Identification of three conserved linear B cell epitopes on the SARS-CoV-2 spike protein

Machine learning accelerates the discovery of epitope-based dual-bioactive peptides against skin infections

OBJECTIVES

Skin injuries and infections are an inevitable part of daily human life, particularly with chronic wounds, becoming an increasing socioeconomic burden. In treating skin infections and promoting wound healing, bioactive peptides may hold significant potential, particularly those possessing antimicrobial and anti-inflammatory properties. However, obtaining these peptides solely through traditional wet laboratory experiments is costly and time-consuming, and peptides identified by current computer-assisted predictive models largely lack validation of their effects via wet laboratory experiments. Consequently, this study aimed to integrate computer-assisted methods and traditional wet laboratory experiments to identify anti-inflammatory and antimicrobial peptides.

METHODS

We developed a computer-assisted mining pipeline to screen potential peptides from the epitopes of the major histocompatibility complex class II.

RESULTS

The peptide AIMP1 was identified, with the ability to physically damage Escherichia coli by increasing bacterial cell membrane permeability, and with the ability to inhibit inflammation by binding to endotoxin-lipopolysaccharide. Additionally, in an LPS-induced inflammation animal model, AIMP1 slightly increased levels of proinflammatory cytokines (TNF-α, IL-1β, and IL-6), and in a skin wound infection animal model, AIMP1 effectively accelerated healing, reduced levels of these pro-inflammatory cytokines, and showed no acute hepatotoxicity or nephrotoxicity.

CONCLUSIONS

In conclusion, this study not only developed a computer-assisted mining pipeline for identifying anti-inflammatory and antimicrobial peptides but also successfully pinpointed the peptide AIMP1, demonstrating its therapeutic potential for skin injury treatment.

Recombinant porcine interferon δ8 inhibited porcine deltacoronavirus infection in vitro and in vivo

Porcine deltacoronavirus (PDCoV) poses a significant threat to both the pig industry and public safety, and has recently been identified in humans. Currently, there are no commercially available vaccines or antiviral treatments for PDCoV. In this study, recombinant porcine interferon δ8 (rINF-δ8) expressed by the HEK 293F expression system was used to evaluated its antiviral activity against PDCoV both in vitro and in vivo. Results demonstrated that rIFN-δ8 displayed non-toxic to ST cells and primary PAMs, and effectively inhibited PDCoV replication in a dose-dependent manner in vitro, with complete suppression of virus replication at a concentration of 2 μg/ml. Treatment of piglets with two doses of 25 μg/kg of rIFN-δ8 reduced clinical symptoms, decreased virus shedding, alleviated intestinal damage, and lowered the viral load in the jejunum and ileum. Furthermore, the levels of interferon-stimulated genes (ISGs) such as Viper, Mx1, ISG15, IFIT1, OSA, and IFITM1 were significantly increased both in vitro and in vivo, with elevated ISG levels sustained for at least 3 days in vivo. These findings suggest that rIFN-δ8 has the potential to serve as an effective antiviral agent for preventing PDCoV in pigs in the future.

Identification of a novel conserved B-cell epitope in p15 of the African swine fever virus

African Swine Fever Virus (ASFV), a highly contagious DNA virus, causes severe economic losses to the global swine industry. The ASFV p15 protein, which is found in the core shell, is essential to the assembly of viral particles. In addition, protein p15 is a candidate target for the development of diagnostic reagents for African Swine Fever (ASF) because of its excellent immunogenicity. In this research, we prepared the p15 protein using eukaryotic expression system and validated it with sera from ASFV-infected pigs. The p15 protein could be well identified by the sera from ASFV-infected pigs, suggesting that some linear epitopes are located in the p15 protein. Furthermore, we successfully prepared two lgG1 subclass monoclonal antibodies (1E6-A7 and 3D6-D4) specific against p15 using hybridoma technology. Using the peptide scanning method, we discovered the two mAbs well recognized the same linear epitope23LEIINNLCML32. The23LEIINNLCML32 epitope in the ASFV p15 N-terminus was identified and characterized for the first time, and it reacted well with the ASFV-positive serum, implying that it was a natural B cell linear epitope. These findings may help in the development of novel serologic diagnosis tools and the improvement of antiviral drug designs for ASF.

Identification of two novel B-cell epitopes located on the spike protein of swine acute diarrhea syndrome coronavirus

Swine acute diarrhea syndrome coronavirus (SADS-CoV) is an emerging alpha-coronavirus that causes diarrhea in piglets and results in serious economic losses. During SADS-CoV infection, the spike protein (S) serves as a crucial structural component of the virion, interacting with receptors and eliciting the production of neutralizing antibodies. Due to the potential risk of zoonotic transmission of SADS-CoV, the identification and screening of epitopes on the S glycoproteins will be crucial for development of sensitive and specific diagnostic tools. In this study, we immunized BALB/c mice with recombinant SADS-CoV S trimer protein and generated two S1-specific monoclonal antibodies (mAbs): 8D6 and 6E9, which recognized different linear B-cell epitopes. The minimal fragment recognized by mAb 8D6 was mapped to 311NPDQRD316, the minimal fragment recognized by mAb 6E9 was mapped to 492ARFVDRL498. Homology analysis of the regions corresponding to 13 typical strains of different SADS-CoV subtypes showed high conservation of these two epitopes. These findings contribute to a deeper understanding of the structure of the SADS-CoV S protein, which is valuable for vaccine design and holds potential for developing diagnostic methods to detect SADS-CoV.

