Structure-Based Development of SARS-CoV-2 Spike Interactors.

Area of Science:

• Virology
• Structural Biology
• Drug Discovery

Background:

• Coronaviruses, including SARS-CoV-2, utilize their surface spike glycoprotein to infect host cells.
• The spike protein's receptor-binding domain (RBD) binds to human angiotensin-converting enzyme 2 (ACE2) to facilitate viral entry.
• Interfering with the spike protein-ACE2 interaction is a key strategy for inhibiting viral entry.

Purpose of the Study:

• To engineer novel, soluble, and stable molecules (S-plugs) that inhibit the binding of the SARS-CoV-2 spike protein to the ACE2 receptor.
• To computationally optimize S-plugs for enhanced thermostability and binding affinity to the spike protein.
• To provide a foundation for developing therapeutics and diagnostics against ACE2-accessing coronaviruses.

Main Methods:

• Utilized structural data of the SARS-CoV-2 spike protein-ACE2 interaction.
• Employed computational approaches including stability prediction with single-point mutations and molecular dynamics simulations.
• Characterized the engineered S-plug molecules for their conformation, thermostability, and binding affinities.

Main Results:

• Developed S-plug3, a highly stable α-helical molecule with a melting temperature of 54 °C.
• S-plug3 demonstrated low nanomolar binding affinities to the spike protein's RBD and S1 domains.
• S-plug3 effectively targets the same interface as ACE2 and shows low nanomolar binding to the SARS-CoV-2 Delta variant spike protein (K_D = 29.2 ± 0.6 nM).

Conclusions:

• The engineered S-plugs, particularly S-plug3, are potent inhibitors of the SARS-CoV-2 spike protein-ACE2 interaction.
• S-plug3's stability and broad binding profile make it a promising candidate for therapeutic and diagnostic applications.
• These findings represent a significant step towards developing novel interventions against coronaviruses that utilize the ACE2 pathway.