Rapid, accurate and serotype independent pipeline for in silico epitope mapping of SARS-CoV-2 antigens: a combined machine learning and Chou’s pseudo amino acid composition method

Here,a new integrated machine learning and Chou’s pseudo amino acid composition method has been proposed for in silico epitope mapping of severe acute respiratorysyndrome-like coronavirus antigens.For this,a training dataset including 266 linear B-cell epitopes,1,267 T-cell epitopes and 1,280 non-epitopes were prepared.The epitope sequences were then converted to numerical vectors using Chou’s pseudo amino acid composition method.The vectors were then introduced to the support vector machine,random forest,artificial neural network,and K-nearest neighbor algorithms for the classification process.The algorithm with the highest performance was selected for the epitope mapping procedure.Based on the obtained results,the random forest algorithm was the most accurate classifier with an accuracy of 0.934 followed by K-nearest neighbor,artificial neural network,and support vector machine respectively.Furthermore,the efficacies of predicted epitopes by the trained random forest algorithm were assessed through their antigenicity potential as well as affinity to human B cell receptor and MHC-I/II alleles using the VaxiJen score and molecular docking,respectively.It was also clear that the predicted epitopes especially the B-cell epitopes had high antigenicity potentials and good affinities to the protein targets.According to the results,the suggested method can be considered for developing specific epitope predictor software as well as an accelerator pipeline for designing serotype independent vaccine against the virus.

Prediction of promiscuous T cell epitopes in RNA dependent RNA polymerase of Chikungunya virus

Objective: To explore RNA dependent RNA polymerase of Chikungunya virus(CHIKV) and develop T cell based epitopes with high antigenicity and good binding affinity for the human leukocyte antigen(HLA) classes as targets for epitopes based CHIKV vaccine. Methods: In this study we downloaded 371 non-structural protein 4 protein sequences of CHIKV belonging to different regions of the world from the US National Institute of Allergy and Infectious Diseases(NIAID) virus pathogen resource database. All the sequences were aligned by using CLUSTALW software and a consensus sequence was developed by using Uni Pro U Gene Software version 1.2.1. PropredⅠand Propred software were used to predict HLAⅠ and HLAⅡ binding promiscuous epitopes from the consensus sequence of non-structural protein 4 protein. The predicted epitopes were analyzed to determine their antigenicity through Vaxijen server version 2.0. All the HLAⅠ binding epitopes were scanned to determine their immunogenic potential through the Immune Epitope Database(IEDB). All the predicted epitopes of our study were fed to IEDB database to determine whether they had been tested earlier. Results: Twenty two HLA class Ⅱ epitopes and eight HLA classⅠepitopes were predicted. The promiscuous epitopes WMNMEVKII at position 486–494 and VRRLNAVLL at 331–339 were found to bind with 37 and 36 of the 51 HLA class Ⅱ alleles respectively. Epitope MANRSRYQS at position 58–66 and epitopes YQSRKVENM at positions 64–72 were predicted to bind with 12 and 9 HLAⅠI alleles with antigenicity scores of 0.754 9 and 1.013 0 respectively. Epitope YSPPINVRL was predicted to bind 18 HLAⅠ alleles and its antigenicity score was 1.425 9 and immunogenicity score was 0.173 83. This epitope is very useful in the preparation of a universal vaccine against CHIKV infection. Conclusions: Epitopes reported in this study showed promiscuity, antigenicity as well as good binding affinity for the HLA classes. These epitopes will provide the baseline for development of efficacious vaccine for CHIKV.

Conservation of T cell epitopes between seasonal influenza viruses and the novel influenza A H7N9 virus

A novel avian influenza A(H7N9) virus recently emerged in the Yangtze River delta and caused diseases, often severe, in over 130 people. This H7N9 virus appeared to infect humans with greater ease than previous avian influenza virus subtypes such as H5N1 and H9N2. While there are other potential explanations for this large number of human infections with an avian influenza virus, we investigated whether a lack of conserved T-cell epitopes between endemic H1N1 and H3N2 influenza viruses and the novel H7N9 virus contributes to this observation. Here we demonstrate that a number of T cell epitopes are conserved between endemic H1N1 and H3N2 viruses and H7N9 virus. Most of these conserved epitopes are from viral internal proteins. The extent of conservation between endemic human seasonal influenza and avian influenza H7N9 was comparable to that with the highly pathogenic avian influenza H5N1. Thus, the ease of inter-species transmission of H7N9 viruses(compared with avian H5N1 viruses) cannot be attributed to the lack of conservation of such T cell epitopes. On the contrary, our findings predict significant T-cell based cross-reactions in the human population to the novel H7N9 virus. Our findings also have implications for H7N9 virus vaccine design.

