9HM2

A swapped dimeric form of ZO1/TJP1 PDZ2 in complex with the C-terminal peptide from protein E of SARS-CoV-2

Summary for 9HM2

• Entry DOI: 10.2210/pdb9hm2/pdb
• Descriptor: Tight junction protein ZO-1, Envelope small membrane protein, IODIDE ION, ... (4 entities in total)
• Functional Keywords: pdz2, scaffolding, cell adhesion, tight junction
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 21986.85

Authors

Alvarez, F.,Mechaly, A.,Haouz, A.,Caillet-Saguy, C. (deposition date: 2024-12-06, release date: 2025-10-22, Last modification date: 2026-01-28)

Primary citation

Alvarez, F.,Larrous, F.,Mechaly, A.,Bardiaux, B.,Goor, Q.,Haouz, A.,Seon-Meniel, B.,de Sousa, R.A.,Bourg, S.,Desmaele, D.,Figadere, B.,Wolff, N.,Munier-Lehmann, H.,Caillet-Saguy, C.
HTRF-based identification of small molecules targeting SARS-CoV-2 E protein interaction with ZO-1 PDZ2.
Sci Rep, 16:2034-2034, 2025

PubMed Abstract: The SARS-CoV-2 E protein through its C-terminal PDZ-binding motif (PBM) interacts with several host PDZ-containing proteins, including Zonula occludens-1 (ZO-1) protein via its PDZ2 domain, thereby contributing to viral pathogenesis. Targeting this interaction represents a potential therapeutic strategy. In this study, we determined the X-ray structure of the E PBM peptide in complex with the ZO-1 PDZ2 domain at 1.7 Å resolution. The structure revealed a domain-swapped dimer conformation of ZO-1 PDZ2, with the E PBM peptide conventionally bound within the PDZ domain's canonical binding groove, exhibiting key interactions characteristic of type II PBM/PDZ interactions. To identify potential inhibitors of the E PBM/ZO-1 PDZ2 interaction, we performed a Homogeneous Time-Resolved Fluorescence (HTRF) screening using a protein-protein interaction-focused library of 1000 compounds. This led to the identification of 36 hits that disrupted this interaction. Subsequent cytotoxicity and dose-response assays narrowed the selection to 14 promising compounds. Docking simulations showed that some compounds bind within or near the PBM-binding pocket, supporting a competitive mechanism of interaction inhibition, while others bind at a central interface between the two PDZ monomers, suggesting an inhibition of dimerization, which in turn prevents PBM binding. Thus, the E PBM/ZO-1 PDZ2 interaction can be inhibited through both direct and indirect mechanisms. Finally, antiviral assays using a NanoLuciferase-expressing recombinant SARS-CoV-2 demonstrated that one compound, C19, significantly reduced viral replication, highlighting its potential as a candidate for further therapeutic development.

PubMed: 41457070
DOI: 10.1038/s41598-025-31755-y

Experimental method

X-RAY DIFFRACTION (1.72 Å)