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Chauhan S, Kumar R, Khan N, Verma S, Sehgal R, Tripathi PK, Farooq U. Designing peptide-based vaccine candidates for Plasmodium falciparum erythrocyte binding antigen 175. Biologicals 2020; 67:42-48. [PMID: 32718776 DOI: 10.1016/j.biologicals.2020.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 11/30/2022] Open
Abstract
Plasmodium falciparum leads to a virulent form of malaria. Progress has been achieved in understanding the mechanisms involved in the malarial infection, still there is no effective vaccine to prevent severe infection. An effective vaccine against malaria should be one which can induce immune responses against multiple epitopes in the context of predominantly occurring HLA alleles. In this study, an integrated approach was employed to identify promiscuous peptides of a well-defined sequence of erythrocyte binding antigen-175 and promiscuous peptides for HLA alleles were designed using bioinformatics tools. A peptide with 15 amino acids (ILAIAIYESRILKRK) was selected based on its high binding affinity score and synthesized. This promiscuous peptide was used as stimulating antigen in lymphoproliferative responses to evaluate the cellular immune response. It was observed this peptide evokes lymphoproliferative and cytokine responses in individuals naturally exposed to the malaria parasite. The intensity of PBMCs proliferation was observed to be higher in sera obtained from P. falciparum exposed as compared to unexposed healthy individuals, suggesting earlier recognition of peptide of this region by T cells. Furthermore, the binding mode of HLA-peptide complex and their interaction may lead to a rational and selective peptide-based vaccine candidate design approach which can be used as a malaria prophylaxis.
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Affiliation(s)
- Shakti Chauhan
- Molecular and Immune-parasitology Laboratory, Shoolini University, Solan, India
| | - Rajender Kumar
- Department of Clinical Microbiology, Umeå University, SE-90185, Umeå, Sweden
| | - Nazam Khan
- Molecular and Immune-parasitology Laboratory, Shoolini University, Solan, India
| | - Swati Verma
- Department of Microbiology, Maharaja Ganga Singh University, Bikaner, India
| | - Rakesh Sehgal
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | | | - Umar Farooq
- Molecular and Immune-parasitology Laboratory, Shoolini University, Solan, India.
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Khan N, Kumar R, Chauhan S, Farooq U. An immunoinformatics approach to promiscuous peptide design for the Plasmodium falciparum erythrocyte membrane protein-1. MOLECULAR BIOSYSTEMS 2018; 13:2160-2167. [PMID: 28856362 DOI: 10.1039/c7mb00332c] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Plasmodium falciparum erythrocyte membrane protein-1 (Pfemp-1), a variant adhesion molecule, can act as a key component of immunity against malaria. In the current selection of malaria vaccines, no efficient vaccines are available that can be employed for its proper treatment. Unfortunately, resistance to post-infection treatments is increasing and therefore there is a pressing need to develop an efficient vaccine. Peptide-based vaccines can be effective tools against malaria but HLA restriction is a major hindrance which can be conquered by using promiscuous peptides. In this work, we employed a combined in silico and experimental approach to identify promiscuous peptides for the treatment of malaria. At first, using the immunoinformatics approach, promiscuous peptides were predicted from two conserved domains, CIDR-1 and DBL-3γ, of the Pfemp-1 antigen. These peptides were selected on the basis of their predicted binding affinity with different HLA class-I & class-II alleles. A total of 13 peptides were selected based on their predicted IFN-γ and IL-4 induction ability as well as their hydrophobicity. Out of these 13, the peptide C6 was synthesised and experimentally evaluated for further rationalization, HLA-peptide complex modelling and binding interaction analysis. Interestingly, the peptide C6 (SFIHIYLYRNIRIQL) showed an encouraging immunological response and T-cell proliferation in the immunological assay. This valuable content can aid the better design of more potent and selective vaccine candidates against infectious diseases.
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Affiliation(s)
- Nazam Khan
- Department of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, HP, India.
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Chauhan V, Singh MP, Ratho RK. Identification of T cell and B cell epitopes against Indian HCV-genotype-3a for vaccine development- An in silico analysis. Biologicals 2018. [PMID: 29519752 DOI: 10.1016/j.biologicals.2018.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Hepatitis C virus (HCV) infects almost 150 million people and is a leading cause of liver disease worldwide. It has been classified into seven genotypes; the most common genotype affecting Indian population is genotype 3 (60-70%). Currently there is no vaccine for any genotype of HCV. In order to develop peptide based vaccine against HCV, it is important to identify the conservancy in the circulating genotypes, along with the Human Leucocyte Antigen (HLA) alleles in the target population. The present study aims to identify conserved CD4 and CD8 T cells and B cell epitopes against Indian HCV-genotype-3a using an in silico analysis. In the present study, 28 promiscuous CD4 T cell epitopes and some CD8 epitopes were identified. The NS4 region was predicted to be the most antigenic with maximum number of conserved and promiscuous CD4 T cell epitopes and CD8 T cell epitopes having strong and intermediate affinity towards a number of HLA alleles prevalent in Indian population. Additionally, some linear B cell epitopes were also identified, which could generate neutralizing antibodies. In order to ascertain the binding pattern of the identified epitopes with HLA alleles, molecular docking analysis was carried out. The authors suggest further experimental validation to investigate the immunogenicity of the identified epitopes.
