Efforts for developing vaccine against Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) is crucial in prevention of SARS re-emergence. The global outbreak of SARS was contained since 2003. However concerns remain over the possibility of future recurrences, especially with recent reports of laboratory-acquired infections and the presence of sporadic cases, raising a serious concern. SARS-CoV spike S protein (1255aa) is an important target in developing safe and effective vaccines. In this study multiple bio-informatics and immunoinformatics implementation tools from NCBI and IEDB were used for epitopes prediction from spike S protein. The predicted epitopes were further assessed for population coverage against the whole world population. Our results demonstrated that the epitopes 38-RGVYYPDEI -46 , 200-YQPIDVVRD -208 and 388-VVKGDDVRQ -396 elicit and stimulate B cell since they got higher score in Emini and Kolaskar and tongaonker software. For T-cell: the epitopes 47-FRSDTLYLT -55, 195-YVYKGYQPI -203 and 880-FAMQMAYRF -888 were found to interact with both MHC-1 and MHC-II alleles. Moreover 851-MIAAYTAAL -859 showed higher affinity to MHC-1 alleles while 782-FNFSQILPD -790 interacted only with MHC-II alleles. The population coverage epitope set for MHC-1 and MHC-II predicted epitopes was 82.16% and 99.97% respectively. All predicted epitopes against T cell (MHC-I/MHC-II) demonstrated strong potentiality as promising peptides vaccine with population coverage epitope set against the whole world of 100%. Taken together eight epitopes were proposed to interact with B and T cells and act as peptide vaccine against SARS-CoV virus. In vitro and in vivo studies are recommended to prove the effectiveness of these epitopes as a peptide vaccine.
Infectious laryngotracheitis virus (ILTV) is a gallid herpesvirus type 1, a member of the genus Iltovirus. It causes an infection in the upper respiratory tract mainly trachea which results in significant economic losses in the poultry industry worldwide. Vaccination against ILTV produced latent infected carriers’ birds, which become a source of virus transmission to nonvaccinated flocks. Thus this study aimed to design safe multiepitopes vaccine against glycoprotein B of ILT virus using immunoinformatic tools. Forty-four sequences of complete envelope glycoprotein B were retrieved from GenBank of National Center for Biotechnology Information (NCBI) and aligned for conservancy by multiple sequence alignment (MSA). Immune Epitope Database (IEDB) analysis resources were used to predict and analyze candidate epitopes that could act as a promising peptide vaccine. For B cell epitopes, thirty-one linear epitopes were predicted using Bepipred. However eight epitopes were found to be on both surface and antigenic epitopes using Emini surface accessibility and antigenicity, respectively. Three epitopes (190KKLP193, 386YSSTHVRS393, and 317KESV320) were proposed as B cell epitopes. For T cells several epitopes were interacted with MHC class I with high affinity and specificity, but the best recognized epitopes were 118YVFNVTLYY126, 335VSYKNSYHF343, and 622YLLYEDYTF630. MHC-II binding epitopes, 301FLTDEQFTI309,277FLEIANYQV285, and 743IASFLSNPF751, were proposed as promising epitopes due to their high affinity for MHC-II molecules. Moreover the docked ligand epitopes from MHC-1 molecule exhibited high binding affinity with the receptors; BF chicken alleles (BF2 2101 and 0401) expressed by the lower global energy of the molecules. In this study nine epitopes were predicted as promising vaccine candidate against ILTV. In vivo and in vitro studies are required to support the effectiveness of these predicted epitopes as a multipeptide vaccine through clinical trials.
