1School of Chinese Materia Medica Beijing University of Chinese Medicine Beijing 100102 China2School of Basic Medical Sciences Beijing University of Chinese Medicine Beijing 100029 China3Institute of Basic Research of Clinical Medicine China Academy of Chinese Medical Sciences Beijing 100700 China
Correspondence should be addressed to Yun Wang wangyunbucmeducn and Cheng-ke Cai cck98126com
Received 5 January 2015 Revised 10 June 2015 Accepted 7 July 2015
Academic Editor Josiah Poon
Copyright copy 2015 Bai-xia Zhang et al This is an open access article distributed under the Creative Commons Attribution Licensewhich permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited
Due to the proved clinical efficacy Shuang-Huang-Lian (SHL) has developed a variety of dosage forms However the in-depthresearch on targets and pharmacological mechanisms of SHL preparations was scarce In the presented study the bioinformaticsapproaches were adopted to integrate relevant data and biological information As a result a PPI networkwas built and the commontopological parameters were characterized The results suggested that the PPI network of SHL exhibited a scale-free property andmodular architecture The drug target network of SHL was structured with 21 functional modules According to certain modulesand pharmacological effects distribution an antitumor effect and potential drug targets were predicted A biological network whichcontained 26 subnetworks was constructed to elucidate the antipneumoniamechanism of SHLWe also extracted the subnetwork toexplicitly display the pathwaywhere one effective component acts on the pneumonia related targets In conclusions a bioinformaticsapproach was established for exploring the drug targets pharmacological activity distribution effective components of SHL andits mechanism of antipneumonia Above all we identified the effective components and disclosed the mechanism of SHL from theview of system
1 Introduction
Traditional Chinese Medicine (TCM) one of the main itemsof complementary and alternative medicine is a healthcarefocused medical system As the main characteristics formulais the most important part which has been utilized fortreating diseases and promoting the health of humans forthousands of years in TCM practice [1] As known herbalformula is the most important part which has been utilizedfor treating diseases and promoting the health of humans forthousands of years in TCM practice In the formula eachherb contains many compounds that offer multitarget multi-component synergy and multidimensional pharmacologicalactions Taking these concerns there is a considerable chal-lenge for researchers to disclose the mechanisms of formulausing conventional pharmacological methods Fortunatelywith the development of pharmaceutical chemistry more
and more public databases of Traditional Chinese Medicinewere built such as Traditional Chinese Medicine IntegratedDatabase (TCMID) Traditional Chinese Medicine Infor-mation Database (TCM-ID) TCMGeneDIT and ChineseTraditional Medicine Herbs Database [2 3] Based on thesequalitative databases some valuable information could beaddressed by system biological technology to identify somemechanisms of herbal formula
Shuang-Huang-Lian (SHL) one of the famous modernformulae prepared from three medicinal herbs including FlosLonicerae Radix Scutellariae and Fructus Forsythiae mainlyhas antibacterial antivirus and anti-inflammation activitieswhich is put into clinic for treatment of the diseases includingacute respiratory tract infection bacterial infection andpneumonia [4] Currently SHL has been developed in avariety of dosage forms due to its proved clinical efficacyfor example SHL capsule SHL soft capsule SHL tablet SHL
Hindawi Publishing Corporatione Scientific World JournalVolume 2015 Article ID 291680 9 pageshttpdxdoiorg1011552015291680
2 The Scientific World Journal
Components of Shuang-Huang-Lian
103 out of 116 have similar drugs
Similar drugs
Drug target
Protein-proteininteraction network
Pharmacologicaleffects distribution
Drug-targetnetwork
Moduleanalysis
Antipneumoniabiological network
Mechanism ofantipneumonia
Figure 1 The workflow of SHL network construction and analysis
oral liquid SHLmixture and SHL injection However the in-depth researches on holistic and synergetic pharmacologicalmechanisms of SHL preparations were scarce and the studieson the targets of multicomponents and pharmacologicalactivity of SHL are necessary for setup
In this study a bioinformatics strategy as shown inFigure 1 was adapted to explore the novel targets and activityof SHLHopefully the approach could arouse a newparadigmfor investigating and explaining the roles of herbal formulas
2 Data Source and Methods
21 Data Sources The components of SHL came fromTraditional Chinese Medicine Basic Information Databaseof State Administration of Traditional Chinese Medicineof Peoplersquos Republic of China (httpcoworkcintcmcomenginewindexjsp) and A Handbook on Analysis of theActive Composition in TCM [5] (Supplementary Table 1 inSupplementary Material available online at httpdxdoiorg1011552015291680) The drug targeting proteins data comesfrom DrugBank database [6] The context of network comesfrom REACTOME database [7] protein-protein interactions(PPI) come from REACTOME database [7] and HPRDdatabase [8] Pharmacological effects data is collected fromDrugBank database The proteins related to pneumonia arederived from the SciClips database
22 Similar Drugs of the SHL Components Are Predicted onDrugBank Database Based on two-dimensional structuralsimilarity we could obtain the similar drugs (SupplementaryTable 2) which exist in the DrugBank database by themoduleof the ldquoChemQuery Structure Searchrdquo in DrugBank (httpwwwdrugbankcastructuressearchsmall molecule drugsstructure) In order to obtain the most credible results twoconditions need to be satisfied (1) the parameter of similaritythreshold was higher than 06 and the other parametersrsquovalues were default (2) the most similar drug to eachcomponent was retained
23 Network Construction In order to construct the TCMcomplex system model identify effective cluster and illus-trate the mechanisms further we put forward the directedTCM grammar systems (dTGS) [9 10] which are based onthe theory of Entity Grammar system [11] dTGS is a tetrad119866 = (119881 119865 119875 119878) whereas 119881 is the character set representingbasic element 119865 is a finite set of relations for119881 119881 and 119865wereviewed as entity 119875 is a set of rules to deduce relationshipsbetween entities and 119878 is the starting entity According todifferent objective we can write different reasoning engineProviding a starting condition (starting entity) dTGS canobtain the result of relationship among entities automaticallyWith these relationships among entities we can constructnetworks In this paper we use dTGS as framework to findthe relationships between components and other entitiesThe results after reasoning and rearranging were visualizedwith Cytoscape Thus we can construct the drug-targetnetwork and the antipneumonia biological network of SHLThe application of dTGS was more flexible compared totraditional network analysis methods According to differentobjective we can define different 119881 119865 119875 and 119878
Due to the various objectives and data the 119881 119865 119875 and119878 of the PPI network and antipneumonia biological networkshould be defined respectively
The 119881 119865 119875 and 119878 of the PPI network are as follows
herbX(A) represents the components existing in thecorresponding herb herbX(AC) represents the rela-tionship of the components of the corresponding herband its similar drug drugtarget(CB) represents therelationship of similar drug and its target link(BD)and link(DE) represent the relationship of nodes inthe background network which was prior knowledge
1198751are used to deduce the relations of chemical
components and their targets 1198752and 119875
3are used to
deduce the related proteins of components in PPInetworks ldquolink(CB)rdquo as prior knowledge representsrelations of nodes in PPI network ldquonet(AB 119873)rdquo isthe results which are obtained by reasoning engine119873 is the cumulative distance from component A toprotein E which is less than 10
The Scientific World Journal 3
(4) 119878 = 1198781cup 1198782
1198781is the set of entities with structure link(BD) in
background network for deduction 1198782is the starting
point of reasoning with structure herbX(A)
The 119881 119865 119875 and 119878 of the antipneumonia biological net-work is described by the following
pos neg 119884 isin 119885lowastIn(A) and out(B) A isin 119881
1 B isin 119881
2
link(AB 119883 119884) defines that A(protein) acts onB(protein) with an effect described in 119883 andthrough 119884 reactions so that the distance numberis 119884 If process happens in one reaction 119884 equals1 In in(A) and out(B) A represents the targets ofcompounds while B represents the pneumonia-related proteins totalnet(AB 119883 119884) represents thatA (target protein) affects B (pneumonia-relatedprotein) with an effect described in 119883 by reactions of119884 minet(AB 119883 119884) defines that A (target protein)can affect B (pneumonia-related protein) with aneffect described in119883 by multiple pathway but we justretain the shortest path with 119884 reactions
= 119873 + 1 119873 = 119884 minus F length(119884) rArr forward(CDE119872)1198751tags the starting point of derivation by in(A) from
link(AB 119883 119884) and the tagged link(AB 119883 119884) isnamed as totalnet(AB 119883 119884)119875
2cup1198753cup1198754cup1198755is the set
of rules to deduce the eventual effects and distances oftarget proteins to other downstream proteins in thenetwork In link(AB 119883 119884) totalnet(AB posD)and minnet(AB 119883 119884) ldquo119883rdquo and ldquoposrdquo and ldquo119884rdquo andldquoDrdquo represent the same data type respectively justbecause they located in the same position119875
2indicates
that if the effect of A on B is positive and theeffect of B on C is positive too then the effectof A on C is positive Meanwhile if A affects Bthrough D reactions and B affects C through Ereactions then the distance of A to C is D plus ESimilar derivations are defined in 119875
3 1198754 and 119875
5
They may be used as many times as necessary to thefinal pneumonia-related protein 119875
6is a rule used to
identify the shortest distance from a target protein toa pneumonia-related protein when the paths betweenthem are too complicated to analyze In 119875
6 if B is
a pneumonia-related protein in totalnet(AB 119883 119884)then minD totalnet(AB 119883 119884) = 119872 indicatesthat the shortest distance from A to B is119872 which isextracted by minnet(AB 119883119872) In the constructionof target network 119875
6will be used as many times
as necessary to the target protein pneumonia-relatedprotein pairs 119875
7cup 1198758cup 1198759cup 11987510cup 11987511
were used todescribe the detailed pathway from A to B with theclear steps of119884The forward(CDE119872)was the finalresult used to construct the network After connectingeach of the forward(CDE119872) we could get thedetailed pathway from A to B
(4) 119878 = 1198781cup 1198782
1198781is the set of entities with structure link(AB 119883 119884)
in background network for deduction 1198782is the set of
starting and end point proteins described by in(A)and out(B)
3 Results and Discussion
31 Topology Analysis of SHL PPI Network As shown inFigure 2 (clear node label can be seen in Figure 2) theSHL PPI network there are 1953 nodes and 3112 edges Thenetwork diameter is 12 which means the greatest distancebetween any pair of vertices is 12 The node degree distribu-tion indicated that the PPI of SHL followed the power lawwith a degree exponent of 0969 (1198772 = 0647) The Clus-tering coefficient is 0322 The connected component is 10Network centralization is 03112 And network heterogeneityas 6017 These common topological parameters suggestedthat the network exhibited scale-free property and modulararchitecture
4 The Scientific World Journal
Figure 2 PPI Network of SHL The components in SHL Network are yellow diamonds The targets are shown as blue squares In the PPInetwork there are 92 components (Supplementary Table 3) acting on 129 targets which interact with 1787 proteins
32 Drug-TargetNetwork In order to express the relationshipbetween SHL components more clearly we constructed adrug-target network of SHL As shown in Figure 3 we totallylabeled the 21 modules Most of them match the commontargets However it may be worth nothing that some noveltargets are detected such as thirteen components of themodule (6) act on the same targets PYGM which playan important role in regulation of cell cycle and cellularmacromoleculemetabolic processThese biological processesare closely related to cell proliferation and tumorigenesis(anticancer effect) Following the same strategy it is easyto help us to understand the functional classifications ofeach SHL component based on the modules in drug-targetnetwork
33 Pharmacological Effects Distribution of SHL In the PPINetwork of SHL we counted pharmacological effects of
all the proteins frequency statistical results are presentedin Figure 4 The results indicate that five in top ten phar-macological effects of SHL are linked with antineoplasticagents protein kinase inhibitors enzyme inhibitors growthinhibitors and phytogenic antineoplastic agents which sug-gested that SHLmight directed against tumor effect Further-more two pharmacological effects focused on antioxidantsand anti-inflammatory agents which could help tumor sup-pression For sure the novel pharmacological effects of SHLneed further empirical data form bench to bedside
34 The Anti-Pneumonia Mechanism of SHL Using the dataderived from the Reactome database as context we con-structed the biological network of the effective components ofSHL acting on the pneumonia related targets Circular noderepresents disease related targets diamond node representseffective components of SHL square node represents proteins
The Scientific World Journal 5
Quercetinrarr3rarr o rarr120573rarrDrarr glucoside
Q03736
ForsythialanA
MTP
DihydrooroxylinA Eriodictyol
SOAT2
DR4L2
UD3A1 Rivularin
SkullcapflavoneII
SkullcapflavoneI
HCK
ATPB
PK3CG
Chrysin
Q9AIU0
NorwogoninQ5G940
ForsythosideAIsomartynoside
Baicalein
PYGM
4-O-Caffeoylquinicacid
Oroxylin oroxylinA
Neobaicalein
5-Caffeoylquinicacid
LeucosceptosideA
Quercetin
ST17B
HIBCH
ATPA
ATPG
PIM1Wogonin
LuteolinCorymbosin
Geranial2-Pentadecanone
Cornoside
LYSCAT1A1
OctadecanoicacidAcetophenone
Butylatedhydroxyanisole ACO13
Phenethylalcohol
Cymene
p-cymene P03437
P26137Stigmasterol
RORA
120573-sitosterol
P00720
MIF
Caffeicacid
P16113
PYRD
Norlapachol
Q02768 Q3IWB0Q08210
PAEP S14L2
Palmiticacid
OPSDPPT1
TPPC3
GCH1
PNPH
P83812
P45563
Q9X1H9
MYP2
HNF4G
TRPA1
CP2C8
TRPM8ECE1
MyrtanolIsoborneol
GBB1
RASK
FNTA
Myrcene
RAE1
GBG1
PA2GDP0A433
Guanine
P0A9M5
Q84EX5
Q9X1T2
OPRKTRPV3
LALBA
Rengyol
PHOS
FNTB
PGTA
PGTB2
GDIA
Caryophyllene
120573-ocimene
DihydrobaicaleinP54965
P25553
COX7C COX5BCOX8A AK1C2
COX3 COX6C
COX2COX1
COX5A
SOAT1
Matairesinol
DimethylmatairesinolArctigenin
ForsythialanB
PRGR
COX7B
ETUD1
ERR3
Oleanolicacid
Pinoresinol
ESR1
Epipinoresinol
n-heneicosane
ERG7
120572-terpineol
Nonacosane
NCOA2P22637
ST2A1
ST2B1DHB1
P33517
P07445
Phillygenol
Ursolicacid
Q48473
KAPCAGLTP
Q8ZRP8
Q7KZA3
PA21BFABP6
COX41NR1H4
2120572-hydroxybetulinicacid
Betulinicacid
CX7A1HEMHCX6A2
ADH1G
P31224
Q8GGK7
EST1CX6B1
Isomenthone
Camphene
Isichlorogenticacid
45-Dicaffeoylquinicacid
Menthone
P00183
ForsythosideB
