Computational Biology and Bioinformatics 2015; 3(1): 6-20 Published online March 4, 2015 (http://www.sciencepublishinggroup.com/j/cbb) doi: 10.11648/j.cbb.20150301.12 ISSN: 2330-8265 (Print); ISSN: 2330-8281 (Online) In-Silico Evaluation of the Capsid Proteins of FMDV as Potential Vaccine Candidates F. M. N. Hassan 1 , Md. Shaifur Rahman 2, * , K. M. T. Rahman 3 , Sharmin S. Sumi 4 , Md. F. Islam 5 , Md. Badrul Alam 1 , Md. Giasuddin 6 , Khondoker M. Hossain 1 1 Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna-9208, Bangladesh 2 Tissue Banking and Biomaterial Research Unit, Atomic Energy Research Establishment, BAEC, Dhaka-1349, Bangladesh 3 Research and Development Division, Incepta Vaccine Limited, Dhaka, Bangladesh 4 Department of Biochemistry, University of Alberta,Edmonton, Alberta, Canada T6G 2H7 5 Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5 Canada 6 Bangladesh Livestock Research Institute (BLRI), Savar, Dhaka -1341, Bangladesh Email address: mdshaifur@gmail.com (M. S. Rahman) To cite this article: F. M. N. Hassan, Md. Shaifur Rahman, K. M. T. Rahman, Sharmin S. Sumi, Md. F. Islam, Md. Badrul Alam, Md. Giasuddin, Khondoker M. Hossain. In-Silico Evaluation of the Capsid Proteins of FMDV as Potential Vaccine Candidates. Computational Biology and Bioinformatics. Vol. 3, No. 1, 2015, pp. 6-20. doi: 10.11648/j.cbb.20150301.12 Abstract: In this study, the capsid proteins of four major serotypes of Foot and Mouth Disease Virus (FMDV) were assessed as the vaccine candidates. Different protein sequences regarding FMDV capsid of O, A, Asia 1 and C type were identified from NCBI Genome Database and UniprotKB. Phylogenetic tree of the four serotypes was developed using ClustalW software. HMMTOP, RANKPEP, Swiss-Model and Vaxign software were used for comparing the capsid proteins in terms of their feasibility as vaccine candidates. The virus and viral serotype were identified from the cultured disease sample using RT-PCR. Our results revealed that different capsid proteins of the four serotypes vary in their suitability to be considered as peptide vaccine components. Viral protein 1 (VP1) for Asia 1 serotype represented the best result as a vaccine candidate. The VP1 region of Asia 1 serotype amplified based on the result of dry lab analysis. Our findings provide a future indication of multivalent vaccine development against FMDV. Keywords: Reverse Vaccinology, FMDV, Capsid Protein, Viral Protein 1, Vaccine Candidate 1. Introduction Vaccines have been developed for generating effective immunogenicity to prevent diseases throughout previous decades [1-2]. Different methodologies have been exploited so far to develop vaccines against life threatening diseases of human and animals [2]. Reverse vaccinology has come out as one of the most modern system of vaccine development in recent years [3]. It takes advantages of genomic and proteomic data regarding pathogenic organisms already available in the databases. Antigenic materials of certain pathogens can be analyzed by using different computational resources and tools. Results from the computational approach can be utilized to develop vaccine within 1-2 years through further experimental approaches. However, foot and mouth disease (FMD) is an economically important and highly contagious viral disease. The FMDV viral particle (25-30 nm) contains an icosahedral capsid consisting of proteins and no envelope [4-5]. The virus possesses a positive-sense single stranded RNA (SS RNA) (about 8.3 kb) genome that encodes a polyprotein which is subsequently processed to yield structural and non- structural proteins [8-9]. Globally, the virus exists in seven immunologically distinct serotypes; the Southern African Territories [SAT] types 1-3 and Eurasian types namely O, A, C and Asia 1, with multiple subtypes within each serotype [10]. Among these serotypes show some regionality; the O serotype is the most common while four serotypes (O, A, Asia 1, C) are available in south Asian countries [4]. The RNA genome of FMDV goes through a high rate of mutation because of error prone replication by the RNA polymerase which results in high genetic diversity [11-12]. Additionally, persistent infection, recombination, and quasi-species dynamics have also been reported as contributing factors to