Entry Inhibitors of SARS-CoV-2 Targeting the Transmembrane Domain of the Spike Protein

Entry Inhibitors of SARS-CoV-2 Targeting the Transmembrane Domain of the Spike Protein

Viruses

10.3390/v17070989

https://doi.org/10.3390/v17070989

Kristin V. Lyles, Shannon Stone, Priti Singh, Lila D. Patterson, Janhavi Natekar, Heather Pathak, Rohit K. Varshnaya, Amany Elsharkawy, Dongning Liu, Shubham Bansal, Oluwafoyinsola O. Faniyi, Sijia Tang, Xiaoxiao Yang, Nagaraju Mulpuri, Donald Hamelberg, CongBao Kang, Binghe Wang, Mukesh Kumar, Ming Luo

coronavirus, spike protein, Transmembrane domain, antiviral, entry inhibitor, pan-coronavirus

16 July 2025

Lyles, K. V., Stone, S., Singh, P., Patterson, L. D., Natekar, J., Pathak, H., Varshnaya, R. K., Elsharkawy, A., Liu, D., Bansal, S., Faniyi, O. O., Tang, S., Yang, X., Mulpuri, N., Hamelberg, D., Kang, C., Wang, B., Kumar, M., & Luo, M. (2025). Entry Inhibitors of SARS-CoV-2 Targeting the Transmembrane Domain of the Spike Protein. Viruses, 17(7), 989. https://doi.org/10.3390/v17070989

Despite current vaccines and therapeutics targeting SARS-CoV-2, the causative agent of the COVID-19 pandemic, cases remain high causing a burden on health care systems. Spike-protein mediated membrane fusion of SARS-CoV-2 is a critical step in viral entry. Herein, we describe entry inhibitors identified by first screening a library of about 160 compounds and then analogue synthesis. Specifically, compound 261 was found to inhibit SARS-CoV-2 infection in a tissue model with IC50 of 0.3 µM. Using NMR, we found that 261 interacts with key residues in the aromatic-rich region of the spike protein directly next to the transmembrane domain. Molecular dynamic simulations of the 261 binding pocket in the spike protein was also mapped to the transmembrane domain, consistent with NMR findings. The amino acids in the binding site are conserved among different coronaviruses known to infect humans; therefore, inhibitors targeting this conserved binding site could be a useful addition to current therapeutics and may have pan-coronavirus antiviral activities.

Attribution 4.0 International (CC BY 4.0)

This research / project is supported by the NIH - Research Program Cooperative Agreement (U19)
Grant Reference no. : AI171954-01

This research / project is supported by the NIH - Outstanding Investigator Award (R35)
Grant Reference no. : GM153718

https://oar.a-star.edu.sg/communities-collections/articles/22287

1999-4915

Experimental Drug Development Centre

https://doi.org/10.3390/v17070989