ABSTRACT
Nucleocapsid phosphoprotein sheaths the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA (positive strand) and assists in virion assembly. This occurs via an interaction with membrane protein and genomic elements involved in transcription and replication. It is important to study these interactions and infer details of the mechanisms behind the connection. Virtual screening for inhibitor mining is also a swift approach for repurposing drugs as well as finding new leads. In this chapter, we describe a swift computational approach in guiding us to interaction, inhibition, and drug-like phytocompound screening against pathogenic agents, especially in pandemics when difficulty in commuting and smooth availability of resources is reduced, leading to plummeted experimental work. We present a case study on virtual screening of phytochemicals against nucleocapsid using a docking approach, followed by ADMET profiling of top compounds. © 2022 Elsevier Inc. All rights reserved.
ABSTRACT
The COVID-19 virus spread around the globe very rapidly during early 2020. Identification of the evolution pattern, and genome scale mutations in SARS-CoV-2 is essential to study the dynamics of this disease. The genomic sequences of thousands of SARS-CoV-2 infected patients from different countries are publicly available for sequence based in-depth analysis. In this study, the DNA sequences of SARS-CoV-2 from the COVID-19 infected patients (having or lacking a travel history) from Pakistan and India, the two highest populous neighboring countries in South Asia, have been analyzed by using computational tools of phylogenetics. These analyses revealed that the SARS-CoV-2 strain in Pakistani traveler COVID-19 patients is closely related to Iranian strains, the strain in non-traveler patients is related to the strain of Wuhan, China. Likewise, in India, the SARS-CoV-2 strains in travelers and non-travelers are closely related to Italy, Germany, and Mexico. The selected approach has also been utilized to find out the identical genomic regions and similar strains around the world. Collectively, our study suggested distinct strains and routes of viral transmission in Pakistan and India. These differences may infer partially the reason for the decline phase in viral propagation in Pakistan two months after the peak COVID-19 load, and rapid viral propagation in India making it the second worst-hit country in the world after the USA.