E2^UbcH5B-derived peptide ligands target HECT E3-E2 binding site and block the Ub-dependent SARS-CoV-2 egression: A...

Area of Science:

• Biochemistry and Molecular Biology
• Virology
• Structural Biology

Background:

• Homologous to E6AP carboxyl-terminus (HECT)-type E3 ligases mediate protein degradation via the ubiquitin-proteasomal system, interacting with E2 ubiquitin-conjugating enzymes.
• Enveloped viruses like SARS-CoV-2 utilize the host cell's ESCRT machinery and HECT E3 ligase activity for viral egress.

Purpose of the Study:

• To characterize the binding of E2^UbcH5B to various HECT domains.
• To identify E2^UbcH5B-specific peptide inhibitors targeting SARS-CoV-2 viral egress.

Main Methods:

• In silico analysis of E2^UbcH5B-HECT domain interactions.
• Molecular dynamics simulations to assess binding pocket dynamics.
• MM-PBSA free energy calculations.
• Peptide-based inhibition assays with mutant validation.

Main Results:

• Molecular dynamics revealed increased opening of the E2^UbcH5B-binding pocket upon complex formation with HECT domains.
• Specific residues (Trp, Tyr, Phe, Cys) in HECT domains were identified as key interaction points with E2^UbcH5B.
• Two E2^UbcH5B-derived peptides demonstrated binding to HECT domains, with mutations impairing this interaction.

Conclusions:

• Peptide-driven inhibition of E2-to-HECT ubiquitin loading is a potential strategy to limit SARS-CoV-2 egression.
• The identified peptides may serve as novel therapeutics against SARS-CoV-2 infection by disrupting viral spread.