Life Science Journal 2014;11(8s) http://www.lifesciencesite.com 552 Binding Affinities of Dengue Virus Envelope Glycoprotein Residues with Human Leukocyte Antigen Alleles: Dry Lab Candidates for Synthetic Vaccines Hamid Nawaz Tipu a , Masroor. E. Babar* b , Tanveer Hussain c a Combined Military Hospital, KhuzdarCantt. Pakistan b Virtual University of Pakistan, Lahore. c Department of Livestock Production, University of Veterinary and Animal Sciences, Lahore, Pakistan. Emails: HNT: hnt1779@yahoo.com, MEB: masroorbabar@hotmail.com , TH: tanveer.hussain@uvas.edu.pk Abstract: Determining dengue virus four serotypes E protein nanomeric epitopes that bind strongly with HLA alleles were identified through computer generated databases and prediction tools to identify individuals/populations who are likely to respond to vaccines. FASTA sequences of E proteins retrieved from NCBI proteins database were fed into MEGA6 software for conserved sequence identification. Binding of conserved sequence as well as nanomeric peptides from entire E protein length with HLA I and II alleles were determined using NetMHC 3.4 and NetMHCII pan 3.0 servers respectively. Conserved sequence among four serotypes did not bind HLA alleles. Individual E protein analysis identified total 97 nanomeric epitopes from four serotypes that qualified as strong binders. HLA specific E protein epitope prediction can help identify synthetic peptide vaccine candidates and predict responses as well. [Hamid Nawaz Tipu, Masroor. E. Babar, Tanveer Hussain. Binding Affinities of Dengue Virus Envelope Glycoprotein Residues with Human Leukocyte Antigen Alleles: Dry Lab Candidates for Synthetic Vaccines. Life Sci J 2014;11(8s):552-557]. (ISSN:1097-8135). http://www.lifesciencesite.com . 115 Keywords Dengue virus envelope (E) protein, Human Leukocyte Antigen, Bioinformatics, Vaccine Candidate Introduction Dengue virus, belonging to flaviviridae family, is transmitted to humans by infective females of mosquitoes Aedes aegypti and Aedes albopictus [1- 2].World Health Organization (WHO) has declared dengue infection endemic in South Asia. About 50- 100 million cases of dengue fever and 500,000 cases of dengue hemorrhagic fever are reported annually, resulting in around 24,000 deaths [3]. Pakistan is at very high risk of large epidemics owing to overcrowded cities, unsafe drinking water, inadequate sanitation and large number of refugees [3]. First outbreak was officially reported in 1994, though virus is believed to have existed in the country since long ago[4]. Since then, existence of virus has been reported from various parts of the country. In 2011, infection rapidly assumed proportion of epidemic; more than 250 people were reported dead in provincial capital city Lahore [5]. Dengue virus is an RNA virus with 11 Kilobases genome that encodes three structural proteins, nucleocapsid or core protein (C), a membrane associated protein (M), an envelope protein (E) and seven nonstructural proteins [6]. E protein binds cellular receptors and mediates fusion of viral and cellular membranes during viral entry into the cells [7]. The native E protein forms a homodimer, with each subunit consisting of three beta barrel domains, named domain I (EDI), domain II (EDII) and domain III (EDIII). The hydrophobic viral fusion peptide is located at the tip of EDII [8] and is well conserved among different serotypes. Figure 1 illustrates structure of E protein. There are four antigenically distinct serotypes of the virus (DENV 1-4) [9]. Antibody epitopes are both unique to each serotype as well as shared among them. Previous infection results in antibody formation that despite cross reactivity with all four serotypes (and other flaviviruses), prevents against re infection with same serotype only. In fact, infection with a new serotype may actually exacerbate the disease [8]. Following infection, patients develop antibodies against structural as well as nonstructural proteins [10]. Since E protein is the main antigen on the surface and is involved in fusion, it is the main target of neutralizing antibodies. However, exact serotype specific epitopes against which antibodies arise remain poorly defined [8, 11]. For a vaccine to be successful it must induce antibodies against all four serotypes but dengue vaccine development has been very slow due to these ill-defined antibodies inducing epitopes. Development of epitopic vaccines using small segments of viral proteome provides effective and controlled immune response reducing lethal effects of live vaccine [12]. However, it must take into account binding of epitopes with human leukocyte antigen (HLA), the complexity of which is compounded by extreme HLA polymorphism. T cells recognize an antigen when presented with human leukocyte antigen complex on the surface of antigen presenting cells. HLA alleles how differential binding affinities for various antigens, both foreign and self, and this determines