Peptide Binder with High-Affinity for the SARS-CoV-2 Spike Receptor-Binding Domain

Abstract

Rapid antigen detection tests are urgently needed for the early diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The discovery of a binder with high affinity and selectivity for the biomarkers presented by SARS-CoV-2 is crucial to the development of the rapid antigen detection method. We utilized the surface biopanning to identify a peptide binder R1 from a phage-displayed peptide library consisting of 10 9 independent phage recombinants. The R1 peptide exhibited high-affinity for specific binding with the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein with a dissociation constant K D of (7.5 ± 1.9) × 10 −10 M, which maintained high binding affinity with the RBD derived from Gamma, Lambda, Delta, and Omicron variants. The composition and sequence dependence of binding characteristics in R1−RBD interactions was revealed by the binding affinity fluctuations between RBD and the scrambled sequences or single-site mutants of R1. The R1functionalized gold nanoparticles possessed concentration-dependent response to RBD and selectivity over bovine serum albumin and human serum albumin. The peptide binder R1 shows the potential to be used for constructing a rapid detection method for the early-stage diagnostics for SARS-CoV-2.

FcγRIIIA affinity chromatography complements conventional functional characterization of rituximab

“…K D value is inversely proportional to the concentration of bound species. 32 The binding affinities of Rituximab were similar to the control upon addition of glucose in varying concentrations, as listed in Table 2. Similar K D values indicated no change in the affinity for the ligand protein that is, FcγRIIIA.…”

“…The reported affinity constant value of Rituximab for this variant was similar to the value reported by Dekkers et al 31 The increased K D values indicated decreased affinity for the ligand protein that is, FcγRIIIA. K D value is inversely proportional to the concentration of bound species 32 …”

Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets

“…Finally, Nsp13 is a helicase, that unwinds the RNA and promotes efficient transcription 25 , while Nsp15 serves as a uridine-specific endoribonuclease that facilitates the evasion of the host immune response 26 . Of the SARS-CoV-2 proteins, peptide binding has previously been shown for S receptor binding domain 27 , 28 , Nsp3 Ubl1 11 , 29 , Nsp5 30 , and suggested for Nsp10 31 , Nsp14 32 , and Nsp16 33 based on computational analysis. Furthermore, a potential peptide binding site in Nsp9 has been suggested from structural analysis 34 .…”

pH-Sensitive and Biodegradable Mn3(PO4)2·3H2O Nanoparticles as an Adjuvant of Protein-Based Bivalent COVID-19 Vaccine to Induce Potent and Broad-Spectrum Immunity

“…The SARS-CoV-2 spike glycoprotein S1 subunit mainly contains a receptor-binding domain (RBD) and an N -terminal domain (NTD). In fact, the RBD domain is responsible for engaging the human angiotensin-converting enzyme 2 (hACE2) receptors during viral infection and contains a wide range of neutralizing epitopes to effectively induce secretion of neutralizing antibodies to protect host cells from viral infection. , Therefore, the S1 subunit could be employed as an effective target in COVID-19 protein vaccines to elicit protective immune responses. − …”

“…In fact, the RBD domain is responsible for engaging the human angiotensinconverting enzyme 2 (hACE2) receptors during viral infection and contains a wide range of neutralizing epitopes to effectively induce secretion of neutralizing antibodies to protect host cells from viral infection. 37,38 Therefore, the S1 subunit could be employed as an effective target in COVID-19 protein vaccines to elicit protective immune responses. 39−41 In this work, we prepared a novel Mn 3 (PO 4 ) 2 •3H 2 O nanoparticle (nano-MnP) by simply optimizing the ratio of Na 2 HPO 4 and NaH 2 PO 4 in MnCl 2 solution for the first time.…”