Camphor
Borneol
Linolenyalcohol
FADS2
PGH2
ELOV4
FADS1
Cynarin
Acteoside
CDK1Wogonoside
CDK8CDK4CDK6
PGH1
TRPV1
NAC1
ACM2 ACHA2
SuspensineA
LonicerinBaicalin
ACES 5HT3A
Arctiin
TOP2A
Matairesionoside
Phillyrin
Astragalin
Chlorogenic
IsochlorogenicacidB
CDK2
CDK5 CDK7
CDK9
EGFR Hyperoside
AK1C3
Rutin
Isoquercetin
Wogonin-7-120573-D-glcUA
Pinoresinol-120573-D-glucoside
7-Methoxybaicalein
(-)Bicuculline
(-)Egenine
(1) (3)(2)(4) (5)
(6) (8)(7)(10)(9) (11)
(12)(13)
(14) (15) (16) (17) (18) (19) (20)(21)
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Luteolinrarr7rarrOrarr120573rarrDrarr glucoside
3572998400-Tetrahydroxyavone
572998400-Trihydroxyflavone
5-Hydroxy-74998400- dimethoxyflavone
(-)-7998400-O-Methylegenine
Figure 3 Drug-target Network of SHL The components are yellow diamonds The targets are shown as blue squares
Ant
ineo
plas
tic ag
ents
Ana
lges
ics
nonn
arco
ticA
ntia
nxie
ty ag
ents
GA
BA an
tago
nists
Sym
path
omim
etic
sAd
juva
nts
anes
thes
iaA
ntic
hole
stere
mic
agen
tsSy
mpa
thom
imet
icA
ntifu
ngal
agen
tsA
ntid
epre
ssiv
e age
nts
seco
nd-g
ener
atio
nEx
cita
tory
amin
o ac
id an
tago
nists
Card
iova
scul
ar ag
ents
Ant
ispas
mod
ics
Ant
inar
cotic
agen
tsO
piat
e ant
agon
ists
Tryp
anoc
idal
agen
tsRe
nal a
gent
sA
ntim
usca
rinic
sD
iagn
ostic
agen
tsD
opam
ine u
ptak
e inh
ibito
rsA
ntic
holin
ergi
c age
nts
Lipo
xyge
nase
inhi
bito
rsC
ofac
tor
Nep
hrop
athi
c cys
tinos
is th
erap
yH
epar
ins
Ant
i-HIV
agen
tsPs
ycho
tropi
c dru
gsVi
tam
in D
3 re
cept
or in
hibi
tor
Enzy
me r
epla
cem
ent a
gent
sVi
tam
ins (
vita
min
D)
Fert
ility
agen
tsLe
ukot
riene
anta
goni
stsFr
ibic
acid
der
ivat
ives
Cor
ticos
tero
idA
mph
etam
ines
Alp
ha-a
dren
ergi
c blo
ckin
g ag
ents
Col
orin
g ag
ents
Mon
oam
ine o
xida
se in
hibi
tors
Pharmacological effects distribution
0
10
20
30
40
50
60
70
80
Figure 4 The pharmacological distribution of all 112 components in SHL
6 The Scientific World Journal
Palmitoylatedmyristoylated
eNOSdimer
Serumalbumin
PalmitylatedN-Myristoylated
eNOS
N-myristoylated eNOS(Gly2)
Aldehyde reductase
Nitricoxide
synthaseendothelial
Isomenthone
Ca(4)CaM Caveolin-1
PhosphorylatedHSL
complex
Fattyacid
bindingprotein
adipocyte
Thrombin activation
peptide
DihydrooroxylinA
Adenosine aminohydrolase
Factor IX
activation peptide
complex (prothrombinase)
Acteoside
Dihydrofolate reductase
FactorXa
Caimpermeable
AMPAreceptors
Factor VIIIa
B A3
acidic polypeptide
Activated thrombin
(factorIIa)
Luteolinrarr7rarrOrarr ararrDrarr glucoside
VaXa
eNOS caveolin-1 CaMeNOS Caveolin-1 CaM HSP90
eNOS caveolin-1
Na+
Ca2+ NH4+Na+
Ca2+
dimer FABP4
Glu
H+PALM
AMP
L-GlnGluL-Ala
Higherfattyacid
Inosinedeoxyinosine
THF
Ribose 1-phosphatedeoxyribose 1-phosphate
Hyp
Pi
2OG
TPN GluH+
Figure 5 The antipneumonia biological network of SHL
involved in the pathway parallelogram node represents com-plex hexagon node represents micromolecule and trianglenode represents biological reaction The edge with trianglearrow represents positive regulation edge with T-shapedarrow represents negative regulation and the undirected edgemeans the direction is uncertain (Figure 5) This biologicalnetwork which included 4 components 5 pneumonia relatedtargets and 26 subnetworks could overall exhibit the effectivecomponents and the mechanism of antipneumonia on amolecular level
This biological network included 26 subnetworks that4 components that acted on 5 pneumonia related targetsAll of these subnetworks intertwined to play the role ofantipneumonia collectively and demonstrated the features ofbiological systems simultaneously such as robustness redun-dancy crosstalk and so forth In order to clearly show theantipneumonia mechanism of SHL effective components wecould extracted 26 subnetworks respectivelyThis paper took2 extracted subnetworks as examples the biological pathwaywhere luteolin-7-o-120572-D-glucoside acted on serum albumin(Figure 6) and the biological pathway where dihydrooroxylinA acted on thrombin activation peptide (Figure 7)
As target of luteolin-7-o-120572-D-glucoside endothelial nitricoxide synthase (eNOS) translocated from Golgi to caveolaeafter N-myristoylation and palmitoylationWith depalmitoy-lation of eNOS dimer it produced PALM After the reactionof PALM and CoASH palmitic acid converted to palmitoyl-CoA accompanyied with energy transformation After aseries of signal transduction ofmicromolecule (NH4+ L-GlnNa+ etc) the content of serum albumin changed As thebiomarker in the early stage this pathway could elucidatethe course of the change That is luteolin-7-o-120572-D-glucosideacting on eNOS leads to the increase of vasopermeability
and serum albumin influxed into the interval of capillariesaccelerated the speed of catabolism and affected the contentof serum albumin at last [12 13]
Figure 7 shows the initial two steps of blood coagulationthe formation process of thrombin activation peptide andthe activation of thrombin As the target of dihydrooroxylinA adenosine aminohydrolase was hydrolyzed dephosphory-lated and oxidated After some amino acid was taken up andGluR2 transferred the Ca2+ impermeable AMPA receptorand aspartic acid receptor were activated and then extrudedof Ca2+ Factor Xa was activated by Ca2+ and Ca2+ alsocould accelerate the combination of factors Xa and Va [14]Factor Va had no activity itself but it could enhance activityof factor Xa and accelerated the formation of thrombin[15] Thrombin could accelerate the blood coagulation andwound healing thus treating alimentary tract hemorrhage ofsevere pneumonia In conclusion dihydrooroxylin A actingon thrombin plays the role of antipneumonia by acceleratingthe hemostasis of the alimentary tract
By summarizing the 26 subnetworks of SHL effectivecomponents cluster acting on pneumonia-related targets wegot 3 main pathways where SHL played the role of antip-neumonia (1) regulating the activity of caveolin-1 existingin the signal pathway of inflammatory and endothelial cellsaffects the response of inflammatory cell to the inflamma-tion further influencing the process of inflammation (2)accelerating the blood coagulation and wound healing thustreating alimentary tract hemorrhage of severe pneumonia(3) affecting the content of serum albumin promoting therepair of lung tissue and enhancing the immune function
Biological network shows 4 components could act on5 targets within 10 biological reactions Other componentsin SHL may also act on pneumonia-related targets but
The Scientific World Journal 7
AMP
PALM
L-Gln
Serum albumin
PalmitylatedN-myristoylated
eNOS
Nitricoxide
synthaseendothelial
Palmitoylatedmyristoylated
eNOS dimer
N-myristoylated eNOS (Gly2)
Na+
NH4+
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Figure 6 The antipneumonia biological pathway of luteolin-7-o-120572-D-glucoside
Ca impermeable
AMPA receptors
Glu
Adenosine aminohydrolase
DihydrooroxylinA
Inosinedeoxyinosine
Hyp
Ribose 1-phosphatedeoxyribose 1-phosphate
Pi
complex (prothrombinase)
Factor Xa
Thrombin activation
peptide
Va Xa
Na+Ca2+
Na+Ca2+
H+
Figure 7 The antipneumonia biological pathway of dihydrooroxylin A
8 The Scientific World Journal
the number of biological reactions will be more When wedefined the reactions as 15 biological network contained 5components and 9 pneumonia-related targets If the reactionwas 20 43 components and 13 targets were included in thebiological network The 4 components by contrast weremore quickly and efficiently acting on pneumonia-relatedtargets Compared with the components in SHL whichstudied frequently such as chlorogenic acid forsythin andbaicalin the content of four components within the networkwas lower but they may play the same role of pneumoniatreatment
4 Conclusion
Based on the public databases of TCM DrugBank databaseand directed TCM grammar systems we have built a PPInetwork drug target network and antipneumonia biologicalnetwork of SHL By the modules analysis we predicted thatSHL has the potential to be an antitumor candidate Thisresultmay provide a novel clue for further experimental stud-ies of SHL In future the predicted novel pharmacologicaleffects of SHL should be further validated from bench tobedside The antipneumonia biological network systemati-cally explained the reason why SHL could play the role ofantipneumonia and identified its effective components Allthese are helpful to guide the quality control and further studyof SHL
Studies have already demonstrated that SHL had thepharmacological actions of antimicrobial antiviral anti-pyretic anti-inflammatory antioxidant antiarrhythmic andenhanced immunity [16ndash19] but they only focused on indi-vidual component pharmacological action or pathway Thecomponent they studied could be extracted and was with ahigh content Compared with these studies our study couldelucidate the mechanism holistically and on the molecularlevel Meanwhile enclosing the synergistic effect of variouscomponents and the cross of pathways we not only addressedthat luteolin-7-120572-D-glucoside [20] dihydrooroxylin A [2122] and acteoside [23] played an anti-inflammatory role butalso predicted that isomenthone could act on pneumonia-related targets through biological network of SHL thusplaying the role of antipneumonia
The thought of this study accords with the networkpharmacology but the method we adopted is different fromother related works [24 25] The whole process of otherrelated works is carried out manually and the batch pro-cessing is impossible With the characteristic of flexibilitydTGS could solve these problems effectively Carrying out theTCM research under the guidance of network pharmacologyis more quick and systematic than traditional methodsMeanwhile dTGS provides a novel strategy for the study ofTCM and other complex systems
Because the research results were based on the inferenceof data included in the existing database or literature andbecause we do not take into account the quantity of compo-nents and the specific interactional environment thismethodstill has some limitations With further study of the complexsystems such as TCM formula and related disease the data
we used will be more complete and the results we got will bemore precise and integrity
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Authorsrsquo Contribution
Bai-xia Zhang Jian Li andHaoGu contributed equally to thiswork
Acknowledgments
This work was supported by National Science and Technol-ogy Major Projects for ldquomajor new drugs innovation anddevelopmentrdquo (Grant no 2011ZX09201-201-15) the NationalNatural Science Foundation of China (Grant nos 81173568and 81373985) and Program for New Century ExcellentTalents in University (Grant no NCET-11-0605)The fundershad no role in study design data collection and analysisdecision to publish or preparation of the paper
References
[1] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[2] X Chen H Zhou Y B Liu et al ldquoDatabase of traditionalChinese medicine and its application to studies of mechanismand to prescription validationrdquo British Journal of Pharmacologyvol 149 no 8 pp 1092ndash1103 2006
[3] Z L Ji H Zhou J F Wang L Y Han C J Zheng and YZ Chen ldquoTraditional Chinese medicine information databaserdquoJournal of Ethnopharmacology vol 103 no 3 501 pages 2006
[4] J Ye X Song Z Liu et al ldquoDevelopment of an LC-MS methodfor determination of three active constituents of Shuang-huang-lian injection in rat plasma and its application to the druginteraction study of Shuang-huang-lian freeze-dried powdercombined with levofloxacin injectionrdquo Journal of Chromatog-raphy B Analytical Technologies in the Biomedical and LifeSciences vol 898 pp 130ndash135 2012
[5] H Liu Y X Qiao B Liu and J J Zhou ldquoTransformation oftraditional Chinese medicine database into data warehouserdquoChinese Pharmaceutical Journal vol 9 pp 645ndash648 2006
[6] V Law C Knox Y Djoumbou et al ldquoDrugBank 40 sheddingnew light on drug metabolismrdquo Nucleic Acids Research vol 42no 1 pp D1091ndashD1097 2014
[7] D Croft A F Mundo R Haw et al ldquoThe Reactome pathwayknowledgebaserdquoNucleic Acids Research vol 42 no 1 ppD472ndashD477 2014
[8] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[9] L Ji R L Ren H Gu et al ldquodTGSmethod for effective compo-nents identification from traditional Chinese medicine formulaand mechanism analysisrdquo Evidence-Based Complementary andAlternativeMedicine vol 2013 Article ID 840427 9 pages 2013
The Scientific World Journal 9
[10] J Yan Y Wang S-J Luo and Y-J Qiao ldquoTCM grammarsystems an approach to aid the interpretation of the molecularinteractions in Chinese herbal medicinerdquo Journal of Ethnophar-macology vol 137 no 1 pp 77ndash84 2011
[11] W Yun ldquoEntity grammar systems a grammatical tool for study-ing the hierarchal structures of biological systemsrdquo Bulletin ofMathematical Biology vol 66 no 3 pp 447ndash471 2004
[12] B Ruot I Papet F Bechereau et al ldquoIncreased albumin plasmaefflux contributes to hypoalbuminemia only during earlyphase of sepsis in ratsrdquo The American Journal of PhysiologymdashRegulatory Integrative and Comparative Physiology vol 284 no3 pp R707ndashR713 2003
[13] J U Hedlund L-O Hansson and A B Ortqvist ldquoHypoal-buminemia in hospitalized patients with community-acquiredpneumoniardquo Archives of Internal Medicine vol 155 no 13 pp1438ndash1442 1995
[14] E Persson P J Hogg and J Stenflo ldquoEffects of Ca2+ bindingon the protease module of factor Xa and its interaction withfactor Va evidence for two Gla-independent Ca2+-binding sitesin factor Xardquo The Journal of Biological Chemistry vol 268 no30 pp 22531ndash22539 1993
[15] E A Norstroslashm S Tran M Steen and B Dahlback ldquoEffectsof factor Xa and protein S on the individual activated proteinC-mediated cleavages of coagulation factor Vardquo The Journal ofBiological Chemistry vol 281 no 42 pp 31486ndash31494 2006
[16] W Zhou X X Zhu A L Yin et al ldquoEffect of various absorptionenhancers based on tight junctions on the intestinal absorptionof forsythoside A in Shuang-Huang-Lian application to itsantivirus activityrdquo Pharmacognosy Magazine vol 10 no 37 pp9ndash17 2014
[17] X Gao M Guo Q Li et al ldquoPlasma metabolomic profiling toreveal antipyretic mechanism of Shuang-Huang-Lian injectionon yeast-induced pyrexia ratsrdquo PLoS ONE vol 9 no 6 ArticleID e100017 2014
[18] R Gao Y N Lin G Liang B Yu and Y Gao ldquoComparativepharmacokinetic study of chlorogenic acid after oral admin-istration of lonicerae japonicae flos and shuang-huang-lian innormal and febrile ratsrdquo Phytotherapy Research vol 28 no 1pp 144ndash147 2014
[19] Y Gao L Fang R Cai et al ldquoShuang-Huang-Lian exertsanti-inflammatory and anti-oxidative activities in lipopoly-saccharide-stimulated murine alveolar macrophagesrdquo Phy-tomedicine vol 21 no 4 pp 461ndash469 2014
[20] CM Park andY-S Song ldquoLuteolin and luteolin-7-O-glucosideinhibit lipopolysaccharide-induced inflammatory responsesthrough modulation of NF-120581BAp-1PI3K-AKT signaling cas-cades in RAW 2647 cellsrdquo Nutrition Research and Practice vol7 no 6 pp 423ndash429 2013
[21] H Lee Y O Kim H Kim et al ldquoFlavonoid wogonin frommedicinal herb is neuroprotective by inhibiting inflammatoryactivation of microgliardquo The FASEB Journal vol 17 no 13 pp1943ndash1944 2003
[22] Y-C Chen L-L Yang and T J-F Lee ldquoOroxylin A inhi-bition of lipopolysaccharide-induced iNOS and COX-2 geneexpression via suppression of nuclear factor-120581B activationrdquoBiochemical Pharmacology vol 59 no 11 pp 1445ndash1457 2000
[23] J He X-P Hu Y Zeng et al ldquoAdvanced research on acteosidefor chemistry and bioactivitiesrdquo Journal of Asian Natural Prod-ucts Research vol 13 no 5 pp 449ndash464 2011
