title: Computational prediction and analysis of envelop glycoprotein epitopes of DENV-2 and DENV-3 Pakistani isolates: a first step towards Dengue vaccine development.
abstract: Dengue fever of tropics is a mosquito transmitted devastating disease caused by dengue virus (DENV). There is no effective vaccine available, so far, against any of its four serotypes (DENV-1, DENV-2, DENV-3, and DENV-4). There is a need for the development of preventive and therapeutic vaccines against DENV to decrease the prevalence of dengue fever, especially in Pakistan. In this research, linear and conformational B-cell epitopes of envelope glycoprotein of DENV-2 and DENV-3 (the most prevalent serotypes in Pakistan) were predicted. We used Kolaskar and Tongaonkar method for linear epitope prediction, Emini's method for surface accessibility prediction and Karplus and Schulz's algorithm for flexibility determination. To propose three dimensional epitopes, the E proteins for both serotypes were homology modeled by using Phyre2 V 2.0 server, and ElliPro was used for the prediction of surface epitopes on their globular structure. Total 21 and 19 linear epitopes were predicted for DENV-2 and DENV-3 Pakistani isolates respectively. Whereas, 5 and 4 discontinuous epitopes were proposed for DENV-2 and DENV-3 Pakistani isolates respectively. Moreover, the values of surface accessibility, flexibility and solvent-accessibility can be helpful in analyzing vaccines against DENV-2 and DENV-3. In conclusion, the proposed continuous and discontinuous antigenic peptides can be valuable candidates for diagnostic and therapeutics of DENV.
authors.affiliation: National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors.forename: Hafsa
authors.initials: H
authors.lastname: Amat-ur-Rasool
authors.affiliation: National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors.forename: Anam
authors.initials: A
authors.lastname: Saghir
authors.affiliation: National Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Idrees
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D053059:Dengue Vaccines / Q000737:chemistry; D000939:Epitopes / Q000737:chemistry*; D008969:Molecular Sequence Data; D010154:Pakistan; D020539:Sequence Analysis, Protein; D017361:Viral Nonstructural Proteins / Q000737:chemistry* / Q000276:immunology
chemical_list: D053059:Dengue Vaccines; D000939:Epitopes; C079340:NS1 protein, Dengue virus type 2; C546113:NS1 protein, Dengue virus type 3; D017361:Viral Nonstructural Proteins