VOLUME 2 | NUMBER 2 | JUN | 2012 |82
Available online at www.ijntps.org | ISSN: 2277 – 2782 INTERNATIONAL JOURNAL OF NOVEL TRENDS IN PHARMACEUTICAL SCIENCES
Molecular Mechanics And Drug Docking Studies On Klebsheilla Pneumonia
(Multidrug Efflux System Protein) Using Insilico Protocols
Hepzibah. W1*, John William
1 S and Balaji. M
2
1Department of Advanced Zoology and Biotechnology, (SECNARM), Loyola College, Chennai-34. Tamilnadu. 2Director, Akshaya Neuroinformatics Research Center, Chennai-5. Tamilnadu
INTRODUCTION
K. pneumoniae is a gram negative bacterium. It is
facultative anaerobic. It is rod-shaped and measures 2 µm
by 0.5 µm. In 1882, Friedlander C. Uber first
discovered Klebsiella to be a pathogen that caused
pneumonia (8). Many hospital cases around the world have
been linked to K. pneumoniae. Therefore, more studies of
the strains were important and performed. The bacterium
was isolated and sequenced from a patient in 2004. K.
pneumoniae is commonly found in the gastrointestinal tract
and hands of hospital personnel (3). The reason for its
pathogenicity is the thick capsule layer surrounding the
bacterium. It is 160 nm thick of fine fibers that protrudes
out from the outer membrane at right angles(6) (5). Another
site on the human body that this bacteria can be found is
the nasopharynx. Its habitat is not limited to humans but is
ubiquitous to the ecological environment. This includes
surface water, sewage, and soil (4).
The complete genome was determined in 2006 at
the Genome Sequencing Center at Washington University in
St. Louis. The genome was named Klebsiella
pneumoniae subsp. pneumoniae MGH 78578. It includes
one chromosome of 5.3 Mbp. The GC content is 57%. There
are five plasmids, pKPN3, pKPN4, pKPN5, pKPN6, and
pKPN7. Respectively, each plasmid length is 0.18 Mbp, 0.11
Mbp, 0.089 Mbp, 0.0043 Mbp, and 0.0035 Mbp. The DNA is
circular. The sequence of K. pneumoniae genome was found
to be closely related that of Escherichia coli K-12 (1).
K. pneumoniae contains a capsule around its cell.
Known as K antigen, it is to protect the bacteria from
phagocytosis. "K. pneumoniae strains of serotypes 01:Kl,
01:K10, and O1:K16, which have only the K antigen exposed
at the cell surface, resist complement-mediated killing by
impeding complement activation. It is also clear that
purified capsular polysaccharides (K antigen) from nine
different serotypes (able or unable to mask the LPS) were
unable to activate complement ." In 1992, K.
pneumoniae could be determined apart from other species
ofKlebsiella. Two oligonucleotide probes and the
hydroxylated fatty acid C14:0-2OH are distinctive of K.
pneumoniae (2). CPS and LPS O side chain are two of the
most important virulence factors of K. pneumoniae (7)
Research Materials
• NCBI ,PUBMED, PUBMED CENTRAL,OMIM,MICROBIAL
GENOME DATABASES,CPH MODEL 2.0 SERVER, Discovery
studio software, MOLSOFT ,RAPPER,PATCHDOCK SERVER
Literature collection: The gene information of Human
Pathogens Klebsheilla pneumonia was collected through
Article Info
Article history
Received 20 May 2012
Revised 25 May 2012
Accepted 19 Jun 2012
Available online 30 Jun 2012
Keywords
Micro-organisms , Protein Modeling
and Drug Docking
Abstract
Klebsiella pneumonia is a necrotizing process with a predilection for debilitated
people. It has a high mortality rate of approximately 50% even with antimicrobial therapy.
The mortality rate approaches 100% for persons with alcoholism and bacteremia.
Klebsiella bacteremia and sepsis produce clinical manifestations similar to those caused by
other gram-negative enteric organisms. Morbidity and mortality rates are comparable to
those for other gram-negative organisms that cause sepsis and septic shock. In neonatal
units, outbreaks caused by ESBL-producing strains present a more serious problem and
may be associated with increased mortality .The primary aim of the present research
investigation is to find out whether the best plant extract compound inhibits the potential
Human pathogens using in-silico methods.
