Strategy 

Project Strategy

COVID-19 Project is divided into three stages.

Publication

This is the first stage of the project. The goal is to improve the binding affinity of soluble ACE2 to the SARS-CoV-2 spike protein and also design a small protein (decoy) that binds to the spike protein RBD (receptor binding domain) with a high affinity. You can help us by identifying all relevant protein structures and amino acid side chain interactions (use Precise and Not Sequential learning pattern).

We will run MD simulations of the viral spike protein with human ACE2 and with a designed decoy, and send the results for publication in the next two months. The first step is to buid a MD system for the complex of RBD and soluble ACE2 (residue 18-615) using PDB 6M17. We want to send the manuscript to Biochemistry.

Internal Funding (up to $10,000)

I will write up a grant proposal and submit it before the end of April. You can help by working on the literature review.

We are planning to use Calu-3 cells and pseudovirus expressing SARS-CoV-2 spike protein but please collect references for viral entry studies with various cell lines (types) and viral models. Please help us by writing methodology.

External Funding ($1-2 million)