Submission Details
Molecule(s):
N#Cc1c([C@H]2CN(C(=N)N)C[C@@H](C(=O)CCl)N2CCc2c[nH]c3ncccc23)[nH]c2cc(S(N)(=O)=O)ccc12
C[C@]1(c2cc(C#N)c3ccc(S(N)(=O)=O)cc3c2)C[C@](Cc2c[nH]c3ncccc23)(C(=O)CCl)C[C@@H]1CC(=N)N
Design Rationale:
My design rationale was primarily to connect the fragments "by eye", but with the assistance of visualization tools such as UCSF Chimera, minimization using smina, and (QM)MM energy minimization using AmberTools suite of applications (antechamber, sander, sqm, etc).
Other Notes:
I have written a blog post here (https://www.sidneypaulymer.com/posts/covid-19-therapeutics-design-of-inhibitors-of-the-sars-cov-2-main-protease) with additional insights. If the reviewers are interested in any of the other candidates referenced in the Appendix of my blog post, please contact me and I can send a PDB file of the protein/ligand complex of interest.