IDENTIFICATION OF POTENTIAL

QUORUM SENSING INHIBITOR BY

MOLECULAR DOCKING ANALYSIS

Submitted by: Guided by:

Saurabh P Kaner Dr. N.R Kotagale
B.Pharm (4th Year) M.Pharm (Ph.D)
1.Introduction
Content
2.Rationale to select Pseudomonas aeruginosa
3.Quorum sensing system in P.aeruginos
3.1 Transmission of P. aeruginosa
4.System used in quorum sensing
4.1 Las system
5. Molecular docking in Las R
5.1Protein preparation
5.2 Ligand preparation
5.3 Receptor gride generation
5.4 Ligand docking
6. Result
7.Conclusion
 1.Introduction
• Quorum sensing
• Quorum means Number of members of group require to be
present to transact business or carry out an activity legally.
• Quorum sensing is a bacterial communication system by which
they develop resistance.
• It facilate
-production of multiple virulence factors
- biofilm formation
- swarming motility once a population threshold is reached.
 2.Rationale to selectPseudomonas auriginosa

• Pseudomonas aeruginosa is a gram negative organism

that is commonly found in soil and water
• Pseudomonas aeruginosa is a well known biofilm
former, which efficiently colonises on different surfaces
leading to chronic infections that are difficult to
eradicate.
• It is an opportunistic pathogen and is only able to infect
hosts with defective immune system function
• Several of these virulence factors have been
demonstrated to be regulated by quorum sensing (QS).
3.Quorum sensing in Pseudomonas aeruginosa

- P. Aeruginosa infect the host cell , forming colonies in it,

after it forms more bacterial colonies (biofilm) , its secret
chemical (quorum sensing) that produces resistance to
drugs.
- Biofilm formation
3.1Transmission of P. Aeruginosa-:

-Pseudomonas aeruginosa lives in the environment and can be

spread to people in healthcare settings when they are exposed
to water or soil that is contaminated with these germs.
-Resistant strains of the germ can also spread in healthcare
settings from one person to another through contaminated
hands, equipment, or surfaces.

Biofilm is a self secreted extra polymeric substance in bacteria

which act as the chemical signaling molecule by which bacteria
develop resistance
4.System used in quorum sensing in pseudomonas
aeruginosa
• There are 4 system of quorum sensing in pseudomonas
aeruginosa with autoinducers

System Autoinducers
Las 3oxoC 12hsl
Rhl N-butyl-L-hsl
PQS 2-alkyle quinolone
IQS 2(2-Hydroxyphenylethiazole-4-
carbaldehyde)

Autoinducers are small molecule that controll quorum sensing

 4.1 Las system

• Las

Las1
autoinducer

3-oxo-C12HSL form biofilm

Las R Host cell DNA/RNA Production of

infect various chemical
 5.Molecular docking Analysis in Las R

• Molecular docking is performed in four important step

1. Protein preparation
2. Ligand preparation
3. Receptors grid generation
4. Molecular docking (ligand docking )
5.1Protein preparation
• For further studies on
docking we select LasR
system .
• We search crystal structure
of LasR on protein data
bank of various resolution
• We select 3xie structure
for further studies at it has
low resolution
Crystal structure search on protein data bank
Year PDB ID Ligand Resolution

2007 2UVO OHN 1.8 Å

2009 3IX3 OHN 1.4 Å

2021 6V7W OHN 3.0 Å

2013 4NG2 OHN 2.41 Å

2020
6V7X OHN 2.90 Å
5.2Ligand preparation
Methotrexa Not 2019

• From the literature search we select eight te Reported

Niclosamide Not 2013

drugs on which docking in not done Reported

Paracetamol NotReported 2021

(ReportedWi
th AbaR)

Omeprazole Not 2019

Reported

Chlorpromaz Not 2019

ine Reported
Not 2020
Ciprofloxaci
Reported
n
2012
Iberin Not
Reported
Thioridiazi Not 2013
ne Reported
5.3Receptors grid generation
• For receptors grid generation the receptor grid generation module of
GLIDE (Gride base ligand docking with energetics) software was used
to generate a grid for molecular docking purpose

• The co-crystalized natural ligand OHN was use as a reference for grid
generation
• The inner grid box of 10A° was define around the centroid of the
bound ligand whereas the outer box extended upto 20A°
• Outer box defines the volume in which grid potential are computed
5.4 Ligand docking

The set of optimized ligands was docked using the Ligand Docking
module of GLID
Molecular docking analysis was carried out using the Glide v7.5
module in Maestro v11.2
For study the binding potential of the active compounds in the
active site of the LasR protein.
Calculations were carried out using an X-ray crystal structure of
protein (PDB code: 3IX3, resolution: 1.4 Å) bound to its natural
ligand OHN.
 6.Result

Docking Score
• The docking score and the GlideScore are the same with a minor
difference
Glide score
• Glide Score is an empirical scoring function that approximates the ligand
binding free energy.
• Scoring function used to predict binding affinity between two molecules
after they have been docked
Comparison between glide score and docking score
e le e
SL m
id zo azin
2H sa r a
rid
C1 clo ep io er
in
3O Ni Om Th Ib
0

-1

-2

Docking Score
-3
Glide Score

-4

-5

-6

-7

-8

-9
 LIGAND INTERACTION DIAGRAM

Molecular docking of 3OC12HSL(Natural ligand) in its Molecular docking of Methotrexate in 3OC12HSL

binding site (natural ligand) binding site
 7.CONCLUSION

• The molecular docking analysis revealed that methotrexate,

niclosamide, and paracetamol show better binding interactions with
LasR as compared to the natural ligand 3OC12HSL.
• These drugs showed better docking scores and significant number of H-
bond interactions (four to six) within the ligand binding domain of LasR
• It can be conclude that this drug and their derivatives through
modification provide more quorum sensing inhibitors.
 8.Reference

• Molecular Insights into Quorum Sensing in the Human Pathogen Pseudomonas aeruginosa from the Structure
of the Virulence Regulator LasR Bound to Its Autoinducer https://doi.org/10.1074/jbc.M700556200
• Lee, J., Zhang, L. The hierarchy quorum sensing network in Pseudomonas aeruginosa. Protein Cell 6, 26–41
(2015) available from . https://doi.org/10.1007/s13238-014-0100-x
• Molecular Insights into Quorum Sensing in the Human Pathogen Pseudomonas aeruginosa from the Structure
of the Virulence Regulator LasR Bound to Its Autoinducer * Bottomley, Matthew J. et al. Journal of Biological
Chemistry, Volume 282, Issue 18, 13592 – 13600 Available from
https://doi.org/10.1074/jbc.M700556200https://
www.jbc.org/action/showCitFormats?doi=10.1074%2Fjbc.M700556200&pii=S0021-9258%2817%2947436-9
• Growth and Laboratory Maintenance of Pseudomonas aeruginosa Annette E. LaBauve and Matthew J. Wargo
doi: 10.1002/9780471729259.mc06e01s25
• Discovery of quorum sensing inhibitors of P.fluorescens P07 by using receptor based
pharmacophore model and virtual screening* Author* Ting Ding , Tingting li Received:15 Feb 2019;
Received in Revised form 3 April 2019; Accepted:8 April 2019 journal
DOI.org/10.1016/j.Iwt.2019.04.030