Background The spread of a novel coronavirus termed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in China and other countries is of great concern worldwide with no effective vaccine. This study aimed to design a novel vaccine construct against SARS-CoV-2 from the spike S protein and orf1ab polyprotein using immunoinformatics tools. The vaccine was designed from conserved epitopes interacted against B and T lymphocytes by the combination of highly immunogenic epitopes with suitable adjuvant and linkers. Results The proposed vaccine composed of 526 amino acids and was shown to be antigenic in Vaxigen server (0.6194) and nonallergenic in Allertop server. The physiochemical properties of the vaccine showed isoelectric point of 10.19. The instability index (II) was 31.25 classifying the vaccine as stable. Aliphatic index was 84.39 and the grand average of hydropathicity (GRAVY) was − 0.049 classifying the vaccine as hydrophilic. Vaccine tertiary structure was predicted, refined and validated to assess the stability of the vaccine via Ramachandran plot and ProSA-web servers. Moreover, solubility of the vaccine construct was greater than the average solubility provided by protein sol and SOLpro servers indicating the solubility of the vaccine construct. Disulfide engineering was performed to reduce the high mobile regions in the vaccine to enhance stability. Docking of the vaccine construct with TLR4 demonstrated efficient binding energy with attractive binding energy of − 338.68 kcal/mol and − 346.89 kcal/mol for TLR4 chain A and chain B respectively. Immune simulation significantly provided high levels of immunoglobulins, T-helper cells, T-cytotoxic cells and INF-γ. Upon cloning, the vaccine protein was reverse transcribed into DNA sequence and cloned into pET28a(+) vector to ensure translational potency and microbial expression. Conclusion A unique vaccine construct from spike S protein and orf1ab polyprotein against B and T lymphocytes was generated with potential protection against the pandemic. The present study might assist in developing a suitable therapeutics protocol to combat SARSCoV-2 infection.
Background Small ruminant morbillivirus or peste des petits ruminants virus (PPRV) is an acute and highly contagious viral disease of goats, sheep, and other livestock. This study aimed at predicting an effective multiepitope vaccine against PPRV from the immunogenic proteins haemagglutinin (H), matrix (M), fusion (F), and nucleoprotein (N) using immunoinformatics tools. Materials and Methods The sequences of the immunogenic proteins were retrieved from GenBank of the National Center for Biotechnology Information (NCBI). BioEdit software was used to align each protein from the retrieved sequences for conservancy. Immune Epitope Database (IEDB) analysis resources were used to predict B and T cell epitopes. For B cells, the criteria for electing epitopes depend on the epitope linearity, surface accessibility, and antigenicity. Results Nine epitopes from the H protein, eight epitopes from the M protein, and ten epitopes from each of the F and N proteins were predicted as linear epitopes. The surface accessibility method proposed seven surface epitopes from each of the H and F proteins in addition to six and four epitopes from the M and N proteins, respectively. For antigenicity, only two epitopes 142PPERV146 and 63DPLSP67 were predicted as antigenic from H and M, respectively. For T cells, MHC-I binding prediction tools showed multiple epitopes that interacted strongly with BoLA alleles. For instance, the epitope 45MFLSLIGLL53 from the H protein interacted with four BoLA alleles, while 276FKKILCYPL284 predicted from the M protein interacted with two alleles. Although F and N proteins demonstrated no favorable interaction with B cells, they strongly interacted with T cells. For instance, 358STKSCARTL366 from the F protein interacted with five alleles, followed by 340SQNALYPMS348 and 442IDLGPAISL450 that interacted with three alleles each. The epitopes from the N protein displayed strong interaction with BoLA alleles such as 490RSAEALFRL498 that interacted with five alleles, followed by two epitopes 2ATLLKSLAL10 and 304QQLGEVAPY312 that interacted with four alleles each. In addition to that, four epitopes 3TLLKSLALF11, 356YFDPAYFRL364, 360AYFRLGQEM368, and 412PRQAQVSFL420 interacted with three alleles each. Conclusion Fourteen epitopes were predicted as promising vaccine candidates against PPRV from four immunogenic proteins. These epitopes should be validated experimentally through in vitro and in vivo studies.
Sudan Ebola virus is single stranded negative sense RNA genome belonging to Filovirus Filoviridae family that causes hemorrhagic fever. There is no treatment or vaccine for it, thus the aim of this study is to design a peptide vaccine using immuoinformatics approaches to analyse the glycoprotein of the all strain of SUDV, to determine the conserved region which is further studied to predict all possible epitopes that can be used as a peptide vaccine. A total of 21 Sudan Ebola virus glycoprotein retrieved from NCBI database were aligned to determine the conservancy and to predict the epitopes using IEDB analysis resource. Three epitopes predicted as a peptide vaccine for B cell (PPPPDGVR, ETFLQSPP, LQSPPIRE). For T cell four epitopes showed high affinity to MHC class I (FLYDRLAST, IIIAIIALL, MHNQNALVC and RTYTILNRK) and high coverage against Sudan and the whole world population. Also in MHC class II, Four epitopes that interact with most frequent MHC class II alleles (FAEGVIAFL, FLRATTELR, FLYDRLAST and FVWVIILFQ) with high coverage against Sudan and the whole world population. We recommend in vivo and in vitro study to prove the effectiveness of these predicted epitopes as a peptide vaccine.
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