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Affiliation(s)
- Varun Chauhan
- Department of Virology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, Punjab 160012, India
| | - Mini P Singh
- Department of Virology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, Punjab 160012, India.
| | - Radha K Ratho
- Department of Virology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, Punjab 160012, India
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Prediction and analysis of promiscuous T cell-epitopes derived from the vaccine candidate antigens of Leishmania donovani binding to MHC class-II alleles using in silico approach. INFECTION GENETICS AND EVOLUTION 2017; 53:107-115. [PMID: 28549876 DOI: 10.1016/j.meegid.2017.05.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 03/20/2017] [Accepted: 05/22/2017] [Indexed: 12/27/2022]
Abstract
Visceral leishmaniasis is a dreadful infectious disease and caused by the intracellular protozoan parasites, Leishmania donovani and Leishmania infantum. Despite extensive efforts for developing effective prophylactic vaccine, still no vaccine is available against leishmaniasis. However, advancement in immunoinformatics methods generated new dimension in peptide based vaccine development. The present study was aimed to identify T-cell epitopes from the vaccine candidate antigens like Lipophosphogylcan-3(LPG-3) and Nucleoside hydrolase (NH) from the L. donovani using in silico methods. Available best tools were used for the identification of promiscuous peptides for MHC class-II alleles. A total of 34 promiscuous peptides from LPG-3, 3 from NH were identified on the basis of their 100% binding affinity towards all six HLA alleles, taken in this study. These peptides were further checked computationally to know their IFN-γ and IL4 inducing potential and nine peptides were identified. Peptide binding interactions with predominant HLA alleles were done by docking. Out of nine docked promiscuous peptides, only two peptides (QESRILRVIKKKLVR, RILRVIKKKLVRKTL), from LPG-3 and one peptide (FDKFWCLVIDALKRI) from NH showed lowest binding energy with all six alleles. These promiscuous T-cell epitopes were predicted on the basis of their antigenicity, hydrophobicity, potential immune response and docking scores. The immunogenicity of predicted promiscuous peptides might be used for subunit vaccine development with immune-modulating adjuvants.
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Binder TMC, Kelsch R, Wikner JM, Aly L, Brendel C, Alster I, Kühnl P, Finckh U, Eiermann TH. A rare ancestral HLA-DRB1(∗)15:01̃DQB1(∗)02:01 haplotype and its reversion in the same Western European family. Hum Immunol 2015; 76:124-8. [PMID: 25636575 DOI: 10.1016/j.humimm.2015.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 12/17/2014] [Accepted: 01/14/2015] [Indexed: 11/20/2022]
Abstract
The HLA-DR and -DQ loci are close neighbors on chromosome 6 that are highly linked. Many common associations between HLA-DR and DQ-alleles are known, normally transmitted as HLA-DR̃DQ haplotypes from one generation to another. Reports of very recent genetic rearrangements between HLA-DR and -DQ are rarely found in the literature. In Europeans haplotypes containing DRB1(∗)15:01, DQB1(∗)02:01, and DQA1(∗)05:01 have not been reported before. We report the finding of the rare HLA haplotype A(∗)24:02̃C(∗)07:02̃B(∗)07:02̃MICA(∗)008:01̃DRB5(∗)01:01̃DRB1(∗)15:01̃DQA1(∗)05:01̃DQB1(∗)02:01̃DPB1(∗)04:01 in a German stem cell donor with East Frisian ancestry. Our observation suggests a rare ancestral recombination between the DR and DQ loci. In order to investigate this haplotype, we typed 50/74 members of the family encompassing four generations for HLA classes I and II by serological and molecular methods. The rare haplotype was identified in 12 heterozygous carriers. Furthermore, we identified and further characterized a putative crossing over event resulting in its reversion to a common haplotype.
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Affiliation(s)
- Thomas M C Binder
- Diagnostic Center, Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Reinhard Kelsch
- Institute of Transfusion Medicine and Transplantation Immunology, University Clinics of Muenster, Muenster, Germany
| | - Julia M Wikner
- Diagnostic Center, Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Anesthesiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lilian Aly
- Diagnostic Center, Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Neurology, Klinikum Rechts der Isar, Munich, Germany
| | - Cornelia Brendel
- Department of Hematology, Oncology and Immunology, Philipps University Marburg and Universitätsklinikum Giessen und Marburg, Germany
| | - Ina Alster
- Diagnostic Center, Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Kühnl
- Diagnostic Center, Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Thomas H Eiermann
- Diagnostic Center, Institute of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Jasti S, Rakh S, Pantula V, Murthy KJR, Valluri VL. Genetic affinity of two south Indian ethnic groups with other populations. Int J Immunogenet 2008; 35:243-9. [DOI: 10.1111/j.1744-313x.2008.00763.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Khan F, Pandey AK, Borkar M, Tripathi M, Talwar S, Bisen PS, Agrawal S. Effect of Sociocultural Cleavage on Genetic Differentiation: A Study from North India. Hum Biol 2008; 80:271-86. [DOI: 10.3378/1534-6617-80.3.271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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