Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19

Debmalya Barh; Sandeep Tiwari; Marianna E Weener; Vasco Azevedo; Aristóteles Góes-Neto; M Michael Gromiha; Preetam Ghosh

doi:10.1016/j.compbiomed.2020.104051

Multi-omics-based identification of SARS-CoV-2 infection biology and candidate drugs against COVID-19

Comput Biol Med. 2020 Nov:126:104051. doi: 10.1016/j.compbiomed.2020.104051. Epub 2020 Oct 10.

Authors

Debmalya Barh¹, Sandeep Tiwari², Marianna E Weener³, Vasco Azevedo², Aristóteles Góes-Neto⁴, M Michael Gromiha⁵, Preetam Ghosh⁶

Affiliations

¹ Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India. Electronic address: dr.barh@gmail.com.
² Laboratório de Genética Celular e Molecular, Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
³ Clinical Research Center, Oftalmic, CRO, 119334, Bardina Str.22/4, Moscow, Russia.
⁴ Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.
⁵ Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IIT-M), Chennai, 600036, India.
⁶ Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA.

Abstract

SARS-CoV-2 has ushered a global pandemic with no effective drug being available at present. Although several FDA-approved drugs are currently under clinical trials for drug repositioning, there is an on-going global effort for new drug identification. In this paper, using multi-omics (interactome, proteome, transcriptome, and bibliome) data and subsequent integrated analysis, we present the biological events associated with SARS-CoV-2 infection and identify several candidate drugs against this viral disease. We found that: (i) Interactome-based infection pathways differ from the other three omics-based profiles. (ii) Viral process, mRNA splicing, cytokine and interferon signaling, and ubiquitin mediated proteolysis are important pathways in SARS-CoV-2 infection. (iii) SARS-CoV-2 infection also shares pathways with Influenza A, Epstein-Barr virus, HTLV-I, Measles, and Hepatitis virus. (iv) Further, bacterial, parasitic, and protozoan infection pathways such as Tuberculosis, Malaria, and Leishmaniasis are also shared by this virus. (v) A total of 50 candidate drugs, including the prophylaxis agents and pathway specific inhibitors are identified against COVID-19. (vi) Betamethasone, Estrogen, Simvastatin, Hydrocortisone, Tositumomab, Cyclosporin A etc. are among the important drugs. (vii) Ozone, Nitric oxide, plasma components, and photosensitizer drugs are also identified as possible therapeutic candidates. (viii) Curcumin, Retinoic acids, Vitamin D, Arsenic, Copper, and Zinc may be the candidate prophylaxis agents. Nearly 70% of our identified agents are previously suggested to have anti-COVID-19 effects or under clinical trials. Among our identified drugs, the ones that are not yet tested, need validation with caution while an appropriate drug combination from these candidate drugs along with a SARS-CoV-2 specific antiviral agent is needed for effective COVID-19 management.

Keywords: COVID-19; Candidate drugs; Infection pathways; Interactome; Prophylaxis agents; Proteome; SARS-CoV-2; Transcriptome.

MeSH terms

Antiviral Agents* / chemistry
Antiviral Agents* / pharmacokinetics
Antiviral Agents* / therapeutic use
Betacoronavirus* / genetics
Betacoronavirus* / metabolism
COVID-19
Coronavirus Infections* / drug therapy
Coronavirus Infections* / genetics
Coronavirus Infections* / metabolism
Databases, Genetic*
Drug Discovery*
Humans
Models, Biological*
Pandemics*
Pneumonia, Viral* / drug therapy
Pneumonia, Viral* / genetics
Pneumonia, Viral* / metabolism
Proteomics
SARS-CoV-2

Substances

Antiviral Agents