RESEARCH ARTICLE
▼ To whom correspondence should be addressed:
H Hepzibah. W
E-Mail address: [email protected]
Hepzibah et al., Molecular Mechanics and Drug Docking Studies On
System Protein) using Insilico Protocols
VOLUME 2 | NUMBER 2 | JUN | 2012
NCBI –PMC (Pub Med central database).
Gene identification: The genome information and gene
functional studies are identified using Comparative genome
database – Microbial genome databases (MBGDB).
Sequence retrieval system: The best identified potential
microbial proteins sequences were collected through NCBI
database in FASTA format in order to perform molecular
modelling.
Protein modeling: The protein sequences are applied into
CPH SERVER (An Automated Homology Modelling Server)
in order to convert the sequence into 3 D structure.
RESULTS AND DISCUSSION
>gi|238547966|dbj|BAH64317.1| multidrug efflux system protein [Klebsiella pneumoniae subsp.
pneumoniae NTUH-K2044]
MTDLPASVRWQLWIVAFGFFMQSLDTTIVNTALPSMAKSLGESPLHMHMIIVSYVLTVAVMLPASGWLAD
RVGVRNIFFTAIVLFTAGSLFCAQASTLDQLVMARVLQGVGGAMMVPVGRLTVMKIVPRDQYMAAMTFVT
LPGQVGPLLGPALGGVLVEYASWHWIFLINIPVGIVGAIATLCLMPNYTMQTRRFDLSGFLLLAAGMATL
TLALDGQKGLGISPAWLAGLVAVGLCALLLYLWHARGNARALFSLNLFRNRTFSLGLGGSFAGRIGSGML
PFMTPVFLQIGLGFSPFHAGLMMIPMVLGSMGMKRIVVQVVNRFGYRRVLVASTLGLAAVSLLFMFSALA
GWYYVLPLVLFLQGMINASRFSSMNTLTLKDLPDDLASSGNS
MSLDAASTHQVFLYTYLSMAAIIALPALIFSRVPDDVGSNIVLRRRNRSGS
nd Drug Docking Studies On Klebsheilla Pneumonia (Mu
The genome information and gene
ed using Comparative genome
Microbial genome databases (MBGDB).
The best identified potential
microbial proteins sequences were collected through NCBI
database in FASTA format in order to perform molecular
The protein sequences are applied into
CPH SERVER (An Automated Homology Modelling Server)
in order to convert the sequence into 3 D structure.
Molecular visualization tools:
of proteins files are viewed with the
STUDIO SOFTWARE to find out the structural and functional
regions of the 3D structure of the pathogen proteins.
Molecular drug docking:
performed using PATCHDOCK server
docking software) in order to identify the binding affinities
of the pathogen proteins and to identify the (
Quercitrin, Chlorogenic acid, Hyperoside and Rutoside
Chemical Compounds.
Figure: 1Chromosome map
>gi|238547966|dbj|BAH64317.1| multidrug efflux system protein [Klebsiella pneumoniae subsp.
MTDLPASVRWQLWIVAFGFFMQSLDTTIVNTALPSMAKSLGESPLHMHMIIVSYVLTVAVMLPASGWLAD
RVGVRNIFFTAIVLFTAGSLFCAQASTLDQLVMARVLQGVGGAMMVPVGRLTVMKIVPRDQYMAAMTFVT
LPGQVGPLLGPALGGVLVEYASWHWIFLINIPVGIVGAIATLCLMPNYTMQTRRFDLSGFLLLAAGMATL
TLALDGQKGLGISPAWLAGLVAVGLCALLLYLWHARGNARALFSLNLFRNRTFSLGLGGSFAGRIGSGML
PFMTPVFLQIGLGFSPFHAGLMMIPMVLGSMGMKRIVVQVVNRFGYRRVLVASTLGLAAVSLLFMFSALA
GWYYVLPLVLFLQGMINASRFSSMNTLTLKDLPDDLASSGNSLLSMVMQLSMSIGVTIAGLLLGLYGQQH
MSLDAASTHQVFLYTYLSMAAIIALPALIFSRVPDDVGSNIVLRRRNRSGS
(Multidrug Efflux
|83
Molecular visualization tools: The modelled 3 D structure
of proteins files are viewed with the help of DISCOVERY
STUDIO SOFTWARE to find out the structural and functional
regions of the 3D structure of the pathogen proteins.
