3D Modeling of Non-coding RNA Interactions

Singh, Krishna Pal; Gupta, Shailendra

doi:10.1007/978-3-031-08356-3_11

Cited by 2 publications

(2 citation statements)

References 146 publications

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“…MiRNA sequences were given as input to MC Fold and among the multiple predicted secondary structures, the one with minimum energy was selected and then submitted to MC Sym, to predict the stable tertiary structures. MC Sym generates structures by examining the conformational search space of RNA [34].…”

Section: Shortlisted Mirnas 3d Structure Predictionmentioning

confidence: 99%

In-silico Elucidation of the Role of ABC-Transporter Genes Expression Regulation by OncomiRs (miR-21, miR-15, and miR-let-7) in Drug Efflux and Chemoresistance in Breast Cancer

Khalaf,

Suleiman,

Suwaid

2023

Math.Biol.Bioinf.

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Breast cancer is the most common and aggressive malignancy in females with a high prevalence rate of 77.9 million worldwide. Chemotherapy and tyrosine kinase inhibitors have been used to treat invasive and malignant tumors; however, invasive tumors have showed resistance to conventional therapies. ABC transporters play a crucial role in breast cancer due to their chemo-resistance and drug efflux abilities. Additionally, chemo-resistant roles of ABC transporters have been reported in several cancers such as cervical cancer, colon cancer, esophageal squamous cell carcinoma, glioma and HCC. The goal of this study was to identify the tumor suppressor role of miR-21, miR-15 and miR-let-7 to chemo-resistant genes majorly ABCA1, ABCB1 and ABCC1 in breast cancer. TargetScan, miRWalk, and miRDB were employed to predict microRNA-mRNA interactions. MC-Sym and RNAComposer were utilized for the tertiary structure prediction of shortlisted miRNAs and mRNAs. For molecular docking and visualization, HDOCK and PyMOL were employed. The present study identified 10, 7 and 13 interactions between microRNAs (miR-21, miR-15, and miR-let-7) and oncogenes (ABCA1, ABCB1, ABCC1) through miRWalk, miRDB and TargetScan respectively. RNA22 predicted the binding sites of microRNAs such as 22 miR-21, 11 miR-15 and 58 miR-let-7 on ABCA1, ABCB1 and ABCC1, respectively. Out of multiple docked complexes, the top 3 were shortlisted for visualization based on maximum confidence score and least binding affinity. The present study identifies the interactions of two novel (miR-15a-5p and let-7c-5p) microRNAs with ABCA1, ABCB1 and ABCC1 regions due to their maximum interactions. The findings of this research may help in developing miRNA drugs that could target ABC transporters specifically ABCA1, ABCB1 and ABCC1 to inhibit increased drug efflux and chemoresistance in breast cancer.

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Section: Shortlisted Mirnas 3d Structure Predictionmentioning

confidence: 99%

In-silico Elucidation of the Role of ABC-Transporter Genes Expression Regulation by OncomiRs (miR-21, miR-15, and miR-let-7) in Drug Efflux and Chemoresistance in Breast Cancer

Khalaf,

Suleiman,

Suwaid

2023

Math.Biol.Bioinf.

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“…A deep understanding of these mechanisms based on non-covalent binding of lncRNA to mRNA, DNA, miRNA, and RNA-binding proteins, in which steric complementarities play an important role, is impossible without an analysis of 3D structures. Although such studies have not yet been reported for NSCLC, the methods of 3D analysis and structural modeling are developing, and it was shown that folding and maintaining the structure seem to be important for encoding lncRNA functions and interactions [23,24].…”

Section: Introductionmentioning

confidence: 99%

Various LncRNA Mechanisms in Gene Regulation Involving miRNAs or RNA-Binding Proteins in Non-Small-Cell Lung Cancer: Main Signaling Pathways and Networks

Braga,

Fridman,

Burdennyy

et al. 2023

IJMS

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Long non-coding RNAs (lncRNAs) are crucial players in the pathogenesis of non-small-cell lung cancer (NSCLC). A competing binding of lncRNAs and mRNAs with microRNAs (miRNAs) is one of the most common mechanisms of gene regulation by lncRNAs in NSCLC, which has been extensively researched in the last two decades. However, alternative mechanisms that do not depend on miRNAs have also been reported. Among them, the most intriguing mechanism is mediated by RNA-binding proteins (RBPs) such as IGF2BP1/2/3, YTHDF1, HuR, and FBL, which increase the stability of target mRNAs. IGF2BP2 and YTHDF1 may also be involved in m6A modification of lncRNAs or target mRNAs. Some lncRNAs, such as DLGAP1-AS2, MALAT1, MNX1-AS1, and SNHG12, are involved in several mechanisms depending on the target: lncRNA/miRNA/mRNA interactome and through RBP. The target protein sets selected here were then analyzed using the DAVID database to identify the pathways overrepresented by KEGG, Wikipathways, and the Reactome pathway. Using the STRING website, we assessed interactions between the target proteins and built networks. Our analysis revealed that the JAK-STAT and Hippo signaling pathways, cytokine pathways, the VEGFA-VEGFR2 pathway, mechanisms of cell cycle regulation, and neovascularization are the most relevant to the effect of lncRNA on NSCLC.

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3D Modeling of Non-coding RNA Interactions

Cited by 2 publications

References 146 publications

In-silico Elucidation of the Role of ABC-Transporter Genes Expression Regulation by OncomiRs (miR-21, miR-15, and miR-let-7) in Drug Efflux and Chemoresistance in Breast Cancer

In-silico Elucidation of the Role of ABC-Transporter Genes Expression Regulation by OncomiRs (miR-21, miR-15, and miR-let-7) in Drug Efflux and Chemoresistance in Breast Cancer

Various LncRNA Mechanisms in Gene Regulation Involving miRNAs or RNA-Binding Proteins in Non-Small-Cell Lung Cancer: Main Signaling Pathways and Networks

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