Send Orders for Reprints to reprints@benthamscience.net Current Pharmaceutical Biotechnology, 2013, 14, 000-000 1 1389-2010/13 $58.00+.00 © 2013 Bentham Science Publishers Design, Virtual Screening and Docking Study of Novel NS3 Inhibitors by Targeting Protein-protein Interacting Sites of Dengue Virus - A Novel Approach Pratap Parida 1* , R.N.S. Yadav 1 , Kishore Sarma 2 and Lalit Mohan Nainwal 3 1 Centre for Studies in Biotechnology, DIbrugarh University, Assam-786004, India; 2 Department of Life Sciences and Bioinformatics, Assam University, Silachar-788011, Assam, India; 3 Department of Pharmaceutical Sciences, Dibrugarh University, India Abstract: Currently dengue is a serious disease which has become a global burden in the last decade. Unfortunately, there are no effective drugs and vaccines against this disease. DENV non-structural protein (NS) 3, which is viral protease which is a potential target for antiviral therapy. Targeting this we performed homology modeling and protein-protein docking study of NS3 with NRBP (Nuclear Receptor Binding Protein) of human as it has been proved that NS3 of DENV interacts with NRBP which causes cellular trafficking in human cell. To carry out search of novel DENV protease inhibi- tors by in silico screening panduratin molecule was selected. 65 novel compounds were designed which involved substi- tuting positions 1-5 of the benzyl ring A (4hydroxy-panduratinA) with various substituents. The protein-protein docking showed that the aminoacid residues of NS3 which were interacting with NRBP were found to be Ala 325, Asp 324, Phe 326, Asp 335, Glu 336, Glu 328, Asp 485, Gln 478, Arg 459, Gly 446 and Leu 480. These residues were targeted by the ligands which showed excellent binding affinity as binding energy. The ligand PKP10 showed lowest binding energy. It is also observed that the interface residues participated in the protein-protein interaction are being inhibited by the ligands. Keywords: Dengue, Homology Modeling, Protein-protein docking, Protein-ligand docking, Panduratin. INTRODUCTION Dengue is a disease, caused by dengue virus infection which has emerged as an endemic disease in over 100 coun- tries in the last decade [1]. The virus is a member of the Flaviviridae causes DF (Dengue fever), DHF/DSS (dengue hemorrhagic fever/ Dengue shock syndrome). There are our serotypes; DENV1, DENV2, DENV3 and DENV4. The ma- jor and the important of the dengue virus is the type DENV3. The RNA genome of DEN2 contains 10,723 nucleotides. This genome encodes a large polyprotein precursor of 3,391 amino acid residues which consist of three structural proteins (C, prM and E) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, NS5). The structural pro- teins of DENV serotypes are encoded from the 5-terminal which absorbs quarter of the genome whereas the remaining two-thirds encode the nonstructural proteins. The order of the proteins within the polyprotein is NH2-C-prM(M)-E- NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5-COOH [2, 3]. Adding up two small hydrophobic proteins are released from the 5 polyprotein, one of them is derived from the C- terminus of the anchored capsid protein after cleavage of the mature capsid is released [4]. The NS3 protein is the second largest viral proteinase which generates the termini of sev- eral nonstructural proteins [5]. NS2B is a cofactor NS3 viral serine protease activity which plays a key role in flaviviral polyprotein [6]. Due to high sequence similarity in NS3 *Address correspondence to this author at the Centre for Studies in Biotech- nology, DIbrugarh University, Assam-786004, India; Tel:/Fax: ???????????; E-mail: pratapparida2007yahoo.com@gmail.com within the flavivirus genus and the conservation of the diba- sic recognition sequence in polypeptide substrates, an antivi- ral inhibitor against DENV may be very effective against in all its serotypes. Further non-structural 3 (NS3) protein of dengue virus type 2 interacts with human nuclear receptor binding protein (NRBP) as a result it causes in alterations membrane structure which helps in replication of the virus which strongly attracts towards the drug development against NS3 [7]. The NRBP participates in sub cellular trafficking between the endoplasmic reticulum and Golgi apparatus through interactions with the Rho-type GTPases [8-9]. The challenging attempt is to design one novel and most effective antiviral therapy is the development of inhibitors directed against the viral NS3 serine protease, which is the main and an essential component of the maturation dengue virus poly- protein. Hence it is more important to understand the functional and interaction activity of the viral NS3 with the NRBP pro- tein such as binding pattern, hydrogen and hydrophobic in- teractions, disulfide bridges etc., especially with which amino acid of the host protein they interact. Modeling the interaction of two macro molecules is very complex. Many forces such as hydrophobic, van der Waals, or stacking inter- actions between amino acids, hydrogen bonding, and electro- static forces are involved in the intermolecular association of the proteins. In this study, the homology modeling and protein-protein interaction of NS3 of DENV3 with NRBP was done to identify the residues of target viral protein. Further, new competitive