[24] L An and F Feng ldquoNetwork pharmacology-based antioxi-dant effect study of Zhi-Zi-da-huang decoction for alcoholic
liver diseaserdquo Evidence-Based Complementary and AlternativeMedicine vol 2015 Article ID 492470 6 pages 2015
[25] F Zhao L Guochun Y Yang L Shi L Xu and L Yin ldquoA net-work pharmacology approach to determine active ingredientsand rationality of herb combinations of Modified-Simiaowanfor treatment of goutrdquo Journal of Ethnopharmacology vol 168pp 1ndash16 2015
2 The Scientific World Journal
Components of Shuang-Huang-Lian
103 out of 116 have similar drugs
Similar drugs
Drug target
Protein-proteininteraction network
Pharmacologicaleffects distribution
Drug-targetnetwork
Moduleanalysis
Antipneumoniabiological network
Mechanism ofantipneumonia
Figure 1 The workflow of SHL network construction and analysis
oral liquid SHLmixture and SHL injection However the in-depth researches on holistic and synergetic pharmacologicalmechanisms of SHL preparations were scarce and the studieson the targets of multicomponents and pharmacologicalactivity of SHL are necessary for setup
In this study a bioinformatics strategy as shown inFigure 1 was adapted to explore the novel targets and activityof SHLHopefully the approach could arouse a newparadigmfor investigating and explaining the roles of herbal formulas
2 Data Source and Methods
21 Data Sources The components of SHL came fromTraditional Chinese Medicine Basic Information Databaseof State Administration of Traditional Chinese Medicineof Peoplersquos Republic of China (httpcoworkcintcmcomenginewindexjsp) and A Handbook on Analysis of theActive Composition in TCM [5] (Supplementary Table 1 inSupplementary Material available online at httpdxdoiorg1011552015291680) The drug targeting proteins data comesfrom DrugBank database [6] The context of network comesfrom REACTOME database [7] protein-protein interactions(PPI) come from REACTOME database [7] and HPRDdatabase [8] Pharmacological effects data is collected fromDrugBank database The proteins related to pneumonia arederived from the SciClips database
22 Similar Drugs of the SHL Components Are Predicted onDrugBank Database Based on two-dimensional structuralsimilarity we could obtain the similar drugs (SupplementaryTable 2) which exist in the DrugBank database by themoduleof the ldquoChemQuery Structure Searchrdquo in DrugBank (httpwwwdrugbankcastructuressearchsmall molecule drugsstructure) In order to obtain the most credible results twoconditions need to be satisfied (1) the parameter of similaritythreshold was higher than 06 and the other parametersrsquovalues were default (2) the most similar drug to eachcomponent was retained
23 Network Construction In order to construct the TCMcomplex system model identify effective cluster and illus-trate the mechanisms further we put forward the directedTCM grammar systems (dTGS) [9 10] which are based onthe theory of Entity Grammar system [11] dTGS is a tetrad119866 = (119881 119865 119875 119878) whereas 119881 is the character set representingbasic element 119865 is a finite set of relations for119881 119881 and 119865wereviewed as entity 119875 is a set of rules to deduce relationshipsbetween entities and 119878 is the starting entity According todifferent objective we can write different reasoning engineProviding a starting condition (starting entity) dTGS canobtain the result of relationship among entities automaticallyWith these relationships among entities we can constructnetworks In this paper we use dTGS as framework to findthe relationships between components and other entitiesThe results after reasoning and rearranging were visualizedwith Cytoscape Thus we can construct the drug-targetnetwork and the antipneumonia biological network of SHLThe application of dTGS was more flexible compared totraditional network analysis methods According to differentobjective we can define different 119881 119865 119875 and 119878
Due to the various objectives and data the 119881 119865 119875 and119878 of the PPI network and antipneumonia biological networkshould be defined respectively
The 119881 119865 119875 and 119878 of the PPI network are as follows
herbX(A) represents the components existing in thecorresponding herb herbX(AC) represents the rela-tionship of the components of the corresponding herband its similar drug drugtarget(CB) represents therelationship of similar drug and its target link(BD)and link(DE) represent the relationship of nodes inthe background network which was prior knowledge
1198751are used to deduce the relations of chemical
components and their targets 1198752and 119875
3are used to
deduce the related proteins of components in PPInetworks ldquolink(CB)rdquo as prior knowledge representsrelations of nodes in PPI network ldquonet(AB 119873)rdquo isthe results which are obtained by reasoning engine119873 is the cumulative distance from component A toprotein E which is less than 10
The Scientific World Journal 3
(4) 119878 = 1198781cup 1198782
1198781is the set of entities with structure link(BD) in
background network for deduction 1198782is the starting
point of reasoning with structure herbX(A)
The 119881 119865 119875 and 119878 of the antipneumonia biological net-work is described by the following
pos neg 119884 isin 119885lowastIn(A) and out(B) A isin 119881
1 B isin 119881
2
link(AB 119883 119884) defines that A(protein) acts onB(protein) with an effect described in 119883 andthrough 119884 reactions so that the distance numberis 119884 If process happens in one reaction 119884 equals1 In in(A) and out(B) A represents the targets ofcompounds while B represents the pneumonia-related proteins totalnet(AB 119883 119884) represents thatA (target protein) affects B (pneumonia-relatedprotein) with an effect described in 119883 by reactions of119884 minet(AB 119883 119884) defines that A (target protein)can affect B (pneumonia-related protein) with aneffect described in119883 by multiple pathway but we justretain the shortest path with 119884 reactions
= 119873 + 1 119873 = 119884 minus F length(119884) rArr forward(CDE119872)1198751tags the starting point of derivation by in(A) from
link(AB 119883 119884) and the tagged link(AB 119883 119884) isnamed as totalnet(AB 119883 119884)119875
2cup1198753cup1198754cup1198755is the set
of rules to deduce the eventual effects and distances oftarget proteins to other downstream proteins in thenetwork In link(AB 119883 119884) totalnet(AB posD)and minnet(AB 119883 119884) ldquo119883rdquo and ldquoposrdquo and ldquo119884rdquo andldquoDrdquo represent the same data type respectively justbecause they located in the same position119875
2indicates
that if the effect of A on B is positive and theeffect of B on C is positive too then the effectof A on C is positive Meanwhile if A affects Bthrough D reactions and B affects C through Ereactions then the distance of A to C is D plus ESimilar derivations are defined in 119875
3 1198754 and 119875
5
They may be used as many times as necessary to thefinal pneumonia-related protein 119875
6is a rule used to
identify the shortest distance from a target protein toa pneumonia-related protein when the paths betweenthem are too complicated to analyze In 119875
6 if B is
a pneumonia-related protein in totalnet(AB 119883 119884)then minD totalnet(AB 119883 119884) = 119872 indicatesthat the shortest distance from A to B is119872 which isextracted by minnet(AB 119883119872) In the constructionof target network 119875
6will be used as many times
as necessary to the target protein pneumonia-relatedprotein pairs 119875
7cup 1198758cup 1198759cup 11987510cup 11987511
were used todescribe the detailed pathway from A to B with theclear steps of119884The forward(CDE119872)was the finalresult used to construct the network After connectingeach of the forward(CDE119872) we could get thedetailed pathway from A to B
(4) 119878 = 1198781cup 1198782
1198781is the set of entities with structure link(AB 119883 119884)
in background network for deduction 1198782is the set of
starting and end point proteins described by in(A)and out(B)
3 Results and Discussion
31 Topology Analysis of SHL PPI Network As shown inFigure 2 (clear node label can be seen in Figure 2) theSHL PPI network there are 1953 nodes and 3112 edges Thenetwork diameter is 12 which means the greatest distancebetween any pair of vertices is 12 The node degree distribu-tion indicated that the PPI of SHL followed the power lawwith a degree exponent of 0969 (1198772 = 0647) The Clus-tering coefficient is 0322 The connected component is 10Network centralization is 03112 And network heterogeneityas 6017 These common topological parameters suggestedthat the network exhibited scale-free property and modulararchitecture
4 The Scientific World Journal
Figure 2 PPI Network of SHL The components in SHL Network are yellow diamonds The targets are shown as blue squares In the PPInetwork there are 92 components (Supplementary Table 3) acting on 129 targets which interact with 1787 proteins
32 Drug-TargetNetwork In order to express the relationshipbetween SHL components more clearly we constructed adrug-target network of SHL As shown in Figure 3 we totallylabeled the 21 modules Most of them match the commontargets However it may be worth nothing that some noveltargets are detected such as thirteen components of themodule (6) act on the same targets PYGM which playan important role in regulation of cell cycle and cellularmacromoleculemetabolic processThese biological processesare closely related to cell proliferation and tumorigenesis(anticancer effect) Following the same strategy it is easyto help us to understand the functional classifications ofeach SHL component based on the modules in drug-targetnetwork
33 Pharmacological Effects Distribution of SHL In the PPINetwork of SHL we counted pharmacological effects of
all the proteins frequency statistical results are presentedin Figure 4 The results indicate that five in top ten phar-macological effects of SHL are linked with antineoplasticagents protein kinase inhibitors enzyme inhibitors growthinhibitors and phytogenic antineoplastic agents which sug-gested that SHLmight directed against tumor effect Further-more two pharmacological effects focused on antioxidantsand anti-inflammatory agents which could help tumor sup-pression For sure the novel pharmacological effects of SHLneed further empirical data form bench to bedside
34 The Anti-Pneumonia Mechanism of SHL Using the dataderived from the Reactome database as context we con-structed the biological network of the effective components ofSHL acting on the pneumonia related targets Circular noderepresents disease related targets diamond node representseffective components of SHL square node represents proteins
The Scientific World Journal 5
Quercetinrarr3rarr o rarr120573rarrDrarr glucoside
Q03736
ForsythialanA
MTP
DihydrooroxylinA Eriodictyol
SOAT2
DR4L2
UD3A1 Rivularin
SkullcapflavoneII
SkullcapflavoneI
HCK
ATPB
PK3CG
Chrysin
Q9AIU0
NorwogoninQ5G940
ForsythosideAIsomartynoside
Baicalein
PYGM
4-O-Caffeoylquinicacid
Oroxylin oroxylinA
Neobaicalein
5-Caffeoylquinicacid
LeucosceptosideA
Quercetin
ST17B
HIBCH
ATPA
ATPG
PIM1Wogonin
LuteolinCorymbosin
Geranial2-Pentadecanone
Cornoside
LYSCAT1A1
OctadecanoicacidAcetophenone
Butylatedhydroxyanisole ACO13
Phenethylalcohol
Cymene
p-cymene P03437
P26137Stigmasterol
RORA
120573-sitosterol
P00720
MIF
Caffeicacid
P16113
PYRD
Norlapachol
Q02768 Q3IWB0Q08210
PAEP S14L2
Palmiticacid
OPSDPPT1
TPPC3
GCH1
PNPH
P83812
P45563
Q9X1H9
MYP2
HNF4G
TRPA1
CP2C8
TRPM8ECE1
MyrtanolIsoborneol
GBB1
RASK
FNTA
Myrcene
RAE1
GBG1
PA2GDP0A433
Guanine
P0A9M5
Q84EX5
Q9X1T2
OPRKTRPV3
LALBA
Rengyol
PHOS
FNTB
PGTA
PGTB2
GDIA
Caryophyllene
120573-ocimene
DihydrobaicaleinP54965
P25553
COX7C COX5BCOX8A AK1C2
COX3 COX6C
COX2COX1
COX5A
SOAT1
Matairesinol
DimethylmatairesinolArctigenin
ForsythialanB
PRGR
COX7B
ETUD1
ERR3
Oleanolicacid
Pinoresinol
ESR1
Epipinoresinol
n-heneicosane
ERG7
120572-terpineol
Nonacosane
NCOA2P22637
ST2A1
ST2B1DHB1
P33517
P07445
Phillygenol
Ursolicacid
Q48473
KAPCAGLTP
Q8ZRP8
Q7KZA3
PA21BFABP6
COX41NR1H4
2120572-hydroxybetulinicacid
Betulinicacid
CX7A1HEMHCX6A2
ADH1G
P31224
Q8GGK7
EST1CX6B1
Isomenthone
Camphene
Isichlorogenticacid
45-Dicaffeoylquinicacid
Menthone
P00183
ForsythosideB
Camphor
Borneol
Linolenyalcohol
FADS2
PGH2
ELOV4
FADS1
Cynarin
Acteoside
CDK1Wogonoside
CDK8CDK4CDK6
PGH1
TRPV1
NAC1
ACM2 ACHA2
SuspensineA
LonicerinBaicalin
ACES 5HT3A
Arctiin
TOP2A
Matairesionoside
Phillyrin
Astragalin
Chlorogenic
IsochlorogenicacidB
CDK2
CDK5 CDK7
CDK9
EGFR Hyperoside
AK1C3
Rutin
Isoquercetin
Wogonin-7-120573-D-glcUA
Pinoresinol-120573-D-glucoside
7-Methoxybaicalein
(-)Bicuculline
(-)Egenine
(1) (3)(2)(4) (5)
(6) (8)(7)(10)(9) (11)
(12)(13)
(14) (15) (16) (17) (18) (19) (20)(21)
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Luteolinrarr7rarrOrarr120573rarrDrarr glucoside
3572998400-Tetrahydroxyavone
572998400-Trihydroxyflavone
5-Hydroxy-74998400- dimethoxyflavone
(-)-7998400-O-Methylegenine
Figure 3 Drug-target Network of SHL The components are yellow diamonds The targets are shown as blue squares
Ant
ineo
plas
tic ag
ents
Ana
lges
ics
nonn
arco
ticA
ntia
nxie
ty ag
ents
GA
BA an
tago
nists
Sym
path
omim
etic
sAd
juva
nts
anes
thes
iaA
ntic
hole
stere
mic
agen
tsSy
mpa
thom
imet
icA
ntifu
ngal
agen
tsA
ntid
epre
ssiv
e age
nts
seco
nd-g
ener
atio
nEx
cita
tory
amin
o ac
id an
tago
nists
Card
iova
scul
ar ag
ents
Ant
ispas
mod
ics
Ant
inar
cotic
agen
tsO
piat
e ant
agon
ists
Tryp
anoc
idal
agen
tsRe
nal a
gent
sA
ntim
usca
rinic
sD
iagn
ostic
agen
tsD
opam
ine u
ptak
e inh
ibito
rsA
ntic
holin
ergi
c age
nts
Lipo
xyge
nase
inhi
bito
rsC
ofac
tor
Nep
hrop
athi
c cys
tinos
is th
erap
yH
epar
ins
Ant
i-HIV
agen
tsPs
ycho
tropi
c dru
gsVi
tam
in D
3 re
cept
or in
hibi
tor
Enzy
me r
epla
cem
ent a
gent
sVi
tam
ins (
vita
min
D)
Fert
ility
agen
tsLe
ukot
riene
anta
goni
stsFr
ibic
acid
der
ivat
ives
Cor
ticos
tero
idA
mph
etam
ines
Alp
ha-a
dren
ergi
c blo
ckin
g ag
ents
Col
orin
g ag
ents
Mon
oam
ine o
xida
se in
hibi
tors
Pharmacological effects distribution
0
10
20
30
40
50
60
70
80
Figure 4 The pharmacological distribution of all 112 components in SHL
6 The Scientific World Journal
Palmitoylatedmyristoylated
eNOSdimer
Serumalbumin
PalmitylatedN-Myristoylated
eNOS
N-myristoylated eNOS(Gly2)
Aldehyde reductase
Nitricoxide
synthaseendothelial
Isomenthone
Ca(4)CaM Caveolin-1
PhosphorylatedHSL
complex
Fattyacid
bindingprotein
adipocyte
Thrombin activation
peptide
DihydrooroxylinA
Adenosine aminohydrolase
Factor IX
activation peptide
complex (prothrombinase)
Acteoside
Dihydrofolate reductase
FactorXa
Caimpermeable
AMPAreceptors
Factor VIIIa
B A3
acidic polypeptide
Activated thrombin
(factorIIa)
Luteolinrarr7rarrOrarr ararrDrarr glucoside
VaXa
eNOS caveolin-1 CaMeNOS Caveolin-1 CaM HSP90
eNOS caveolin-1
Na+
Ca2+ NH4+Na+
Ca2+
dimer FABP4
Glu
H+PALM
AMP
L-GlnGluL-Ala
Higherfattyacid
Inosinedeoxyinosine
THF
Ribose 1-phosphatedeoxyribose 1-phosphate
Hyp
Pi
2OG
TPN GluH+
Figure 5 The antipneumonia biological network of SHL
involved in the pathway parallelogram node represents com-plex hexagon node represents micromolecule and trianglenode represents biological reaction The edge with trianglearrow represents positive regulation edge with T-shapedarrow represents negative regulation and the undirected edgemeans the direction is uncertain (Figure 5) This biologicalnetwork which included 4 components 5 pneumonia relatedtargets and 26 subnetworks could overall exhibit the effectivecomponents and the mechanism of antipneumonia on amolecular level
