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A Docking Study on Various Secondary Metabolites from
W. somnifera
on
Tetrahydrodipicolinate N-Succinyltransferase Protein Involved in The
Lysine Biosysnthesis Pathway in
P. aeruginosa
Nagwani AK* and Kashyap D
Department of Microbiology & Bioinformatics, University Teaching Department, Bilaspur University, Bilaspur, India
*Corresponding author: Nagwani AK, Department of Microbiology & Bioinformatics, University Teaching Department, Bilaspur University, Bilaspur, India,
Tel: +91-9039950450; E-mail: amitkn52@gmail.com
Received date: June 9, 2018; Accepted date: June 11, 2018; Published date: June 18, 2018
Copyright: © 2018 Nagwani AK, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Abstract
A crucial survival factor for leading pathogen (carrying 40-60% mortality rate) is Tetrahydrodipicolinate N-
Succinyltransferase (DAPD EC 2.3.1.117) involves in lysine biosynthesis pathway of P. aeruginosa. Targeting the
lysine biosynthesis pathway is a opportunistic and logical site to inhibit the effect of this organism. Withania
somnifera, also known as “Indian ginseng”, a reputed herb in ayurvedic medicine, constituting various steroidal
lactones (withanolides, withaferins) and saponins which shown various pharmacological activities. We described the
docking of 11 secondary metabolites from Withania somnifera into the three dimensional structure of DapD protein
of P. aeruginosa using swiss-dock server. Simultaneously, we have checked the ADME values and
pharmacokinetics values of these secondary metabolites against the target protein. We have followed the “Lipnski
rule of 5” principle and “Molinspiration” tool. Dihydowithaferin, 4-B, Hydroxywithanolide, Withanoloide E,
Withanoloide F, Withanoloide D, Withanoloide A) have potential to be used as medicine to treat P.aeruginosa
infections. Several known antibiotics also studied along with this approach for comparison purpose.
Background/Objectives: Withania somnifera additionally referred to as “Ashwagandha” and “Indian ginseng” is
a medicative plant constituting (isopelletierine, anaferine, cuseohygrine, and anahygrine, etc.), hormone lactones
(withanolides, withaferins) and saponins., P.aeruginosa is a leading gram negative opportunist infectious agent,
carrying a high 40-60% death rate and causes grievous infections in people with compromised immune systems.
Tetrahydrodipicolinate N-Succinyltransferase (DAPD Europetwo.3.1.117) potential targets for brand spanking new
antibacterial drug medication.
Methods/Statistical analysis: The tying up method involves the prediction of matter conformation and
orientation (or posing) inside a targeted binding web site. Swiss Dock may be a tying up internet server. All
calculations are performed on the server aspect, so for tying up run’s don't need any machine power from the user.
The ligands were neutralized and checked for his or her ADME properties victimization computer code
Molinspiration obtainable at machine resources for Drug Discovery (CRDD). The secondary metabolites and
antibiotics were conjointly subjected to Lipinski Rule of 5 value's on server The Supercomputing Facility for
Bioinformatics & machine Biology (SCFBio), Indian Institute of Technology, N. Delhi.
Findings: Among the eleven secondary metabolites from Withania somnifera and seven antibiotics we elect for
docking, Ciproflaxin, Cephalosporin, Tobramycin, and Azlocillin showing the higher result compare to alternative
compounds. Results of ADME properties showed Compounds as 4-B hydroxywithanolide, 2-3 dihydowitaferin A,
Withanoloide E,Withanoloide D, Withanoloide A, and Withanoloide F has higher ADME values then the
unremarkably used antibiotics (Azlocillin, Ciproflaxin, Ticarcillin, and antibiotic). Results of Lipinski rule of five values
are given below in one table. Secondary metabolites like 4-B hydroxywithanolide, 2-3 dihydowitaferin A,
Withanoloide E, Withanoloide D, and Withanoloide F showed higher results for Lipinski rule of five compare to
antibiotics like Alocillin, Mefoxin, Meropenem, and Tobramycin.
