Borneol Ester Derivatives as Entry Inhibitors of a Wide Spectrum of SARS-CoV-2 Viruses

Abstract

In the present work we studied the antiviral activity of the home library of monoterpenoid derivatives using the pseudoviral systems of our development, which have glycoproteins of the SARS-CoV-2 virus strains Wuhan and Delta on their surface. We found that borneol derivatives with a tertiary nitrogen atom can exhibit activity at the early stages of viral replication. In order to search for potential binding sites of ligands with glycoprotein, we carried out additional biological tests to study the inhibition of the re-receptor-binding domain of protein S. For the compounds that showed activity on the pseudoviral system, a study using three strains of the infectious SARS-CoV-2 virus was carried out. As a result, two leader compounds were found that showed activity on the Wuhan, Delta, and Omicron strains. Based on the biological results, we searched for the potential binding site of the leader compounds using molecular dynamics and molecular docking methods. We suggested that the compounds can bind in conserved regions of the central helices and/or heptad repeats of glycoprotein S of SARS-CoV-2 viruses.

Keywords: SARS-CoV-2; borneol; coronavirus surface protein S-spike; molecular docking; molecular dynamics; pseudoviral system; terpene.

Figure 6

(A)—Structures of compounds 11, 21, and 36 containing a similar structural fragment. (B)—Surface viral proteins hemagglutinin (HA) of influenza virus and glycoprotein (S-protein) SARS-CoV-2. The secondary structures of proteins that make up the first HA1 and S1 subunits are shown in gray. The receptor binding domain (RBD) of the S-protein is shown in red. α-Heptad repeats (HR), make up the second HA2 and S2 subunits. The Arbidol binding sites in both surface proteins are located between the α-helix of the two protomers. The amino acids included in the binding site are colored according to their pharmacophoric signatures. The Camphecene binding site is located at the HA proteolysis site. Surface proteins were visualized based on the PDB [26] codes of HAs of the A/H1N1 4LXV strain [61] and the SARS-CoV-2 6VXX S-protein [62].

Figure 1

Scheme of work with the pseudovirus system. Experimental work with pseudoviruses includes several stages: (Stage 1) is the assembly of viral particles by transfection of the HEK293 cell line using three plasmids—core, reporter and envelope; (Stage 2) is the determination of the ability of pseudoviral particles to infect target cells; and (Stage 3) is the direct neutralization assay using immune sera or chemotherapeutic agents to determine their ability to block pseudoviruses from entering target cells.

Figure 2

Infectivity of pseudoviral particles containing the SARS-CoV-2 protein on the S surface in HEK293T, HEK293T-hACE2 (stable) and HEK293T-hACE2-TMPRSS2 (transient). At 48 h post-infection, pseudovirus entry was analyzed by determining luciferase activity in cell lysates.

Figure 3

First class compounds—camphor derivatives.

Figure 4

Compounds of the second class—ester derivatives based on (-)-borneol.

Figure 5

Compounds of the third class—isobornylamine-based amides.

Figure 7

Mutations of amino acid residues in different strains of the SARS-CoV-2 virus considered in this study.

Figure 8

(A)—is the result of the estimation of the acidity constant of the leader compounds by quantum chemistry; (B)—is the weighted atomic population map of compound 21 based on the results of molecular dynamic simulations; (C)—is the comparison of a number of amino acid residues of part S2 of SARS-CoV-2 of various strains, and replacements are shown in red font; H-bond is the frequency of formation (in %) of hydrogen bonds between ligand atoms and amino acids.

Figure 9

(A)—full-length visualization of the surface protein: S1 and S2 surface protein subunits, TMD—transmembrane domain, CHR, HR1, HR2—central and heptad repeats 1 and 2, respectively, FP1, FP2—fusion peptides; (B)—location of agents 11 and 21 in the supposed binding site: hydrogen bonds are shown with a yellow dashed line, π-cation interaction—with a green dashed line. The ranked IC₅₀ values illustrate the antiviral activity against different SARS-CoV-2 virus strains.