Phage-Displayed Mimotopes of SARS-CoV-2 Spike Protein Targeted to Authentic and Alternative Cellular Receptors

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).

Receptor-binding domain-anchored peptides block binding of severe acute respiratory syndrome coronavirus 2 spike proteins with cell surface angiotensin-converting enzyme 2

“…Frontiers in Microbiology 06 frontiersin.org pathogen invasions in this lab (Zhao et al, 2012) or others (Hall et al, 2009;Wei et al, 2020). This study and several other efforts (Anand et al, 2021;Sokullu et al, 2021;Ballmann et al, 2022;Labriola et al, 2022;Petrenko et al, 2022;Sevenich et al, 2022;Yang et al, 2022) demonstrated that PhD was a plausible method for generating possible therapeutics to treat COVID-19 as well. For example, Petrenko used phage-displayed spike S1 protein mimotopes to search for "all" cellular receptors, including authentic and alternative ones.…”

“…For example, Petrenko used phage-displayed spike S1 protein mimotopes to search for “all” cellular receptors, including authentic and alternative ones. Interestingly, FGFR3 was identified as an alternative receptor to S proteins ( Petrenko et al, 2022 ). Since FGFR3 manifested a distribution pattern different from that of ACE2, Petrenko’s work expanded the area of SARS-CoV-2 targets and might lead to the discovery of novel pathogenesis of SARS-CoV-2.…”

“…Here, we report that two SEAL peptides were obtained via phage displaying against S-RBD and S-trimer proteins, and preliminary functional studies demonstrated weak blocking effects at high concentrations. Encouragingly, while this project was ongoing, three groups reported their results obtained by protocols mainly relying on PhD (Petrenko et al, 2022;Sevenich et al, 2022;Yang et al, 2022Yang et al, ). 10.3389/fmicb.2022 The promises and limitations of these studies were also discussed.…”

Construction, Characterization, and Application of a Nonpathogenic Virus-like Model for SARS-CoV-2 Nucleocapsid Protein by Phage Display

“…Petrenko et al described a model termed “phage mimicry” to display the viral receptor-binding site on the spike protein by phage display and by employing recombinant filamentous bacteriophages. They used the model to investigate the binding mechanism of the virus to the corresponding receptor in vitro [ 11 ]. Further, Yang et al used phage display technology to research the specific binding of SARS-CoV-2.…”

The Breadth of Bacteriophages Contributing to the Development of the Phage-Based Vaccines for COVID-19: An Ideal Platform to Design the Multiplex Vaccine

“…In a recent study, the SARS-CoV-2 spike S1, the protein’s phage mimotopes which resemble the shape of the viral receptor-binding (RB) sites, were created. Utilizing recombinant bacteriophages with surface mimotopes may provide a molecular probe for analyzing viral infectivity and could be effective in COVID-19 vaccine development [ 59 ]. Another study used mycobacteriophages to show SARS-CoV-2 RB motif segments.…”