Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) has become a global public health emergency. G-quadruplex, one of the non-canonical secondary structures, has shown potential antiviral values. However, little is known about the G-quadruplexes of the emerging SARS-CoV-2. Herein, we characterized the potential G-quadruplexes in both positive and negative-sense viral strands. The identified potential G-quadruplexes exhibited similar features to the G-quadruplexes detected in the human transcriptome. Within some bat- and pangolin-related betacoronaviruses, the G-tracts rather than the loops were under heightened selective constraints. We also found that the amino acid sequence similar to SUD (SARS-unique domain) was retained in SARS-CoV-2 but depleted in some other coronaviruses that can infect humans. Further analysis revealed that the amino acid residues related to the binding affinity of G-quadruplexes were conserved among 16,466 SARS-CoV-2 samples. Moreover, the dimer of the SUD-homology structure in SARS-CoV-2 displayed similar electrostatic potential patterns to the SUD dimer from SARS. Considering the potential value of G-quadruplexes to serve as targets in antiviral strategy, our fundamental research could provide new insights for the SARS-CoV-2 drug discovery.
Highlights
The coronavirus disease 2019 (COVID-19) pandemic, which first broke out in China, has rapidly become a global public health emergency within a few months (Lai et al, 2020)
Fifteen of the 24 PG4s (67.5%) were located in the positive-sense strand (Table 1); most of them were harbored in non-structural proteins including nsp1, nsp3, nsp4, nsp5, nsp10, and nsp14, with the remaining ones located in the spike protein, orf3a, and the membrane protein
G-quadruplexes have shown tremendous potential for the development of anticancer (Han and Hurley, 2000; Balasubramanian et al, 2011; Miller and Rodriguez, 2011; Neidle, 2017) and antiviral drugs (Perrone et al, 2015; Ruggiero and Richter, 2018, 2020), as G-quadruplexes can interfere with many biological processes that are critical to cancer cells and viruses
Summary
The coronavirus disease 2019 (COVID-19) pandemic, which first broke out in China, has rapidly become a global public health emergency within a few months (Lai et al, 2020). Since 2000, humans have suffered at least three coronavirus outbreaks, and they were severe acute respiratory syndrome (SARS) in 2003 (Zhong et al, 2003; Peiris et al, 2004; Zumla et al, 2016; Cui et al, 2019), Middle East respiratory syndrome (MERS) in 2012 (Zumla et al, 2016; Cui et al, 2019), and COVID-19. Scientists identified and sequenced the virus early in this outbreak, and named it SARS-CoV-2 (Gorbalenya et al, 2020). The clinical chest CT (computed tomography) and nucleic acid testing are the most typical methods of diagnosing COVID-19 (Jin et al, 2020; Zu et al, 2020). Despite the great efforts of the researchers, no specific clinical drugs or vaccines had developed to cope with COVID-19 by the end of September 2020
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