Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing

Article

Islam, Md. Ariful, Kibria, Md. Kaderi, Hossen, Md. Bayazid, Reza, Md. Selim, Tasmia, Samme Amena, Tuly, Khanis Farhana, Mosharof, Md. Parvez, Kabir, Syed Rashel, Kabir, Md. Hadiul, Mollah, Md. Nurul Haque and Mosharof, P.. 2023. "Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing." Scientific Reports. 13 (1). https://doi.org/10.1038/s41598-023-31276-6
Article Title

Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing

ERA Journal ID201487
Article CategoryArticle
AuthorsIslam, Md. Ariful, Kibria, Md. Kaderi, Hossen, Md. Bayazid, Reza, Md. Selim, Tasmia, Samme Amena, Tuly, Khanis Farhana, Mosharof, Md. Parvez, Kabir, Syed Rashel, Kabir, Md. Hadiul, Mollah, Md. Nurul Haque and Mosharof, P.
Journal TitleScientific Reports
Journal Citation13 (1)
Article Number4685
Number of Pages19
Year2023
PublisherNature Publishing Group
Place of PublicationUnited Kingdom
ISSN2045-2322
Digital Object Identifier (DOI)https://doi.org/10.1038/s41598-023-31276-6
Web Address (URL)https://www.nature.com/articles/s41598-023-31276-6
AbstractSome recent studies showed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and idiopathic pulmonary fibrosis (IPF) disease might stimulate each other through the shared genes. Therefore, in this study, an attempt was made to explore common genomic biomarkers for SARS-CoV-2 infections and IPF disease highlighting their functions, pathways, regulators and associated drug molecules. At first, we identified 32 statistically significant common differentially expressed genes (cDEGs) between disease (SARS-CoV-2 and IPF) and control samples of RNA-Seq profiles by using a statistical r-package (edgeR). Then we detected 10 cDEGs (CXCR4, TNFAIP3, VCAM1, NLRP3, TNFAIP6, SELE, MX2, IRF4, UBD and CH25H) out of 32 as the common hub genes (cHubGs) by the protein–protein interaction (PPI) network analysis. The cHubGs regulatory network analysis detected few key TFs-proteins and miRNAs as the transcriptional and post-transcriptional regulators of cHubGs. The cDEGs-set enrichment analysis identified some crucial SARS-CoV-2 and IPF causing common molecular mechanisms including biological processes, molecular functions, cellular components and signaling pathways. Then, we suggested the cHubGs-guided top-ranked 10 candidate drug molecules (Tegobuvir, Nilotinib, Digoxin, Proscillaridin, Simeprevir, Sorafenib, Torin 2, Rapamycin, Vancomycin and Hesperidin) for the treatment against SARS-CoV-2 infections with IFP diseases as comorbidity. Finally, we investigated the resistance performance of our proposed drug molecules compare to the already published molecules, against the state-of-the-art alternatives publicly available top-ranked independent receptors by molecular docking analysis. Molecular docking results suggested that our proposed drug molecules would be more effective compare to the already published drug molecules. Thus, the findings of this study might be played a vital role for diagnosis and therapies of SARS-CoV-2 infections with IPF disease as comorbidity risk. © 2023, The Author(s).
KeywordsSARS‑CoV‑2; idiopathic pulmonary fibrosis (IPF) disease; Bioinformatics; genetic influence; COVID-19
ANZSRC Field of Research 20204299. Other health sciences
Byline AffiliationsUniversity of Rajshahi, Bangladesh
School of Business
Permalink -

https://research.usq.edu.au/item/z25zz/bioinformatics-based-investigation-on-the-genetic-influence-between-sars-cov-2-infections-and-idiopathic-pulmonary-fibrosis-ipf-diseases-and-drug-repurposing

Log in to edit

Download files

Published Version
s41598-023-31276-6.pdf
License: CC BY 4.0
File access level: Anyone

  • 16
    total views
  • 9
    total downloads
  • 6
    views this month
  • 2
    downloads this month

