Original Article IN SILICO PEPTIDE BASED VACCINE DESIGN AGAINST NON-STRUCTURAL PROTEIN 5 OF HEPATITIS C VIRUS VIKAS KAUSHIK, GAUTAM CHAUHAN, JOGINDER SINGH* School of Biotechnology and Biosciences, Lovely Professional University, Phagwara, Punjab, India. Email: joginder.15005@lpu.co.in Received: 04 May 2014 Revised and Accepted: 01 Sep 2014 ABSTRACT Objective: Hepatitis C virus (HCV) is the cause of hepatitis C in human. A hepatitis C infection does not show any noticeable symptoms in the very early stages of the infection, but a chronic infection can ultimately lead to cirrhosis. The chronic condition results in liver failure or cancer. Protein- Protein interactions play a vital role in the pathogenesis of any pathogen. Protein-Protein interactions maps designed and created in this research provide accurate and valuable resource for better understanding of the pathogenicity pathways of Hepatitis C Virus. The objective of the study was to predict the epitope against non-structural protein NS (5a) of Hepatitis C Virus which could be used as suitable vaccine candidate against Hepatitis C virus infections. Methods: A specific protein-protein interaction is selected on the basis of its significance in the pathway leading to replication of Hepatitis C genome i. e. Interaction between Hepatitis C Nonstructural protein 5A (NS5A) with sh3 domain of Fyn tyrosine protein kinase. Epitopes was predicted and screened by using various bioinformatics tools. Each of the predicted structure was docked with MHC Class I and class II molecules using PatchDock and FireDock. Results: The MVGLNSYRI epitope was selected on the basis of half life of dissociation and binding score. The average score of half-life of disassociation (t1/2) for MVGLNSYRI was 20 hrs, which is the greater than the other epitopes. Structure based modeling of epitopes was done and further the energy was optimized. Then after that the binding score was calculated, which was again best in case of MVGLNSYRI. Conclusion: These findings conclude that the designed protein-protein interaction maps and predicted epitopes can be of great use in the wet laboratory formulations of vaccines against Hepatitis C Virus. Keywords: Bioinformatics, Protein-protein interaction, HCV, Vaccine, 3D structure. INTRODUCTION Hepatitis C virus (HCV) is the cause of hepatitis C in humans. A hepatitis C infection does not show any noticeable symptoms in the very early stages of the infection, but a chronic infection can ultimately lead to cirrhosis. The chronic condition results in liver failure or cancer. Hepatitis C spread mostly through blood to blood contact, unsterilized equipment used for intravenous drug transfer. The number of people affected by hepatitis C infection worldwide is approximately 200 million per annum which is responsible for hundreds of thousands of deaths each year. Hepatitis C virus infects only humans and chimpanzees. The knowledge about hepatitis C infection was first reported in the year 1989[1]. It belongs to the genus Hepacivirus and is a member of family flaviviridae [2]. It is an enveloped positive sense single stranded RNA virus with approximately 55-65 nm. Despite the discovery of HCV over 15 years ago, knowledge of the HCV lifecycle has been limited by inability to grow the virus in cell culture, as well as by the lack of small-animal models of HCV infection [3]. HCV has an RNA genome which consists of 9600 nucleotide bases. It consists of UTRs at 5’ and 3’ ends of the RNA. The genome contains a non-coding region (5’-3’) and a coding region. HCV genome comes with a high genetic variability caused due to the mutations that happens frequently during the viral replication. These mutations vary in different genomic regions of HCV [4]. Structural proteins of HCV are core protein (E1 and E2) which are primarily present in the coding region of the genome and non-structural proteins (NS2, NS3, NS4, NS4A, NS4B, NS5, NS5A, NS5B) [2]. The proteins encoded by Hepatitis C genome (structural and non- structural proteins) are primarily responsible for the pathogenesis of Hepatitis C virus. The Hepatitis C viral proteins interact with the proteins present in the human host cells and generate certain signaling pathways which in turn regulate the replication of Hepatitis C genome and its survival in human cells. The no- structural NS1 protein is a hydrophobic transmembrane protein which basically form hydrophilic pores and there by regulating the permeability of the membrane for the propagation of viral assembly and release of viral particles to increase infectivity, NS2 protein works as to attract the envelope proteins to the assembly site and favours viral assembly, NS3 has helicase as well as protease activity. It plays a central role in the process of viral replication. It has its major role in unwinding of viral RNA alone and in complex with NS4A, NS4A functions as cofactor for proper working of NS3 protein for increased enzymatic activities. NS4A also forms complex with NS4B and NS5A to facilitate viral replication on the endoplasmic reticulum membrane, NS4B is associated with NS5B so as to modify its polymerase activity, thus showing its role in carcinogenesis. NS4B favours viral replication as it is involved in the formation of the membranous structure which acts as a platform for viral replication to happen, NS5A is necessary for the viral replication as well as viral assembly, NS5B works as RNA dependent RNA polymerase [5]. The overall pathogenicity of Hepatitis C virus depends upon the interactions between the proteins coded by its genome and their interactions with the human proteins which together result in manipulations to the originally occurring cellular processes and the pathways, thereby increasing pathogenicity. Thus in order to further known the pathogenicity pathways, various protein-protein interactions can be extracted and used in the construction of pathways. Protein–protein interaction maps provide information about the proteins which are highly involved in the viral replication and life cycle. Thus, maps provide a more easy and illustrative way of acquiring knowledge about important interactions between different proteins which are involved in the viral replication. By studying the interaction map for Hepatitis C protein NS5A various assertions can be made supporting the fact that it is the International Journal of Pharmacy and Pharmaceutical Sciences ISSN- 0975-1491 Vol 6, Issue 9, 2014 Innovare Academic Sciences