Fig. 4

Molecular docking analysis with compounds of coffee and Omicron spike protein-ACE2 complex. a Co-immunoprecipitation using 293 T cells expressing SARS-CoV-2 spike-HA and ACE2 to verify that 5 compounds can inhibit the binding of ACE2 and spike. After anti-HA pulldown, adding 5 compounds (100 μM), ACE2, and spike antibodies were used to detect by immunoblotting. b Surface view of Caffeine, CGA, isoCGA-A, isoCGA-B and isoCGA-C docking to Omicron spike protein (S)-ACE2 complex (PDB ID: 7T9L). The best pose of each compound was shown as sticks. The binding area of compounds is indicated by red dashed rectangle. 3D visualization of hydrogen bond interactions between Caffeine, CGA, isoCGA-A, isoCGA-B and isoCGA-C with Omicron S-ACE2 complex amino acids. Four hydrogen bond interactions were formed between Caffeine and the complex amino acids Gln506 (S), Thr324 (ACE2), Asn330 (ACE2) and Gly354 (ACE2). One hydrogen bond interaction was formed between CGA and the complex amino acids Arg357 (ACE2). Seven hydrogen bond interactions were formed between isoCGA-A and the complex amino acids Gly504 (S), Lys353 (ACE2), Gly354 (ACE2), Asp355 (ACE2) and Arg393 (ACE2). Six hydrogen bond interactions were formed between isoCGA-B and the complex amino acids Arg403 (S), Ser496 (S), His505 (S), Lys353 (ACE2) and Arg393 (ACE2). Two hydrogen bond interactions were formed between isoCGA-C and the complex amino acids Lys353 (ACE2) and Arg393 (ACE2). Hydrogen bonds are shown as black dashed lines