Pathway enrichment analysis of virus-host interactome and prioritization of novel compounds targeting the spike glycoprotein receptor binding domain-human angiotensin-converting enzyme 2 interface to combat SARS-CoV-2

Abstract

SARS-CoV-2 has become a pandemic causing a serious global health concern. The absence of effective drugs for treatment of the disease has caused its rapid spread on a global scale. Similarly to the SARS-CoV, the SARS-CoV-2 is also involved in a complex interplay with the host cells. This infection is characterized by a diffused alveolar damage consistent with the Acute Respiratory Disease Syndrome (ARDS). To explore the complex mechanisms of the disease at the system level, we used a network medicine tools approach. The protein-protein interactions (PPIs) between the SARS-CoV and the associated human cell proteins are crucial for the viral pathogenesis. Since the cellular entry of SARS-CoV-2 is accomplished by binding of the spike glycoprotein binding domain (RBD) to the human angiotensin-converting enzyme 2 (hACE2), a molecule that can bind to the spike RDB-hACE2 interface could block the virus entry. Here, we performed a virtual screening of 55 compounds to identify potential molecules that can bind to the spike glycoprotein and spike-ACE2 complex interface. It was found that the compound ethyl 1-{3-[(2,4-dichlorobenzyl) carbamoyl]-1-ethyl-6-fluoro-4-oxo-1,4-dihydro-7-quinolinyl}-4-piperidine carboxylate (the S54 ligand) and ethyl 1-{3-[(2,4-dichlorobenzyl) carbamoyl]-1-ethyl-6-fluoro-4-oxo-1,4-dihydro-7-quinolinyl}-4 piperazine carboxylate (the S55 ligand) forms hydrophobic interactions with Tyr41A, Tyr505B and Tyr553B, Leu29A, Phe495B, respectively of the spike glycoprotein, the hotspot residues in the spike glycoprotein RBD-hACE2 binding interface. Furthermore, molecular dynamics simulations and free energy calculations using the MM-GBSA method showed that the S54 ligand is a stronger binder than a known SARS-CoV spike inhibitor SSAA09E3 (N-(9,10-dioxo-9, 10-dihydroanthracen-2-yl) benzamide).Communicated by Ramaswamy H. Sarma.

Keywords: SARS-CoV-2; molecular docking; molecular dynamics; protein–protein interactions (PPIs); spike glycoprotein; virtual screening.

Figure 1.

Extended interactome construction of SARS-CoV-human interactions obtained from the viral proteins (orange colour) and associated human proteins showing 374 nodes and 5827 edges.

Figure 2.

GO/pathway terms specific for upregulated genes from the first neighbour nodes of the spike glycoprotein representing: the biological function (a), molecular function (b), and pathway analysis (c) (60 nodes). The bars represent the number of genes associated with the terms. The percentage of genes per term is shown as a bar label. Terms with up- and down-regulated genes are shown in red and green, respectively. The colour gradient shows the gene proportion of each cluster associated with the term. Equal proportions of the two clusters are represented in white.

Figure 3.

Functional assessment analysis of the spike glycoprotein first neighbour proteins. The genes recognized as close neighbours of the spike glycoprotein are highlighted in different colours based on their functional enrichment: genes for the viral entry into the host cell and the viral receptor activity are shown in green, genes for the heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules in grey, genes for the transition metal ion homeostasis in light blue, genes for the natural killer cell-mediated immunity in dark blue, genes for the glycogen catabolic process in red, genes for the regulation of humoral immune response mediated by circulating immunoglobulin in pink, genes for the MHC protein binding in sky blue, and genes for the immunoregulatory interactions between a lymphoid and a non-lymphoid cell in yellow. The genes shown in the subnetwork (orange) show the interaction of CLEC4M protein with the human ACE2 protein (receptor for the spike glycoprotein), and the genes which are involved in the viral entry into the host.

Figure 4.

(a) Blind docking of using the spike glycoprotein RBD (grey) for ligand specificity search. Active pocket (pockets A to E) regions show clusters of ligands in different sites. (b) Pie chart showing the percentage of ligands at different active sites bound to the spike glycoprotein RBD.

Figure 5.

Binding interactions of the S54 and SSAA093 ligands at the interface of the spike glycoprotein RBD-hACE2 complex.

Figure 6.

Superimposed conformations of the S54 and SSAA093 ligands at the interface of the spike glycoprotein RBD-hACE2 complex. The S54 ligand is shown in green, while the SSAA093 ligand is shown in red.

Figure 7.

Backbone root-mean-square deviation (RMSD) over time for complexes with the reference SSAA093, the S54, and the S55 ligand.

Figure 8.

Number of intermolecular H-bonds for complexes with the reference SSAA093 ligand (left), the S54 (middle), and the S55 ligand (right).

Figure 9.

Overlay of the spike glycoprotein complexes with the reference SSAA093 ligand (tan), the S54 ligand (light blue), and the S55 ligand (pink) after 300 ns MD simulation with top contributing amino acid residues (yellow) shown.

Figure 10.

Binding interactions of the S54 and the S55 ligand at the interface of the spike glycoprotein RBD-hACE2 complex after 300 ns MD simulations.

Figure 11.

Per residue root-mean-square fluctuation (RMSF) for complexes with the reference SSAA093, the S54 ligand, and the S55 ligand.