IN SILICO MOLECULAR DOCKING OF ANTIVIRAL DRUGS AGAINST NS5-METHYLTRANSFERASE OF DENGUE VIRUS

Saurabh Chaudhary, Ajay Kumar, *Vivek Srivastava

Department of Biotechnology, Faculty of Engineering & Technology, Rama University, Kanpur, Uttar Pradesh, India

Dengue is the most prevalent mosquito-borne virus, with nearly 400 million annual cases worldwide (Bhatt et al., 2013). Dengue fever and dengue hemorrhagic fever are the quickly spreading mosquito-borne diseases in the universe today, for an watched 30-fold expand from claiming accounted cases in the most recent 50 years a long time (WHO, 2009). The WHO estimates that, globally, 2.5 billion people are at risk, and annually, 50-100 million people become infected, of which approximately 0.5 million require hospitalization (WHO, 2014) and 22,000 deaths occur each year in areas where it is endemic (CDC, 2014).The disease has four viral serotypes (DENV-1, DENV-2, DENV-3, and DENV-4), and its spectrum ranges from asymptomatic infection to dengue fever, dengue hemorrhagic fever (DHF), and dengue shock syndrome (DSS), and may lead the patient to death (Gubler, 1998). All four serotypes of dengue virus are transmitted to

humans by the Aedes aegypti and Aedes albopictus mosquitoes (Wrigh et al., 2009). The positive-sense flavivirus RNA genome of 11 kb forms a single open reading frame that is translated into an ~370 kDa polyprotein precursor containing the structural proteins and seven non-structural proteins known as NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5. NS5 is about 900 amino acids long, largest (104 kDa) and the most conserved protein in DENV. It is also a bifunctional enzyme with a methyltransferase domain (MTase; residues 1-296) at its N-terminal end and a RNA-dependent RNA polymerase (RdRp; residues 320-900) (Wyles, 2013) C-terminal end (Egloff et al., 2002). Its enzymatic activities form attractive target for antiviral development (Davidson, 2009; Noble, 2012; Lim et al., 2013. Present study comprises molecular docking of four antiviral drugs such as Quinacrine, Amodiaquine, Berberine and Prochlorperazine against NS5-methyltransferase of dengue virus using in silico approach.

*Address for Correspondence : Dr. Vivek Srivastava , Department of Biotechnology, Faculty of Engineering & Technology, Rama University, Kanpur, Uttar Pradesh, India,

Email : viveksrivastavabio@rediffmail.com

ABSTRACT

Dengue is a mosquito-borne viral disease that has rapidly spread in all regions of world. Dengue fever is a severe, flu-like illness that affects infants, young children and adults. Currently there is no specific treatment for DENV. In the present study, four known drugs, Quinacrine, Amodiaquine, Berberine and Prochlorperazine have been docked with NS5-methyltransferase of Dengue viruses using Autodock 4.2 tool. Quinacrine showed minimum binding energy −6.83 kcal/mol with NS5-methyltransferase (PDB ID-3EVG), and Amodiaquine, Berberine and Prochlorperazine have -6.64 kcal/mol, -6.22 kcal/mol and 6.67 kcal/mol, respectively. Further the best-docked complexes were analyzed through Python Molecular Viewer software for their interaction studies. Thus from the Complex scoring and binding ability it is deciphered that Quinacrine is a good promising drug for NS5-methyltransferase of dengue virus as drug target. Observations made in this study may extend an assuring platform for developing anti-viral competitive inhibitors against DENV infection.Keywords: Docking; NS5-methyltransferase; AutoDock4.2; Antiviral drugs; dengue virus

INTRODUCTION

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MATERIALS AND METHODSProtein preparationThe 3D coordinates of the Crystal structure of dengue-2 virus methyltransferase complexed with S-adenosyl-L-homocysteine (PDB Id: 3EVG) was retrieved from Protein Databank (http://www.rcsb. org/).

Inhibitors datasetChemical structures of Quinacrine, Amodiaquine, Berberine and Prochlorperazine were downloaded in .sdf format from pubchem compound database (Kim et al., 2016). They were later converted in .pdb format with the help of open babel (O'Boyle et al., 2011) tool. All the drugs were subjected to energy minimization using the HyperChem software (HyperChem (TM) Release 7.5).

