A Strategy Based on Loop Analysis to Develop Peptide Epitopes: Application to SARS-CoV-2 Spike Protein

Abstract

Many current strategies for inducing an immune response rely on the production of an antigenic protein. Such methods can be problematic if the folding of the antigenic protein is incorrect. To avoid this problem, we propose a method based on grafting specific regions of the chosen antigenic protein onto biocompatible polymeric matrices, so that they can mimic portions of the antigenic protein. These regions are selected following the criterion according to which they are not folded, are exposed to the solvent and are not already present in the human body, so that they are not recognized by the immune system as self. Regions are selected using the primary sequence of the protein and, where possible, its tertiary structure. The application of this strategy to the Spike protein of SARS-CoV-2 is presented.

Keywords: COVID-19; SARS-CoV-2; bioconjugate polymers; hybrid protein-polymer; loop regions.

FIGURE 1

Location of the proposed regions in the Spike protein and comparison with Spike proteins from other coronavirus. (A) Top: schematic view of the Spike protein with the specifications of the different domains: NTD, N-Terminal Domain; RBD, Receptor Binding Domain; RBM, Receptor Binding Motif; FP, Fusion Peptide; HR1, Heptad Repeat 1; HR2, Heptad Repeat 2; TM, TransMembrane region; CP, Cytoplasmic Domain. The S1 domain consists of the NTD and RBD regions. Bottom: primary sequence of Spike protein in SARS-CoV-2 in the prefusion state (Wrapp et al., 2020; PDB code 6vsb, chain A). Helices are colored in yellow, sheets are colored in green and the missing regions in the crystal structure are colored in blue. The regions reported in the text are underlined. (B) 3D structure of Spike protein in SARS-CoV-2 in the prefusion state (Wrapp et al., 2020; PDB code 6vsb) where the regions reported in the text are colored in green for each monomer. (C) 3D structure of Spike protein in MERS-CoV in the prefusion state (Yuan et al., 2017; PDB code 5 × 5c). The regions corresponding to the ones reported in text are colored in green for each monomer. (D) 3D structure of Spike protein in SARS-CoV in the prefusion state (Yuan et al., 2017; PDB code 5 × 58). The regions corresponding to the ones reported in text are colored in green for each monomer. The equivalent residues in MERS-CoV and SARS-CoV were obtained by multiple alignment using the ClustalW software (Larkin et al., 2007). The figures were prepared with Chimera software (Pettersen et al., 2004).