Indo American Journal of Pharmaceutical Research, 2014

ISSN NO: 2231-6876

STRUCTURE BASED DRUG DESIGN FROM PANDURATIN A AGAINST NS2B/NS3

PROTEIN
Pratap Parida, RNS Yadav
Centre for Studies in Biotechnology, Dibrugarh University, Assam 786 004, India.
ARTICLE INFO
Article history
Received 04/12/2014
Available online
19/12/2014
Keywords
Catalytic Triad,
Dengue,
Docking,
NS2B/NS3,
Panduratin A.

ABSTRACT
The NS2B/NS3 protein of dengue virus umpires the processing of viral polyprotein inside the
host cell and is considered to be an important target of virus replication. The NS2B/NS3 has a
serine protease domain with a catalytic triad (His51, Asp75 and Ser135). The catalytic triad is
responsible for the post-translational proteolytic processing of the polyprotein as well as it is
also an essential component for the viral replication. In this study, we docked three drugs
such as Mycophenolic acid, Ribavirin and Panduratin A onto the catalytic triad pocket of
NS2B/NS3 protein for selection of potent lead molecules against dengue virus. Based on the
docking score we found that panduratin scores better docking energy against the target
protein. Further we docked some Panduratin A derivatives to the same binding pocket after
studying the bioavailability. The catalytic triad was well blocked by the drugs as well as some
derivatives of Panduratin A found to be have better binding energy than Mycophenolic acid
and Ribavirin.

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Please cite this article in press as Pratap Parida et al. Structure Based drug design from Panduratin A against NS2B/NS3 protein.
Indo American Journal of Pharm Research.2014:4(12).

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Corresponding author
Pratap Parida
Centre for Studies in Biotechnology,
Dibrugarh University, Assam-786004, India.
pratap_parida2007@yahoo.com,
91-9864413857

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INTRODUCTION
Dengue viruses cause dengue disease. It belongs to the family flaviviridae. Dengue viruses transmitted through to human by
the vector, Aedes aegypti mosquito. Dengue viruses consist of ten proteins which comprises of three structural proteins and seven
nonstructural proteins. The three structural proteins are capsid protein (C), membrane protein (prM), and envelope protein (E) [1-3].
The seven nonstructural proteins are NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5 [2-3].
The NS3 protein encompases a serine protease at the N-terminal region that binds to NS2B cofactor for the formation of
polypeptide [4-5]. The NS3-NS2B complex is responsible for viral replication and maturation of infectious viral proteins [6]. The
interference with the NS2B-NS3 complex may hamper the replication of the dengue virus [7]. Currently NS3-NS2B is targeted for
drug development [8-13].
The NS3 protease of dengue virus has a serine protease catalytic triad (His51, Asp75 and Ser135) having trypsin like
character [4, 14]. The NS2B provides cofactor activity for proteolytic and catalytic activity of viral proteins [6].
Hence, we used mycophenolic acid (MPA), Ribavirin and Panduratin A derivatives for blocking the interaction of the NS2B
cofactor so that the proteolytic activity of the virus can be prevented.
MATERIALS AND METHODS
Protein structure retrieval and preparation
The 3D structure of the dengue virus NS2B/NS3 Protease having 1.50 resolution was retrieved from RCSB (Research
Collaboratory for Structural Bioinformatics), Protein Databank (PDB, http://www.pdb.org). The PDB ID of the selected protein was
found to be 2FOM [15]. Initially the protein was attached with water molecules and ligands which were removed using Pymol.
Identification of lead molecules
Three different lead molecules (MPA, Ribavirin and Panduratin A) were extracted from NCBI PubChem Compound database
(http://www.ncbi.nlm.nih.gov/pccompound/). The Pubchem Ids of the compounds were 446541, 37542 and 6483648 for MPA,
Ribavirin and Panduratin A respectively.
Drug Likeness, Bioactivity and Bioavailability
Before docking study, we studied the drug likeness, bioactivity and bioavailability of the drugs using Molinspiration
(www.molinspiration.com) and Osiris property explorer (http://www.organic-chemistry.org/prog/peo/). All the compounds were
screened for molecular physicochemical properties such as absorption, distribution, metabolism, excretion and toxicity
(ADME/Tox), pertinent to the drug design. It provides the selective screening of compounds to have drug like properties. OSIRIS
Property explorer was used for the prediction of the mutagenicity, tumourogenicity, irritating, reproductive effects, drug likeness and
drug scores of the selected compounds.
Selection of potential inhibitor
All the lead molecules were docked to the catalytic triad (His51-Asp75-ser135) of dengue NS3 protein. The molecules were
found to be having better toxicity scores. We performed the docking studies using Patchdock [16] of all the lead molecules for
selecting best potent lead molecule and analogue design against dengue virus. Based on the lowest interaction energy we selected
panduratin A for analogue design with various substitutions. Though we have already developed some ligands in our previous study
[10], we did not go for further substitution in the Panduratin A molecule.
Docking of receptor with Panduratin A derivatives
The 3D structure and the ligands were subjected for docking using patchdock. Patchdock is an online server which helps in
prediction of protein-ligand interaction which is a part of Critical Assessment of Prediction of Interactions (CAPRI). The algorithm of
Patchdock is based on image sequestration and object identification techniques. The algorithm divides the surface of the molecule into
two parts based on the surface structure. The normal parts such as concave, convex or flat surface are identified by segmentation
algorithm. These parts are then sorted out and the one with hot spot residues are maintained. When these parts are identified, the shape
matching algorithms such as Geometric Hashing and Pose-Clustering are applied for superimposition for matching the identified parts.
After matching the parts, all the complexes which are having unacceptable penetration of receptor residues to the ligand molecules are
filtered. Lastly all the selected ligand molecules are ranked on the basis of geometric conformations.