Molecular dockingDocking of Quinacrine, Amodiaquine, Berberine and Prochlorperazine done using molecular docking program AutoDock (Morris et al., 1998). Gasteiger charges are added to the ligand and maximum 6 numbers of active torsions are given to the lead compounds using AutoDock tool

(http://autodock.scripps.edu/resources/adt). Kollman charges and the solvation term were added to the protein structure. The Lamarckian genetic algorithm implemented in Autodock was used for docking.

RESULTS & DISCUSSIONInfection with one of four dengue virus serotypes (DENV1-4) can lead to febrile illness and flu-like symptoms, or can progress to the more severe dengue hemorrhagic fever or dengue shock syndrome. Development of the more severe hemorrhagic fever is more likely if recovery from infection by one dengue serotype is followed by subsequent infection by a second serotype (Wilson and Chen, 2015).Individual MTase and RdRp domains in full-length NS5 have conserved protein folds. The MTase (residues 1–262) adopts the SAM-dependent methyltransferase fold composed of four helices surrounding a central 7-stranded β-sheet (Klema et al., 2016, Egloff et al., 2002) is shown in Fig. 1. The active site, containing a catalytic K61-D146-K180-E216 (KDKE) motif, is positioned in the center of the β-sheet.

Fig. 1: Overall fold of the DENV NS5 monomer. The MTase domain is shown in cyan, and the RdRp domain is colored by region (thumb, red; palm, green; fingers, blue; domain linker, orange; priming loop, yellow). SAH is shown as a space-filling model and colored by atom type. Two zinc ions are shown as gray spheres (Klema et al., 2016).

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In docking studies of known antiviral drugs with active site of NS5-methyltransferase, best autodock score was used as criteria to interpret the best conformation among the 10 conformations,

generated by AutoDock 4.2 program. The docking result of these drugs with NS5-methyltransferase was shown in Table 1.

Table 1: Docking results of known antiviral drugs with NS5-methyltransferase.

Compound Name PubChem CID

BE IME IE TorE VdwE EE

Quinacrine 237 -6.83 -9.51 -1.13 2.68 -8.89 -0.62

Amodiaquine 2165 -6.64 -8.73 -0.44 2.09 -8.49 -0.25

Berberine 2353 -6.22 -6.82 -0.34 0.6 -6.78 -0.04

Prochlorperazine 4917 -6.67 -7.86 -1.02 1.19 -6.93 -0.94

BE= Binding Energy; IME: Intermolecular Energy; IE= Internal Energy; TorE= Torsional; Energy; VdwE= vdW + Hbond + desolv Energy; EE= Electrostatic energy.

Fig.2: Docked complex of Quinacrine with NS5-methyltransferase.

Further, the docked complexes were analyzed through Python Molecular Viewer software for their interaction studies. Docked complex of

Quinacrine with NS5-methyltransferase is shown in fig.1.

Fig.3: Docked complex of Amodiaquine with

NS5-methyltransferase.

Fig.4: Docked complex of Berberine with .

NS5-methyltransferase.

Fig.5: Docked complex of Prochlorperazine with

NS5-methyltransferase.

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Protein is represented as cartoon model with white color and red sticks represent drug molecule. The active site, containing a catalytic K61-D146-K180-E216 (KDKE) motif is represented as sticks and ball model with color by atom type. In docked complex of Quinacrine with catalytic trade of NS5-methyltransferase shows one H-bond between NS5-methyltransferase residue ASP146:OD2 with Quinacrine H atom (Fig. 2). Docked complex of Amodiaquine, Berberine and Prochlorperazine with catalytic site of NS5-methyltransferase were shown in Fig.3, Fig. 4 & Fig. 5 respectively. One H-bond formed between NS5-methyltransferase residue ASP146:OD2 with Amodiaquine and Prochlorperazine H atom, respectively (Fig.3 & Fig.5).

CONCLUSIONThe results obtained from this study would be useful in understanding the inhibitory mode of Quinacrine, Amodiaquine, Berberine and Prochlorperazine with catalytic site of NS5-methyltransferase and accurately predicting the activities of drugs on the basis of docking scores. Here we concluded that the Quinacrine be a novel inhibitor for NS5-methyltransferase preventing Dengue.

ACKNOWLEDGMENTThe authors would like to thank Faculty of Engineering & Technology, Rama University, Kanpur Uttar Pradesh, India for providing facilities to carry out this study.

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