Endogenous piRNAs Can Interact with the Omicron Variant of the SARS-CoV-2 Genome
Rakhmetullina A. Akimniyazova A. Niyazova T. Pyrkova A. Kamenova S. Kondybayeva A. Ryskulova A.-G. Ivashchenko A. Zielenkiewicz P.
April 2023MDPI
Current Issues in Molecular Biology
2023#45Issue 42950 - 2964 pp.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the COVID-19 pandemic, can still infect populations in many countries around the globe. The Omicron strain is the most mutated variant of SARS-CoV-2. The high transmissibility of the strain and its ability to evade immunity necessitate a priority study of its properties in order to quickly create effective means of preventing its spread. The current research aimed to examine the in silico interaction between PIWI-interacting RNAs (piRNAs) and the SARS-CoV-2 genome (gRNA) to identify endogenous piRNAs and propose synthetic piRNAs with strong antiviral activity for drug development. This study used validated bioinformatic approaches regarding the interaction of more than eight million piRNAs with the SARS-CoV-2 genome. The piRNAs’ binding sites (BSs) in the 5′UTR were located with overlapping nucleotide sequences termed clusters of BSs. Several BSs clusters have been found in the nsp3, nsp7, RNA-dependent RNA polymerase, endoRNAse, S surface glycoprotein, ORF7a, and nucleocapsid. Sixteen synthetic piRNAs that interact with gRNA have been proposed with free binding energy ranging from −170 kJ/mol to −175 kJ/mol, which can be used to create drugs that suppress the reproduction of SARS-CoV-2.
coronavirus genome , Omicron , piRNAs , replication , SARS-CoV-2 , translation
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Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, 02-106, Poland
Department of Technology of Production of Livestock Products, A. Baitursynov Kostanay Regional University, Kostanay, 110000, Kazakhstan
Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty, 050040, Kazakhstan
Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, 050040, Kazakhstan
Center for Bioinformatics and Nanomedicine, Almaty, 050060, Kazakhstan
Department of Population Health and Social Sciences, Kazakhstan’s Medical University “KSPH”, Almaty, 050060, Kazakhstan
Institute of Biochemistry and Biophysics
Department of Technology of Production of Livestock Products
Higher School of Medicine
Faculty of Biology and Biotechnology
Center for Bioinformatics and Nanomedicine
Department of Population Health and Social Sciences
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