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

2020 ◽  
Author(s):  
Alexander Norman ◽  
Charlotte Franck ◽  
Mary Christie ◽  
Paige M. E. Hawkins ◽  
Karishma Patel ◽  
...  
Keyword(s):  
Cyclic Peptide ◽  
Dissociation Constants ◽  
Surface Protein ◽  
Peptide Ligands ◽  
Spike Protein ◽  
Mrna Display ◽  
Affinity Ligand ◽  
Protein Receptor ◽  
C Terminus ◽  
Diagnostic Applications

ABSTRACTThe 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 (KD) in the nanomolar range (15-550 nM) to the RBD. The highest affinity ligand could be used as an affinity reagent to detect spike protein in solution by ELISA, and the co-crystal 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.

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

2021 ◽  
Author(s):  
Alexander Norman ◽  
Charlotte Franck ◽  
Mary Christie ◽  
Paige M. E. Hawkins ◽  
Karishma Patel ◽  
...  
Keyword(s):  
Cyclic Peptide ◽  
Peptide Ligands ◽  
Spike Protein ◽  
Mrna Display

scholarly journals Effects of common mutations in the SARS-CoV-2 Spike RBD domain and its ligand the human ACE2 receptor on binding affinity and kinetics

2021 ◽  
Author(s):  
Michael I Barton ◽  
Stuart MacGowan ◽  
Mikhail A Kutuzov ◽  
Omer Dushek ◽  
Geoffrey J Barton ◽  
...  
Keyword(s):  
South Africa ◽  
Cell Surface ◽  
Immune Escape ◽  
Surface Protein ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Cell Surface Protein ◽  
Kinetics Analysis ◽  
Protein Receptor ◽  
The Uk

The interaction between the SARS-CoV-2 virus Spike protein receptor binding domain (RBD) and the ACE2 cell surface protein is required for viral infection of cells. Mutations in the RBD domain are present in SARS-CoV-2 variants of concern that have emerged independently worldwide. For example, the more transmissible B.1.1.7 lineage has a mutation (N501Y) in its Spike RBD domain that enhances binding to ACE2. There are also ACE2 alleles in humans with mutations in the RBD binding site. Here we perform a detailed affinity and kinetics analysis of the effect of five common RBD mutations (K417N, K417T, N501Y, E484K and S477N) and two common ACE2 mutations (S19P and K26R) on the RBD/ACE2 interaction. We analysed the effects of individual RBD mutations, and combinations found in new SARS-CoV-2 variants first identified in the UK (B.1.1.7), South Africa (B.1.351) and Brazil (P1). Most of these mutations increased the affinity of the RBD/ACE2 interaction. The exceptions were mutations K417N/T, which decreased the affinity. Taken together with other studies, our results suggest that the N501Y and S477N mutations primarily enhance transmission, the K417N/T mutations facilitate immune escape, and the E484K mutation facilitates both transmission and immune escape.

scholarly journals Effects of common mutations in the SARS-CoV-2 Spike RBD and its ligand, the human ACE2 receptor on binding affinity and kinetics

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Michael I Barton ◽  
Stuart A MacGowan ◽  
Mikhail A Kutuzov ◽  
Omer Dushek ◽  
Geoffrey John Barton ◽  
...  
Keyword(s):  
Cell Surface ◽  
Binding Site ◽  
Receptor Binding ◽  
Immune Escape ◽  
Surface Protein ◽  
Spike Protein ◽  
Receptor Binding Domain ◽  
Cell Surface Protein ◽  
Kinetics Analysis ◽  
Protein Receptor