Molecular drug docking: The drug docking studies were
performed using PATCHDOCK server- automated molecular
in order to identify the binding affinities
of the pathogen proteins and to identify the (Caffeic acid,
acid, Hyperoside and Rutoside )
>gi|238547966|dbj|BAH64317.1| multidrug efflux system protein [Klebsiella pneumoniae subsp.
MTDLPASVRWQLWIVAFGFFMQSLDTTIVNTALPSMAKSLGESPLHMHMIIVSYVLTVAVMLPASGWLAD
RVGVRNIFFTAIVLFTAGSLFCAQASTLDQLVMARVLQGVGGAMMVPVGRLTVMKIVPRDQYMAAMTFVT
LPGQVGPLLGPALGGVLVEYASWHWIFLINIPVGIVGAIATLCLMPNYTMQTRRFDLSGFLLLAAGMATL
TLALDGQKGLGISPAWLAGLVAVGLCALLLYLWHARGNARALFSLNLFRNRTFSLGLGGSFAGRIGSGML
PFMTPVFLQIGLGFSPFHAGLMMIPMVLGSMGMKRIVVQVVNRFGYRRVLVASTLGLAAVSLLFMFSALA
LLSMVMQLSMSIGVTIAGLLLGLYGQQH
Hepzibah et al., Molecular Mechanics and Drug Docking Studies On Klebsheilla Pneumonia (Multidrug Efflux
System Protein) using Insilico Protocols
84 | VOLUME 2 | NUMBER 2 | JUN | 2012
Figure: 2 3 Dimensional structure of (Klebsheilla pneumonia (multidrug efflux system protein).
Discovery studio software – Atom model
Figure: 3 3 Dimensional structure of Klebsheilla pneumonia (multidrug efflux system protein).
Discovery studio software – Solid Ribbon model
Hepzibah et al., Molecular Mechanics and Drug Docking Studies On Klebsheilla Pneumonia (Multidrug Efflux
System Protein) using Insilico Protocols
VOLUME 2 | NUMBER 2 | JUN | 2012 |85
Figure : 4 Molecular docking Klebsheilla pneumonia (multidrug efflux system protein) and
Caffeic acid
Figure: 5 Molecular docking Klebsheilla pneumonia (multidrug efflux system protein) and
Chlorogenic acid
Hepzibah et al., Molecular Mechanics and Drug Docking Studies On Klebsheilla Pneumonia (Multidrug Efflux
System Protein) using Insilico Protocols
86 | VOLUME 2 | NUMBER 2 | JUN | 2012
Figure: 6 Molecular docking Klebsheilla pneumonia (multidrug efflux system protein) and Rutin
Figure: 7Molecular docking Klebsheilla pneumonia (multidrug efflux system protein) and
Quercitrin
Hepzibah et al., Molecular Mechanics and Drug Docking Studies On Klebsheilla Pneumonia (Multidrug Efflux
System Protein) using Insilico Protocols
VOLUME 2 | NUMBER 2 | JUN | 2012 |87
Figure: 8 Molecular docking Klebsheilla pneumonia (multidrug efflux system protein) and
Hyperoside
Table: 1
Pathogens Receptor
protein
Caffeic acid Quercitrin Chlorogenic
acid
Hyperoside Rutoside
Klebsheilla
pneumonia
(multidrug efflux
system protein )
-156.98 -309.09 -285.93 -328.08 -429.00
Discussion
Multiple drug resistance or Multidrug resistance is a
condition enabling a disease-causing organism to resist
distinct drugs or chemicals of a wide variety of structure
and function targeted at eradicating the organism.
Organisms that display multidrug resistance can be
pathologic cells, including bacterial and neoplastic (tumor)
cells.
Until recently, research and development (R&D)
efforts have provided new drugs in time to treat bacteria
that became resistant to older antibiotics. That is no longer
the case. The potential crisis at hand is the result of a
marked decrease in industry R&D, and the increasing
prevalence of resistant bacteria. Infectious disease
physicians are alarmed by the prospect that effective
antibiotics may not be available to treat seriously ill patients
in the near future.