Export as

Related outputs

Parental role and peer support in adolescent suicidal behavior in eight South-East Asian countries
Sultana, Moomtahin, Gow, Jeff, Mosharof, Parvez, Rahman, Habibur, Koly, Kamrun N., Rahman, Md Ashfikur, Huq, Nafisa, Rawal, Lal B., Kumar, Manasi and Mahumud, Rashidul Alam. 2023. "Parental role and peer support in adolescent suicidal behavior in eight South-East Asian countries." Journal of Affective Disorders. 332, pp. 221-230. https://doi.org/10.1016/j.jad.2023.03.092
Meta-Data Analysis to Explore the Hub of the Hub-Genes That Influence SARS-CoV-2 Infections Highlighting Their Pathogenetic Processes and Drugs Repurposing
Mosharaf, Md. Parvez, Kibria, Md. Kaderi, Hossen, Md. Bayazid, Islam, Md. Ariful, Reza, Md. Selim, Mahumud, Rashidul Alam, Alam, Khorshed, Gow, Jeffrey and Mollah, Md. Nurul Haque. 2022. "Meta-Data Analysis to Explore the Hub of the Hub-Genes That Influence SARS-CoV-2 Infections Highlighting Their Pathogenetic Processes and Drugs Repurposing." Vaccines. 10 (8), pp. 1-22. https://doi.org/10.3390/vaccines10081248
Comprehensive In Silico Analysis of RNA Silencing-Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.)
Akond, Zobaer, Rahman, Hafizur, Ahsan, Md. Asif, Mosharaf, Md. Parvez, Alam, Munirul and Mollah, Md. Nurul Haque. 2022. "Comprehensive In Silico Analysis of RNA Silencing-Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.)." BioMed Research International. 2022. https://doi.org/10.1155/2022/4955209
Identification of host transcriptome-guided repurposable drugs for SARS-CoV-1 infections and their validation with SARS-CoV-2 infections by using the integrated bioinformatics approaches
Ahmed, Fee Faysal, Reza, Md. Selim, Sarker, Md. Shahin, Islam, Md. Samiul, Mosharaf, Md. Parvez, Hasan, Sohel and Mollah, Md. Nurul Haque. 2022. "Identification of host transcriptome-guided repurposable drugs for SARS-CoV-1 infections and their validation with SARS-CoV-2 infections by using the integrated bioinformatics approaches." PLoS One. 17 (4 April). https://doi.org/10.1371/journal.pone.0266124
Disclosing Potential Key Genes, Therapeutic Targets and Agents for Non-Small Cell Lung Cancer: Evidence from Integrative Bioinformatics Analysis
Mosharaf, Md. Parvez, Reza, Md. Selim, Gov, Esra, Mahumud, Rashidul Alam and Mollah, Md. Nurul Haque. 2022. "Disclosing Potential Key Genes, Therapeutic Targets and Agents for Non-Small Cell Lung Cancer: Evidence from Integrative Bioinformatics Analysis." Vaccines. 10 (5). https://doi.org/10.3390/vaccines10050771
Computational identification of host genomic biomarkers highlighting their functions, pathways and regulators that influence SARS‑CoV‑2 infections and drug repurposing
Mosharaf, Md. Parvez, Reza, Md. Selim, Kibria, Md. Kaderi, Ahmed, Fee Faysal, Kabir, Md. Hadiul, Hasan, Sohel and Mollah, Md. Nurul Haque. 2022. "Computational identification of host genomic biomarkers highlighting their functions, pathways and regulators that influence SARS‑CoV‑2 infections and drug repurposing." Scientific Reports. 12 (1). https://doi.org/10.1038/s41598-022-08073-8
Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework
Ahmed, Fee Faysal, Khatun, Mst. Shamima, Mosharaf, Md. Parvez and Mollah, Md. Nurul Haque. 2021. "Prediction of Protein-protein Interactions in Arabidopsis thaliana Using Partial Training Samples in a Machine Learning Framework." Current Bioinformatics. 16 (6), pp. 865-879. https://doi.org/10.2174/1574893616666210204145254
Psychological impact of COVID-19 among frontline financial services workers in Bangladesh
Rana, Rezwanul Hasan and Islam, Ariful. 2021. "Psychological impact of COVID-19 among frontline financial services workers in Bangladesh." Journal of Workplace Behavioral Health: employee assistance practice and research. 36 (3), pp. 238-249. https://doi.org/10.1080/15555240.2021.1930021
Computational prediction of protein ubiquitination sites mapping on Arabidopsis thaliana
Mosharaf, Md. Parvez, Hassan, Md. Mehedi, Ahmed, Fee Faysal, Khatun, Mst. Shamima, Moni, Mohammad Ali and Mollah, Md. Nurul Haque. 2020. "Computational prediction of protein ubiquitination sites mapping on Arabidopsis thaliana." Computational Biology and Chemistry. 85. https://doi.org/10.1016/j.compbiolchem.2020.107238
In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.)
Mosharaf, Md. Parvez, Rahman, Hafizur, Ahsan, Md. Asif, Akond, Zobaer, Ahmed, Fee Faysal, Islam, Md. Mazharul, Moni, Mohammad Ali and Mollah, Md. Nurul Haque. 2020. "In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.)." PLoS One. 15 (12 December). https://doi.org/10.1371/journal.pone.0228233
Determinants of bank profitability for the selected private commercial banks in Bangladesh: a panel data analysis
Islam, Md. Ariful and Rana, Rezwanul Hasan. 2017. "Determinants of bank profitability for the selected private commercial banks in Bangladesh: a panel data analysis." Banks and Bank Systems. 12 (3), pp. 179-192. https://doi.org/10.21511/bbs.12(3-1).2017.03