This biological network included 26 subnetworks that4 components that acted on 5 pneumonia related targetsAll of these subnetworks intertwined to play the role ofantipneumonia collectively and demonstrated the features ofbiological systems simultaneously such as robustness redun-dancy crosstalk and so forth In order to clearly show theantipneumonia mechanism of SHL effective components wecould extracted 26 subnetworks respectivelyThis paper took2 extracted subnetworks as examples the biological pathwaywhere luteolin-7-o-120572-D-glucoside acted on serum albumin(Figure 6) and the biological pathway where dihydrooroxylinA acted on thrombin activation peptide (Figure 7)
As target of luteolin-7-o-120572-D-glucoside endothelial nitricoxide synthase (eNOS) translocated from Golgi to caveolaeafter N-myristoylation and palmitoylationWith depalmitoy-lation of eNOS dimer it produced PALM After the reactionof PALM and CoASH palmitic acid converted to palmitoyl-CoA accompanyied with energy transformation After aseries of signal transduction ofmicromolecule (NH4+ L-GlnNa+ etc) the content of serum albumin changed As thebiomarker in the early stage this pathway could elucidatethe course of the change That is luteolin-7-o-120572-D-glucosideacting on eNOS leads to the increase of vasopermeability
and serum albumin influxed into the interval of capillariesaccelerated the speed of catabolism and affected the contentof serum albumin at last [12 13]
Figure 7 shows the initial two steps of blood coagulationthe formation process of thrombin activation peptide andthe activation of thrombin As the target of dihydrooroxylinA adenosine aminohydrolase was hydrolyzed dephosphory-lated and oxidated After some amino acid was taken up andGluR2 transferred the Ca2+ impermeable AMPA receptorand aspartic acid receptor were activated and then extrudedof Ca2+ Factor Xa was activated by Ca2+ and Ca2+ alsocould accelerate the combination of factors Xa and Va [14]Factor Va had no activity itself but it could enhance activityof factor Xa and accelerated the formation of thrombin[15] Thrombin could accelerate the blood coagulation andwound healing thus treating alimentary tract hemorrhage ofsevere pneumonia In conclusion dihydrooroxylin A actingon thrombin plays the role of antipneumonia by acceleratingthe hemostasis of the alimentary tract
By summarizing the 26 subnetworks of SHL effectivecomponents cluster acting on pneumonia-related targets wegot 3 main pathways where SHL played the role of antip-neumonia (1) regulating the activity of caveolin-1 existingin the signal pathway of inflammatory and endothelial cellsaffects the response of inflammatory cell to the inflamma-tion further influencing the process of inflammation (2)accelerating the blood coagulation and wound healing thustreating alimentary tract hemorrhage of severe pneumonia(3) affecting the content of serum albumin promoting therepair of lung tissue and enhancing the immune function
Biological network shows 4 components could act on5 targets within 10 biological reactions Other componentsin SHL may also act on pneumonia-related targets but
The Scientific World Journal 7
AMP
PALM
L-Gln
Serum albumin
PalmitylatedN-myristoylated
eNOS
Nitricoxide
synthaseendothelial
Palmitoylatedmyristoylated
eNOS dimer
N-myristoylated eNOS (Gly2)
Na+
NH4+
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Figure 6 The antipneumonia biological pathway of luteolin-7-o-120572-D-glucoside
Ca impermeable
AMPA receptors
Glu
Adenosine aminohydrolase
DihydrooroxylinA
Inosinedeoxyinosine
Hyp
Ribose 1-phosphatedeoxyribose 1-phosphate
Pi
complex (prothrombinase)
Factor Xa
Thrombin activation
peptide
Va Xa
Na+Ca2+
Na+Ca2+
H+
Figure 7 The antipneumonia biological pathway of dihydrooroxylin A
8 The Scientific World Journal
the number of biological reactions will be more When wedefined the reactions as 15 biological network contained 5components and 9 pneumonia-related targets If the reactionwas 20 43 components and 13 targets were included in thebiological network The 4 components by contrast weremore quickly and efficiently acting on pneumonia-relatedtargets Compared with the components in SHL whichstudied frequently such as chlorogenic acid forsythin andbaicalin the content of four components within the networkwas lower but they may play the same role of pneumoniatreatment
4 Conclusion
Based on the public databases of TCM DrugBank databaseand directed TCM grammar systems we have built a PPInetwork drug target network and antipneumonia biologicalnetwork of SHL By the modules analysis we predicted thatSHL has the potential to be an antitumor candidate Thisresultmay provide a novel clue for further experimental stud-ies of SHL In future the predicted novel pharmacologicaleffects of SHL should be further validated from bench tobedside The antipneumonia biological network systemati-cally explained the reason why SHL could play the role ofantipneumonia and identified its effective components Allthese are helpful to guide the quality control and further studyof SHL
Studies have already demonstrated that SHL had thepharmacological actions of antimicrobial antiviral anti-pyretic anti-inflammatory antioxidant antiarrhythmic andenhanced immunity [16ndash19] but they only focused on indi-vidual component pharmacological action or pathway Thecomponent they studied could be extracted and was with ahigh content Compared with these studies our study couldelucidate the mechanism holistically and on the molecularlevel Meanwhile enclosing the synergistic effect of variouscomponents and the cross of pathways we not only addressedthat luteolin-7-120572-D-glucoside [20] dihydrooroxylin A [2122] and acteoside [23] played an anti-inflammatory role butalso predicted that isomenthone could act on pneumonia-related targets through biological network of SHL thusplaying the role of antipneumonia
The thought of this study accords with the networkpharmacology but the method we adopted is different fromother related works [24 25] The whole process of otherrelated works is carried out manually and the batch pro-cessing is impossible With the characteristic of flexibilitydTGS could solve these problems effectively Carrying out theTCM research under the guidance of network pharmacologyis more quick and systematic than traditional methodsMeanwhile dTGS provides a novel strategy for the study ofTCM and other complex systems
Because the research results were based on the inferenceof data included in the existing database or literature andbecause we do not take into account the quantity of compo-nents and the specific interactional environment thismethodstill has some limitations With further study of the complexsystems such as TCM formula and related disease the data
we used will be more complete and the results we got will bemore precise and integrity
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Authorsrsquo Contribution
Bai-xia Zhang Jian Li andHaoGu contributed equally to thiswork
Acknowledgments
This work was supported by National Science and Technol-ogy Major Projects for ldquomajor new drugs innovation anddevelopmentrdquo (Grant no 2011ZX09201-201-15) the NationalNatural Science Foundation of China (Grant nos 81173568and 81373985) and Program for New Century ExcellentTalents in University (Grant no NCET-11-0605)The fundershad no role in study design data collection and analysisdecision to publish or preparation of the paper
References
[1] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[2] X Chen H Zhou Y B Liu et al ldquoDatabase of traditionalChinese medicine and its application to studies of mechanismand to prescription validationrdquo British Journal of Pharmacologyvol 149 no 8 pp 1092ndash1103 2006
[3] Z L Ji H Zhou J F Wang L Y Han C J Zheng and YZ Chen ldquoTraditional Chinese medicine information databaserdquoJournal of Ethnopharmacology vol 103 no 3 501 pages 2006
[4] J Ye X Song Z Liu et al ldquoDevelopment of an LC-MS methodfor determination of three active constituents of Shuang-huang-lian injection in rat plasma and its application to the druginteraction study of Shuang-huang-lian freeze-dried powdercombined with levofloxacin injectionrdquo Journal of Chromatog-raphy B Analytical Technologies in the Biomedical and LifeSciences vol 898 pp 130ndash135 2012
[5] H Liu Y X Qiao B Liu and J J Zhou ldquoTransformation oftraditional Chinese medicine database into data warehouserdquoChinese Pharmaceutical Journal vol 9 pp 645ndash648 2006
[6] V Law C Knox Y Djoumbou et al ldquoDrugBank 40 sheddingnew light on drug metabolismrdquo Nucleic Acids Research vol 42no 1 pp D1091ndashD1097 2014
[7] D Croft A F Mundo R Haw et al ldquoThe Reactome pathwayknowledgebaserdquoNucleic Acids Research vol 42 no 1 ppD472ndashD477 2014
[8] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[9] L Ji R L Ren H Gu et al ldquodTGSmethod for effective compo-nents identification from traditional Chinese medicine formulaand mechanism analysisrdquo Evidence-Based Complementary andAlternativeMedicine vol 2013 Article ID 840427 9 pages 2013
The Scientific World Journal 9
[10] J Yan Y Wang S-J Luo and Y-J Qiao ldquoTCM grammarsystems an approach to aid the interpretation of the molecularinteractions in Chinese herbal medicinerdquo Journal of Ethnophar-macology vol 137 no 1 pp 77ndash84 2011
[11] W Yun ldquoEntity grammar systems a grammatical tool for study-ing the hierarchal structures of biological systemsrdquo Bulletin ofMathematical Biology vol 66 no 3 pp 447ndash471 2004
[12] B Ruot I Papet F Bechereau et al ldquoIncreased albumin plasmaefflux contributes to hypoalbuminemia only during earlyphase of sepsis in ratsrdquo The American Journal of PhysiologymdashRegulatory Integrative and Comparative Physiology vol 284 no3 pp R707ndashR713 2003
[13] J U Hedlund L-O Hansson and A B Ortqvist ldquoHypoal-buminemia in hospitalized patients with community-acquiredpneumoniardquo Archives of Internal Medicine vol 155 no 13 pp1438ndash1442 1995
[14] E Persson P J Hogg and J Stenflo ldquoEffects of Ca2+ bindingon the protease module of factor Xa and its interaction withfactor Va evidence for two Gla-independent Ca2+-binding sitesin factor Xardquo The Journal of Biological Chemistry vol 268 no30 pp 22531ndash22539 1993
[15] E A Norstroslashm S Tran M Steen and B Dahlback ldquoEffectsof factor Xa and protein S on the individual activated proteinC-mediated cleavages of coagulation factor Vardquo The Journal ofBiological Chemistry vol 281 no 42 pp 31486ndash31494 2006
[16] W Zhou X X Zhu A L Yin et al ldquoEffect of various absorptionenhancers based on tight junctions on the intestinal absorptionof forsythoside A in Shuang-Huang-Lian application to itsantivirus activityrdquo Pharmacognosy Magazine vol 10 no 37 pp9ndash17 2014
[17] X Gao M Guo Q Li et al ldquoPlasma metabolomic profiling toreveal antipyretic mechanism of Shuang-Huang-Lian injectionon yeast-induced pyrexia ratsrdquo PLoS ONE vol 9 no 6 ArticleID e100017 2014
[18] R Gao Y N Lin G Liang B Yu and Y Gao ldquoComparativepharmacokinetic study of chlorogenic acid after oral admin-istration of lonicerae japonicae flos and shuang-huang-lian innormal and febrile ratsrdquo Phytotherapy Research vol 28 no 1pp 144ndash147 2014
[19] Y Gao L Fang R Cai et al ldquoShuang-Huang-Lian exertsanti-inflammatory and anti-oxidative activities in lipopoly-saccharide-stimulated murine alveolar macrophagesrdquo Phy-tomedicine vol 21 no 4 pp 461ndash469 2014
[20] CM Park andY-S Song ldquoLuteolin and luteolin-7-O-glucosideinhibit lipopolysaccharide-induced inflammatory responsesthrough modulation of NF-120581BAp-1PI3K-AKT signaling cas-cades in RAW 2647 cellsrdquo Nutrition Research and Practice vol7 no 6 pp 423ndash429 2013
[21] H Lee Y O Kim H Kim et al ldquoFlavonoid wogonin frommedicinal herb is neuroprotective by inhibiting inflammatoryactivation of microgliardquo The FASEB Journal vol 17 no 13 pp1943ndash1944 2003
[22] Y-C Chen L-L Yang and T J-F Lee ldquoOroxylin A inhi-bition of lipopolysaccharide-induced iNOS and COX-2 geneexpression via suppression of nuclear factor-120581B activationrdquoBiochemical Pharmacology vol 59 no 11 pp 1445ndash1457 2000
[23] J He X-P Hu Y Zeng et al ldquoAdvanced research on acteosidefor chemistry and bioactivitiesrdquo Journal of Asian Natural Prod-ucts Research vol 13 no 5 pp 449ndash464 2011
[24] L An and F Feng ldquoNetwork pharmacology-based antioxi-dant effect study of Zhi-Zi-da-huang decoction for alcoholic
liver diseaserdquo Evidence-Based Complementary and AlternativeMedicine vol 2015 Article ID 492470 6 pages 2015
[25] F Zhao L Guochun Y Yang L Shi L Xu and L Yin ldquoA net-work pharmacology approach to determine active ingredientsand rationality of herb combinations of Modified-Simiaowanfor treatment of goutrdquo Journal of Ethnopharmacology vol 168pp 1ndash16 2015
The Scientific World Journal 3
(4) 119878 = 1198781cup 1198782
1198781is the set of entities with structure link(BD) in
background network for deduction 1198782is the starting
point of reasoning with structure herbX(A)
The 119881 119865 119875 and 119878 of the antipneumonia biological net-work is described by the following
pos neg 119884 isin 119885lowastIn(A) and out(B) A isin 119881
1 B isin 119881
2
link(AB 119883 119884) defines that A(protein) acts onB(protein) with an effect described in 119883 andthrough 119884 reactions so that the distance numberis 119884 If process happens in one reaction 119884 equals1 In in(A) and out(B) A represents the targets ofcompounds while B represents the pneumonia-related proteins totalnet(AB 119883 119884) represents thatA (target protein) affects B (pneumonia-relatedprotein) with an effect described in 119883 by reactions of119884 minet(AB 119883 119884) defines that A (target protein)can affect B (pneumonia-related protein) with aneffect described in119883 by multiple pathway but we justretain the shortest path with 119884 reactions
= 119873 + 1 119873 = 119884 minus F length(119884) rArr forward(CDE119872)1198751tags the starting point of derivation by in(A) from
link(AB 119883 119884) and the tagged link(AB 119883 119884) isnamed as totalnet(AB 119883 119884)119875
2cup1198753cup1198754cup1198755is the set
of rules to deduce the eventual effects and distances oftarget proteins to other downstream proteins in thenetwork In link(AB 119883 119884) totalnet(AB posD)and minnet(AB 119883 119884) ldquo119883rdquo and ldquoposrdquo and ldquo119884rdquo andldquoDrdquo represent the same data type respectively justbecause they located in the same position119875
2indicates
that if the effect of A on B is positive and theeffect of B on C is positive too then the effectof A on C is positive Meanwhile if A affects Bthrough D reactions and B affects C through Ereactions then the distance of A to C is D plus ESimilar derivations are defined in 119875
3 1198754 and 119875
5
They may be used as many times as necessary to thefinal pneumonia-related protein 119875
6is a rule used to
identify the shortest distance from a target protein toa pneumonia-related protein when the paths betweenthem are too complicated to analyze In 119875
6 if B is
a pneumonia-related protein in totalnet(AB 119883 119884)then minD totalnet(AB 119883 119884) = 119872 indicatesthat the shortest distance from A to B is119872 which isextracted by minnet(AB 119883119872) In the constructionof target network 119875
6will be used as many times
as necessary to the target protein pneumonia-relatedprotein pairs 119875
7cup 1198758cup 1198759cup 11987510cup 11987511
were used todescribe the detailed pathway from A to B with theclear steps of119884The forward(CDE119872)was the finalresult used to construct the network After connectingeach of the forward(CDE119872) we could get thedetailed pathway from A to B
