Elucidating Interactions Between SARS-CoV-2 Trimeric Spike Protein and ACE2 Using Homology Modeling and Molecular Dynamics Simulations

Abstract

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19). As of October 21, 2020, more than 41.4 million confirmed cases and 1.1 million deaths have been reported. Thus, it is immensely important to develop drugs and vaccines to combat COVID-19. The spike protein present on the outer surface of the virion plays a major role in viral infection by binding to receptor proteins present on the outer membrane of host cells, triggering membrane fusion and internalization, which enables release of viral ssRNA into the host cell. Understanding the interactions between the SARS-CoV-2 trimeric spike protein and its host cell receptor protein, angiotensin converting enzyme 2 (ACE2), is important for developing drugs and vaccines to prevent and treat COVID-19. Several crystal structures of partial and mutant SARS-CoV-2 spike proteins have been reported; however, an atomistic structure of the wild-type SARS-CoV-2 trimeric spike protein complexed with ACE2 is not yet available. Therefore, in our study, homology modeling was used to build the trimeric form of the spike protein complexed with human ACE2, followed by all-atom molecular dynamics simulations to elucidate interactions at the interface between the spike protein and ACE2. Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) and in silico alanine scanning were employed to characterize the interacting residues at the interface. Twenty interacting residues in the spike protein were identified that are likely to be responsible for tightly binding to ACE2, of which five residues (Val445, Thr478, Gly485, Phe490, and Ser494) were not reported in the crystal structure of the truncated spike protein receptor binding domain (RBD) complexed with ACE2. These data indicate that the interactions between ACE2 and the tertiary structure of the full-length spike protein trimer are different from those between ACE2 and the truncated monomer of the spike protein RBD. These findings could facilitate the development of drugs and vaccines to prevent SARS-CoV-2 infection and combat COVID-19.

Keywords: COVID-19; SARS-CoV-2; homology modeling; molecular dynamics simulations; spike protein.

Figure 1

The genomic structure of Severe Acute Respiratory Syndrome Coronavirus-2. There are 14 open reading frames (ORFs) within the two primary transcriptional units ORF1a and ORF1b. S, Spike protein; E, Envelope protein; M, Membrane protein; N, Nucleocapsid protein; ns, Non-structural protein; RBD, Receptor binding domain; TM, Transmembrane region; S1, spike protein subunit 1; S2, spike protein subunit 2.

Figure 2

(A) Homology model of the wild-type trimeric form of Severe Acute Respiratory Syndrome Coronavirus-2 spike protein complexed with ACE2. The template structures are in green and red. The chain A, chain B, and chain C of the trimeric spike protein, and ACE2 are colored in yellow, magenta, cyan and brown, respectively. (B) Superimposition of the template structures (green and blue) and the modeled trimeric form of the spike protein (yellow, magenta, and cyan) complexed with ACE2 (brown).

Figure 3

Root mean square deviation (RMSD) plot for the trimeric form of Severe Acute Respiratory Syndrome Coronavirus-2 spike protein (Chain A in red, Chain B in cyan, Chain C in green) and ACE2 (brown) during the 100 ns molecular dynamics simulations. The X-axis indicates time in ns and the Y-axis represents RMSD values in Å.

Figure 4

The root mean square fluctuation (RMSF) plot for Cα atoms in chain A (green), B (cyan), and C (brown) of the trimeric form of Severe Acute Respiratory Syndrome Coronavirus-2 spike protein and ACE2 (red) during the 100 ns molecular dynamics simulations. The X axis indicates residue number and Y axis represents RMSF value in Å.

Figure 5

Pie chart of statistics of the 4 clusters of Severe Acute Respiratory Syndrome Coronavirus-2 spike protein complexed with ACE2. Number of structures and percentages are indicated in each pie segment.

Figure 6

Superimposition of the spike protein-ACE2 complexes using the full-length trimeric spike protein (Magenta) and the truncated spike protein RBD monomer (Cyan). The interacting residues are represented by stick model illustrations, while the rest of the ACE2 proteins are depicted in ribbon model form. The five new interacting residues identified using the full-length trimeric spike protein complexed with ACE2 are labeled.

Figure 7

Hydrogen bonds between the trimeric spike protein and ACE2. The residues involved in the hydrogen bond formation are shown in stick. The trimeric spike (Chain A–Green and Chain B–Cyan) and ACE2 (Yellow) are shown in ribbons.