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RESULTS AND DISCUSSION

Protein structure retrieval and preparation
The three dimensional structure of the protein (PDB ID-2FOM) retrieved from Protein data bank was attached with Chlorine
and Glycerol which were removed before docking study. The cleaned protein structure is given in Figure 1.

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Figure 2: The three lead molecules. (a) Mycophenolic Acid (b) Ribavirin (C) Panduratin A.

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Figure 1: A: The NS2B/NS3 protein with two glycerol molecule labeled as Gol 202 and 203 in red colored stick. The dotted
magenta color represents the chloride ion attached to the protein before docking. B: The cleaned protein with its C-terminal
and N-terminal ends.

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Identification of lead molecules & drug likeness and bioavailability

Prior to docking study of the three lead molecules (Figure 2), all the molecules were tested for bioavailability and toxicity
studies. All the three compounds showed good bioavailability and bioavailability properties without violating Lipinski rule. The
molecules satisfying Lipinski rule with several physicochemical properties were reported in Table 1. Several undesired effect study
such as mutagenecity, tumorigenecity, irritancy, reproductive effect along with drug conform behavior of the molecules were studied
and reported in Figure 3-5.
Table 1: Various physicochemical properties of the three lead molecules.
Compounds
MPA
Ribavirin
Panduratin A

MF
C17H20O6
C8H12N4O5
C26H30O4

MW (g/mol)
320.337
244.204
406.514

Log P
3.2
-1.8
6

HBD
2
4
2

HBA
6
7
4

GL
0.28
0.31
0.06

ICM
0.08
0.21
0.04

KI
-0.22
-0.21
-0.24

NRL
0.82
-1.45
0.35

PI
0.02
-0.20
-0.03

EI
0.76
0.71
0.19

MF: Molecular Formula, MW: Molecular Weight, HBD: Hydrogen Bond Donor, HBA: Hydrogen Bond Acceptor, GL: GPCR
Ligand, ICM: Ion Channel Modulator, KI: Kinase inhibitor NRL: Nuclear receptor ligand, PI: Protease inhibitor, EI: Enzyme
inhibitor.

Figure 3: Drug likeness score of MPA.

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Figure 4: Drug Likeness score of Ribavirin.

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Figure 5: Drug Likeness score of Panduratin A.

Figure 6: Docking Study of three lead molecules. Hydrophobic and hydrogen bond forming residues of NS2B/NS3. The
catalytic triad residues of NS2B/NS3 marked in magenta color. The hydrogen interactions were in yellow dash line.

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Selection of potential inhibitor

All the lead molecules successfully docked into the catalytic triad binding pocket of dengue NS3 protein. All the molecules
found to be properly inhibiting the catalytic triad of the NS3 protein. The compound MPA interacts with eight residues of the NS3
protein excluding the catalytic triad. It forms four hydrogen interactions with Gly 151, Asn152, Gly153 and Val154 (Figure 6). It
forms patchdock docking score of 2818. The compound ribavirin also blocks the catalytic triad including twelve other interactions. It
forms a hydrogen interaction with the residue Ser135 which falls under the catalytic triad domain of NS3 protein (Figure 6). The
docking score of ribavirin more than MPA which is 3364. Similarly the compound Panduratin A forms 3698 docking score which is
more than both the previous compounds MPA and ribavirin. It also blocks the catalytic triad of NS3 protein by forming one hydrogen
interaction with Ser135 (Figure 6). The comparative study of the docking scores of the ligands given in Figure 7 suggests that
Panduratin A molecules is a better inhibitor than MPA and Ribavirin. Since we have already designed some potential derivatives of
Panduratin A against dengue NS3 protein in our previous study [10] we docked the molecules using patchdock server. These
molecules include various substituents such as the hydroxyl group (OH), nitro group (NO2), halogen group (Cl), and alkyl group
(CH3) in the 2nd and 3rd positions of the benzyl ring A and are as presented in Figures 8. Further we studied different
physicochemical properties of these molecules and are reported in Table 2.