(4) 119878 = 1198781cup 1198782
1198781is the set of entities with structure link(AB 119883 119884)
in background network for deduction 1198782is the set of
starting and end point proteins described by in(A)and out(B)
3 Results and Discussion
31 Topology Analysis of SHL PPI Network As shown inFigure 2 (clear node label can be seen in Figure 2) theSHL PPI network there are 1953 nodes and 3112 edges Thenetwork diameter is 12 which means the greatest distancebetween any pair of vertices is 12 The node degree distribu-tion indicated that the PPI of SHL followed the power lawwith a degree exponent of 0969 (1198772 = 0647) The Clus-tering coefficient is 0322 The connected component is 10Network centralization is 03112 And network heterogeneityas 6017 These common topological parameters suggestedthat the network exhibited scale-free property and modulararchitecture
4 The Scientific World Journal
Figure 2 PPI Network of SHL The components in SHL Network are yellow diamonds The targets are shown as blue squares In the PPInetwork there are 92 components (Supplementary Table 3) acting on 129 targets which interact with 1787 proteins
32 Drug-TargetNetwork In order to express the relationshipbetween SHL components more clearly we constructed adrug-target network of SHL As shown in Figure 3 we totallylabeled the 21 modules Most of them match the commontargets However it may be worth nothing that some noveltargets are detected such as thirteen components of themodule (6) act on the same targets PYGM which playan important role in regulation of cell cycle and cellularmacromoleculemetabolic processThese biological processesare closely related to cell proliferation and tumorigenesis(anticancer effect) Following the same strategy it is easyto help us to understand the functional classifications ofeach SHL component based on the modules in drug-targetnetwork
33 Pharmacological Effects Distribution of SHL In the PPINetwork of SHL we counted pharmacological effects of
all the proteins frequency statistical results are presentedin Figure 4 The results indicate that five in top ten phar-macological effects of SHL are linked with antineoplasticagents protein kinase inhibitors enzyme inhibitors growthinhibitors and phytogenic antineoplastic agents which sug-gested that SHLmight directed against tumor effect Further-more two pharmacological effects focused on antioxidantsand anti-inflammatory agents which could help tumor sup-pression For sure the novel pharmacological effects of SHLneed further empirical data form bench to bedside
34 The Anti-Pneumonia Mechanism of SHL Using the dataderived from the Reactome database as context we con-structed the biological network of the effective components ofSHL acting on the pneumonia related targets Circular noderepresents disease related targets diamond node representseffective components of SHL square node represents proteins
The Scientific World Journal 5
Quercetinrarr3rarr o rarr120573rarrDrarr glucoside
Q03736
ForsythialanA
MTP
DihydrooroxylinA Eriodictyol
SOAT2
DR4L2
UD3A1 Rivularin
SkullcapflavoneII
SkullcapflavoneI
HCK
ATPB
PK3CG
Chrysin
Q9AIU0
NorwogoninQ5G940
ForsythosideAIsomartynoside
Baicalein
PYGM
4-O-Caffeoylquinicacid
Oroxylin oroxylinA
Neobaicalein
5-Caffeoylquinicacid
LeucosceptosideA
Quercetin
ST17B
HIBCH
ATPA
ATPG
PIM1Wogonin
LuteolinCorymbosin
Geranial2-Pentadecanone
Cornoside
LYSCAT1A1
OctadecanoicacidAcetophenone
Butylatedhydroxyanisole ACO13
Phenethylalcohol
Cymene
p-cymene P03437
P26137Stigmasterol
RORA
120573-sitosterol
P00720
MIF
Caffeicacid
P16113
PYRD
Norlapachol
Q02768 Q3IWB0Q08210
PAEP S14L2
Palmiticacid
OPSDPPT1
TPPC3
GCH1
PNPH
P83812
P45563
Q9X1H9
MYP2
HNF4G
TRPA1
CP2C8
TRPM8ECE1
MyrtanolIsoborneol
GBB1
RASK
FNTA
Myrcene
RAE1
GBG1
PA2GDP0A433
Guanine
P0A9M5
Q84EX5
Q9X1T2
OPRKTRPV3
LALBA
Rengyol
PHOS
FNTB
PGTA
PGTB2
GDIA
Caryophyllene
120573-ocimene
DihydrobaicaleinP54965
P25553
COX7C COX5BCOX8A AK1C2
COX3 COX6C
COX2COX1
COX5A
SOAT1
Matairesinol
DimethylmatairesinolArctigenin
ForsythialanB
PRGR
COX7B
ETUD1
ERR3
Oleanolicacid
Pinoresinol
ESR1
Epipinoresinol
n-heneicosane
ERG7
120572-terpineol
Nonacosane
NCOA2P22637
ST2A1
ST2B1DHB1
P33517
P07445
Phillygenol
Ursolicacid
Q48473
KAPCAGLTP
Q8ZRP8
Q7KZA3
PA21BFABP6
COX41NR1H4
2120572-hydroxybetulinicacid
Betulinicacid
CX7A1HEMHCX6A2
ADH1G
P31224
Q8GGK7
EST1CX6B1
Isomenthone
Camphene
Isichlorogenticacid
45-Dicaffeoylquinicacid
Menthone
P00183
ForsythosideB
Camphor
Borneol
Linolenyalcohol
FADS2
PGH2
ELOV4
FADS1
Cynarin
Acteoside
CDK1Wogonoside
CDK8CDK4CDK6
PGH1
TRPV1
NAC1
ACM2 ACHA2
SuspensineA
LonicerinBaicalin
ACES 5HT3A
Arctiin
TOP2A
Matairesionoside
Phillyrin
Astragalin
Chlorogenic
IsochlorogenicacidB
CDK2
CDK5 CDK7
CDK9
EGFR Hyperoside
AK1C3
Rutin
Isoquercetin
Wogonin-7-120573-D-glcUA
Pinoresinol-120573-D-glucoside
7-Methoxybaicalein
(-)Bicuculline
(-)Egenine
(1) (3)(2)(4) (5)
(6) (8)(7)(10)(9) (11)
(12)(13)
(14) (15) (16) (17) (18) (19) (20)(21)
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Luteolinrarr7rarrOrarr120573rarrDrarr glucoside
3572998400-Tetrahydroxyavone
572998400-Trihydroxyflavone
5-Hydroxy-74998400- dimethoxyflavone
(-)-7998400-O-Methylegenine
Figure 3 Drug-target Network of SHL The components are yellow diamonds The targets are shown as blue squares
Ant
ineo
plas
tic ag
ents
Ana
lges
ics
nonn
arco
ticA
ntia
nxie
ty ag
ents
GA
BA an
tago
nists
Sym
path
omim
etic
sAd
juva
nts
anes
thes
iaA
ntic
hole
stere
mic
agen
tsSy
mpa
thom
imet
icA
ntifu
ngal
agen
tsA
ntid
epre
ssiv
e age
nts
seco
nd-g
ener
atio
nEx
cita
tory
amin
o ac
id an
tago
nists
Card
iova
scul
ar ag
ents
Ant
ispas
mod
ics
Ant
inar
cotic
agen
tsO
piat
e ant
agon
ists
Tryp
anoc
idal
agen
tsRe
nal a
gent
sA
ntim
usca
rinic
sD
iagn
ostic
agen
tsD
opam
ine u
ptak
e inh
ibito
rsA
ntic
holin
ergi
c age
nts
Lipo
xyge
nase
inhi
bito
rsC
ofac
tor
Nep
hrop
athi
c cys
tinos
is th
erap
yH
epar
ins
Ant
i-HIV
agen
tsPs
ycho
tropi
c dru
gsVi
tam
in D
3 re
cept
or in
hibi
tor
Enzy
me r
epla
cem
ent a
gent
sVi
tam
ins (
vita
min
D)
Fert
ility
agen
tsLe
ukot
riene
anta
goni
stsFr
ibic
acid
der
ivat
ives
Cor
ticos
tero
idA
mph
etam
ines
Alp
ha-a
dren
ergi
c blo
ckin
g ag
ents
Col
orin
g ag
ents
Mon
oam
ine o
xida
se in
hibi
tors
Pharmacological effects distribution
0
10
20
30
40
50
60
70
80
Figure 4 The pharmacological distribution of all 112 components in SHL
6 The Scientific World Journal
Palmitoylatedmyristoylated
eNOSdimer
Serumalbumin
PalmitylatedN-Myristoylated
eNOS
N-myristoylated eNOS(Gly2)
Aldehyde reductase
Nitricoxide
synthaseendothelial
Isomenthone
Ca(4)CaM Caveolin-1
PhosphorylatedHSL
complex
Fattyacid
bindingprotein
adipocyte
Thrombin activation
peptide
DihydrooroxylinA
Adenosine aminohydrolase
Factor IX
activation peptide
complex (prothrombinase)
Acteoside
Dihydrofolate reductase
FactorXa
Caimpermeable
AMPAreceptors
Factor VIIIa
B A3
acidic polypeptide
Activated thrombin
(factorIIa)
Luteolinrarr7rarrOrarr ararrDrarr glucoside
VaXa
eNOS caveolin-1 CaMeNOS Caveolin-1 CaM HSP90
eNOS caveolin-1
Na+
Ca2+ NH4+Na+
Ca2+
dimer FABP4
Glu
H+PALM
AMP
L-GlnGluL-Ala
Higherfattyacid
Inosinedeoxyinosine
THF
Ribose 1-phosphatedeoxyribose 1-phosphate
Hyp
Pi
2OG
TPN GluH+
Figure 5 The antipneumonia biological network of SHL
involved in the pathway parallelogram node represents com-plex hexagon node represents micromolecule and trianglenode represents biological reaction The edge with trianglearrow represents positive regulation edge with T-shapedarrow represents negative regulation and the undirected edgemeans the direction is uncertain (Figure 5) This biologicalnetwork which included 4 components 5 pneumonia relatedtargets and 26 subnetworks could overall exhibit the effectivecomponents and the mechanism of antipneumonia on amolecular level
This biological network included 26 subnetworks that4 components that acted on 5 pneumonia related targetsAll of these subnetworks intertwined to play the role ofantipneumonia collectively and demonstrated the features ofbiological systems simultaneously such as robustness redun-dancy crosstalk and so forth In order to clearly show theantipneumonia mechanism of SHL effective components wecould extracted 26 subnetworks respectivelyThis paper took2 extracted subnetworks as examples the biological pathwaywhere luteolin-7-o-120572-D-glucoside acted on serum albumin(Figure 6) and the biological pathway where dihydrooroxylinA acted on thrombin activation peptide (Figure 7)
As target of luteolin-7-o-120572-D-glucoside endothelial nitricoxide synthase (eNOS) translocated from Golgi to caveolaeafter N-myristoylation and palmitoylationWith depalmitoy-lation of eNOS dimer it produced PALM After the reactionof PALM and CoASH palmitic acid converted to palmitoyl-CoA accompanyied with energy transformation After aseries of signal transduction ofmicromolecule (NH4+ L-GlnNa+ etc) the content of serum albumin changed As thebiomarker in the early stage this pathway could elucidatethe course of the change That is luteolin-7-o-120572-D-glucosideacting on eNOS leads to the increase of vasopermeability
and serum albumin influxed into the interval of capillariesaccelerated the speed of catabolism and affected the contentof serum albumin at last [12 13]
Figure 7 shows the initial two steps of blood coagulationthe formation process of thrombin activation peptide andthe activation of thrombin As the target of dihydrooroxylinA adenosine aminohydrolase was hydrolyzed dephosphory-lated and oxidated After some amino acid was taken up andGluR2 transferred the Ca2+ impermeable AMPA receptorand aspartic acid receptor were activated and then extrudedof Ca2+ Factor Xa was activated by Ca2+ and Ca2+ alsocould accelerate the combination of factors Xa and Va [14]Factor Va had no activity itself but it could enhance activityof factor Xa and accelerated the formation of thrombin[15] Thrombin could accelerate the blood coagulation andwound healing thus treating alimentary tract hemorrhage ofsevere pneumonia In conclusion dihydrooroxylin A actingon thrombin plays the role of antipneumonia by acceleratingthe hemostasis of the alimentary tract
By summarizing the 26 subnetworks of SHL effectivecomponents cluster acting on pneumonia-related targets wegot 3 main pathways where SHL played the role of antip-neumonia (1) regulating the activity of caveolin-1 existingin the signal pathway of inflammatory and endothelial cellsaffects the response of inflammatory cell to the inflamma-tion further influencing the process of inflammation (2)accelerating the blood coagulation and wound healing thustreating alimentary tract hemorrhage of severe pneumonia(3) affecting the content of serum albumin promoting therepair of lung tissue and enhancing the immune function
Biological network shows 4 components could act on5 targets within 10 biological reactions Other componentsin SHL may also act on pneumonia-related targets but
The Scientific World Journal 7
AMP
PALM
L-Gln
Serum albumin
PalmitylatedN-myristoylated
eNOS
Nitricoxide
synthaseendothelial
Palmitoylatedmyristoylated
eNOS dimer
N-myristoylated eNOS (Gly2)
Na+
NH4+
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Figure 6 The antipneumonia biological pathway of luteolin-7-o-120572-D-glucoside
Ca impermeable
AMPA receptors
Glu
Adenosine aminohydrolase
DihydrooroxylinA
Inosinedeoxyinosine
Hyp
Ribose 1-phosphatedeoxyribose 1-phosphate
Pi
complex (prothrombinase)
Factor Xa
Thrombin activation
peptide
Va Xa
Na+Ca2+
Na+Ca2+
H+
Figure 7 The antipneumonia biological pathway of dihydrooroxylin A
8 The Scientific World Journal
the number of biological reactions will be more When wedefined the reactions as 15 biological network contained 5components and 9 pneumonia-related targets If the reactionwas 20 43 components and 13 targets were included in thebiological network The 4 components by contrast weremore quickly and efficiently acting on pneumonia-relatedtargets Compared with the components in SHL whichstudied frequently such as chlorogenic acid forsythin andbaicalin the content of four components within the networkwas lower but they may play the same role of pneumoniatreatment
4 Conclusion
Based on the public databases of TCM DrugBank databaseand directed TCM grammar systems we have built a PPInetwork drug target network and antipneumonia biologicalnetwork of SHL By the modules analysis we predicted thatSHL has the potential to be an antitumor candidate Thisresultmay provide a novel clue for further experimental stud-ies of SHL In future the predicted novel pharmacologicaleffects of SHL should be further validated from bench tobedside The antipneumonia biological network systemati-cally explained the reason why SHL could play the role ofantipneumonia and identified its effective components Allthese are helpful to guide the quality control and further studyof SHL
Studies have already demonstrated that SHL had thepharmacological actions of antimicrobial antiviral anti-pyretic anti-inflammatory antioxidant antiarrhythmic andenhanced immunity [16ndash19] but they only focused on indi-vidual component pharmacological action or pathway Thecomponent they studied could be extracted and was with ahigh content Compared with these studies our study couldelucidate the mechanism holistically and on the molecularlevel Meanwhile enclosing the synergistic effect of variouscomponents and the cross of pathways we not only addressedthat luteolin-7-120572-D-glucoside [20] dihydrooroxylin A [2122] and acteoside [23] played an anti-inflammatory role butalso predicted that isomenthone could act on pneumonia-related targets through biological network of SHL thusplaying the role of antipneumonia
The thought of this study accords with the networkpharmacology but the method we adopted is different fromother related works [24 25] The whole process of otherrelated works is carried out manually and the batch pro-cessing is impossible With the characteristic of flexibilitydTGS could solve these problems effectively Carrying out theTCM research under the guidance of network pharmacologyis more quick and systematic than traditional methodsMeanwhile dTGS provides a novel strategy for the study ofTCM and other complex systems
Because the research results were based on the inferenceof data included in the existing database or literature andbecause we do not take into account the quantity of compo-nents and the specific interactional environment thismethodstill has some limitations With further study of the complexsystems such as TCM formula and related disease the data
we used will be more complete and the results we got will bemore precise and integrity
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Authorsrsquo Contribution
Bai-xia Zhang Jian Li andHaoGu contributed equally to thiswork
Acknowledgments
This work was supported by National Science and Technol-ogy Major Projects for ldquomajor new drugs innovation anddevelopmentrdquo (Grant no 2011ZX09201-201-15) the NationalNatural Science Foundation of China (Grant nos 81173568and 81373985) and Program for New Century ExcellentTalents in University (Grant no NCET-11-0605)The fundershad no role in study design data collection and analysisdecision to publish or preparation of the paper
References
[1] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[2] X Chen H Zhou Y B Liu et al ldquoDatabase of traditionalChinese medicine and its application to studies of mechanismand to prescription validationrdquo British Journal of Pharmacologyvol 149 no 8 pp 1092ndash1103 2006
[3] Z L Ji H Zhou J F Wang L Y Han C J Zheng and YZ Chen ldquoTraditional Chinese medicine information databaserdquoJournal of Ethnopharmacology vol 103 no 3 501 pages 2006
