Structural analysis of ACE2 variant N720D demonstrates a higher binding affinity to TMPRSS2

Area of Science:

• Virology
• Genetics
• Structural Biology

Background:

• Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes the angiotensin-converting enzyme 2 (ACE2) receptor for cellular entry.
• Genetic variations in the ACE2 gene can influence the interaction with the SARS-CoV-2 S-protein.
• The N720D variant is located in the collectrin-like domain (CLD) near the TMPRSS2 cleavage site.

Purpose of the Study:

• To investigate the structural and thermodynamic effects of the ACE2 N720D variant.
• To assess the impact of the N720D variant on the binding and cleavage by TMPRSS2.
• To understand how this variant influences SARS-CoV-2 S-protein interaction and viral entry.

Main Methods:

• Molecular dynamics simulations (DynaMut, HDOCK, PRODIGY) were used to analyze ACE2 structure, stability, and TMPRSS2 binding affinity.
• Thermodynamic stability was assessed via free energy change (ΔΔG).
• Molecular dynamics simulations (100 ns) were performed on ACE2 apo and ACE2-TMPRSS2 complexes.

Main Results:

• The N720D variant exhibited increased structural dynamics and a more favorable binding affinity (Kd = 3.2 × 10⁻¹⁰ M) to TMPRSS2.
• While the N720D variant showed reduced overall stability (RMSD, RMSF), the D720-TMPRSS2 complex displayed slower dynamics.
• A significant change in free energy (ΔΔG: -0.470 kcal/mol) was observed for the N720D variant.

Conclusions:

• The N720D variant enhances ACE2 flexibility, particularly in loop regions, creating a more favorable site for TMPRSS2 binding and cleavage.
• This increased efficiency in TMPRSS2 processing can facilitate SARS-CoV-2 S-protein binding and subsequent viral entry.
• Understanding ACE2 variants like N720D is crucial for comprehending viral pathogenesis and developing therapeutic strategies.