Developing Rationally Designed Small Molecules to Inhibit SARS‐CoV‐2 Spike Protein‐Human ACE2 Receptor Interactions

Dufresne, Jason; Kapanadze, Tinatini; Grove, Laurie

Targeting the binding domain of SARS‐CoV‐2 spike protein (S protein) with rationally designed small molecules is expected to disrupt S protein‐human ACE2 (hACE2) interactions. First, we set out to establish a small molecule library using traditional structure‐based drug design strategies and various computational tools. Small molecule design began by utilizing FTMap to identify “hotspots” on the S protein binding domain (Chain B), which has been shown to interact with the hACE2 receptor (PDB file 6LZG). A hotspot was identified in the S protein‐hACE2 binding domain. Within the probe cluster for this hotspot, the phenol probe was found to have strong interactions with the surrounding amino acids and thus selected as the initial scaffold. Based on the residues surrounding the hotspot, additional substituents were added to the scaffold to improve binding affinity to the S protein. AutoDock was used to sequentially evaluate the binding affinity of each small molecule to assess the effects of various substituents and geometries, thereby refining the small molecule library. Over 200 unique small molecules were rationally designed, which revealed two preferred substructures: fluorene and naphthalene‐based molecules. The lead molecule from the fluorene substructure had a binding affinity of ‐9.1 kcal/mol (jmol156), and the lead molecule from the naphthalene substructure had a binding affinity of ‐8.5 kcal/mol (tmol35) (Figure 1). These molecules most strongly interact with Tyr505 via pi‐stacking and Asn501, Gly496, Tyr453 and Gln493 via hydrogen bonding (Figure 2). Additionally, Tyr453 of the S protein, which participates in binding with hACE2, is partially blocked by both lead molecules. Overall, the jmol156 and tmol35 molecules show two preferred substructures that can be used for future drug design and demonstrate potential to serve as a starting point for in vitro testing.