[4] J Ye X Song Z Liu et al ldquoDevelopment of an LC-MS methodfor determination of three active constituents of Shuang-huang-lian injection in rat plasma and its application to the druginteraction study of Shuang-huang-lian freeze-dried powdercombined with levofloxacin injectionrdquo Journal of Chromatog-raphy B Analytical Technologies in the Biomedical and LifeSciences vol 898 pp 130ndash135 2012
[5] H Liu Y X Qiao B Liu and J J Zhou ldquoTransformation oftraditional Chinese medicine database into data warehouserdquoChinese Pharmaceutical Journal vol 9 pp 645ndash648 2006
[6] V Law C Knox Y Djoumbou et al ldquoDrugBank 40 sheddingnew light on drug metabolismrdquo Nucleic Acids Research vol 42no 1 pp D1091ndashD1097 2014
[7] D Croft A F Mundo R Haw et al ldquoThe Reactome pathwayknowledgebaserdquoNucleic Acids Research vol 42 no 1 ppD472ndashD477 2014
[8] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[9] L Ji R L Ren H Gu et al ldquodTGSmethod for effective compo-nents identification from traditional Chinese medicine formulaand mechanism analysisrdquo Evidence-Based Complementary andAlternativeMedicine vol 2013 Article ID 840427 9 pages 2013
The Scientific World Journal 9
[10] J Yan Y Wang S-J Luo and Y-J Qiao ldquoTCM grammarsystems an approach to aid the interpretation of the molecularinteractions in Chinese herbal medicinerdquo Journal of Ethnophar-macology vol 137 no 1 pp 77ndash84 2011
[11] W Yun ldquoEntity grammar systems a grammatical tool for study-ing the hierarchal structures of biological systemsrdquo Bulletin ofMathematical Biology vol 66 no 3 pp 447ndash471 2004
[12] B Ruot I Papet F Bechereau et al ldquoIncreased albumin plasmaefflux contributes to hypoalbuminemia only during earlyphase of sepsis in ratsrdquo The American Journal of PhysiologymdashRegulatory Integrative and Comparative Physiology vol 284 no3 pp R707ndashR713 2003
[13] J U Hedlund L-O Hansson and A B Ortqvist ldquoHypoal-buminemia in hospitalized patients with community-acquiredpneumoniardquo Archives of Internal Medicine vol 155 no 13 pp1438ndash1442 1995
[14] E Persson P J Hogg and J Stenflo ldquoEffects of Ca2+ bindingon the protease module of factor Xa and its interaction withfactor Va evidence for two Gla-independent Ca2+-binding sitesin factor Xardquo The Journal of Biological Chemistry vol 268 no30 pp 22531ndash22539 1993
[15] E A Norstroslashm S Tran M Steen and B Dahlback ldquoEffectsof factor Xa and protein S on the individual activated proteinC-mediated cleavages of coagulation factor Vardquo The Journal ofBiological Chemistry vol 281 no 42 pp 31486ndash31494 2006
[16] W Zhou X X Zhu A L Yin et al ldquoEffect of various absorptionenhancers based on tight junctions on the intestinal absorptionof forsythoside A in Shuang-Huang-Lian application to itsantivirus activityrdquo Pharmacognosy Magazine vol 10 no 37 pp9ndash17 2014
[17] X Gao M Guo Q Li et al ldquoPlasma metabolomic profiling toreveal antipyretic mechanism of Shuang-Huang-Lian injectionon yeast-induced pyrexia ratsrdquo PLoS ONE vol 9 no 6 ArticleID e100017 2014
[18] R Gao Y N Lin G Liang B Yu and Y Gao ldquoComparativepharmacokinetic study of chlorogenic acid after oral admin-istration of lonicerae japonicae flos and shuang-huang-lian innormal and febrile ratsrdquo Phytotherapy Research vol 28 no 1pp 144ndash147 2014
[19] Y Gao L Fang R Cai et al ldquoShuang-Huang-Lian exertsanti-inflammatory and anti-oxidative activities in lipopoly-saccharide-stimulated murine alveolar macrophagesrdquo Phy-tomedicine vol 21 no 4 pp 461ndash469 2014
[20] CM Park andY-S Song ldquoLuteolin and luteolin-7-O-glucosideinhibit lipopolysaccharide-induced inflammatory responsesthrough modulation of NF-120581BAp-1PI3K-AKT signaling cas-cades in RAW 2647 cellsrdquo Nutrition Research and Practice vol7 no 6 pp 423ndash429 2013
[21] H Lee Y O Kim H Kim et al ldquoFlavonoid wogonin frommedicinal herb is neuroprotective by inhibiting inflammatoryactivation of microgliardquo The FASEB Journal vol 17 no 13 pp1943ndash1944 2003
[22] Y-C Chen L-L Yang and T J-F Lee ldquoOroxylin A inhi-bition of lipopolysaccharide-induced iNOS and COX-2 geneexpression via suppression of nuclear factor-120581B activationrdquoBiochemical Pharmacology vol 59 no 11 pp 1445ndash1457 2000
[23] J He X-P Hu Y Zeng et al ldquoAdvanced research on acteosidefor chemistry and bioactivitiesrdquo Journal of Asian Natural Prod-ucts Research vol 13 no 5 pp 449ndash464 2011
[24] L An and F Feng ldquoNetwork pharmacology-based antioxi-dant effect study of Zhi-Zi-da-huang decoction for alcoholic
liver diseaserdquo Evidence-Based Complementary and AlternativeMedicine vol 2015 Article ID 492470 6 pages 2015
[25] F Zhao L Guochun Y Yang L Shi L Xu and L Yin ldquoA net-work pharmacology approach to determine active ingredientsand rationality of herb combinations of Modified-Simiaowanfor treatment of goutrdquo Journal of Ethnopharmacology vol 168pp 1ndash16 2015
4 The Scientific World Journal
Figure 2 PPI Network of SHL The components in SHL Network are yellow diamonds The targets are shown as blue squares In the PPInetwork there are 92 components (Supplementary Table 3) acting on 129 targets which interact with 1787 proteins
32 Drug-TargetNetwork In order to express the relationshipbetween SHL components more clearly we constructed adrug-target network of SHL As shown in Figure 3 we totallylabeled the 21 modules Most of them match the commontargets However it may be worth nothing that some noveltargets are detected such as thirteen components of themodule (6) act on the same targets PYGM which playan important role in regulation of cell cycle and cellularmacromoleculemetabolic processThese biological processesare closely related to cell proliferation and tumorigenesis(anticancer effect) Following the same strategy it is easyto help us to understand the functional classifications ofeach SHL component based on the modules in drug-targetnetwork
33 Pharmacological Effects Distribution of SHL In the PPINetwork of SHL we counted pharmacological effects of
all the proteins frequency statistical results are presentedin Figure 4 The results indicate that five in top ten phar-macological effects of SHL are linked with antineoplasticagents protein kinase inhibitors enzyme inhibitors growthinhibitors and phytogenic antineoplastic agents which sug-gested that SHLmight directed against tumor effect Further-more two pharmacological effects focused on antioxidantsand anti-inflammatory agents which could help tumor sup-pression For sure the novel pharmacological effects of SHLneed further empirical data form bench to bedside
34 The Anti-Pneumonia Mechanism of SHL Using the dataderived from the Reactome database as context we con-structed the biological network of the effective components ofSHL acting on the pneumonia related targets Circular noderepresents disease related targets diamond node representseffective components of SHL square node represents proteins
The Scientific World Journal 5
Quercetinrarr3rarr o rarr120573rarrDrarr glucoside
Q03736
ForsythialanA
MTP
DihydrooroxylinA Eriodictyol
SOAT2
DR4L2
UD3A1 Rivularin
SkullcapflavoneII
SkullcapflavoneI
HCK
ATPB
PK3CG
Chrysin
Q9AIU0
NorwogoninQ5G940
ForsythosideAIsomartynoside
Baicalein
PYGM
4-O-Caffeoylquinicacid
Oroxylin oroxylinA
Neobaicalein
5-Caffeoylquinicacid
LeucosceptosideA
Quercetin
ST17B
HIBCH
ATPA
ATPG
PIM1Wogonin
LuteolinCorymbosin
Geranial2-Pentadecanone
Cornoside
LYSCAT1A1
OctadecanoicacidAcetophenone
Butylatedhydroxyanisole ACO13
Phenethylalcohol
Cymene
p-cymene P03437
P26137Stigmasterol
RORA
120573-sitosterol
P00720
MIF
Caffeicacid
P16113
PYRD
Norlapachol
Q02768 Q3IWB0Q08210
PAEP S14L2
Palmiticacid
OPSDPPT1
TPPC3
GCH1
PNPH
P83812
P45563
Q9X1H9
MYP2
HNF4G
TRPA1
CP2C8
TRPM8ECE1
MyrtanolIsoborneol
GBB1
RASK
FNTA
Myrcene
RAE1
GBG1
PA2GDP0A433
Guanine
P0A9M5
Q84EX5
Q9X1T2
OPRKTRPV3
LALBA
Rengyol
PHOS
FNTB
PGTA
PGTB2
GDIA
Caryophyllene
120573-ocimene
DihydrobaicaleinP54965
P25553
COX7C COX5BCOX8A AK1C2
COX3 COX6C
COX2COX1
COX5A
SOAT1
Matairesinol
DimethylmatairesinolArctigenin
ForsythialanB
PRGR
COX7B
ETUD1
ERR3
Oleanolicacid
Pinoresinol
ESR1
Epipinoresinol
n-heneicosane
ERG7
120572-terpineol
Nonacosane
NCOA2P22637
ST2A1
ST2B1DHB1
P33517
P07445
Phillygenol
Ursolicacid
Q48473
KAPCAGLTP
Q8ZRP8
Q7KZA3
PA21BFABP6
COX41NR1H4
2120572-hydroxybetulinicacid
Betulinicacid
CX7A1HEMHCX6A2
ADH1G
P31224
Q8GGK7
EST1CX6B1
Isomenthone
Camphene
Isichlorogenticacid
45-Dicaffeoylquinicacid
Menthone
P00183
ForsythosideB
Camphor
Borneol
Linolenyalcohol
FADS2
PGH2
ELOV4
FADS1
Cynarin
Acteoside
CDK1Wogonoside
CDK8CDK4CDK6
PGH1
TRPV1
NAC1
ACM2 ACHA2
SuspensineA
LonicerinBaicalin
ACES 5HT3A
Arctiin
TOP2A
Matairesionoside
Phillyrin
Astragalin
Chlorogenic
IsochlorogenicacidB
CDK2
CDK5 CDK7
CDK9
EGFR Hyperoside
AK1C3
Rutin
Isoquercetin
Wogonin-7-120573-D-glcUA
Pinoresinol-120573-D-glucoside
7-Methoxybaicalein
(-)Bicuculline
(-)Egenine
(1) (3)(2)(4) (5)
(6) (8)(7)(10)(9) (11)
(12)(13)
(14) (15) (16) (17) (18) (19) (20)(21)
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Luteolinrarr7rarrOrarr120573rarrDrarr glucoside
3572998400-Tetrahydroxyavone
572998400-Trihydroxyflavone
5-Hydroxy-74998400- dimethoxyflavone
(-)-7998400-O-Methylegenine
Figure 3 Drug-target Network of SHL The components are yellow diamonds The targets are shown as blue squares
Ant
ineo
plas
tic ag
ents
Ana
lges
ics
nonn
arco
ticA
ntia
nxie
ty ag
ents
GA
BA an
tago
nists
Sym
path
omim
etic
sAd
juva
nts
anes
thes
iaA
ntic
hole
stere
mic
agen
tsSy
mpa
thom
imet
icA
ntifu
ngal
agen
tsA
ntid
epre
ssiv
e age
nts
seco
nd-g
ener
atio
nEx
cita
tory
amin
o ac
id an
tago
nists
Card
iova
scul
ar ag
ents
Ant
ispas
mod
ics
Ant
inar
cotic
agen
tsO
piat
e ant
agon
ists
Tryp
anoc
idal
agen
tsRe
nal a
gent
sA
ntim
usca
rinic
sD
iagn
ostic
agen
tsD
opam
ine u
ptak
e inh
ibito
rsA
ntic
holin
ergi
c age
nts
Lipo
xyge
nase
inhi
bito
rsC
ofac
tor
Nep
hrop
athi
c cys
tinos
is th
erap
yH
epar
ins
Ant
i-HIV
agen
tsPs
ycho
tropi
c dru
gsVi
tam
in D
3 re
cept
or in
hibi
tor
Enzy
me r
epla
cem
ent a
gent
sVi
tam
ins (
vita
min
D)
Fert
ility
agen
tsLe
ukot
riene
anta
goni
stsFr
ibic
acid
der
ivat
ives
Cor
ticos
tero
idA
mph
etam
ines
Alp
ha-a
dren
ergi
c blo
ckin
g ag
ents
Col
orin
g ag
ents
Mon
oam
ine o
xida
se in
hibi
tors
Pharmacological effects distribution
0
10
20
30
40
50
60
70
80
Figure 4 The pharmacological distribution of all 112 components in SHL
6 The Scientific World Journal
Palmitoylatedmyristoylated
eNOSdimer
Serumalbumin
PalmitylatedN-Myristoylated
eNOS
N-myristoylated eNOS(Gly2)
Aldehyde reductase
Nitricoxide
synthaseendothelial
Isomenthone
Ca(4)CaM Caveolin-1
PhosphorylatedHSL
complex
Fattyacid
bindingprotein
adipocyte
Thrombin activation
peptide
DihydrooroxylinA
Adenosine aminohydrolase
Factor IX
activation peptide
complex (prothrombinase)
Acteoside
Dihydrofolate reductase
FactorXa
Caimpermeable
AMPAreceptors
Factor VIIIa
B A3
acidic polypeptide
Activated thrombin
(factorIIa)
Luteolinrarr7rarrOrarr ararrDrarr glucoside
VaXa
eNOS caveolin-1 CaMeNOS Caveolin-1 CaM HSP90
eNOS caveolin-1
Na+
Ca2+ NH4+Na+
Ca2+
dimer FABP4
Glu
H+PALM
AMP
L-GlnGluL-Ala
Higherfattyacid
Inosinedeoxyinosine
THF
Ribose 1-phosphatedeoxyribose 1-phosphate
Hyp
Pi
2OG
TPN GluH+
Figure 5 The antipneumonia biological network of SHL
involved in the pathway parallelogram node represents com-plex hexagon node represents micromolecule and trianglenode represents biological reaction The edge with trianglearrow represents positive regulation edge with T-shapedarrow represents negative regulation and the undirected edgemeans the direction is uncertain (Figure 5) This biologicalnetwork which included 4 components 5 pneumonia relatedtargets and 26 subnetworks could overall exhibit the effectivecomponents and the mechanism of antipneumonia on amolecular level
This biological network included 26 subnetworks that4 components that acted on 5 pneumonia related targetsAll of these subnetworks intertwined to play the role ofantipneumonia collectively and demonstrated the features ofbiological systems simultaneously such as robustness redun-dancy crosstalk and so forth In order to clearly show theantipneumonia mechanism of SHL effective components wecould extracted 26 subnetworks respectivelyThis paper took2 extracted subnetworks as examples the biological pathwaywhere luteolin-7-o-120572-D-glucoside acted on serum albumin(Figure 6) and the biological pathway where dihydrooroxylinA acted on thrombin activation peptide (Figure 7)
As target of luteolin-7-o-120572-D-glucoside endothelial nitricoxide synthase (eNOS) translocated from Golgi to caveolaeafter N-myristoylation and palmitoylationWith depalmitoy-lation of eNOS dimer it produced PALM After the reactionof PALM and CoASH palmitic acid converted to palmitoyl-CoA accompanyied with energy transformation After aseries of signal transduction ofmicromolecule (NH4+ L-GlnNa+ etc) the content of serum albumin changed As thebiomarker in the early stage this pathway could elucidatethe course of the change That is luteolin-7-o-120572-D-glucosideacting on eNOS leads to the increase of vasopermeability
and serum albumin influxed into the interval of capillariesaccelerated the speed of catabolism and affected the contentof serum albumin at last [12 13]
Figure 7 shows the initial two steps of blood coagulationthe formation process of thrombin activation peptide andthe activation of thrombin As the target of dihydrooroxylinA adenosine aminohydrolase was hydrolyzed dephosphory-lated and oxidated After some amino acid was taken up andGluR2 transferred the Ca2+ impermeable AMPA receptorand aspartic acid receptor were activated and then extrudedof Ca2+ Factor Xa was activated by Ca2+ and Ca2+ alsocould accelerate the combination of factors Xa and Va [14]Factor Va had no activity itself but it could enhance activityof factor Xa and accelerated the formation of thrombin[15] Thrombin could accelerate the blood coagulation andwound healing thus treating alimentary tract hemorrhage ofsevere pneumonia In conclusion dihydrooroxylin A actingon thrombin plays the role of antipneumonia by acceleratingthe hemostasis of the alimentary tract
By summarizing the 26 subnetworks of SHL effectivecomponents cluster acting on pneumonia-related targets wegot 3 main pathways where SHL played the role of antip-neumonia (1) regulating the activity of caveolin-1 existingin the signal pathway of inflammatory and endothelial cellsaffects the response of inflammatory cell to the inflamma-tion further influencing the process of inflammation (2)accelerating the blood coagulation and wound healing thustreating alimentary tract hemorrhage of severe pneumonia(3) affecting the content of serum albumin promoting therepair of lung tissue and enhancing the immune function
Biological network shows 4 components could act on5 targets within 10 biological reactions Other componentsin SHL may also act on pneumonia-related targets but
The Scientific World Journal 7
AMP
PALM
L-Gln
Serum albumin
PalmitylatedN-myristoylated
eNOS
Nitricoxide
synthaseendothelial
Palmitoylatedmyristoylated
eNOS dimer
N-myristoylated eNOS (Gly2)
Na+
NH4+
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Figure 6 The antipneumonia biological pathway of luteolin-7-o-120572-D-glucoside
Ca impermeable
AMPA receptors
Glu
Adenosine aminohydrolase
DihydrooroxylinA
Inosinedeoxyinosine
Hyp
Ribose 1-phosphatedeoxyribose 1-phosphate
Pi
complex (prothrombinase)
Factor Xa
Thrombin activation
peptide
Va Xa
Na+Ca2+
Na+Ca2+
H+
Figure 7 The antipneumonia biological pathway of dihydrooroxylin A
8 The Scientific World Journal
