2. Saskara Putra

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Molecular docking study of HIV NS3 protease inhibitors on dengue virus Raghunath Satpathy1, Gyan Ranjan Satpathy2, Prangya Ranjan Rout2 1

MIRC Laboratory, Department of Biotechnology, MITS Engineering College, Rayagada, Odisha, 765017, India; E-mail: [email protected] 2 Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, Odisha, 769008, India ABSTRACT Dengue virus belongs to the family Flaviviridae and is a major emerging pathogen for which the development of drugs, vaccines and antiviral therapy has seen little success. The NS3 viral protease is a potential target for antiviral drugs since it is required for virus replication. In this work, the HIV NS3 protease inhibitors were used to evaluate binding affinity on dengue virus NS3 protease. All total 19 inhibitors were obtained from Pubchem database and after energy minimization docking was performed by taking NS3 protease of dengue virus as a receptor (PDB ID 2FOM). Interestingly the docking energy for the two of the ligands having Pubchem database ID CID 482206 and CID 484561 shows highest value equally as -400.08. Conformation of ligands, sequence and structure analysis has been performed to observe the relationship between the Dengue and HIV NS3 protease enzyme. Keywords: dengue virus, NS3 protease inhibitor, docking study, antiviral drugs

INTRODUCTION Dengue virus (DENV) is considered as one of the most important global pathogens and also it represents a global pandemic type of infection [1]. The current estimate indicates approximately 2.5 billion people worldwide at risk for dengue infection among which 1.5 million infected individuals presenting with clinical symptoms and 500,000 infections progressing to the serious disease states of dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Each year, dengue infections result in 25000 deaths, primarily in children [2]. After malaria, DENV is the most common mosquito borne pathogen that infects humans and mostly transmitted by mosquitoes of the Aedes genus among infected human hosts, with the main vector Aedes aegypti. Aedes albopictus and Aedes polynesiensis have also been implicated in dengue outbreaks [3]. There is currently no specific treatment for dengue disease [4]. There are five basic types non structural proteins NS1, NS2, NS3, NS4, NS5 along with subtypes are present in case of dengue virus which are associated unwinding double stranded DNA during viral replication [5]. These non-structural proteins forms the replication complex which includes the NS3 protease with its NS2B as cofactor and the protein serve as potential inhibitory targets for antiviral agents since [6]. These functional roles were supported by recent flavivirus helicase crystal structures and a recently solved crystal structure of linked NS3 protease domains suggested the protease domain enhanced binding of RNA to the NS3 helicase [7]. The NS3 protease is a primary target for development of dengue antiviral drugs since the NS2-NS3B protease is required for virus replication and protease inhibitors have a successful history as being developed into antiviral drugs [8]. Research Article, Biotechnol. Bioinf. Bioeng. 2011, 1(2):179-182 © 2011 Society for Applied Biotechnology. Printed in India.

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MATERIALS AND METHODS The HIV NS3 inhibior molecules were retrieved from pubchem data base present in NCBI server (http://pubchem.ncbi.nlm.nih.gov/). In total 19 numbers of inhibitor were collected and the structure were drawn by Marvin sketch 5.0 tool (http://www.chemaxon.com/marvin/sketch/index.jsp) and corresponding 3D structure were obtained. The molecules were then energy minimised by PRODRG server [9]. Prodrg is an on line tool for energy minimization of small molecules where the energy minimization of is performed by using Gromos 96 force field. Then molecular docking was performed by the dengue NS3 protease enzyme obtained from Protein Data Bank (2FOM) using HEX tool [10]. From the docking result various conformations of the ligand were analysed by Swiss PDB Viewer tool [11]. Also the protein sequence comparison and motif prediction was performed among the NS3 protease of dengue and HIV virus.

