In silico drug discovery for COVID-19 using gene expression profiles of mouse infected by MHV and those of human cell lines infected by SARS-CoV-2

Presentation at EUSTM2020
https://eustm-2020.heysummit.com/talks/in-silico-drug-discovery-for-covid-19-using-gene-expression-profiles-of-mouse-infected-by-mhv-and-those-of-human-cell-lines-infected-by-sars-cov-2/

Also published in PLoS ONE
https://doi.org/10.1371/journal.pone.0238907

Transcript

1. In silico drug discovery for COVID-19 using gene expression profiles of mouse infected by MHV and those of human cell lines infected by SARS-CoV-2 Y-h. Taguchi Department of Physics, Chuo University, Tokyo 112-8551, Japan Turki Turki Department of Computer Science, King Abdulaziz University, Jeddah, Saudi Arabia 7th Annual Congress of the European Society for Translational Medicine on Covid-19 (EUSTM-2020) 21-25 September, 2020 (Virtual Congress)
2. Y-h. Taguchi, Turki Turki Novel Method for Detection of Genes With Altered Expression Caused by Coronavirus Infection and Screening of Candidate Drugs for SARS-CoV-2 doi: 10.20944/preprints202004.0431.v2 Y-h. Taguchi, Turki Turki A New Advanced In silico Drug Discovery Method for Novel Coronavirus (SARS-CoV-2) with Tensor Decomposition- based Unsupervised Feature Extraction doi: 10.20944/preprints202004.0524.v2
3. Data set 1 Data set 1 Data set 2 Data set 2 Calu3 NHBE A549 MOI 0.2 MOI 2.0 ACE2 expressed SARS-CoV-2 3 3 3 3 3 Control 3 3 3 3 3 Number of samples (Biological replicates) Mouse (in vivo) Human cell lines (in vitro)
4. Data set 1 Data set 1 Data set 2 Data set 2
5. Data set 2 Data set 2 Genotype Tissue PBS vs MHV Biological replicates Technical replicates Genes Data set 1 Data set 1 Cell lines SARS-CoV-2 vs Control Biological replicates Genes )
6. Data set 1 Data set 1 Genotype Tissue PBS vs MHV Biological replicates Technical replicates 1st 1st 1st 1st 2nd
7. 1st Cell lines SARS-CoV-2 vs Control Biological replicates Data set 2 Data set 2 1st 1st 2nd
8. Data set 1 Data set 1 Data set 2 Data set 2 l 6 =3 l 4 =5
9. Data set 1 Data set 1 Data set 2 Data set 2 l 6 =3 l 4 =5 Enrichr Biological validations overlap with …. • proteins interact with SARS proteins • genes altered by SARS infection Drug repositioning • Drugs whose treatment alter expression of genes whose expression altered by SARS infection.
10. Data set 1 Data set 1 proteins interact with SARS proteins
11. Data set 2 Data set 2
12. genes altered by SARS infection Data set 1 Data set 1 Data set 2 Data set 2
13. Data set 2 (continued) Data set 2 (continued)
14. Drug repositioning Data set 1 Data set 1 Data set 2 Data set 2
15. Data set 1 Data set 1 Primaquine Primaquine is known to inhibit the replication of Newcastle disease virus, which is in the family of paramyxoviruses that are enveloped, non-segmented, negative-sense single-stranded RNA viruses. Meloxicam Meloxicam is known to have cytotoxic and antiproliferative activity on virus-transformed tumor cells, including myelocytomatosis virus and Rous sarcoma virus. Pyrogallol Pyrogallol was reported to have anti-virus effects on human influenza virus strain A/Udorn/72, avian influenza virus A/ swan/ Shimane/ 499 /83, herpes simplex virus-1, vesicular stomatitis virus, and retrovirus. Data set 2 Data set 2 Meloxicam Meloxicam is known to exert cytotoxic and antiproliferative activities towards virus-transformed tumor cells, including myelocytomatosis virus and Rous sarcoma virus. Gentamicin Gentamicin is known to be a bactericidal antibiotic, it also exhibits antiviral activity Dibromochloromethane Dibromochloromethane was announced as a possible antiviral drug by the Agency forToxic Substances and Disease Registry
16. Drug Perturbations from GEO Data set 2 Data set 2
17. LINCS L1000 Chem Pert, C646, Chelerythrine chloride, Canertinib BX-795, Sorafenib, QL-X-138, Radicicol,A-443654,CGP-60474, Alvocidib, QL-XII-47, Mitoxantrone, Geldanamycin, These are possible SARS-CoV-2 drug repositioning target.
18. Term Overlap P-value Adjusted P-value Ivermectin-7.5 mg/kg in CMC-Rat-Liver-1d-dn 12/277 2.98E-06 9.93E-06 Ivermectin-7.5 mg/kg in CMC-Rat-Liver-5d-dn 12/289 4.60E-06 1.44E-05 Ivermectin-7.5 mg/kg in CMC-Rat-Liver-3d-dn 11/285 2.29E-05 5.56E-05 Ivermectin-7.5 mg/kg in CMC-Rat-Liver-1d-up 10/323 3.28E-04 5.39E-04 Ivermectin-7.5 mg/kg in CMC-Rat-Liver-5d-up 8/311 4.06E-03 5.10E-03 Ivermectin-7.5 mg/kg in CMC-Rat-Liver-3d-up 8/315 4.38E-03 5.46E-03 In our second preprint, ivermectin ivermectin was one of hits! DrugMatrix in Enrichr Enrichr https://asia.nikkei.com/Spotlight/Coronavirus/Parasite-killing-drug-ivermectin-heads-into-coronavirus-trials Originally, discovered by Japanese Prof. Omura, Novel prize winner.
19. Validations 1: Comparison with gold standard PPI with SARS-CoV-2 Proteins Data set 1 Data set 1
20. Data set 2 Data set 2
21. Validations 2: Comparison with gold standard drug repositioning with SARS-CoV-2 Data set 1 Data set 1
22. Data set 2 Data set 2
23. Conclusions We have identified two set of genes whose expression altered by SARS-CoV-2 in vivo (mouse) and in vitro (human cell lines), respectively. Two gene sets are coincident with known SARS-CoV protein interacting human proteins and genes whose expression is altered by SARS-CoV infection. Drug repositioning, including ivermectin, are performed with identifying drugs that affect two set of genes. Validations: Coincidence with gold standard SARS-CoV-2 PPI and drug repositioning proposed for SARS-CoV-2. Our strategy might be promising.