scholarly journals A novel computational approach for drug repurposing using systems biology

2018 ◽  
Vol 34 (16) ◽  
pp. 2817-2825 ◽  
Author(s):  
Azam Peyvandipour ◽  
Nafiseh Saberian ◽  
Adib Shafi ◽  
Michele Donato ◽  
Sorin Draghici
Keyword(s):  
Systems Biology ◽  
Drug Repurposing ◽  
Computational Approach

scholarly journals A Biologically-Based Computational Approach to Drug Repurposing for Anthrax Infection

Toxins ◽  
2017 ◽  
Vol 9 (3) ◽  
pp. 99 ◽  
Author(s):  
Jane Bai ◽  
Theodore Sakellaropoulos ◽  
Leonidas Alexopoulos
Keyword(s):  
Drug Repurposing ◽  
Computational Approach ◽  
Anthrax Infection

scholarly journals Drug Repurposing for Japanese Encephalitis Virus Infection by Systems Biology Methods

2018 ◽  
Author(s):  
Bo-Min Lv ◽  
Xin-Yu Tong ◽  
Yuan Quan ◽  
Meng-Yuan Liu ◽  
Qing-Ye Zhang ◽  
...  
Keyword(s):  
Systems Biology ◽  
Japanese Encephalitis Virus ◽  
Japanese Encephalitis ◽  
Antiviral Agents ◽  
Drug Repurposing ◽  
Enrichment Analysis ◽  
Potential Effect ◽  
Encephalitis Virus ◽  
Mice Model ◽  
Japanese Encephalitis Virus Infection

Japanese encephalitis is a zoonotic disease caused by Japanese encephalitis virus (JEV). It is mainly epidemic in Asia with an estimated 69,000 cases occurring per year. However, no approved agents are available for the treatment of JEV infection, and existing vaccines cannot resist various types of JEV strains. Drug repurposing is a new concept for finding new indication of existing drugs, and recently, it has been used to discover new antiviral agents. Identifying host proteins involved in the progress of JEV infection and using these proteins as targets are the center of drug repurposing for JEV infection. In this study, based on the gene expression data of JEV infection and the phenome-wide association study (PheWAS) data, we identified 286 genes participating in the progress of JEV infection using the systems biology methods. The enrichment analysis of these genes suggested that the genes identified by our methods were predominantly related to viral infection pathways and immune response-related pathways. We found that bortezomib which can target these genes may have potential effect on the treatment of JEV infection. Subsequently, we evaluated the antiviral activity of bortezomib using the JEV-infected mice model. The results showed that bortezomib can lower JEV-induced lethality in mice, alleviate suffering in JEV-infected mice and reduce the damage in brains caused by JEV infection. This work provides a new method for the development of antiviral agents.

scholarly journals A computational approach to drug repurposing against SARS-CoV-2 RNA dependent RNA polymerase (RdRp)

2020 ◽  
pp. 1-8 ◽  
Author(s):  
Giovanni Ribaudo ◽  
Alberto Ongaro ◽  
Erika Oselladore ◽  
Giuseppe Zagotto ◽  
Maurizio Memo ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Drug Repurposing ◽  
Computational Approach ◽  
Rna Dependent Rna Polymerase

scholarly journals Deciphering The Molecular Pathogenesis Behind Neurological Manifestations of SARS-CoV-2 And Drug Repurposing, A Systems Biology Approach

2021 ◽  
Author(s):  
maryam mozafar ◽  
Seyed Amir Mirmotalebisohi ◽  
Marzieh Sameni ◽  
Zeinab Dehghan ◽  
Yalda Khazaei-Poul ◽  
...  
Keyword(s):  
Systems Biology ◽  
Regulatory Networks ◽  
Target Genes ◽  
Viral Infections ◽  
Drug Repurposing ◽  
Enrichment Analysis ◽  
Neurological Complications ◽  
Functional Enrichment ◽  
Neurological Manifestations ◽  
Ppi Networks

Abstract Introduction: As the COVID-19 pandemic spreads worldwide, reports about the neurological complications of SARS-CoV-2 are excessively increasing. However, there is still insufficient high-throughput data on neuronal cells infected with SARS-CoV-2 to help predict its neural pathogenesis. HCoV-OC43 is another member of the beta coronavirus family that has confirmed neuro-invasive effects and has available neural omics data. This study predicts the critical genes, biological processes, and pathways mediating in SARS-CoV-2 neurological manifestations using a systems biology approach.Method: We retrieved raw data related to SARS-CoV-2 and HCoV-OC43 infections from gene expression omnibus datasets (GSE147507 and GSE13879 respectively). We constructed gene regulatory networks for both infections, detected significant regulatory motifs by FANMOD software, and created their subnetworks. We also constructed PPI networks and identified the MCODE clusters. In the intersection of merged subnetworks of two viruses, the most critical genes were verified in GRN & PPI networks. We drug-repurposed for the selected target genes and performed the functional enrichment analysis using DAVID and String databases.Results: Some of the top KEGG pathway results included NF-kappa B, Toll-like receptor, NOD-like receptor, MAPK, and Neurotrophin signaling pathways. The most essential identified genes included IL6, TNF, HOXA5, POU2F2, ITGB3, STAT1, YY1, E2F6, ESR1, FOXO3, FOXO1, MEF2A, ATF3, ATF4, DDIT3, TCF4, BCL2L2, and BMP4. These genes were also involved in mechanisms of other viral infections of the nervous system. This study repurposes nine medicines with effects on COVID-19 neurological complications. Some of the repurposed drugs were previously registered in clinical trials for COVID-19 treatment.Conclusion: We recommended some identified crucial genes and medications to investigate further their potential role in treating COVID-19 neurological complications.

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