Computational Design of Peptides to Block Binding of the SARS-CoV-2 Spike Protein to Human ACE2

Xiaoqiang Huang; Robin Pearce; Yang Zhang

It has been confirmed that SARS-CoV-2 initiates its entry into host cells by binding to the angiotensin-converting enzyme 2 (ACE2) via the receptor binding domain (RBD) of its spike protein 7, 8 . Therefore, it is possible to develop new therapeutics to block SARS-CoV-2 from binding to ACE2. Although small molecule compounds are commonly preferred as therapeutics, they are not effective at blocking protein-protein interactions (PPIs) where a deep binding pocket may be missing at the interface 9 . On the contrary, peptide binders are more suitable for disrupting PPIs by specifically binding to the interface binding region 10 . More importantly, small peptides have reduced immunogenicity 11 . These positive features make peptides great candidates to serve as therapeutics 12, 13 . Recently, Zhang et al 14 reported that the natural 23-mer peptide (a.a. cut from the human ACE2 (hACE2) α1 helix can strongly bind to SARS-CoV-2 RBD with a disassociation constant (Kd) of 47 nM, which was comparable to that of the full-length hACE2 . CC-BY-NC-ND 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.28.013607 doi: bioRxiv preprint binding to SARS-CoV-2 RBD 15 ; they also showed that a shorter 12-mer peptide (a.a. [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] from the same helix was not able to bind the virus RBD at all. In an earlier report, Han et al 16 performed a study to identify the critical determinants on hACE2 for SARS-CoV entry, and they found that two natural peptides from hACE2 (a.a. 22-44 and 22-57) exhibited a modest antiviral activity to inhibit the binding of SARS-CoV RBD to hACE2 with IC50 values of about 50 μM and 6 μM, respectively, implying that the peptide composed of residues 22-57 had stronger binding affinity for SARS-CoV RBD. They also generated a hybrid peptide by linking two discontinuous fragments from hACE2 (a.a. 22-44 and 351-357) with a glycine, and this 31-mer exhibited a potent antiviral activity with an IC50 of about 0.1 μM, indicating that this artificial peptide had much stronger binding affinity for SARS-CoV RBD than the peptides composed of residues 22-44 or 22-57. Due to the high similarity of the binding interfaces between SARS-CoV RBD/hACE2 and SARS-CoV-2 RBD/hACE2, we think that this artificial peptide may also bind to SARS-CoV-2 more strongly than the peptide 21-43 tested by Zhang et al 14 , which is similar to the peptide 22-44 from Han et al 16 . Although the natural peptides are promising, it has been argued that the sequence of hACE2 is suboptimal for binding the S protein of SARS-CoV-2 17 . Therefore, further redesign of the natural peptides may significantly enhance its binding affinity to the virus RBD and the improved peptide binders may have the potential to inhibit SARS-CoV-2 from entering human cells and hinder its rapid transmission.