Oligomeric State and Drug Binding of the SARS-CoV‑2 Envelope Protein Are Sensitive to the Ectodomain

• Published in: Journal of the American Chemical Society 2024-09, Vol.146 (35), p.24537-24552
• Main Authors: Somberg, Noah H., Sučec, Iva, Medeiros-Silva, João, Jo, Hyunil, Beresis, Richard, Syed, Abdullah M., Doudna, Jennifer A., Hong, Mei
• Format: Article
• Language: English
• Subjects: Amiloride - analogs & derivatives; Amiloride - chemistry; Amiloride - pharmacology; Antiviral Agents - chemistry; Antiviral Agents - metabolism; Antiviral Agents - pharmacology; Coronavirus Envelope Proteins - chemistry; Coronavirus Envelope Proteins - metabolism; Humans; Protein Binding; Protein Domains; Protein Multimerization - drug effects; SARS-CoV-2 - chemistry; SARS-CoV-2 - drug effects; SARS-CoV-2 - metabolism
• ISSN: 0002-7863; 1520-5126; 1520-5126
• DOI: 10.1021/jacs.4c07686

The envelope (E) protein of SARS-CoV-2 is the smallest of the three structural membrane proteins of the virus. E mediates budding of the progeny virus in the endoplasmic reticulum Golgi intermediate compartment of the cell. It also conducts ions, and this channel activity is associated with the pathogenicity of SARS-CoV-2. The structural basis for these functions is still poorly understood. Biochemical studies of E in detergent micelles found a variety of oligomeric states, but recent 19F solid-state NMR data indicated that the transmembrane domain (ETM, residues 8–38) forms pentamers in lipid bilayers. Hexamethylene amiloride (HMA), an E inhibitor, binds the pentameric ETM at the lipid-exposed helix–helix interface. Here, we investigate the oligomeric structure and drug interaction of an ectodomain-containing E construct, ENTM (residues 1–41). Unexpectedly, 19F spin diffusion NMR data reveal that ENTM adopts an average oligomeric state of dimers instead of pentamers in lipid bilayers. A new amiloride inhibitor, AV-352, shows stronger inhibitory activity than HMA in virus-like particle assays. Distance measurements between 13C-labeled protein and a trifluoromethyl group of AV-352 indicate that the drug binds ENTM with a higher stoichiometry than ETM. We measured protein–drug contacts using a sensitivity-enhanced two-dimensional 13C–19F distance NMR technique. The results indicate that AV-352 binds the C-terminal half of the TM domain, similar to the binding region of HMA. These data provide evidence for the existence of multiple oligomeric states of E in lipid bilayers, which may carry out distinct functions and may be differentially targeted by antiviral drugs.