Display of porcine epidemic diarrhea virus spike protein B-cell linear epitope on Lactobacillus mucosae G01 S-layer surface induce a robust immunogenicity in mice

The Porcine epidemic diarrhea virus (PEDV) presents a substantial risk to the domestic pig industry, resulting in extensive and fatal viral diarrhea among piglets. Recognizing the mucosal stimulation triggered by PEDV and harnessing the regulatory impact of lactobacilli on intestinal function, we have developed a lactobacillus-based vaccine that is carefully designed to elicit a strong mucosal immune response. Through bioinformatics analysis, we examined PEDV S proteins to identify B-cell linear epitopes that meet the criteria of being non-toxic, soluble, antigenic, and capable of neutralizing the virus. In this study, a genetically modified strain of Lactobacillus mucosae G01 (L.mucosae G01) was created by utilizing the S layer protein (SLP) as a scaffold for surface presentation. Chimeric immunodominant epitopes with neutralizing activity were incorporated at various sites on SLP. The successful expression of SLP chimeric immunodominant epitope 1 on the surface of L.mucosae G01 was confirmed through indirect immunofluorescence and transmission electron microscopy, revealing the formation of a transparent membrane. The findings demonstrate that the oral administration of L.mucosae G01, which expresses the SLP chimeric immunodominant gene epitope1, induces the production of secreted IgA in the intestine and feces of mice. Additionally, there is an elevation in IgG levels in the serum. Moreover, the levels of cytokines IL-2, IL-4, IFN-γ, and IL-17 are significantly increased compared to the negative control group. These results suggest that L. mucosae G01 has the ability to deliver exogenous antigens and elicit a specific mucosal immune response against PEDV. This investigation presents new possibilities for immunoprophylaxis against PEDV-induced diarrhea.

Identification and Validation of Peptides Specifying SARS-CoV-2 B-Cell Epitopes Eliciting Neutralizing Antibodies

Vaccination is an effective means of inducing immune protection to prevent transmissible diseases. During the Covid-19 pandemic, immunizations using traditional and novel vaccine platforms such as the inactivated SARSCo-V-2 vaccine, adenoviral-vectored, and nucleic acid-based mRNA vaccines have been relatively successful in controlling the rates of infection and hospitalizations. Nevertheless, the danger posed by the emergence of SARS-CoV-2 variants would set the stage for the design of next generation vaccines. To overcome the lack of efficacy of current vaccines against emerging SARS-CoV-2 variants, new vaccines must be able to overcome the reduced effectiveness of the current vaccines. Since the current Covid-19 vaccines are dependent on the whole S-protein of Wuhan strain as the antigen, mutations have rendered the current Covid-19 vaccines less effective against variants of concern (VoCs). Instead of using the whole S-protein, peptide-based epitopes could be predicted using immunoinformatic approaches, simulation of the 3D structures, overlapping peptides covering the whole length of the S-protein or peptide arrays based on synthetic peptide combinatorial libraries comprising peptides recognizable by monoclonal antibodies. B-cell epitopes were predicted, and immunogenicity of peptides was validated in mice by immunizing mice with peptides conjugated to keyhole limpet hemocyanin (KLH) mixed with Montanide 51 as an adjuvant. The immunogenicity of epitopes that could elicit peptide specific IgGs was determined by peptide-based ELISA. Neutralizing activities were determined by cPass and pseudovirus-based neutralization assays.

Advances in rapid detection of SARS-CoV-2 by mass spectrometry

COVID-19 has already been lasting for more than two years and it has been severely affecting the whole world. Still, detection of SARS-CoV-2 remains the frontline approach to combat the pandemic, and the reverse transcription polymerase chain reaction (RT-PCR)-based method is the well recognized detection method for the enormous analytical demands. However, the RT-PCR method typically takes a relatively long time, and can produce false positive and false negative results. Mass spectrometry (MS) is a very commonly used technique with extraordinary sensitivity, specificity and speed, and can produce qualitative and quantitative information of various analytes, which cannot be achieved by RT-PCR. Since the pandemic outbreak, various mass spectrometric approaches have been developed for rapid detection of SARS-CoV-2, including the LC-MS/MS approaches that could allow analysis of several hundred clinical samples per day with one MS system, MALDI-MS approaches that could directly analyze clinical samples for the detection, and efforts for the on-site detection with portable devices. In this review, these mass spectrometric approaches were summarized, and their pros and cons as well as further development were also discussed.