Computational characterization of Plasmodium falciparum proteomic data for screening of potential vaccine candidates Satarudra P. Singh a,b , Feroz Khan c , Bhartendu N. Mishra b, * a Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow, India b Department of Biotechnology, Institute of Engineering and Technology, Uttar Pradesh Technical University, Sitapur Road, Lucknow, India c Metabolic and Structural Biology Division, Central Institute of Medicinal and Aromatic Plants (Council of Scientific and Industrial Research), Lucknow, India ARTICLE INFO Article history: Received 27 June 2009 Accepted 5 November 2009 Available online 31 December 2009 Keywords: Vaccine Proteomics Multiepitope Supertypes Plasmodium falciparum ABSTRACT Advancement in the field of proteomics and bioinformatics offers tremendous opportunities for the devel- opment of novel epitope-based effective vaccine against human malaria. In this study, we have characterized 25 antigens as a vaccine candidate and screened the potential T-lymphocyte epitopes presented by human leukocyte antigen (HLA)-A, -B, and -DR molecules based on the proteomic data of Plasmodium falciparum. Of the 25 proteins, 22 were predicted as probable antigens and two were predicted as adhesions. In addition, seven proteins were predicted to contain signal peptide for secretary pathway and six proteins were found similar to the human and mouse reference proteins, whereas none of the proteins were predicted as allergen. A total of 14,841 peptides were predicted as epitope, presented by HLA class I and II supertypes that covered a broad human population (95%). Our results suggest that HLA-based multistage and multiepitope malaria vaccine would likely be needed to induce broader CD8 + as well as CD4 + T-cell responses. The predicted epitopes may be served as a useful diagnostic reagent for evaluating T-cell responses in the context of natural infection and/or vaccine trials.  2010 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved. 1. Introduction Malaria is the most important parasitic disease of human beings, caused by the parasite Plasmodium falciparum, and is responsible for killing more than 1 million African children annually [1]. In the past decades, several approaches have been used for the develop- ment of malaria vaccines, ranging from the immunization with live-attenuated pathogen to the formulation of safer subunit vac- cines [2,3]. Subunit vaccines currently under development are based on a single or few antigens and may therefore elicit too narrow a breadth of immune response, providing neither optimal protection nor protection on genetically diverse backgrounds, and thus no vaccine candidate has been proved with sufficient efficacy to warrant commercial development [4]. The challenges to devel- oping an effective malaria vaccine include the complex multistage parasitic life cycle, a large 23-Mbp genome encoding more than 5300 proteins, distinct stage-specific expression of the proteins, stage-specific immunity, and antigenic variation within a single strain, as well as major histocompatibility complex (MHC) allelic diversity [2]. Various approaches have been proposed for the identification of P. falciparum antigens that can lead to potential vaccine targets against malaria [5,6]. Synthetic and recombinant multistage, mul- tiepitope P. falciparum malaria antigens have also been designed with the aim of increasing the breadth of the vaccine-induced immune responses to circumvent the escape of potential P. falcipa- rum mutants [7–9]. In recent years, the linear peptides containing minimal T-cell epitopes of P. falciparum circumsporozoite and PfEMP-1 protein antigen have also been evaluated as economical, safe, and readily produced malaria vaccines [10,11]. The Plasmodium spp. parasite developing within the host hepa- tocyte is the major target of protective immune responses induced by immunization with irradiated sporozoites. CD8 + T cells specific for peptide epitopes from proteins expressed by irradiated sporo- zoites in the hepatocyte are considered the primary immune effec- tors and protection is mediated by interferon- released by these CD8 + T cells (as well as other cells) rather than by direct cytotoxic T-cell–mediated lysis. CD4 + T cells that recognize parasite-derived peptide on the hepatocyte may also play a role. The targets of cellular immunity (both at the CD8 + and CD4 + T cell level) are largely unknown; however, it has also been reported that the in- fected hepatocyte may present parasite-derived peptides on MHC molecules to both CD4 + and CD8 + T cells for initiating the specific adaptive immune responses [12]. Therefore, the identification of T-cell epitopes in the antigenic proteins that promiscuously bind to multiple alleles of HLA (human leukocyte antigen) are prime tar- gets for future vaccine and are relevant to the larger proportions of the human population [13,14]. However, the experimental deter- mination of binding specificities even for a single antigen and single * Corresponding author. E-mail address: profbnmishra@gmail.com. Human Immunology 71 (2010) 136 –143 Contents lists available at ScienceDirect 0198-8859/10/$32.00 - see front matter  2010 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved. doi:10.1016/j.humimm.2009.11.009