A recombinant multi epitope, multi stage malaria vaccine candidate expressed in Escherichia coli

Objective To construct and evaluate a recombinant multi epitope, multistage malaria vaccine candidate expressed in Escherichia coli (E coli) Methods A hybrid gene (HGF) encoding several putative immunodominant T or T/B epitopes from MSP 1, MSP 2, Pf155/RESA of Plasmodium falciparum (P falciparum ) and two immune stimulating epitopes from interleukin 1 and tetanus toxin was synthesized Two copies of HGF and a copy of gene encoding Pattaroyo′s Spf66 were connected together to construct a sandwich hybrid gene HGFSP The gene was cloned into an expression vector pWR450 I for production of a fusion protein with β galactosidase Efficacy of this vaccine candidate in inducing specific immunity against malaria parasites was evaluated Results Immunization of different species of animals with purified recombinant peptide showed that the peptide was able to induce remarkable antibody response to the immunized peptide as well as falciparum malaria parasites The epitopes included in the construct could induce antibodies against the intact parasite proteins as demonstrated by western blotting, indicating the epitopes retained their antigenicity in the new peptide construct Antibodies from animals immunized with recombinant HGFSP peptide exhibited good ability in inhibition of the in vitro growth of malaria parasites, augmentation of phagocytosis of the parasites or infected RBC by phagocytes, and facilitation of antibody dependent cell mediated cytotoxicity to the cultured malaria parasites Conclusion The recombinant peptide seems to be a potential candidate which is valuable for further investigation

Effects of the configuration of a multi epitope chimeric malaria DNA vaccine on its antigenicity to mice

Objective Four B and Th cell epitopes were selected from conservative domain of Plasmodium falciparum antigens to construct two groups of chimeric malaria DNA vaccines with different configurations and their antigenicities were studied Methods The partially synthesized oligonucleotide was annealed, PCR amplified and cloned into a mammalian cell expression vector By using a pair of isocaudamers on the vector, different single copies of B epitopes were multiplied and were tenderly stringed into two groups of chimeric DNA vaccine with different configurations BALB/c mice were immunized with these DNA plasmids by either intramuscular or intradermal injections Results The antisera from the immunized mice tested by ELISA showed that only the configuration which had a single copy of universal T helper cell epitope, CS T3, located at the C terminal of the multi copy B cell epitopes induced a high antibody response The T helper cell epitope at any other position of the peptide, or the double T helper cell epitopes configured with the B cell epitopes did not enhance antibody response, and some configurations even decreased the humoral response to a B cell epitope Conclusion This study demonstrated that both combination and configuration of the epitope may affect the antigenicity of a chimeric multiple antigen

Three Candidate Epitope-Vaccines in Combination Inducing High Levels of Multiantibodies Against HIV-1

HIV 1 mutation results in immune evasion, which presents a serious challenge for conventional strategies for developing effective vaccines. So far, much experimental evidence indicates that HIV 1 particles in the blood of patients can be cleaned principally by neutralizing antibodies. Based on these facts, we prepared triple combination of epitope vaccines with the objective of inducing antibodies with predefined multi epitope specificity against HIV 1. According to the sequences of three neutralizing epitopes (RILAVERYLKD, ELDKWA and GPGRAFY, designated E1, E2, and E3, respectively) on HIV 1 envelope proteins, three epitope peptides ((E1)2: C (RILAVERYLKDG) 2; (E2)4: C (ELDKWAG) 4; and (E3)2: C (GPGRAFY) 2) were synthesized and then conjugated with carrier protein keyhole limpet hemocyanin (KLH) or bovine serum albumin (BSA), and used for immunizing rabbits. After the vaccine course, the triple combination of epitope vaccines induced high levels of predefined multi epitope specific antibodies. An immunoblotting analysis demonstrated that the antibodies could recognize the native epitopes on both gp41 protein and V3 loop peptide. Furthermore, we compared the immune responses of three doses of epitope peptides in the candidate epitope vaccine. Strong antibody responses to three epitopes were observed in a dose dependent manner, with increasing dose raising the immune response. This result indicated that immunotolerance did not occur using an epitope vaccine dose of 80 μg. Thus, our results demonstrate that epitope vaccines in combination can synchronously induce high levels of antibodies with predefined multi epitope specificity against HIV 1, and may be used to develop effective vaccines against HIV as a new strategy.

Research Progress of Using Phage Display Technology to Screen Virus Affinity Peptides

Development and application of phage display technology and research progress of virus affinity peptide were summarized in the paper,and a preliminary outlook for future development was put forward. The paper laid a foundation for development of polypeptide drugs and polypeptide vaccine.

Recent advances in synthetic carbohydrate-based human immunodeficiency virus vaccines

An effective vaccine for human immunodeficiency virus(HIV) is urgently needed to prevent HIV infection and progression to acquired immune deficiency syndrome(AIDS). As glycosylation of viral proteins becomes better understood, carbohydrate-based antiviral vaccines against special viruses have attracted much attention. Significant efforts in carbohydrate synthesis and immunogenicity research have resulted in the development of multiple carbohydrate-based HIV vaccines. This review summarizes recent advances in synthetic carbohydrate-based vaccines design strategies and the applications of these vaccines in the prevention of HIV.