Identifying potential human and medicinal plant microRNAs against SARS-CoV-2 3'UTR region: A computational genomics assessment

Naman Mangukia; Priyashi Rao; Kamlesh Patel; Himanshu Pandya; Rakesh M Rawal

doi:10.1016/j.compbiomed.2021.104662

Identifying potential human and medicinal plant microRNAs against SARS-CoV-2 3'UTR region: A computational genomics assessment

Comput Biol Med. 2021 Sep:136:104662. doi: 10.1016/j.compbiomed.2021.104662. Epub 2021 Jul 19.

Authors

Naman Mangukia¹, Priyashi Rao², Kamlesh Patel³, Himanshu Pandya⁴, Rakesh M Rawal⁵

Affiliations

¹ Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India; BioInnovations, Bhayander (West), Mumbai, 401101, Maharashtra, India. Electronic address: namanmangukia@gujaratuniversity.ac.in.
² Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India. Electronic address: priyashi.rao@gujaratuniversity.ac.in.
³ Advait Theragnostics, GUSEC, Gujarat University, Ahmedabad, 380009, Gujarat, India. Electronic address: kamlesh.patel@advaitdx.com.
⁴ Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India. Electronic address: hapandya@gujaratuniversity.ac.in.
⁵ Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India. Electronic address: rakeshrawal@gujaratuniversity.ac.in.

Abstract

The coronavirus disease of 2019 (COVID-19) began as an outbreak and has taken a toll on human lives. The current pandemic requires scientific attention; hence we designed a systematic computational workflow to identify the cellular microRNAs (miRNAs) from human host possessing the capability to target and silence 3'UTR of SARS-CoV-2 genome. Based on this viewpoint, we extended our miRNA search to medicinal plants like Ocimum tenuiflorum, Zingiber officinale and Piper nigrum, which are well-known to possess antiviral properties, and are often consumed raw or as herbal decoctions. Such an approach, that makes use of miRNA of one species to interact and silence genes of another species including viruses is broadly categorized as cross-kingdom interactions. As a part of our genomics study on host-virus-plant interaction, we identified one unique 3'UTR conserved site 'GGAAGAG' amongst 5024 globally submitted SARS-CoV-2 complete genomes, which can be targeted by the human miRNA 'hsa-miR-1236-3p' and by Z. officinale miRNA 'zof-miR2673b'. Additionally, we also predicted that the members of miR477 family commonly found in these three plant genomes possess an inherent potential to silence viral genome RNA and facilitate antiviral defense against SARS-CoV-2 infection. In conclusion, this study reveals a universal site in the SARS-CoV-2 genome that may be crucial for targeted therapeutics to cure COVID-19.

Keywords: Antiviral defense; Computational genomics; Conserved 3′UTR; Medicinal plants; SARS-CoV-2; miRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

3' Untranslated Regions / genetics
COVID-19*
Computational Biology
Genomics
Humans
MicroRNAs* / genetics
Plants, Medicinal* / genetics
RNA, Plant
SARS-CoV-2

Substances

3' Untranslated Regions
MIRN1236 microRNA, human
MicroRNAs
RNA, Plant