Improvements/Applications: Ashwagandha is employed from a few years for several treatments. This analysis
additionally stresses the likelihood of this plant to use for cure of an added chronic infection. The experiment shows
probabilities to develop a brand new drug.
Keywords:
P. aeruginosa
;
W. somnifera
; Tetrahydrodipicolinate N-
Succinyltransferase; Swiss dock; Lysine biosynthesis pathway
Introduction
P. aeruginosa
is associate expedient human infectious agent. It’s an
expedient as a result of it cause infection to healthy people. Instead, it
typically aects immune-compromised patients, like those with
monogenic disorder, cancer, or AIDS.
P. aeruginosa
may be a leading
gram-negative expedient infectious agent and, carrying a 40-60% rate.
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ISSN: 2168-9547
Molecular Biology : Open Access Nagwani and Kashyap, Mol Bio 2018, 7:3
DOI: 10.4172/2168-9547.1000214
Research Article Open Access
Mol Bio, an open access journal
ISSN:2168-9547
Volume 7 • Issue 3 • 1000212
It complicates ninetieth of pancreatic brosis death, and lastly, it's
invariably listed joined of the highest 3 most frequent gram-negative
pathogens everywhere world [1].
P. aeruginosa
conjointly carries a
great deal of chromosome-mobilizing plasmids that a terribly vital to
the organism’s way as a microorganism [2].
P. aeruginosa
attacks mucoviscidosis patients
via
airway and once
it's in, it uses its agellum for visit the hypoxic zone, associate degree
oxygen depleted atmosphere. is can be the transition state for
P.
aeruginosa
undergoes for associate degree aerobic to associate degree
anaerobic microorganism and starts forming biolms anaerobically.
Once this can be fashioned, the
P. aeruginosa
will sense their
population
via
gathering sensing, wherever they secret low mass
pheromones that change them to speak with one another at intervals a
community [3,4]. is oers them the a resistance to several defenses,
as well as anti-Pseudomonas antibiotics like ticarcillin, Mefoxin,
tobramycin, and antibiotic, as a result of once the bacterium sense that
their outer layer of biolm is being destroyed, the inner layers can
grow a lot of powerfully to alter the community [5].
Randomized transpo-son mutagenesis screens had indicated several
genes from the diaminopimelate (DAP) biosynthetic pathway to lysine
in
P. aeruginosa
as essential, suggesting that this gene products as
potential targets for new antibacterial drugs.
P. aeruginosa
mutants
where the dap A sequence had been deleted were viable and able to
grow throughout a mouse internal organ infection model, suggesting
that Dap A is not associate best target for drug development against
this organism [6].
Plants are made during a wide selection of secondary metabolites
like tannins, terpenoids, alkaloids, avonoids etc. that are found to
own antimicrobial properties.
Withania somnifera
(L) Dunal
(Aswaghanda or Indian “Ginseng”) is wide employed in ayurvedic
medicines and is consumed as a dietary supplement round the world.
e major bioactive compounds of Ashwagandha are steroidal lactones
compounds referred to as withanolides. ey conjointly contain many
alkaloids, withanosides, reducing sugars, few avonoids, tannins etc.
[7].
ere are several novel structural variants of withanolides with
modications either of the chemical element skeleton or the
aspectchain and these have typically been delineate as changed
withanolides or ergostan-type steroids associated with withanolides.
Hence, the current study was aimed to spot the potential Dap D
inhibitors from
W. somnifera
by molecular arrival studies exploitation
Swiss Dock net server [8,9].
