Discovery of Cyclic Peptide Ligands to the SARS-CoV-2 Spike Protein Using mRNA Display

Abstract

The COVID-19 pandemic, caused by SARS-CoV-2, has led to substantial morbidity, mortality, and disruption globally. Cellular entry of SARS-CoV-2 is mediated by the viral spike protein, and affinity ligands to this surface protein have the potential for applications as antivirals and diagnostic reagents. Here, we describe the affinity selection of cyclic peptide ligands to the SARS-CoV-2 spike protein receptor binding domain (RBD) from three distinct libraries (in excess of a trillion molecules each) by mRNA display. We identified six high affinity molecules with dissociation constants ( K D ) in the nanomolar range (15–550 nM) to the RBD. The highest affinity ligand could be used as an affinity reagent to detect the spike protein in solution by ELISA, and the cocrystal structure of this molecule bound to the RBD demonstrated that it binds to a cryptic binding site, displacing a β-strand near the C-terminus. Our findings provide key mechanistic insight into the binding of peptide ligands to the SARS-CoV-2 spike RBD, and the ligands discovered in this work may find future use as reagents for diagnostic applications.

SARS-CoV-2 pan-variant inhibitory peptides deter S1-ACE2 interaction and neutralize delta and omicron pseudoviruses

“… [1] , [2] , [3] , [4] , [5] , [6] , [7] , [8] , [9] , [10] , [11] , [12] , [13] , [14] , [15] , [16] , [17] , [18] , [19] , [20] , [21] , [22] , [23] , [24] , [25] , [26] , [27] , [28] , [29] , [30] , [31] , [32] , [33] , [34] , [35] , [36] , [37] , [38] , [39] , [40] , [41] , [42] , [43] , [44] , [45] , [46] , [47] , [48] , [49] , [50] , [51] , [52] , [53] , [54] , [55] , [56] , [57] , [58] , [59] , [60] , [61] , [62] , [63] , [64] , [65] , [66] , [67] , [68] , [69] , [70] , [71] , [72] ...…”

Phage Display-Derived Peptide for the Specific Binding of SARS-CoV-2

“… 24 − 27 There are several SARS-CoV-2-specific peptides either derived from the ACE2 protein via computational design and/or affinity selection 28 , 29 or screened from the mRNA display library. 30 As the RBD is highly exposed outside the viral spike, it is a good target for screening against the phage display peptide library to obtain a potentially sensitive peptide for SARS-CoV-2 virus detection.…”

A Novel Regioselective Approach to Cyclize Phage-Displayed Peptides in Combination with Epitope-Directed Selection to Identify a Potent Neutralizing Macrocyclic Peptide for SARS-CoV-2

“…Several precedent works that used RBD directly for the identification of peptide ligands have been reported; however, many of the identified ligands bound the RBD at locations distal to the RBD-ACE2 binding interface, and were therefore not productive at inhibiting the RBD-ACE2 interaction. 27,28 To avoid the identification of nonproductive peptide ligands, we reasoned that using small RBD epitopes that directly interact with ACE2 for the selection of phagedisplayed macrocyclic peptides will increase the chances of identifying productive macrocyclic peptide ligands that directly block interactions between RBD and ACE2. In this work, we report the successful implementation of this approach for the identification of a potent peptidyl SARS-CoV-2 antiviral and its validation.…”