Y. Xiang; G. Zhai; Y. Li; M. Wang; X. Chen; R. Wang; H. Xie; W. Zhang; G. Ge; Q. Zhang; Y. Xu; A. Caflisch; J. Xu; H. Chen; L. Chen

Journal: Int. J. Biol. Macromol.
Year: 2023
Volume: 226
Pages: 780-792
DOI: 10.1016/j.ijbiomac.2022.12.057
Type of Publication: Journal Article

Angiotensin-Converting Enzyme 2; COVID-19; HEK293 Cells; Humans; Molecular Docking Simulation; Molecular Dynamics Simulation; Protein Binding; SARS-CoV-2; Spike Glycoprotein, Coronavirus


Targeting the interaction between the spike protein receptor binding domain (S-RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and angiotensin-converting enzyme 2 (ACE2) is a potential therapeutic strategy for treating coronavirus disease 2019 (COVID-19). However, we still lack small-molecule drug candidates for this target due to the missing knowledge in the hot spots for the protein-protein interaction. Here, we used NanoBiT technology to identify three Ginkgolic acids from an in-house traditional Chinese medicine (TCM) library, and they interfere with the S-RBD/ACE2 interplay. Our pseudovirus assay showed that one of the compounds, Ginkgolic acid C17:1 (GA171), significantly inhibits the entry of original SARS-CoV-2 and its variants into the ACE2-overexpressed HEK293T cells. We investigated and proposed the binding sites of GA171 on S-RBD by combining molecular docking and molecular dynamics simulations. Site-directed mutagenesis and surface plasmon resonance revealed that GA171 specifically binds to the pocket near R403 and Y505, critical residues of S-RBD for S-RBD interacting with ACE2. Thus, we provide structural insights into developing new small-molecule inhibitors and vaccines against the proposed S-RBD binding site.