Materials and Methods
Selection of docking molecules
e SDF (SQL Server Compact info File) les of eleven varied
chemicals (secondary metabolites) has been downloaded from
Pubchem info of NCBI. For the docking studies. Equally the
commercially oered medicine specically antibiotics like Azlocillin,
Ciproaxin, Levooxocin, Meropenem, Ticarcillin and antibiotic were
taken from the literature.
e ligands were neutralized and checked for their ADME
properties mistreatment code Molinspiration on the market at
machine resources for Drug Discovery (CRDD) (http://
www.molinspiration.com/cgi-bin/properties). It helps in analyzing the
pharmacological medicine and pharmacodynamics of the matter by
assessing the drug like properties.
e secondary metabolites and antibiotics were additionally
subjected to Lipinski Rule of 5 values on server e Supercomputing
Facility for Bioinformatics & machine Biology (SCFBio), Indian
Institute of Technology, N. Delhi. Lipinski rule of ve helps in
characteristic between drug like and non-drug like molecules. It
predicts high likelihood of success or failure because of drug likeness
for molecules compliant with a pair of or a lot of rules [10,11].
Target protein
Tetrahydrodipicolinate N-Succinyltransferase (DAPD European
Economic Community two.3.1.117) could be a succinyl-coenzyme A
(SCoA) dependant accelerator. Dap D shows distinct options at the N
and C terminal domains that area unit structurally completely dierent
from those delineated for Dap D enzymes from gram-negative
microorganism and shows additional similarity to Dap Ds from M.
T.B. e sequence/structure of Dap D super molecule is downloaded
from Protein data Bank (PDB ID-3R5A, B, C) As shown in Figure 1.
Figure 1: 3D structure of
P. seudomonas aeruginos
a Dap D
(PA3666) in complex with CoA and succinate.
Docking
Docking was applied victimisation Swiss Dock internet server [12].
e structure of the target super molecule, similarly as that of the
matter, is oen mechanically ready for arrival. Additionally, the
cumbersome syntax of the arrival engine is hidden behind a clean
internet interface providing cheap various sets of parameters similarly
as sample input les. All calculations area unit performed on the server
aspect, so arrival runs don't need any machine power from the user.
e interpretation of arrival results and their integration into existing
analysis pipelines is greatly expedited by the seamless image of arrival
predictions within the UCSF Chimera molecular viewer, which might
be launched directly from the online browser. e sequence code
3R5A, B, C was used for arrival purpose.
Citation: Nagwani AK and Kashya D (2018) A Docking Study on Various Secondary Metabolites from W. somnifera on Tetrahydrodipicolinate N-
Succinyltransferase Protein Involved in The Lysine Biosysnthesis Pathway in P. aeruginosa. Mol Bio 7: 214. doi:
10.4172/2168-9547.1000214
Page 2 of 6
Mol Bio, an open access journal
ISSN:2168-9547
Volume 7 • Issue 3 • 1000212
Structure of 3R5A, B, C was submitted to Swiss Dock sever. e
series (3R5A) has been used for Swiss Dock that is predicated on
EADock DSS with anoloides and dierent compounds (from
W.
somnifera
) were uploaded for docking.
e Predicted les from Swiss Dock server were analyzed
exploitation UCSF Chimera. UCSF Chimera may be an extremely
protractible program for interactive mental image and analysis of
molecular structures [13]. Discovery Studio beholder version four, 2
were used for mental image of docked ligands. We have a tendency to
were used PyMOL for analysis of docking results. e code free for
academic and analysis purpose [14]. VEGA ZZ was used for format
conversion and mental image of compounds and docking results
[15-17] as shown in Figure 2.
Figure 2a: With anoloide E with Tetrahydrodipicolinate N-
Succinyltransferase viewed in UCSF Chimer.
Figure 2b: With anolide F with Tetrahydrodipicolinate N-
Succinyltransferase viewed in UCSF Chimera.
Figure 2c: 4-B, hydroxywithanoloide E with Tetrahydrodipicolinate
N-Succinyltransferases viewed in UCSF Chimera.
Figure 2d: 2-3dihydrowithaferin with Tetrahydrodipicolinate N-
Succinyltransferase viewed in UCSF Chimer
Figures 2a, 2b, 2c and 2d show the best docking interaction of target
protein and some secondary metabolites [18-21].