The interaction between the SARS-CoV-2 virus Spike protein receptor binding domain (RBD) and the ACE2 cell surface protein is required for viral infection of cells. Mutations in the RBD are present in SARS-CoV-2 variants of concern that have emerged independently worldwide. For example, the B.1.1.7 lineage has a mutation (N501Y) in its Spike RBD that enhances binding to ACE2. There are also ACE2 alleles in humans with mutations in the RBD binding site. Here we perform a detailed affinity and kinetics analysis of the effect of five common RBD mutations (K417N, K417T, N501Y, E484K, and S477N) and two common ACE2 mutations (S19P and K26R) on the RBD/ACE2 interaction. We analysed the effects of individual RBD mutations and combinations found in new SARS-CoV-2 Alpha (B.1.1.7), Beta (B.1.351), and Gamma (P1) variants. Most of these mutations increased the affinity of the RBD/ACE2 interaction. The exceptions were mutations K417N/T, which decreased the affinity. Taken together with other studies, our results suggest that the N501Y and S477N mutations enhance transmission primarily by enhancing binding, the K417N/T mutations facilitate immune escape, and the E484K mutation enhances binding and immune escape.

scholarly journals Potent Cyclic Peptide Inhibitors of FXIIa Discovered by mRNA Display with Genetic Code Reprogramming

2021 ◽  
Author(s):  
Daniel J. Ford ◽  
Nisharnthi M. Duggan ◽  
Sarah E. Fry ◽  
Jorge Ripoll-Rozada ◽  
Stijn M. Agten ◽  
...  
Keyword(s):  
Genetic Code ◽  
Cyclic Peptide ◽  
Peptide Inhibitors ◽  
Mrna Display

scholarly journals Phage-Display Based Discovery and Characterization of Peptide Ligands against WDR5

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1225
Author(s):  
Jiawen Cao ◽  
Tiantian Fan ◽  
Yanlian Li ◽  
Zhiyan Du ◽  
Lin Chen ◽  
...  
Keyword(s):  
Phage Display ◽  
Cyclic Peptide ◽  
Protein Complexes ◽  
Peptide Ligands ◽  
Phage Library ◽  
Cancer Drug ◽  
Protein Protein Interaction ◽  
Phage Display Technique ◽  
Peptide Mimic ◽  
Human Proteins

WD40 is a ubiquitous domain presented in at least 361 human proteins and acts as scaffold to form protein complexes. Among them, WDR5 protein is an important mediator in several protein complexes to exert its functions in histone modification and chromatin remodeling. Therefore, it was considered as a promising epigenetic target involving in anti-cancer drug development. In view of the protein–protein interaction nature of WDR5, we initialized a campaign to discover new peptide-mimic inhibitors of WDR5. In current study, we utilized the phage display technique and screened with a disulfide-based cyclic peptide phage library. Five rounds of biopanning were performed and isolated clones were sequenced. By analyzing the sequences, total five peptides were synthesized for binding assay. The four peptides are shown to have the moderate binding affinity. Finally, the detailed binding interactions were revealed by solving a WDR5-peptide cocrystal structure.

scholarly journals Immunoglobulin G Antibodies against the Endosymbionts of Filarial Nematodes (Wolbachia) in Patients with Pulmonary Dirofilariasis

2003 ◽  
Vol 10 (1) ◽  
pp. 180-181 ◽  
Author(s):  
F. Simón ◽  
G. Prieto ◽  
R. Morchón ◽  
C. Bazzocchi ◽  
C. Bandi ◽  
...  
Keyword(s):  
Immunoglobulin G ◽  
Dirofilaria Immitis ◽  
Surface Protein ◽  
Igg Antibodies ◽  
Healthy Individuals ◽  
Bacterial Endosymbiont ◽  
Filarial Nematodes ◽  
Pulmonary Dirofilariasis ◽  
Diagnostic Applications

ABSTRACT The dog parasite Dirofilaria immitis can infect humans. Patients with pulmonary dirofilariasis were tested for immunoglobulin G (IgG) antibodies against the surface protein of Wolbachia, the bacterial endosymbiont of D. immitis. These patients showed significantly higher IgG titers than healthy individuals from areas in which D. immitis was endemic as well as areas in which it was not endemic. Titration of anti-Wolbachia surface protein IgG could become useful for diagnostic applications.

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