RESULTS AND DISCUSSION The docking of the ligands was carefully observed for its conformation and docking energy. The ligands having Pubchem database ID CID 482206 and CID 484561 shows highest binding affinity as -400.08 (Table 1). The binding position of the highest docking energy were observed (Figure 1A,B). The conformations of the ligand were analysed by Swiss PDB viewer tool. The above two ligands, which shows different conformation after docking (Figure 2A). The rest of 17 ligands were observed to share a similar position in the protein also shows similar conformation (Figure 2B).

(A)

(B)

Figure 1. The binding position of the ligand CID 482206 (A) and CID 484561 (B) shown as pink colour.

(A)

(B)

Figure 2. Showing the conformation of ligands after docking; the conformation of best considered ligands (A) and conformation of rest of the ligands (B).

181 Table 1. Docking energy calculated for the considered ligands by Hex tool. Pubchem Ligand ID CID 482206 CID 482207 CID 482209 CID 482210 CID 482211 CID 484561 CID 484563 CID 484564 CID 484565 CID 484566 CID 484567 CID 484568 CID 484570 CID 484571 CID 484572 CID 484573 CID 484574 CID 3002867

Molecular formula C47H65N7O13 C46H66N8O12 C36H58N6O14S C38H55N5O7 C43H56N6O14S C39H51N5O11S C19H25N3O7S C44H60N6O12S C40H55N5O9S C35H48N4O6S C20H29N3O5S C34H48N6O13S C36H52N6O14S C33H52N6O14S2 C44H61N7O12S C37H48N6O14S2 C32H52N6O13S C21H15NO3S2

Molecular weight (g/mol) 936.058100 923.062640 830.942520 693.872600 913.001540 797.914140 439.482700 897.045200 781.957800 652.843820 423.526360 780.842320 824.894880 820.927780 912.059840 864.938820 760.852680 393.478700

Docking Energy -400.88 -355.44 -358.94 -346.37 -310.67 -400.88 -222.51 -313.19 -292.62 -273.89 -229.06 -251.07 -344.75 -318.63 -342.25 -314.63 -324.20 - 226.72

Further the sequence of the NS3 protease of Dengue (2FOM) and HIV virus (3EKQ) were obtained from PDB and analysed for the similarity. BLAST 2 was used for comparison which shows no significant sequence similarity. Then the two sequences were searched for their common motif by using EMBOSS tool [12]. In case of EMOSS tool the prediction of motif is done by searching the pattern from the Prosite data base within the sequence (Table 2). The result shows none of the sequence having the similar sequence pattern to each other. Table 2. Showing motif prediction along with their positions for the NS3 proteases of HIV and dengue virus protein sequences computed from EMBOSS tool. No. 1 2 3 4 5 6 7 8

Motif (HIV) IGTVLVGP (72-79) LTQIGCT (90-96) KMIVGIGGFVKVRQYDQ IPIEICGHK (45-70) TLWKRPIVTIR (4-14) KEALLDT (20-26) ----------------------------------------------------------------------

Motif (Dengue) EVQVLALE (94-101) LWDVPSPPPVGKA (4-16) SPIVDKKGKVVGLYGNGV VTRSGAYVSAI(137-165) TRGAVLMH (53-60) IGAVSLDFS (123-131) KGILGYSQIGAGVY (33-41) KKDLISY (73-79) RAVQTKPGL (107-115)

The analysis indicates the conformation study of the ligands having its importance while predicting the activity of drug molecule. The docking result suggests that different ligands bind to the same binding site under different receptor conformations. Docking to different ligand conformations also due to change of a receptor-specific conformation [13]. Since the viral proteases are a primary target for antiviral drugs as very since they are common to most viruses and generally

182 important for efficient replication. Again the HIV protease inhibitors could be used for the development of other antiviral protease inhibitors. The applications of HIV inhibitors for the treatment of human rhinovirus and hepatitis C virus protease inhibitors have also entered clinical trials [14,15]. Despite of this application very few antiviral have been approved for human use. The present study shows although HIV and Dengue belongs to different families of virus also the HIV and Dengue NS3 protease are not similar to their sequence and structure but some available HIV NS3 protease inhibitor molecules could be potentially used against Dengue as preventive drugs.

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