Structure analysis of the receptor binding of 2019-nCoV

Abstract

2019-nCoV is a newly identified coronavirus with high similarity to SARS-CoV. We performed a structural analysis of the receptor binding domain (RBD) of spike glycoprotein responsible for entry of coronaviruses into host cells. The RBDs from the two viruses share 72% identity in amino acid sequences, and molecular simulation reveals highly similar ternary structures. However, 2019-nCoV has a distinct loop with flexible glycyl residues replacing rigid prolyl residues in SARS-CoV. Molecular modeling revealed that 2019-nCoV RBD has a stronger interaction with angiotensin converting enzyme 2 (ACE2). A unique phenylalanine F486 in the flexible loop likely plays a major role because its penetration into a deep hydrophobic pocket in ACE2. ACE2 is widely expressed with conserved primary structures throughout the animal kingdom from fish, amphibians, reptiles, birds, to mammals. Structural analysis suggests that ACE2 from these animals can potentially bind RBD of 2019-nCoV, making them all possible natural hosts for the virus. 2019-nCoV is thought to be transmitted through respiratory droplets. However, since ACE2 is predominantly expressed in intestines, testis, and kidney, fecal-oral and other routes of transmission are also possible. Finally, antibodies and small molecular inhibitors that can block the interaction of ACE2 with RBD should be developed to combat the virus.

Keywords: Coronavirus; Molecular modeling; Sequence analysis; Structure analysis.

Fig. 1

Comparison of 2019-nCoV with closely related coronaviruses. A. Identity of 2019-nCoV with closely related coronaviruses in nucleotide sequences. Data are given for the percentage of coverage and sequence identity for the whole genome and the coding region of the entire spike glycoprotein and its receptor-binding domain (RBD). B. Amino acid sequence alignment for RBD of spike glycoprotein from five closely related coronaviruses. GenBank accession numbers are AY274119 for SARS (SARS-CoV isolated during the initial 2002–2003 SARS outbreak, ref. 8), AY525636 for SARSv (SARS-CoV isolated during the mild 2003–2004 outbreak, ref. 9), AY304486 for civet (SARS-CoV-like virus isolated from palm civets, ref. 10), AGZ48806.1 for bat (SARS-CoV-like coronavirus RsSHC014 isolated from bat, ref. 11), and MN908947.3 for nCoV (2019-nCoV). Amino acid residues interacting with ACE2 in the SARS-CoV RBD and conserved ones in other viruses are highlighted in red. Major secondary structures are underlined (double underlines for β-sheet). Major altered amino acids in 2019-nCoV are highlighted in green. Cysteine residues forming disulfide bonds and putative N-linked glycosylation sites are highlighted in yellow and cyan, respectively.

Fig. 2

Comparison of the known structures SARS-CoV RBD and its ACE2 complex with the deduced molecular models of 2019-nCoV RBD. Some structure segments and key amino acid residues are indicated.

Fig. 3

Amino acid sequence alignment of ACE2 molecules from 7 animals. Only the part containing amino acid residues (highlighted in red) in human ACE2 that directly interact with RBD of SARS-CoV is shown. Correspondent amino acids for other animals are also highlighted in red if they are shared by human ACE2. Major secondary structures are underlined (dash-lines for α-helix and double lines for β-sheet). GenBank accession numbers are AAX63775.1 for civet (Paguma larvata), ADN93475.1 for bat (Rhinolophus sinicus), KFQ92425.1 for bird (Nipponia nippon), XP_029140508.1 for snake (Protobothrops mucrosquamatus), XP_018104311.1 for frog (Xenopus laevis), and XP_007889845.1 for fish (Callorhinchus milii).

Fig. 4

Expression of ACE2 in human tissues. Data represent Consensus Normalized eXpression levels for 55 tissue types and 6 blood cell types obtained from The Human Protein Atlas (www.proteinatlas.org).