Modeling the SARS-CoV-2 receptor ACE2 indicates that protein-bound Zn affects distant protein stability and interactions

Abstract

Abstract Molecular Dynamics (MD) is a widely used drug design tool capable of rapidly screening the binding capacity of many candidate inhibitors in a cost-effective manner. This approach has been leveraged to search for molecules that can bind to angiotensin converting enzyme 2 (ACE2) and prevent SARS-CoV-2 viral entry to host cells. However, ACE2 is difficult to model due to an embedded zinc ion (Zn), which introduces complex charge transfer and polarization. Since the embedded Zn is distant from the site of ACE2 binding, many groups have assumed Zn does not impact protein interactions and have excluded Zn while modeling ACE2. Here, we evaluated the impact of Zn by performing MD simulations of Zn-bound and Zn-free versions of the ACE2-spike protein (S1) and ACE2-monoclonal antibody (mAb) systems . We found that excluding Zn had a significant effect on total protein stability and the stability of interacting residues, indicating that Zn can impact distant protein sites. Additionally, we discovered that including protein-bound Zn in MD simulations improved the binding free energy of both systems by −3.26 and −14.8 kcal/mol in the ACE2-S1 and ACE2-mAb systems, respectively. These data suggest that excluding Zn may alter inhibitor selection decisions and should be included for accurate modeling. Interestingly, ACE2-mAb is particularly sensitive to changes in receptor structure, likely reflecting its generation against in vivo Zn-bound ACE2. Collectively, our data demonstrates that excluding Zn significantly impacts MD simulation outcomes which inform inhibitor selection, particularly when modeling receptor-mAb complexes.