Non-Structural Proteins (Nsp): A Marker for Detection of Human Coronavirus Families

Computer-aided drug design for the double-membrane vesicle pore complex inhibitors against SARS-CoV-2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of the ongoing global pandemic, has constituted the worst global health disaster in recent years. However, no antiviral drugs have proved clinically efficacious to combat SARS-CoV-2 infection. The SARS-CoV-2 double-membrane vesicle (DMV) pore complex, particularly for its positively charged residues R1613, R1614, R303, R305, and R306, which are highly conserved across β-coronaviruses and play a critical role in mediating RNA transport and virus replication, has been validated as an effective drug target. Here, we employed computer-aided drug design (CADD) techniques for the first time to screen the antiviral compounds against SARS-CoV-2 by targeting the crystal structure of the SARS-CoV-2 DMV nsp3-4 pore complex. A total of 486,387 drug compounds were subjected to virtual screening, such as toxicity prediction, ADMET prediction, molecular docking, and target analysis. The six compounds (three for each binding site) were selected based on their lowest binding energies. Notably, Compound 391 demonstrated the strongest binding affinity to the critical positively charged residues R1613 and R1614 at binding site 1, meanwhile, Compound 5,157 exhibited the most stable interactions with the essential positively charged residues R303, R305, and R306 at binding site 2. These results demonstrate that Compound 391 and Compound 5,157 exhibit greater potential antiviral effects, which provide a theoretical basis for further confirmation against SARS-CoV-2 in vitro and in vivo studies.

Genomic Evolution Strategy in SARS-CoV-2 Lineage B: Coevolution of Cis Elements

In the SARS-CoV-2 lineage, RNA elements essential for its viral life cycle, including genome replication and gene expression, have been identified. Still, the precise structures and functions of these RNA regions in coronaviruses remain poorly understood. This lack of knowledge points out the need for further research to better understand these crucial aspects of viral biology and, in time, prepare for future outbreaks. In this research, the in silico analysis of the cis RNA structures that act in the alpha-, beta-, gamma-, and deltacoronavirus genera has provided a detailed view of the presence and adaptation of the structures of these elements in coronaviruses. The results emphasize the importance of these cis elements in viral biology and their variability between different viral variants. Some coronavirus variants in some groups, depending on the cis element (stem-loop1 and -2; pseudoknot stem-loop1 and -2, and s2m), exhibited functional adaptation. Additionally, the conformation flexibility of the s2m element in the SARS variants was determined, suggesting a coevolution of this element in this viral group. The variability in secondary structures suggests genomic adaptations that may be related to replication processes, genetic regulation, as well as the specific pathogenicity of each variant. The results suggest that RNA structures in coronaviruses can adapt and evolve toward different viral variants, which has important implications for viral adaptation, pathogenicity, and future therapeutic strategies.

Avian coronavirus infectious bronchitis virus Beaudette strain NSP9 interacts with STAT1 and inhibits its phosphorylation to facilitate viral replication

Avian coronavirus, known as infectious bronchitis virus (IBV), is the causative agent of infectious bronchitis (IB). Viral nonstructural proteins play important roles in viral replication and immune modulation. IBV NSP9 is a component of the RNA replication complex for viral replication. In this study, we uncovered a function of NSP9 in immune regulation. First, the host proteins that interacted with NSP9 were screened. The immune-related protein signal transducer and activator of transcription 1 (STAT1) was identified and the interaction between NSP9 and STAT1 was further confirmed. Furthermore, IBV replication was inhibited in STAT1-overexpressing cells but inversely affected in STAT1 knock-down cells. Importantly, NSP9 inhibited STAT1 phosphorylation. Finally, the expression of JAK/STAT pathway downstream genes IRF7 and ISG20 was significantly decreased in NSP9-overexpressing cells. These results showed the important role of IBV NSP9 in immunosuppression.