Results
We took eleven secondary metabolites from Withania
somnifera and seven antibiotics for docking study.
e docking conrmation with best docking Score had been analyzed.
e results obtained from Swiss-Dock
were analyzed mistreatment UCSF Chimera. Swiss-Dock
results are given in terms of full tness and ΔG Kcal/mol. e number
of hydrogen bond found between the target super molecule and also
the secondary metabolites ranged 1- 3.
Binding mode of available drug molecules
For comparison purpose, a bunch of antibiotics were extensively
utilized for tying up with target macromolecule. square measure able
to analyze that and therefore the results are, Ciproaxin, antibiotic
drug, Tobramycin, and Azlocillin showing sensible interaction in terms
Citation: Nagwani AK and Kashya D (2018) A Docking Study on Various Secondary Metabolites from W. somnifera on Tetrahydrodipicolinate N-
Succinyltransferase Protein Involved in The Lysine Biosysnthesis Pathway in P. aeruginosa. Mol Bio 7: 214. doi:
10.4172/2168-9547.1000214
Page 3 of 6
Mol Bio, an open access journal
ISSN:2168-9547
Volume 7 • Issue 3 • 1000212
of ΔG and nearly all are having sensible binding interactions as shown
in Table 1.
S.no. Antibiotics Energy Simple fitness Full fitness Cluster Rank No. of Hydrogen Bond
1 Azlocillin 110.05 110.05 -1565 0 3
2 Cephalosporin 130.33 130.33 -1484.5 2 1
3 Ciproflaxcin 266.25 266.25 -1382.5 7 2
4 Levoflaxcin 62.47 62.47 -1565 7 1
5 Meropenem 107.12 107.12 -1548.7 5 2
6 Ticarcillin 96.91 96.91 -1564.2 7 2
7 Tobramycin 113.73 113.73 -1525.1 4 3
Table 1: Antibiotics with their docking results.
Binding mode of bioactive compounds from
W. somnifera
Aer analysis of result, we will clearly observe that, aer we have
taken full tness as criteria, we tend to area unit able to found
Scopoletin, Cuscohygrine, Tropine, Cysteine showing high binding
anity to the target macromolecule. Once the results of docking were
analyzed using ΔG as criteria, 4-B hydroxywithanolide, 2-3
dihydowitaferin A, Withanoloide E, Withanoloide D, Withanoloide A,
showed high anity to focus on macromolecule as shown in Table 2.
S.no. Compounds Energy Simple
fitness Full fitness Cluster Rank No. of Hydrogen Bond
1 Dihydowithaferin 274.27 274.27 -1334.1 7 1
2 4-B, Hydroxywithanolide 284.92 284.92 -1320.7 4 2
3 Withanoloide E 313.8 313.8 -1285.9 16 2
4 Withanoloide F 83.49 83.49 -1501.9 22 3
5 Withanoloide D 339.55 339.55 -1253.7 5 2
6 Withanoloide A 266.67 266.67 -1363.4 4 1
7 Choline 77.34 77.34 -1580.3 1 1
8 Tropine 34.67 34.67 -1597.7 7 2
9 Cuscohygrine -5.71 -5.71 -1682.9 4 1
10 cysteine 1.45 1.45 -1626.8 3 3
11 scopoletin 1.66 1.66 -1618.7 38 2
Table 2: Compounds with their docking results.
Results of ADME properties
It showed Compounds as 4-B hydroxywithanolide, 2-3
dihydowitaferin A , Withanoloide E, Withanoloide D, Withanoloide A,
and Withanoloide F has higher ADME values then the normally used
antibiotics (Azlocillin, Ciproaxin, Ticarcillin, and Tobramycin) as
shown in Table 3.
