation in breast cells changes the expression of key genes, which can lead to the occurrence, development, and maintenance of cancer, even related to the development of drug-resistance. Therefore, in this study, we performed methylated DNA immunoprecipitation-sequencing (MeDIP-seq) to reveal the difference in methylation between breast cancer drug-resistant cells and sensitive cells. A total of 55076 differentially methylated genes (DMGs) were detected, including 21061 hypermethylated DMGs and 34015 hypomethylated DMGs. Moreover, Gene Ontology (GO) analysis and KEGG pathway analysis reveal the function and pathway of screening genes. These results indicate that DNA methylation may be involved in regulating the occurrence and development of breast cancer.

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“…related to the progress of human breast cancer [26][27][28][29][30][31]. These data clearly provide useful information for the resistance development of breast cancer.…”

Section: Plos Onementioning

confidence: 73%

Genome-wide DNA methylation analysis of breast cancer MCF-7 / Taxol cells with MeDIP-Seq

Shi

Gong

et al. 2020

PLoS ONE

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“…Hermawan et al retrieved gene expression microarray data of hesperetin-treated NCI-60 cell from the COMPARE public library, and compared these data with the list of breast cancer resistance regulatory genes obtained from Pubmed. Further, KEGG pathway enrichment and molecular docking studies proved that hesperetin was a targeted inhibitor of ABL1, DNMT3B, and MLH1 (Hermawan et al, 2019). The results of this study provided the basis for the application of hesperetin in the clinical application of breast cancer chemical resistance.…”

Section: Gene Expression Microarray In Elucidating the Pharmacologicamentioning

confidence: 63%

High-Throughput Transcriptome Profiling in Drug and Biomarker Discovery

et al. 2020

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The development of new drugs is multidisciplinary and systematic work. High-throughput techniques based on "-omics" have driven the discovery of biomarkers in diseases and therapeutic targets of drugs. A transcriptome is the complete set of all RNAs transcribed by certain tissues or cells at a specific stage of development or physiological condition. Transcriptome research can demonstrate gene functions and structures from the whole level and reveal the molecular mechanism of specific biological processes in diseases. Currently, gene expression microarray and high-throughput RNA-sequencing have been widely used in biological, medical, clinical, and drug research. The former has been applied in drug screening and biomarker detection of drugs due to its high throughput, fast detection speed, simple analysis, and relatively low price. With the further development of detection technology and the improvement of analytical methods, the detection flux of RNAseq is much higher but the price is lower, hence it has powerful advantages in detecting biomarkers and drug discovery. Compared with the traditional RNA-seq, scRNA-seq has higher accuracy and efficiency, especially the single-cell level of gene expression pattern analysis can provide more information for drug and biomarker discovery. Therefore, (sc) RNA-seq has broader application prospects, especially in the field of drug discovery. In this overview, we will review the application of these technologies in drug, especially in natural drug and biomarker discovery and development. Emerging applications of scRNA-seq and the third generation RNA-sequencing tools are also discussed.

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“…The following seventeen plant-based compounds entering clinical trials were obtained from the literature and clinical trial database: catechin, colchicine, curcumin, daidzein, epigallocatechin gallate (EGCG), genistein, hesperetin, hesperidin, homoharringtonine, ingenol mebutate, luteolin, naringenin, paclitaxel, quercetin, resveratrol, vinblastine, and vincristine 16 . The chemical structures were drawn using Chemdraw software and then subjected to conformational search and energy minimization in MOE.…”

Section: Dataset Collectionmentioning

confidence: 99%

“…Molecular docking analysis was performed to screen the binding affinities of several natural products on CEP55-ALIX binding interaction. Molecular docking simulation, RMSD calculation, and visualization of binding interaction were conducted using MOE 2010.12 (Licensed from Faculty of Pharmacy UGM) 16,17 . The PDB ID 3E1R was used as the model of CEP55 considering the available complex with ALIX.…”

Section: Molecular Dockingmentioning

confidence: 99%

CEP55 Inhibitor: Extensive Computational Approach Defining a New Target of Cell Cycle Machinery Agent

Lestari

Utomo

2021

Adv Pharm Bull

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Purpose: Centrosomal protein 55 (CEP55) is a pivotal protein for cytokinesis during cell division. This study aimed to provide a comprehensive information about the CEP55 gene, including its expression pattern in several cancer types, conduct functional domain analysis across species, and perform a computational approach for potential inhibitors of CEP55. Methods: The expression levels of CEP55 in different cancers were analyzed using the Oncomine and TCGA databases. Evolutionary analysis of the CEP55 gene in various species was performed using MEGA-X software. Molecular docking analysis was used to screen the binding affinity of several natural products on CEP55–ALIX binding interaction. Results: High CEP55 expression was observed in 16 datasets of different cancer types. The high expression of the CEP55 protein was associated with worse outcomes in cancer treatments. Phylogenetic and evolutionary analyses revealed that the amino acid residues essential for CEP55 binding and localization were mostly conserved across vertebrates. Seventeen plant-based compounds were docked against the CEP55 protein to determine their binding affinities and illustrated specific sites of interaction for predicting novel protein–drug interactions. Flavanol compounds epigallocatechin gallate and catechin possessed superior binding affinity to all other compounds owing to the substitution of gallic ester or hydroxyl groups on the C3 position. Conclusion: This study provides comprehensive information about the CEP55 gene and insights for designing potent inhibitors against CEP55 signaling.

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Comprehensive bioinformatics study reveals targets and molecular mechanism of hesperetin in overcoming breast cancer chemoresistance

Cited by 26 publications

References 76 publications

Genome-wide DNA methylation analysis of breast cancer MCF-7 / Taxol cells with MeDIP-Seq

Genome-wide DNA methylation analysis of breast cancer MCF-7 / Taxol cells with MeDIP-Seq

High-Throughput Transcriptome Profiling in Drug and Biomarker Discovery

CEP55 Inhibitor: Extensive Computational Approach Defining a New Target of Cell Cycle Machinery Agent

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