Exploring Conformational Transition of 2019 Novel Coronavirus Spike Glycoprotein Between Its Closed and Open States Using Molecular Dynamics Simulations

Mert Gur; Elhan Taka; Sema Zeynep Yilmaz; Ceren Kilinc; Umut Aktas; Mert Golcuk

In December 2019, a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing the coronavirus disease (COVID-19) emerged as a human pathogen in the city of Wuhan, China. Since then, SARS-CoV-2 has spread worldwide rapidly. As of 17 April 2020, there are more than 2,000,000 confirmed COVID-19 cases globally, among them at least 135,000 have resulted in death (World Health Organization). Based on its genome sequence, SARS-CoV-2 belongs to same genus (betacoronavirus) as the severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle-East respiratory syndrome coronavirus (MERS-CoV). SARS-CoV emerged in the Guangdong province of China in 2002 and resulted in an epidemic outbreak infecting 8,098 and killing 774 people (Drosten et al. 2003 , Walls et al. 2020 . MERS-CoV emerged in 2012 in the Arabian Peninsula, where it remains a major public health concern, having infected ~2519 and killed 858 people in 27 countries (Memish et al. 2020 , Walls, Park et al. 2020 . Phylogenetic analyses have suggested that SARS-CoV-2 shares 82% gene sequence identity with SARS-CoV ) and 51.8% gene sequence identity with MERS-CoV (Han and Yang 2020) . Coronaviruses (CoVs) comprise a large and diverse family. Though having such high gene sequence identity with SARS-CoV and MERS-CoV, SARS-CoV-2 appears to be transmitted among humans more readily and much faster than SARS-CoV (Li et al. 2003 , Wrapp et al. 2020 ) and MERS-CoV (Paraskevis et al. 2020 . COVID-19 clinical symptoms are fever, dry cough, severe respiratory failure, and pneumonia ). On 10 March 2020, COVID-19 was declared as a pandemic by the World Health Organization (WHO) (World Health Organization 2020). Currently there is no proven treatment for COVID-19. Thus, there is a pressing need for the development of vaccines and therapeutics for COVID-19.