S.no. Compounds MiLogP TPSA MW Antibiotics MiLogP TPSA MW
1 Dihydowithaferin 3.88 96.36 472.62 Azlocillin 0.99 148.14 461.5
2 4-B, Hydroxywithanolide 2.26 136.82 502.6 Ticarcillin 0.44 124 384.44
3 Withanoloide E 3.18 116.59 486.61 Tobramycin -5.7 268.19 467.52
Citation: Nagwani AK and Kashya D (2018) A Docking Study on Various Secondary Metabolites from W. somnifera on Tetrahydrodipicolinate N-
Succinyltransferase Protein Involved in The Lysine Biosysnthesis Pathway in P. aeruginosa. Mol Bio 7: 214. doi:
10.4172/2168-9547.1000214
Page 4 of 6
Mol Bio, an open access journal
ISSN:2168-9547
Volume 7 • Issue 3 • 1000212
4 Withanoloide F 3.75 104.06 470.61 Ciproflaxin -0.7 74.57 331.35
5 Withanoloide D 4.15 96.36 470.61
6 Withanoloide A 4.15 96.36 470.61
Table 3: Comparison of ADME values.
Results of Lipinski rule of 5
Values given in Table no. 4. Secondary metabolites like 4-B
hydroxywithanolide, 2-3 dihydowitaferin A, Withanoloide E,
Withanoloide D, and Withanoloide F showed higher results for
Lipinski rule of ve compare to antibiotics like Alocillin, Meropenem,
and Antibiotic drug as shown in Table 4.
S.no. Compounds
Molecular
Weight
High
Liphophicity
Molar
Refractivity
Antibiotics Molecular
Weight
High
Liphophicity
Molar
Refractivity
(130.0 to
725.0) (-2 to 6.5) (40-130)
1 Dihydowithaferin 472 3.58 124.56 Azlocillin 460 3 110.85
2 4-B, Hydroxywithanoloide 502 1.73 127.43 Cephalosporin 385 4 84.92
3 Withanoloide E 486 2.75 126.04 Meropenem 383 3 92.27
4 Withanoloide F 470 3.54 126.52 Tobramycin 472 3 101.87
5 Withanoloide D 470 3.5 124.51
6 Withanoloide A 470 3.5
Table 4: Comparison of Lipinski rule of 5 values.
Discussion
Interactions of secondary metabolites and antibiotics at the active
site of Dap D. e two adjacent subunits that kind a lively website cle
however distinct from the binding sites for CoA and succinate. We
found result in form of full tness and ΔG Kcal/mol are reliable
because it is additionally not showing results once there's no suitability
of chemical with target super molecule for binding, whereas with Swiss
dock, whenever results were obtained in terms of full tness. ere
wasn't one case, aer we didn't get results.
Conclusion
All the work done here recommend that the compounds beneath
study (Dihydowithaferin, 4-B, Hydroxywithanolide, Withanoloide E,
Withanoloide F, Withanoloide D, Withanoloide A ) have potential to be
used as drugs to treat
P. aeruginosa
infections in humans.
Acknowledgement
e entire work done by me under the guidance of my professor Mr.
Dharmendra Kashyap and that I am therefore appreciative to him. All
the soware’s and internet tools square measure used from
Bioinformatics laboratory of University Teaching Department,
Bilaspur University. I am therefore appreciative to my family and
friends for their support
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Citation: Nagwani AK and Kashya D (2018) A Docking Study on Various Secondary Metabolites from W. somnifera on Tetrahydrodipicolinate N-
Succinyltransferase Protein Involved in The Lysine Biosysnthesis Pathway in P. aeruginosa. Mol Bio 7: 214. doi:
10.4172/2168-9547.1000214
Page 5 of 6
Mol Bio, an open access journal
ISSN:2168-9547
Volume 7 • Issue 3 • 1000212
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Citation: Nagwani AK and Kashya D (2018) A Docking Study on Various Secondary Metabolites from W. somnifera on Tetrahydrodipicolinate N-
Succinyltransferase Protein Involved in The Lysine Biosysnthesis Pathway in P. aeruginosa. Mol Bio 7: 214. doi:
10.4172/2168-9547.1000214
Page 6 of 6
Mol Bio, an open access journal
ISSN:2168-9547
Volume 7 • Issue 3 • 1000212
