Identification of a Pentasaccharide Lead Compound with High Affinity to the SARS-CoV-2 Spike Protein via In Silico Screening

Abstract

The spike (S) protein on the surface of the SARS-CoV-2 virus is critical to mediate fusion with the host cell membrane through interaction with angiotensin-converting enzyme 2 (ACE2). Additionally, heparan sulfate (HS) on the host cell surface acts as an attachment factor to facilitate the binding of the S receptor binding domain (RBD) to the ACE2 receptor. Aiming at interfering with the HS-RBD interaction to protect against SARS-CoV-2 infection, we have established a pentasaccharide library composed of 14,112 compounds covering the possible sulfate substitutions on the three sugar units (GlcA, IdoA, and GlcN) of HS. The library was used for virtual screening against RBD domains of SARS-CoV-2. Molecular modeling was carried out to evaluate the potential antiviral properties of the top-hit pentasaccharide focusing on the interactive regions around the interface of RBD-HS-ACE2. The lead pentasaccharide with the highest affinity for RBD was analyzed via drug-likeness calculations, showing better predicted druggable profiles than those currently reported for RBD-binding HS mimetics. The results provide significant information for the development of HS-mimetics as anti-SARS-CoV-2 agents.

Keywords: RBD; SARS-CoV-2; heparan sulfate; protein binding; virtual screening.

Figure 1

Structure of the trimeric SARS-CoV-2 S protein showing the open and closed form of RBD (PDB ID: 6VSB) [19].

Figure 2

Structure of the top-hit pentasaccharide AD08043.

Figure 3

Structure of (a) pentosan polysulfate (PPS) [20]; (b) (IdoA2S-GlcNS6S)₄ [6].

Figure 4

The binding molecular model of oligosaccharides of the HS-analogue and SARS-CoV-2 RBD. The green surface indicates the RBD-ACE2-RBD binding interface. AD08043 is colored in purple, PPS is colored in teal, and (IdoA2S-GlcNS6S)₄ is colored in yellow.

Figure 5

Interactions between the interface amino acids of the RBDs of the variants of SARS-CoV-2 and AD08043. (a) Original variant; (b) B.1.1.7 (alpha) variant; (c) B.1.351 (beta) variant; (d) P.1(gamma) variant; (e) B.1.617.2 (delta) variant; and (f) B.1.1.529 (omicron BA.1) variant.

Figure 6

Electrostatic surface rendering of the SARS-CoV-2 RBD-AD08043 complex during the MD simulation. Blue and red surfaces indicate electropositive and electronegative surfaces, respectively. L0, L10, L20, L30, L40, L50, L60, L70, and L80 are colored in pink, orange, yellow, cyan, pale green, salmon, wheat, limon, and gray (e.g., L10 represents the location of AD08043 at 10 ns during the MD simulation period).

Figure 7

Detailed information on the interactions between SARS-CoV-2 RBD and AD08043 at 80 ns during the MD simulation period. Amino acids that produce polar and non-polar interactions with the ligand are colored in red and yellow, respectively.

Figure 8

The FMOs including HOMO and LUMO for (a) AD08043; (b) PPS; and (c) (IdoA2S-GlcNS6S)₄, as calculated at B3LYP-D3/6-31 + G(d,p) level of DFT.

Figure 9

Illustration of the pentasaccharide structures in the library. The carbon atom serial number is shown in the monosaccharide plane structure.