Jul 2026· Journal of Medicinal Chemistry· 0 citations· 27 references
Medicine
TL;DR
The utility of the LW25.13 peptide as a scaffold that can be adapted to different virus variants, which may prove useful for the development of peptides against new coronavirus variants of concern in the future, is illustrated.
Abstract
The starting point of this work was a SARS-CoV-2 neutralizing peptide (LW25.13), which binds to the receptor-binding domain of the viral spike protein and inhibits the attachment of the virus to its cellular receptor ACE2. As LW25.13 is unable to neutralize later SARS-CoV-2 variants, such as omicron, we have extended the neutralization breadth of LW25.13 through structural and bioinformatic analysis. This involved the systematic variation of a range of positions and yielded peptides neutralizing SARS-CoV-2 beta and omicron at low nanomolar concentrations, while preserving the strong neutralizing capacity against earlier virus variants (wild-type, alpha, delta), as well as the proteolytic stability and α-helical conformation of the peptide. This gain in neutralizing breadth illustrates the utility of the peptide as a scaffold that can be adapted to different virus variants, which may prove useful for the development of peptides against new coronavirus variants of concern in the future.
The emergence of the SARS-CoV-2 pandemic led to the spread of highly transmissible variants, such as the Delta variant, which originated in India, underscoring the urgent need to develop new antivirals, therapeutics, and vaccines. In our previous study, we showed that Membrane-Envelope Virus-like Particles exhibit antigenicity and neutralization activity. Hence, our present study was conducted to evaluate whether the M protein alone can form VLPs that elicit an immune response. Using computational methods, we identified key interacting residues in M-protein that contribute to VLP formation and interact with other structural proteins, including Spike (S), Nucleocapsid (N), and Envelope (E). The SARS-CoV-2-M protein was expressed in Sf-21 insect cells, and the resulting VLPs were purified, analyzed for shape and size, and characterized using DLS, FESEM, and TEM. The purified VLPs were injected into BALB/c mice to evaluate their immune response compared with uninfected controls. The biophysical analysis confirms that the particles are round and have a size of ~ 180–200 nm. The serum levels of IgG, IgM, and IgA were found to be higher in immunized mice than in uninfected mice. Further qRT-PCR analysis demonstrated the levels of IFN-γ, IL-2, and IL-12, indicating a TH1-biased immune response against the M protein. Our study demonstrates that the highly conserved M protein can self-assemble into VLPs and elicit humoral and cellular immune response. Furthermore, our study indicates that while M-protein VLPs elicit significant antibodies and cytokine responses, they do not induce detectable neutralizing activity when given alone.
Akash Kumar, K. K. Inampudi, Vikas Kumar et al.· Virology Journal· 0 citations
The results show the value of nanobody technology for identifying novel neutralising epitopes in the S2 region of beta-coronaviruses with potential for the development of new selective anti-viral agents.
John D. Clarke, Luke M. Jones, I. Buckle et al.· Scientific Reports· 0 citations
As the subunit of the SARS-CoV-2 spike protein (SARS-CoV-2 SP), the receptor-binding domain (RBD) can specifically bind to human angiotensin-converting enzyme 2 (ACE2), enabling viral infection of host cells. Therefore, it is of utmost significance to explore probes that can bind to the conserved epitope of the SARS-CoV-2 RBD with good affinity, so as to recognize various SARS-CoV-2 variants for diagnosis, vaccination, and the development of new detection methods. Herein, we biopanned peptide RN3 (sequence: YSIDWVFHHPML) by phage display, which can bind to the SARS-CoV-2 RBD with excellent affinity and selectivity. Molecular dynamics simulation and molecular docking verified that the His8 and Met11 residues in peptide RN3 are bound to the Asn487 and Tyr489 residues of the conserved epitope of the SARS-CoV-2 RBD subunit on the SARS-CoV-2 SP (His8-Asn487 and Met11-Tyr489, respectively) by hydrogen bonding. Alanine scanning confirmed that Met11 of peptide RN3 is the key amino acid for binding to the SARS-CoV-2 SP. The median inhibition concentration for peptide RN3 inhibiting the SARS-CoV-2 SP binding to ACE2 was 37 nM. Subsequently, phage RN3 was used as a capture probe, the SARS-CoV-2 SP-specific binding peptide Pn (sequence: WNLDLSQWLPPMGGGSKKKC) as a detection probe, and Au@Pd NP-based peroxidase-mimicking nanozyme for signal amplification. A phage RN3/antigen/peptide Pn sandwich ELISA was established for the selective detection of SARS-CoV-2 SP with a linear range of 5-1000 pg/mL and a limit of detection of 2.93 pg/mL. This method was applied to double-blind testing of 13 randomized clinical samples, which could distinguish between positive and negative samples. The detected results are well consistent with those of the gold-standard RT-PCR method. Thus, this study proposed phage-displayed dual peptides to construct a reliable and inexpensive ELISA for screening SARS-CoV-2 infection. A similar strategy can be extended to study other pathogens.
Mingyang Wang, Haipeng Yu, Wanjian Liu et al.· Analytical Chemistry· 1 citation
Evaluations utilizing surface plasmon resonance and pseudovirus assays demonstrate that these sublineages exhibit significantly reduced human ACE2 receptor engagement compared to their parental strain, which suggests these variants will soon spread globally and emphasize the critical need for ongoing surveillance to monitor D420N-carrying lineages.
The receptor-binding domain (RBD) of SARS-CoV-2 spike glycoprotein is central to serological diagnostics and vaccine development, but production in eukaryotic expression systems is costly and technically demanding. Here, we describe an Escherichia coli platform to express the wild-type RBD, used as an initial model for the standardization of the methodology. Subsequently, the platform was applied to the alpha and beta variants, demonstrating its adaptability to different RBD variants. Inclusion bodies were purified under denaturing conditions and refolded by size-exclusion chromatography using a linear urea gradient and a redox/anti-aggregation buffer that promotes correct disulfide-bond formation and minimizes aggregation. The procedure yielded ∼36 mg of soluble protein per liter of culture. The refolded recombinant RBDs of wild-type, alpha and beta variants, as well as RDB wild-type produced in Expi293 cells as a control were evaluated in ELISA assays against sera from healthy, vaccinated and convalescent SARS-CoV-2 patients. All recombinant RBDs produced in E. coli were recognized by patients' sera, demonstrating that they retain antigenicity and supporting their use in serological assays as a rapid and scalable source of antigens.
Daniela Roa-Velázquez, J. Filisola-Villaseñor, D. I. Zavala-Vargas et al.· Protein Expression and Purif...· 0 citations
The phylogenetic relationship of the A222V substitution in the S protein relative to various global isolates is investigated, indicating high mutation rates in the S gene, characterised by diverse point mutations.
Kiky Martha, Ariesaka, M. M. Nuryady et al.· 0 citations
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