As bacterial antibiotic resistance continues to
exhaust the supply of effective antibiotics, a global public
health disaster appears likely. Poor financial investment in
antibiotic research has exacerbated the situation. A call to
arms raised by several prestigious scientific organizations a
few years ago rallied the scientific community, and now the
scope of antibacterial research has broadened considerably
Quercitrin is a glycoside formed from the flavonoid
quercetin and the deoxy sugar rhamnose. It is a constituent
of the dye quercitron. It can be found in Tartary buckwheat
(Fagopyrum tataricum)
Caffeic acid is a hydroxycinnamic acid, a naturally
occurring organic compound. This yellow solid consists of
both phenolic and acrylic functional groups. It is found in all
plants because it is a key intermediate in the biosynthesis of
lignin, one of the principal sources of biomass. Caffeic acid
has been shown to inhibit carcinogenesis, although other
experiments show possible carcinogenic effects. It is also
Hepzibah et al., Molecular Mechanics and Drug Docking Studies On Klebsheilla Pneumonia (Multidrug Efflux
System Protein) using Insilico Protocols
88 | VOLUME 2 | NUMBER 2 | JUN | 2012
known as an antioxidant in vitro and also in vivo. Caffeic
acid also shows immunomodulatory and antiinflammtory
activity. 4
Chlorogenic acid is a hydroxycinnamic acid, a
member of a family of naturally occurring organic
compounds. These are esters of polyphenolic caffeic acid
and cyclitol (-)-quinic acid (Clifford, M. N et al., 2003). It is
an important biosynthetic intermediate ( Wout Boerjan , et
al 2003) .It also is one of the phenols found in coffee,
bamboo Phyllostachys edulis (Kweon,Mee-Hyang et al.,
2001), as well as many other plants(Clifford, M. N. (2003)
).This compound, long known as an antioxidant, also slows
the release of glucose into the bloodstream after a
meal(Johnston, K. L et al ., 2003).
Hyperoside is a chemical compound. It is the 3-O-
galactoside of quercetin. It is a medicinally active
compound that can be isolated from Drosera rotundifolia,
from the Stachys plant, from Prunella vulgaris, from Rumex
acetosella, Cuscuta chinensis seeds, from St John's wort and
from Camptotheca acuminata (Shiyou Li , et al., 2005). In
Rheum nobile and R. rhaponticum, it serves as a UV blocker
found in the bracts.It can have a protective antioxidant
effect on cultured PC12 cells. (Zhiyong Liu , et al., 2005).
Rutin, also called rutoside, quercetin-3-O-rutinoside
and sophorin, is a citrus flavonoid glycoside found in
buckwheat, (Kreft S et al., 1999). It can combine with
cations, supplying nutrients from the soil to the cells in
plants. In humans, it attaches to the iron ion Fe2+,
preventing it from binding to hydrogen peroxide, which
would otherwise create a highly-reactive free radical that
may damage cells. It is also an antioxidant.
Furthermore, it has been shown to inhibit in vitro
the vascular endothelial growth factor (Luo; et al., 2008) .in
subtoxic concentrations, so acts as an inhibitor of
angiogenesis. This finding can be potentially relevant for
the control of some cancers (table 2).
Docking is frequently used to predict the binding
orientation of small molecule drug candidates to their
protein targets in order to in turn predict the affinity and
activity of the small molecule. Hence docking plays an
important role in the rational design of drugs. 5
The extracted chemical compound structure and
the predicted three-dimensional structure of Human
pathogen protein were docked using PATCHDOCK server.
Molecular mechanics methods may also be used to provide
semi-quantitative prediction of the binding affinity.
The table (3and 4) in fig (1 and 2) show the binding
affinities between the Ligand and the receptor. The Rutin
shows the high binding affinities (-429.00 /Klebsheilla
pneumoniae) .An overall affinity shows that Hypersoide and
Rutin are the potential inhibitors of the target (Klebsheilla
pneumonia )pathogen proteins.
Conclusion
Antibiotic resistance is an important tool for genetic
engineering. We focus on how the naturally occurring
chemicals inhibit the Multi-drug Resistance (MDR) Human
pathogens (Klebsheilla pneumonia,) protein. Thus, we
identified that the chemical compounds in the plant
products are best agents to reduce the problems associated
to urinary tract infections. So we conclude that Rutin and
Hypersoide are one of the potential drug candidates for
Klebsheilla pneumonia organisms.
The Klebsheilla pneumonia are one of the powerful
pathogens for Multi-Drug Resistance (MDR) in human. The
identified compounds (Quercitrin, Caffeic acid, Chlorogenic
acid, Hyperoside and Rutin) has basically antioxidant activity
whereas these results clearly show that the compounds also
have anti-bacterial properties based on Insilico docking
studies.
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