the number of biological reactions will be more When wedefined the reactions as 15 biological network contained 5components and 9 pneumonia-related targets If the reactionwas 20 43 components and 13 targets were included in thebiological network The 4 components by contrast weremore quickly and efficiently acting on pneumonia-relatedtargets Compared with the components in SHL whichstudied frequently such as chlorogenic acid forsythin andbaicalin the content of four components within the networkwas lower but they may play the same role of pneumoniatreatment
4 Conclusion
Based on the public databases of TCM DrugBank databaseand directed TCM grammar systems we have built a PPInetwork drug target network and antipneumonia biologicalnetwork of SHL By the modules analysis we predicted thatSHL has the potential to be an antitumor candidate Thisresultmay provide a novel clue for further experimental stud-ies of SHL In future the predicted novel pharmacologicaleffects of SHL should be further validated from bench tobedside The antipneumonia biological network systemati-cally explained the reason why SHL could play the role ofantipneumonia and identified its effective components Allthese are helpful to guide the quality control and further studyof SHL
Studies have already demonstrated that SHL had thepharmacological actions of antimicrobial antiviral anti-pyretic anti-inflammatory antioxidant antiarrhythmic andenhanced immunity [16ndash19] but they only focused on indi-vidual component pharmacological action or pathway Thecomponent they studied could be extracted and was with ahigh content Compared with these studies our study couldelucidate the mechanism holistically and on the molecularlevel Meanwhile enclosing the synergistic effect of variouscomponents and the cross of pathways we not only addressedthat luteolin-7-120572-D-glucoside [20] dihydrooroxylin A [2122] and acteoside [23] played an anti-inflammatory role butalso predicted that isomenthone could act on pneumonia-related targets through biological network of SHL thusplaying the role of antipneumonia
The thought of this study accords with the networkpharmacology but the method we adopted is different fromother related works [24 25] The whole process of otherrelated works is carried out manually and the batch pro-cessing is impossible With the characteristic of flexibilitydTGS could solve these problems effectively Carrying out theTCM research under the guidance of network pharmacologyis more quick and systematic than traditional methodsMeanwhile dTGS provides a novel strategy for the study ofTCM and other complex systems
Because the research results were based on the inferenceof data included in the existing database or literature andbecause we do not take into account the quantity of compo-nents and the specific interactional environment thismethodstill has some limitations With further study of the complexsystems such as TCM formula and related disease the data
we used will be more complete and the results we got will bemore precise and integrity
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Authorsrsquo Contribution
Bai-xia Zhang Jian Li andHaoGu contributed equally to thiswork
Acknowledgments
This work was supported by National Science and Technol-ogy Major Projects for ldquomajor new drugs innovation anddevelopmentrdquo (Grant no 2011ZX09201-201-15) the NationalNatural Science Foundation of China (Grant nos 81173568and 81373985) and Program for New Century ExcellentTalents in University (Grant no NCET-11-0605)The fundershad no role in study design data collection and analysisdecision to publish or preparation of the paper
References
[1] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[2] X Chen H Zhou Y B Liu et al ldquoDatabase of traditionalChinese medicine and its application to studies of mechanismand to prescription validationrdquo British Journal of Pharmacologyvol 149 no 8 pp 1092ndash1103 2006
[3] Z L Ji H Zhou J F Wang L Y Han C J Zheng and YZ Chen ldquoTraditional Chinese medicine information databaserdquoJournal of Ethnopharmacology vol 103 no 3 501 pages 2006
[4] J Ye X Song Z Liu et al ldquoDevelopment of an LC-MS methodfor determination of three active constituents of Shuang-huang-lian injection in rat plasma and its application to the druginteraction study of Shuang-huang-lian freeze-dried powdercombined with levofloxacin injectionrdquo Journal of Chromatog-raphy B Analytical Technologies in the Biomedical and LifeSciences vol 898 pp 130ndash135 2012
[5] H Liu Y X Qiao B Liu and J J Zhou ldquoTransformation oftraditional Chinese medicine database into data warehouserdquoChinese Pharmaceutical Journal vol 9 pp 645ndash648 2006
[6] V Law C Knox Y Djoumbou et al ldquoDrugBank 40 sheddingnew light on drug metabolismrdquo Nucleic Acids Research vol 42no 1 pp D1091ndashD1097 2014
[7] D Croft A F Mundo R Haw et al ldquoThe Reactome pathwayknowledgebaserdquoNucleic Acids Research vol 42 no 1 ppD472ndashD477 2014
[8] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[9] L Ji R L Ren H Gu et al ldquodTGSmethod for effective compo-nents identification from traditional Chinese medicine formulaand mechanism analysisrdquo Evidence-Based Complementary andAlternativeMedicine vol 2013 Article ID 840427 9 pages 2013
The Scientific World Journal 9
[10] J Yan Y Wang S-J Luo and Y-J Qiao ldquoTCM grammarsystems an approach to aid the interpretation of the molecularinteractions in Chinese herbal medicinerdquo Journal of Ethnophar-macology vol 137 no 1 pp 77ndash84 2011
[11] W Yun ldquoEntity grammar systems a grammatical tool for study-ing the hierarchal structures of biological systemsrdquo Bulletin ofMathematical Biology vol 66 no 3 pp 447ndash471 2004
[12] B Ruot I Papet F Bechereau et al ldquoIncreased albumin plasmaefflux contributes to hypoalbuminemia only during earlyphase of sepsis in ratsrdquo The American Journal of PhysiologymdashRegulatory Integrative and Comparative Physiology vol 284 no3 pp R707ndashR713 2003
[13] J U Hedlund L-O Hansson and A B Ortqvist ldquoHypoal-buminemia in hospitalized patients with community-acquiredpneumoniardquo Archives of Internal Medicine vol 155 no 13 pp1438ndash1442 1995
[14] E Persson P J Hogg and J Stenflo ldquoEffects of Ca2+ bindingon the protease module of factor Xa and its interaction withfactor Va evidence for two Gla-independent Ca2+-binding sitesin factor Xardquo The Journal of Biological Chemistry vol 268 no30 pp 22531ndash22539 1993
[15] E A Norstroslashm S Tran M Steen and B Dahlback ldquoEffectsof factor Xa and protein S on the individual activated proteinC-mediated cleavages of coagulation factor Vardquo The Journal ofBiological Chemistry vol 281 no 42 pp 31486ndash31494 2006
[16] W Zhou X X Zhu A L Yin et al ldquoEffect of various absorptionenhancers based on tight junctions on the intestinal absorptionof forsythoside A in Shuang-Huang-Lian application to itsantivirus activityrdquo Pharmacognosy Magazine vol 10 no 37 pp9ndash17 2014
[17] X Gao M Guo Q Li et al ldquoPlasma metabolomic profiling toreveal antipyretic mechanism of Shuang-Huang-Lian injectionon yeast-induced pyrexia ratsrdquo PLoS ONE vol 9 no 6 ArticleID e100017 2014
[18] R Gao Y N Lin G Liang B Yu and Y Gao ldquoComparativepharmacokinetic study of chlorogenic acid after oral admin-istration of lonicerae japonicae flos and shuang-huang-lian innormal and febrile ratsrdquo Phytotherapy Research vol 28 no 1pp 144ndash147 2014
[19] Y Gao L Fang R Cai et al ldquoShuang-Huang-Lian exertsanti-inflammatory and anti-oxidative activities in lipopoly-saccharide-stimulated murine alveolar macrophagesrdquo Phy-tomedicine vol 21 no 4 pp 461ndash469 2014
[20] CM Park andY-S Song ldquoLuteolin and luteolin-7-O-glucosideinhibit lipopolysaccharide-induced inflammatory responsesthrough modulation of NF-120581BAp-1PI3K-AKT signaling cas-cades in RAW 2647 cellsrdquo Nutrition Research and Practice vol7 no 6 pp 423ndash429 2013
[21] H Lee Y O Kim H Kim et al ldquoFlavonoid wogonin frommedicinal herb is neuroprotective by inhibiting inflammatoryactivation of microgliardquo The FASEB Journal vol 17 no 13 pp1943ndash1944 2003
[22] Y-C Chen L-L Yang and T J-F Lee ldquoOroxylin A inhi-bition of lipopolysaccharide-induced iNOS and COX-2 geneexpression via suppression of nuclear factor-120581B activationrdquoBiochemical Pharmacology vol 59 no 11 pp 1445ndash1457 2000
[23] J He X-P Hu Y Zeng et al ldquoAdvanced research on acteosidefor chemistry and bioactivitiesrdquo Journal of Asian Natural Prod-ucts Research vol 13 no 5 pp 449ndash464 2011
[24] L An and F Feng ldquoNetwork pharmacology-based antioxi-dant effect study of Zhi-Zi-da-huang decoction for alcoholic
liver diseaserdquo Evidence-Based Complementary and AlternativeMedicine vol 2015 Article ID 492470 6 pages 2015
[25] F Zhao L Guochun Y Yang L Shi L Xu and L Yin ldquoA net-work pharmacology approach to determine active ingredientsand rationality of herb combinations of Modified-Simiaowanfor treatment of goutrdquo Journal of Ethnopharmacology vol 168pp 1ndash16 2015
The Scientific World Journal 5
Quercetinrarr3rarr o rarr120573rarrDrarr glucoside
Q03736
ForsythialanA
MTP
DihydrooroxylinA Eriodictyol
SOAT2
DR4L2
UD3A1 Rivularin
SkullcapflavoneII
SkullcapflavoneI
HCK
ATPB
PK3CG
Chrysin
Q9AIU0
NorwogoninQ5G940
ForsythosideAIsomartynoside
Baicalein
PYGM
4-O-Caffeoylquinicacid
Oroxylin oroxylinA
Neobaicalein
5-Caffeoylquinicacid
LeucosceptosideA
Quercetin
ST17B
HIBCH
ATPA
ATPG
PIM1Wogonin
LuteolinCorymbosin
Geranial2-Pentadecanone
Cornoside
LYSCAT1A1
OctadecanoicacidAcetophenone
Butylatedhydroxyanisole ACO13
Phenethylalcohol
Cymene
p-cymene P03437
P26137Stigmasterol
RORA
120573-sitosterol
P00720
MIF
Caffeicacid
P16113
PYRD
Norlapachol
Q02768 Q3IWB0Q08210
PAEP S14L2
Palmiticacid
OPSDPPT1
TPPC3
GCH1
PNPH
P83812
P45563
Q9X1H9
MYP2
HNF4G
TRPA1
CP2C8
TRPM8ECE1
MyrtanolIsoborneol
GBB1
RASK
FNTA
Myrcene
RAE1
GBG1
PA2GDP0A433
Guanine
P0A9M5
Q84EX5
Q9X1T2
OPRKTRPV3
LALBA
Rengyol
PHOS
FNTB
PGTA
PGTB2
GDIA
Caryophyllene
120573-ocimene
DihydrobaicaleinP54965
P25553
COX7C COX5BCOX8A AK1C2
COX3 COX6C
COX2COX1
COX5A
SOAT1
Matairesinol
DimethylmatairesinolArctigenin
ForsythialanB
PRGR
COX7B
ETUD1
ERR3
Oleanolicacid
Pinoresinol
ESR1
Epipinoresinol
n-heneicosane
ERG7
120572-terpineol
Nonacosane
NCOA2P22637
ST2A1
ST2B1DHB1
P33517
P07445
Phillygenol
Ursolicacid
Q48473
KAPCAGLTP
Q8ZRP8
Q7KZA3
PA21BFABP6
COX41NR1H4
2120572-hydroxybetulinicacid
Betulinicacid
CX7A1HEMHCX6A2
ADH1G
P31224
Q8GGK7
EST1CX6B1
Isomenthone
Camphene
Isichlorogenticacid
45-Dicaffeoylquinicacid
Menthone
P00183
ForsythosideB
Camphor
Borneol
Linolenyalcohol
FADS2
PGH2
ELOV4
FADS1
Cynarin
Acteoside
CDK1Wogonoside
CDK8CDK4CDK6
PGH1
TRPV1
NAC1
ACM2 ACHA2
SuspensineA
LonicerinBaicalin
ACES 5HT3A
Arctiin
TOP2A
Matairesionoside
Phillyrin
Astragalin
Chlorogenic
IsochlorogenicacidB
CDK2
CDK5 CDK7
CDK9
EGFR Hyperoside
AK1C3
Rutin
Isoquercetin
Wogonin-7-120573-D-glcUA
Pinoresinol-120573-D-glucoside
7-Methoxybaicalein
(-)Bicuculline
(-)Egenine
(1) (3)(2)(4) (5)
(6) (8)(7)(10)(9) (11)
(12)(13)
(14) (15) (16) (17) (18) (19) (20)(21)
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Luteolinrarr7rarrOrarr120573rarrDrarr glucoside
3572998400-Tetrahydroxyavone
572998400-Trihydroxyflavone
5-Hydroxy-74998400- dimethoxyflavone
(-)-7998400-O-Methylegenine
Figure 3 Drug-target Network of SHL The components are yellow diamonds The targets are shown as blue squares
Ant
ineo
plas
tic ag
ents
Ana
lges
ics
nonn
arco
ticA
ntia
nxie
ty ag
ents
GA
BA an
tago
nists
Sym
path
omim
etic
sAd
juva
nts
anes
thes
iaA
ntic
hole
stere
mic
agen
tsSy
mpa
thom
imet
icA
ntifu
ngal
agen
tsA
ntid
epre
ssiv
e age
nts
seco
nd-g
ener
atio
nEx
cita
tory
amin
o ac
id an
tago
nists
Card
iova
scul
ar ag
ents
Ant
ispas
mod
ics
Ant
inar
cotic
agen
tsO
piat
e ant
agon
ists
Tryp
anoc
idal
agen
tsRe
nal a
gent
sA
ntim
usca
rinic
sD
iagn
ostic
agen
tsD
opam
ine u
ptak
e inh
ibito
rsA
ntic
holin
ergi
c age
nts
Lipo
xyge
nase
inhi
bito
rsC
ofac
tor
Nep
hrop
athi
c cys
tinos
is th
erap
yH
epar
ins
Ant
i-HIV
agen
tsPs
ycho
tropi
c dru
gsVi
tam
in D
3 re
cept
or in
hibi
tor
Enzy
me r
epla
cem
ent a
gent
sVi
tam
ins (
vita
min
D)
Fert
ility
agen
tsLe
ukot
riene
anta
goni
stsFr
ibic
acid
der
ivat
ives
Cor
ticos
tero
idA
mph
etam
ines
Alp
ha-a
dren
ergi
c blo
ckin
g ag
ents
Col
orin
g ag
ents
Mon
oam
ine o
xida
se in
hibi
tors
Pharmacological effects distribution
0
10
20
30
40
50
60
70
80
Figure 4 The pharmacological distribution of all 112 components in SHL
6 The Scientific World Journal
Palmitoylatedmyristoylated
eNOSdimer
Serumalbumin
PalmitylatedN-Myristoylated
eNOS
N-myristoylated eNOS(Gly2)
Aldehyde reductase
Nitricoxide
synthaseendothelial
Isomenthone
Ca(4)CaM Caveolin-1
PhosphorylatedHSL
complex
Fattyacid
bindingprotein
adipocyte
Thrombin activation
peptide
DihydrooroxylinA
Adenosine aminohydrolase
Factor IX
activation peptide
complex (prothrombinase)
Acteoside
Dihydrofolate reductase
FactorXa
Caimpermeable
AMPAreceptors
Factor VIIIa
B A3
acidic polypeptide
Activated thrombin
(factorIIa)
Luteolinrarr7rarrOrarr ararrDrarr glucoside
VaXa
eNOS caveolin-1 CaMeNOS Caveolin-1 CaM HSP90
eNOS caveolin-1
Na+
Ca2+ NH4+Na+
Ca2+
dimer FABP4
Glu
H+PALM
AMP
L-GlnGluL-Ala
Higherfattyacid
Inosinedeoxyinosine
THF
Ribose 1-phosphatedeoxyribose 1-phosphate
Hyp
Pi
2OG
TPN GluH+
Figure 5 The antipneumonia biological network of SHL
involved in the pathway parallelogram node represents com-plex hexagon node represents micromolecule and trianglenode represents biological reaction The edge with trianglearrow represents positive regulation edge with T-shapedarrow represents negative regulation and the undirected edgemeans the direction is uncertain (Figure 5) This biologicalnetwork which included 4 components 5 pneumonia relatedtargets and 26 subnetworks could overall exhibit the effectivecomponents and the mechanism of antipneumonia on amolecular level
This biological network included 26 subnetworks that4 components that acted on 5 pneumonia related targetsAll of these subnetworks intertwined to play the role ofantipneumonia collectively and demonstrated the features ofbiological systems simultaneously such as robustness redun-dancy crosstalk and so forth In order to clearly show theantipneumonia mechanism of SHL effective components wecould extracted 26 subnetworks respectivelyThis paper took2 extracted subnetworks as examples the biological pathwaywhere luteolin-7-o-120572-D-glucoside acted on serum albumin(Figure 6) and the biological pathway where dihydrooroxylinA acted on thrombin activation peptide (Figure 7)
As target of luteolin-7-o-120572-D-glucoside endothelial nitricoxide synthase (eNOS) translocated from Golgi to caveolaeafter N-myristoylation and palmitoylationWith depalmitoy-lation of eNOS dimer it produced PALM After the reactionof PALM and CoASH palmitic acid converted to palmitoyl-CoA accompanyied with energy transformation After aseries of signal transduction ofmicromolecule (NH4+ L-GlnNa+ etc) the content of serum albumin changed As thebiomarker in the early stage this pathway could elucidatethe course of the change That is luteolin-7-o-120572-D-glucosideacting on eNOS leads to the increase of vasopermeability
and serum albumin influxed into the interval of capillariesaccelerated the speed of catabolism and affected the contentof serum albumin at last [12 13]
