Abstract
The evolution of the SARS-CoV-2 virus during the COVID-19 pandemic was accompanied by the emergence of new heavily mutated viral variants with increased infectivity and/or resistance to detection by the human immune system. To respond to the urgent need for advanced methods and materials to empower a better understanding of the mechanisms of virus’s adaptation to human host cells and to the immuno-resistant human population, we suggested using recombinant filamentous bacteriophages, displaying on their surface foreign peptides termed “mimotopes”, which mimic the structure of viral receptor-binding sites on the viral spike protein and can serve as molecular probes in the evaluation of molecular mechanisms of virus infectivity. In opposition to spike-binding antibodies that are commonly used in studying the interaction of the ACE2 receptor with SARS-CoV-2 variants in vitro, phage spike mimotopes targeted to other cellular receptors would allow discovery of their role in viral infection in vivo using cell culture, tissue, organs, or the whole organism. Phage mimotopes of the SARS-CoV-2 Spike S1 protein have been developed using a combination of phage display and molecular mimicry concepts, termed here “phage mimicry”, supported by bioinformatics methods. The key elements of the phage mimicry concept include: (1) preparation of a collection of p8-type (landscape) phages, which interact with authentic active receptors of live human cells, presumably mimicking the binding interactions of human coronaviruses such as SARS-CoV-2 and its variants; (2) discovery of closely related amino acid clusters with similar 3D structural motifs on the surface of natural ligands (FGF1 and NRP1), of the model receptor of interest FGFR and the S1 spike protein; and (3) an ELISA analysis of the interaction between candidate phage mimotopes with FGFR3 (a potential alternative receptor) in comparison with ACE2 (the authentic receptor).
Highlights
We evaluated the performance of phage mimicry using representatives of major classes of cell surface receptors, which mediate entry of coronaviruses into the host cells: (1) metallopeptidases, including angiotensin-converting enzyme 2 (ACE2) [1,26], and (2) growth factor receptors, including fibroblast growth factor receptor 3 (FGFR3) [35,37,78,79,80,81]
To validate the phage mimicry approach for the discovery of phage mimotopes that correspond to functionally active sites on the surface of the SARS-CoV-2 spike protein, we focused on the SARS-CoV-2 spike protein receptor-binding domain (RBD)
We found that the CUB2 domain of NRP1 has amino acid clusters with similarity to the SARS-CoV-2 spike RBD and phage mimotopes
Summary
The evolution of the SARS-CoV-2 virus during the COVID-19 pandemic was accompanied by the emergence of a diverse assortment of new virus variants having multiple mutations in both receptor- and antibody-binding sites located throughout the spike S protein [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] (Figure 1). To empower increased insight into the evolutionary mechanisms of the SARS-CoV-2 spike protein, we suggest using recombinant filamentous probes [31], displaying on their surface an array of mechanisms of the bacteriophage-based. ~4000 foreign peptides, which produces a unique molecular landscape across the viral bacteriophage-based probes [31], displaying on their surface an array of ~4000 foreign surface that canproduces mimic the structure of viral receptor-binding [32,33,34,35,36,37], as illustrated peptides, which a unique molecular landscape across sites the viral surface that can in Figures 2 and.
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