In Silico Discovery of Small Molecule Modulators Targeting the Achilles' Heel of SARS-CoV-2 Spike Protein

The spike protein of SARS-CoV-2 has been a promising target for developing vaccines and therapeutics due to its crucial role in the viral entry process. Previously reported cryogenic electron microscopy (cryo-EM) structures have revealed that free fatty acids (FFA) bind with SARS-CoV-2 spike protein, stabilizing its closed conformation and reducing its interaction with the host cell target in vitro. Inspired by these, we utilized a structure-based virtual screening approach against the conserved FFA-binding pocket to identify small molecule modulators of SARS-CoV-2 spike protein, which helped us identify six hits with micromolar binding affinities. Further evaluation of their commercially available and synthesized analogs enabled us to discover a series of compounds with better binding affinities and solubilities. Notably, our identified compounds exhibited similar binding affinities against the spike proteins of the prototypic SARS-CoV-2 and a currently circulating Omicron BA.4 variant. Furthermore, the cryo-EM structure of the compound SPC-14 bound spike revealed that SPC-14 could shift the conformational equilibrium of the spike protein toward the closed conformation, which is human ACE2 (hACE2) inaccessible. Our identified small molecule modulators targeting the conserved FFA-binding pocket could serve as the starting point for the future development of broad-spectrum COVID-19 intervention treatments.

Automated summary

Structure-based virtual screening of the conserved free fatty acid (FFA)-binding pocket of SARS-CoV-2 spike protein identified six small molecule modulators with micromolar binding affinities. Further evaluation of commercially available and synthesized analogs led to the discovery of compounds with improved binding affinities and solubilities. The identified compounds exhibited similar binding affinities against both the spike protein of prototypic SARS-CoV-2 and the currently circulating Omicron BA.4 variant. The compound SPC-14 was found to shift the conformational equilibrium of the spike protein towards the closed conformation, rendering it inaccessible to human ACE2. These small molecule modulators targeting the conserved FFA-binding pocket could serve as a starting point for the future development of broad-spectrum COVID-19 intervention treatments.