Molecular basis of pangolin ACE2 engaged by COVID-19 virus

Abstract

The virus caused coronavirus disease 2019 (COVID-19 virus), also called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the seventh coronavirus that can infect humans, and belongs to the genus β-coronavirus in the family Coronaviridae. As of 5 November 2020, SARS-CoV-2 has caused >47000000 confirmed cases and >1200000 related deaths in 219 countries and regions, bringing great challenges to global public health. Currently, there is no approved therapeutics or vaccines for the treatment of this disease. Several studies suggested SARS-CoV-2 might have originated from bats based on phylogenetic analysis, but the intermediate host of the virus is still unknown. Besides humans, cats, dogs, tigers, lions, minks, and other species have been reported to be infected by SARS-CoV-2. Several studies have reported pangolins as the only other mammalian species carrying coronaviruses related to SARS-CoV-2 besides bats, and suggested pangolins might be the intermediate host of SARS-CoV-2. Previously, we and other groups identified the angiotensin converting enzyme 2 (ACE2), the receptor of SARS-CoV, also functions as the entry receptor of SARS-CoV-2 and is recognized by the receptor binding domain (RBD) of the spike protein (S). Then, we elucidated the interaction between SARS-CoV-2 RBD and human ACE2 (hACE2) or cat ACE2 (cACE2), and also found that SARS-CoV-2 had broad potential host range, including domestic animals, companion pets and wild animals. In this study, we investigated the binding features of SARS-CoV-2 and two pangolin coronaviruses (pangolin-CoVs, GX/P2V/2017 and GD/1/2019) that recognize the receptors of both pangolin ACE2 (pACE2) and hACE2 using surface plasmon resonance (SPR) and structural methods. We further determined the crystal structure of SARS-CoV-2 S (RBD) in complex with pACE2 at a 2.3 Å resolution, revealing the similarity in the binding mode between SARS-CoV-2 RBD to hACE2 and to cACE2. Interestingly, we found that the SARS-CoV-2 RBD-pACE2 complex is more similar to the SARS-CoV-2 RBD-hACE2 complex than to SARS-CoV-2 RBD-cACE2 complex. Furthermore, we modeled the interactions of GX/P2V/2017 RBD and GD/1/2019 RBD bound to pACE2 and hACE2, respectively, and found that both viruses adopted similar binding mode as SARS-CoV-2 RBD to pACE2 and hACE2. However, crystal structure and homology modeling implied that the interaction between the three RBDs and pACE2 were slightly weaker than their respective binding to hACE2, which was consistent with the receptor-RBD protein interaction measured by SPR. These results could facilitate better understanding of SARS-CoV-2 evolution, indicate the potential of pangolin-CoVs to enter human population that may lead to another outbreak, and highlight the importance of monitoring pangolin CoVs to prevent possible spillovers.