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Figure 8: The derived drugs of Panduratin A with various substitutions.

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Figure 7: Comparison of docking scores of three lead molecules suggests that Panduratin A scores better than the MPA and
Ribavirin. ACE: Atomic contact energy.

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Table 2: Various physicochemical properties of the Panduratin A derived molecules.

Compounds
1
2
3
4
5
6
7
8
9
10
11
12
13
14

GL
0.09
-0.07
-0.02
-0.06
-0.13
-0.15
0.02
-0.07
-0.05
-0.11
0.01
-0.04
-0.04
-0.01

ICM
-0.23
-0.28
-0.31
-0.20
-0.23
-0.24
-0.18
-0.31
-0.11
-0.24
-0.23
-0.35
-0.09
-0.38

KI
-0.51
-0.28
-0.66
-0.31
-0.35
-0.49
-0.46
-0.37
-0.32
-0.44
-0.62
-0.55
-0.34
-0.61

NRL
0.16
-0.02
-0.07
0.01
-0.08
0.04
0.16
-0.08
0.16
0.08
0.18
0.01
0.08
-0.13

PI
-0.23
-0.28
-0.19
-0.27
-0.28
-0.26
-0.10
-0.35
-0.12
-0.33
-0.16
-0.16
-0.18
-0.13

EI
0.18
0.10
0.08
0.14
0.08
0.12
0.23
0.04
0.16
0.07
0.20
0.17
0.04
0.10

GL: GPCR Ligand, ICM: Ion Channel Modulator, KI: Kinase inhibitor NRL: Nuclear receptor ligand, PI: Protease inhibitor, EI:
Enzyme inhibitor.
Docking of receptor with Panduratin A derivatives
All the panduratin A derivatives successfully docked to catalytic triad binding site. Docking provided a good score of all the
compounds which are represented in Figure 9. We found the docking scores in a range of 2714-3070. The compound number 1
provides highest docking score i.e. 3070. The docking complexes were further analyzed using pymol for idenitification of the
aminoacid which are involved in interaction with the ligands. We observed that all the Panduratin A derivatives block the catalytic
triad of the NS3 protein. However we found that the compound 3, 11, 13 constantly formed hydrogen interaction with Ser135 from the
catalytic triad wherever the rest residues of the catalytic triad His51 and Asp 75 formed hydrophobic interaction (Figure 10-13).

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Figure 9: The docking score of the derived molecules Panduratin A which shows the number compound highest docking score.

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Figure 11: Docking Study of compound 5, 6, 7 & 8. Hydrophobic and hydrogen bond forming residues of NS2B/NS3. The
catalytic triad residues of NS2B/NS3 marked in magenta color. The hydrogen interactions were in yellow dash line.

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Figure 10: Docking of top four compounds. Hydrophobic and hydrogen bond forming residues of NS2B/NS3. The catalytic
triad residues of NS2B/NS3 marked in magenta color. The hydrogen interactions were in yellow dash line.

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Figure 12: Docking Study of compound 9, 10, 11 & 12. Hydrophobic and hydrogen bond forming residues of NS2B/NS3. The
catalytic triad residues of NS2B/NS3 marked in magenta color. The hydrogen interactions were in yellow dash line.

Figure 13: Docking Study of compound 13, & 14. Hydrophobic and hydrogen bond forming residues of NS2B/NS3. The
catalytic triad residues of NS2B/NS3 marked in magenta color. The hydrogen interactions were in yellow dash line.
CONCLUSION
Based on the in silico docking study, we found that Panduratin A has better docking energy than MPA and Ribavirin.
Further, the compound 1 and 2 of Panduratin A also formed more docking energy than MPA and Ribavirin. This study has found
possible binding of drugs which interacts with the catalytic triad of dengue NS2B/NS3 protein. Moreover, it was observed that the
Panduratin A derivatives have greater ability to inhibit dengue virus replication. Hence, Pandurain A derivatives can be concluded as
the future drug candidates for dengue virus before synthesis and clinical trial. The above study may help in finding some inhibitor for
the NS2B/NS3 protein in dengue virus. The future scope can be further added to synthesis and biological activity of the Panduratin A
derivatives as antidengue drugs

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ACKNOWLEDGEMENT
The authors gratefully acknowledge Department of Biotechnology, Government of India.

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Authors Statements
Competing Interests
The authors declare no conflict of interest.

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