Design of novel multi-epitope vaccines against severe acute respiratory syndrome validated through multistage molecular interaction and dynamics

Abstract

Severe acute respiratory syndrome (SARS) is endemic in South China and is continuing to spread worldwide since the 2003 outbreak, affecting human population of 37 countries till present. SARS is caused by the severe acute respiratory syndrome Coronavirus (SARS-CoV). In the present study, we have designed two multi-epitope vaccines (MEVs) composed of cytotoxic T lymphocyte (CTL), helper T lymphocyte (HTL) and B cell epitopes overlap, bearing the potential to elicit cellular as well as humoral immune response. We have used truncated (residues 10–153) Onchocerca volvulus activation-associated secreted protein-1 as molecular adjuvants at N-terminal of both the MEVs. Selected overlapping epitopes of both the MEVs were further validated for stable molecular interactions with their respective human leukocyte antigen class I and II allele binders. Moreover, CTL epitopes were further studied for their molecular interaction with transporter associated with antigen processing. Furthermore, after tertiary structure modelling, both the MEVs were validated for their stable molecular interaction with Toll-like receptors 2 and 4. Codon-optimized cDNA of both the MEVs was analysed for their potential high level of expression in the mammalian cell line (Human) needed for their further in vivo testing. Overall, the present study proposes in silico validated design of two MEVs against SARS composed of specific epitopes with the potential to cause a high level of SARS-CoV specific cellular as well as humoral immune response.

Communicated by Ramaswamy H. Sarma     

Immunoinformatics Approach to Design T-cell Epitope-Based Vaccine Against Hendra Virus

Screening of HLA class II epitope-based peptides as potential vaccine candidates is one of the most rational approach for vaccine development against Hendra virus (HeV) infection, for which currently there is no successful vaccine in practice. In this study, screening of epitopes from HeV proteins viz matrix, glycoprotein, nucleocapsid, fusion, C protein, V protein, W protein and polymerase, followed by highest binding affinity & molecular dynamic simulation of selected T-cell epitopes with their corresponding HLA class II alleles has been done. The server ProPred facilitates the binding prediction of HLA class II allele specific epitopes from the antigenic protein sequences of HeV. PEPstrMOD server was used for PDB structure modeling of the screened epitopes and MODELLER was used for HLA alleles modeling. We docked the selected T-cell epitopes with their corresponding HLA allele structures using the AutoDock 4.2 tool. Further the selected docked complex structures were optimized by NAnoscale Molecular Dynamics program (NAMD) at 5 ps, with the CHARMM-22 force field parameter incorporated in Visual Molecular Dynamics (VMD 1.9.2) and complex structure stability was evaluated by calculating RMSD values. Epitopes IRIFVPATN (Nucleocapsid), MRNLLSQSL (Nucleocapsid), VRRAGKYYS (Matrix) and VRLKCLLCG (Fusion) proteins have shown considerable binding with DRB1*0806, DRB1*1304, DRB1*0701 and DRB1*0301 HLA class II allele respectively. Toxicity, antigenicity and population coverage of epitopes IRIFVPATN, MRNLLSQSL, VRRAGKYYS and VRLKCLLCG were analyzed by Toxin Pred, Vexijen and IEDB tool, respectively. The potential T-cell epitopes can be utilized in designing comprehensive epitope-based vaccines and diagnostic kits against Hendra virus after further in-vivo studies.

     

Reconstructing the Human Genetic History of Mainland Southeast Asia: Insights from Genome-Wide Data from Thailand and Laos

Thailand and Laos, located in the center of Mainland Southeast Asia (MSEA), harbor diverse ethnolinguistic groups encompassing all five language families of MSEA: Tai-Kadai (TK), Austroasiatic (AA), Sino-Tibetan (ST), Hmong-Mien (HM), and Austronesian (AN). Previous genetic studies of Thai/Lao populations have focused almost exclusively on uniparental markers and there is a paucity of genome-wide studies. We therefore generated genome-wide SNP data for 33 ethnolinguistic groups, belonging to the five MSEA language families from Thailand and Laos, and analyzed these together with data from modern Asian populations and SEA ancient samples. Overall, we find genetic structure according to language family, albeit with heterogeneity in the AA-, HM-, and ST-speaking groups, and in the hill tribes, that reflects both population interactions and genetic drift. For the TK speaking groups, we find localized genetic structure that is driven by different levels of interaction with other groups in the same geographic region. Several Thai groups exhibit admixture from South Asia, which we date to ∼600–1000 years ago, corresponding to a time of intensive international trade networks that had a major cultural impact on Thailand. An AN group from Southern Thailand shows both South Asian admixture as well as overall affinities with AA-speaking groups in the region, suggesting an impact of cultural diffusion. Overall, we provide the first detailed insights into the genetic profiles of Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical studies.     

Sequence and Structure Based Binding Prediction Study of HLA Class I and cTAP Binding Peptides for Japanese Encephalitis Vaccine Development

Japanese encephalitis is a major threat in developing countries, even the availability of several conventional vaccines, which demand development of more effective vaccines. The present study used propred I and Immune Epitope Database Artificial Neural Network (ANN) algorithm (IEDB-ANN) to identify the conserve and promiscuous T cell epitopes from JEV proteome followed by structure based analysis of potential epitopes. Among all identified 102 epitopes, ten epitope were promiscuous but two epitopes of glycoprotein viz. ⁵⁵LVTVNPFVA⁶³ and ³⁸IPIVSVASL⁴⁶ were found most promiscuous, highly conserved and high population coverage in comparison of known antigenic positive control peptides. The B cell epitopes of glycoprotein also share these two T cell epitopes revealed by BCPred algorithm which can be a basis to confer the protection by neutralizing antibody combined with an effective cell-mediated response. Further, Autodock 4.2 and NAMD–VMD molecular dynamics simulation were used for docking and molecular dynamics simulation respectively, to validate epitope and allele complex binding stability. The 3D structure models were generated for epitopes and corresponding HLA allele by Pepstr and Modeller 9.10 respectively. Epitope LVTVNPFVA–B5101 allele complex showed best energy minimization and stability over the time window during simulation. Here we also present the binding sequel of epitope LVTVNPFVA and its eventual transport through cTAP1 (PDB ID: 1JJ7) revealed by Autodock 4.2, which is an essential path for HLA class I binding epitopes to elicit immune response. The docking experiment of epitope LVTVNPFVA and cTAP1 very well show a 2 H-bond with a binding energy of ?1.88 kcal/mol and other binding state of epitope forming no H-bond with a binding energy of ?1.13 kcal/mol in the lower area of cTAP1 cavity. These results show a smooth pass through of the epitope across the channel of cTAP1. Overall, identified peptides have potential application in the design and development of short peptide based vaccines and diagnostic agents for Japanese encephalitis.