Figure 7 shows the initial two steps of blood coagulationthe formation process of thrombin activation peptide andthe activation of thrombin As the target of dihydrooroxylinA adenosine aminohydrolase was hydrolyzed dephosphory-lated and oxidated After some amino acid was taken up andGluR2 transferred the Ca2+ impermeable AMPA receptorand aspartic acid receptor were activated and then extrudedof Ca2+ Factor Xa was activated by Ca2+ and Ca2+ alsocould accelerate the combination of factors Xa and Va [14]Factor Va had no activity itself but it could enhance activityof factor Xa and accelerated the formation of thrombin[15] Thrombin could accelerate the blood coagulation andwound healing thus treating alimentary tract hemorrhage ofsevere pneumonia In conclusion dihydrooroxylin A actingon thrombin plays the role of antipneumonia by acceleratingthe hemostasis of the alimentary tract
By summarizing the 26 subnetworks of SHL effectivecomponents cluster acting on pneumonia-related targets wegot 3 main pathways where SHL played the role of antip-neumonia (1) regulating the activity of caveolin-1 existingin the signal pathway of inflammatory and endothelial cellsaffects the response of inflammatory cell to the inflamma-tion further influencing the process of inflammation (2)accelerating the blood coagulation and wound healing thustreating alimentary tract hemorrhage of severe pneumonia(3) affecting the content of serum albumin promoting therepair of lung tissue and enhancing the immune function
Biological network shows 4 components could act on5 targets within 10 biological reactions Other componentsin SHL may also act on pneumonia-related targets but
The Scientific World Journal 7
AMP
PALM
L-Gln
Serum albumin
PalmitylatedN-myristoylated
eNOS
Nitricoxide
synthaseendothelial
Palmitoylatedmyristoylated
eNOS dimer
N-myristoylated eNOS (Gly2)
Na+
NH4+
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Figure 6 The antipneumonia biological pathway of luteolin-7-o-120572-D-glucoside
Ca impermeable
AMPA receptors
Glu
Adenosine aminohydrolase
DihydrooroxylinA
Inosinedeoxyinosine
Hyp
Ribose 1-phosphatedeoxyribose 1-phosphate
Pi
complex (prothrombinase)
Factor Xa
Thrombin activation
peptide
Va Xa
Na+Ca2+
Na+Ca2+
H+
Figure 7 The antipneumonia biological pathway of dihydrooroxylin A
8 The Scientific World Journal
the number of biological reactions will be more When wedefined the reactions as 15 biological network contained 5components and 9 pneumonia-related targets If the reactionwas 20 43 components and 13 targets were included in thebiological network The 4 components by contrast weremore quickly and efficiently acting on pneumonia-relatedtargets Compared with the components in SHL whichstudied frequently such as chlorogenic acid forsythin andbaicalin the content of four components within the networkwas lower but they may play the same role of pneumoniatreatment
4 Conclusion
Based on the public databases of TCM DrugBank databaseand directed TCM grammar systems we have built a PPInetwork drug target network and antipneumonia biologicalnetwork of SHL By the modules analysis we predicted thatSHL has the potential to be an antitumor candidate Thisresultmay provide a novel clue for further experimental stud-ies of SHL In future the predicted novel pharmacologicaleffects of SHL should be further validated from bench tobedside The antipneumonia biological network systemati-cally explained the reason why SHL could play the role ofantipneumonia and identified its effective components Allthese are helpful to guide the quality control and further studyof SHL
Studies have already demonstrated that SHL had thepharmacological actions of antimicrobial antiviral anti-pyretic anti-inflammatory antioxidant antiarrhythmic andenhanced immunity [16ndash19] but they only focused on indi-vidual component pharmacological action or pathway Thecomponent they studied could be extracted and was with ahigh content Compared with these studies our study couldelucidate the mechanism holistically and on the molecularlevel Meanwhile enclosing the synergistic effect of variouscomponents and the cross of pathways we not only addressedthat luteolin-7-120572-D-glucoside [20] dihydrooroxylin A [2122] and acteoside [23] played an anti-inflammatory role butalso predicted that isomenthone could act on pneumonia-related targets through biological network of SHL thusplaying the role of antipneumonia
The thought of this study accords with the networkpharmacology but the method we adopted is different fromother related works [24 25] The whole process of otherrelated works is carried out manually and the batch pro-cessing is impossible With the characteristic of flexibilitydTGS could solve these problems effectively Carrying out theTCM research under the guidance of network pharmacologyis more quick and systematic than traditional methodsMeanwhile dTGS provides a novel strategy for the study ofTCM and other complex systems
Because the research results were based on the inferenceof data included in the existing database or literature andbecause we do not take into account the quantity of compo-nents and the specific interactional environment thismethodstill has some limitations With further study of the complexsystems such as TCM formula and related disease the data
we used will be more complete and the results we got will bemore precise and integrity
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Authorsrsquo Contribution
Bai-xia Zhang Jian Li andHaoGu contributed equally to thiswork
Acknowledgments
This work was supported by National Science and Technol-ogy Major Projects for ldquomajor new drugs innovation anddevelopmentrdquo (Grant no 2011ZX09201-201-15) the NationalNatural Science Foundation of China (Grant nos 81173568and 81373985) and Program for New Century ExcellentTalents in University (Grant no NCET-11-0605)The fundershad no role in study design data collection and analysisdecision to publish or preparation of the paper
References
[1] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[2] X Chen H Zhou Y B Liu et al ldquoDatabase of traditionalChinese medicine and its application to studies of mechanismand to prescription validationrdquo British Journal of Pharmacologyvol 149 no 8 pp 1092ndash1103 2006
[3] Z L Ji H Zhou J F Wang L Y Han C J Zheng and YZ Chen ldquoTraditional Chinese medicine information databaserdquoJournal of Ethnopharmacology vol 103 no 3 501 pages 2006
[4] J Ye X Song Z Liu et al ldquoDevelopment of an LC-MS methodfor determination of three active constituents of Shuang-huang-lian injection in rat plasma and its application to the druginteraction study of Shuang-huang-lian freeze-dried powdercombined with levofloxacin injectionrdquo Journal of Chromatog-raphy B Analytical Technologies in the Biomedical and LifeSciences vol 898 pp 130ndash135 2012
[5] H Liu Y X Qiao B Liu and J J Zhou ldquoTransformation oftraditional Chinese medicine database into data warehouserdquoChinese Pharmaceutical Journal vol 9 pp 645ndash648 2006
[6] V Law C Knox Y Djoumbou et al ldquoDrugBank 40 sheddingnew light on drug metabolismrdquo Nucleic Acids Research vol 42no 1 pp D1091ndashD1097 2014
[7] D Croft A F Mundo R Haw et al ldquoThe Reactome pathwayknowledgebaserdquoNucleic Acids Research vol 42 no 1 ppD472ndashD477 2014
[8] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[9] L Ji R L Ren H Gu et al ldquodTGSmethod for effective compo-nents identification from traditional Chinese medicine formulaand mechanism analysisrdquo Evidence-Based Complementary andAlternativeMedicine vol 2013 Article ID 840427 9 pages 2013
The Scientific World Journal 9
[10] J Yan Y Wang S-J Luo and Y-J Qiao ldquoTCM grammarsystems an approach to aid the interpretation of the molecularinteractions in Chinese herbal medicinerdquo Journal of Ethnophar-macology vol 137 no 1 pp 77ndash84 2011
[11] W Yun ldquoEntity grammar systems a grammatical tool for study-ing the hierarchal structures of biological systemsrdquo Bulletin ofMathematical Biology vol 66 no 3 pp 447ndash471 2004
[12] B Ruot I Papet F Bechereau et al ldquoIncreased albumin plasmaefflux contributes to hypoalbuminemia only during earlyphase of sepsis in ratsrdquo The American Journal of PhysiologymdashRegulatory Integrative and Comparative Physiology vol 284 no3 pp R707ndashR713 2003
[13] J U Hedlund L-O Hansson and A B Ortqvist ldquoHypoal-buminemia in hospitalized patients with community-acquiredpneumoniardquo Archives of Internal Medicine vol 155 no 13 pp1438ndash1442 1995
[14] E Persson P J Hogg and J Stenflo ldquoEffects of Ca2+ bindingon the protease module of factor Xa and its interaction withfactor Va evidence for two Gla-independent Ca2+-binding sitesin factor Xardquo The Journal of Biological Chemistry vol 268 no30 pp 22531ndash22539 1993
[15] E A Norstroslashm S Tran M Steen and B Dahlback ldquoEffectsof factor Xa and protein S on the individual activated proteinC-mediated cleavages of coagulation factor Vardquo The Journal ofBiological Chemistry vol 281 no 42 pp 31486ndash31494 2006
[16] W Zhou X X Zhu A L Yin et al ldquoEffect of various absorptionenhancers based on tight junctions on the intestinal absorptionof forsythoside A in Shuang-Huang-Lian application to itsantivirus activityrdquo Pharmacognosy Magazine vol 10 no 37 pp9ndash17 2014
[17] X Gao M Guo Q Li et al ldquoPlasma metabolomic profiling toreveal antipyretic mechanism of Shuang-Huang-Lian injectionon yeast-induced pyrexia ratsrdquo PLoS ONE vol 9 no 6 ArticleID e100017 2014
[18] R Gao Y N Lin G Liang B Yu and Y Gao ldquoComparativepharmacokinetic study of chlorogenic acid after oral admin-istration of lonicerae japonicae flos and shuang-huang-lian innormal and febrile ratsrdquo Phytotherapy Research vol 28 no 1pp 144ndash147 2014
[19] Y Gao L Fang R Cai et al ldquoShuang-Huang-Lian exertsanti-inflammatory and anti-oxidative activities in lipopoly-saccharide-stimulated murine alveolar macrophagesrdquo Phy-tomedicine vol 21 no 4 pp 461ndash469 2014
[20] CM Park andY-S Song ldquoLuteolin and luteolin-7-O-glucosideinhibit lipopolysaccharide-induced inflammatory responsesthrough modulation of NF-120581BAp-1PI3K-AKT signaling cas-cades in RAW 2647 cellsrdquo Nutrition Research and Practice vol7 no 6 pp 423ndash429 2013
[21] H Lee Y O Kim H Kim et al ldquoFlavonoid wogonin frommedicinal herb is neuroprotective by inhibiting inflammatoryactivation of microgliardquo The FASEB Journal vol 17 no 13 pp1943ndash1944 2003
[22] Y-C Chen L-L Yang and T J-F Lee ldquoOroxylin A inhi-bition of lipopolysaccharide-induced iNOS and COX-2 geneexpression via suppression of nuclear factor-120581B activationrdquoBiochemical Pharmacology vol 59 no 11 pp 1445ndash1457 2000
[23] J He X-P Hu Y Zeng et al ldquoAdvanced research on acteosidefor chemistry and bioactivitiesrdquo Journal of Asian Natural Prod-ucts Research vol 13 no 5 pp 449ndash464 2011
[24] L An and F Feng ldquoNetwork pharmacology-based antioxi-dant effect study of Zhi-Zi-da-huang decoction for alcoholic
liver diseaserdquo Evidence-Based Complementary and AlternativeMedicine vol 2015 Article ID 492470 6 pages 2015
[25] F Zhao L Guochun Y Yang L Shi L Xu and L Yin ldquoA net-work pharmacology approach to determine active ingredientsand rationality of herb combinations of Modified-Simiaowanfor treatment of goutrdquo Journal of Ethnopharmacology vol 168pp 1ndash16 2015
6 The Scientific World Journal
Palmitoylatedmyristoylated
eNOSdimer
Serumalbumin
PalmitylatedN-Myristoylated
eNOS
N-myristoylated eNOS(Gly2)
Aldehyde reductase
Nitricoxide
synthaseendothelial
Isomenthone
Ca(4)CaM Caveolin-1
PhosphorylatedHSL
complex
Fattyacid
bindingprotein
adipocyte
Thrombin activation
peptide
DihydrooroxylinA
Adenosine aminohydrolase
Factor IX
activation peptide
complex (prothrombinase)
Acteoside
Dihydrofolate reductase
FactorXa
Caimpermeable
AMPAreceptors
Factor VIIIa
B A3
acidic polypeptide
Activated thrombin
(factorIIa)
Luteolinrarr7rarrOrarr ararrDrarr glucoside
VaXa
eNOS caveolin-1 CaMeNOS Caveolin-1 CaM HSP90
eNOS caveolin-1
Na+
Ca2+ NH4+Na+
Ca2+
dimer FABP4
Glu
H+PALM
AMP
L-GlnGluL-Ala
Higherfattyacid
Inosinedeoxyinosine
THF
Ribose 1-phosphatedeoxyribose 1-phosphate
Hyp
Pi
2OG
TPN GluH+
Figure 5 The antipneumonia biological network of SHL
involved in the pathway parallelogram node represents com-plex hexagon node represents micromolecule and trianglenode represents biological reaction The edge with trianglearrow represents positive regulation edge with T-shapedarrow represents negative regulation and the undirected edgemeans the direction is uncertain (Figure 5) This biologicalnetwork which included 4 components 5 pneumonia relatedtargets and 26 subnetworks could overall exhibit the effectivecomponents and the mechanism of antipneumonia on amolecular level
This biological network included 26 subnetworks that4 components that acted on 5 pneumonia related targetsAll of these subnetworks intertwined to play the role ofantipneumonia collectively and demonstrated the features ofbiological systems simultaneously such as robustness redun-dancy crosstalk and so forth In order to clearly show theantipneumonia mechanism of SHL effective components wecould extracted 26 subnetworks respectivelyThis paper took2 extracted subnetworks as examples the biological pathwaywhere luteolin-7-o-120572-D-glucoside acted on serum albumin(Figure 6) and the biological pathway where dihydrooroxylinA acted on thrombin activation peptide (Figure 7)
As target of luteolin-7-o-120572-D-glucoside endothelial nitricoxide synthase (eNOS) translocated from Golgi to caveolaeafter N-myristoylation and palmitoylationWith depalmitoy-lation of eNOS dimer it produced PALM After the reactionof PALM and CoASH palmitic acid converted to palmitoyl-CoA accompanyied with energy transformation After aseries of signal transduction ofmicromolecule (NH4+ L-GlnNa+ etc) the content of serum albumin changed As thebiomarker in the early stage this pathway could elucidatethe course of the change That is luteolin-7-o-120572-D-glucosideacting on eNOS leads to the increase of vasopermeability
and serum albumin influxed into the interval of capillariesaccelerated the speed of catabolism and affected the contentof serum albumin at last [12 13]
Figure 7 shows the initial two steps of blood coagulationthe formation process of thrombin activation peptide andthe activation of thrombin As the target of dihydrooroxylinA adenosine aminohydrolase was hydrolyzed dephosphory-lated and oxidated After some amino acid was taken up andGluR2 transferred the Ca2+ impermeable AMPA receptorand aspartic acid receptor were activated and then extrudedof Ca2+ Factor Xa was activated by Ca2+ and Ca2+ alsocould accelerate the combination of factors Xa and Va [14]Factor Va had no activity itself but it could enhance activityof factor Xa and accelerated the formation of thrombin[15] Thrombin could accelerate the blood coagulation andwound healing thus treating alimentary tract hemorrhage ofsevere pneumonia In conclusion dihydrooroxylin A actingon thrombin plays the role of antipneumonia by acceleratingthe hemostasis of the alimentary tract
By summarizing the 26 subnetworks of SHL effectivecomponents cluster acting on pneumonia-related targets wegot 3 main pathways where SHL played the role of antip-neumonia (1) regulating the activity of caveolin-1 existingin the signal pathway of inflammatory and endothelial cellsaffects the response of inflammatory cell to the inflamma-tion further influencing the process of inflammation (2)accelerating the blood coagulation and wound healing thustreating alimentary tract hemorrhage of severe pneumonia(3) affecting the content of serum albumin promoting therepair of lung tissue and enhancing the immune function
Biological network shows 4 components could act on5 targets within 10 biological reactions Other componentsin SHL may also act on pneumonia-related targets but
The Scientific World Journal 7
AMP
PALM
L-Gln
Serum albumin
PalmitylatedN-myristoylated
eNOS
Nitricoxide
synthaseendothelial
Palmitoylatedmyristoylated
eNOS dimer
N-myristoylated eNOS (Gly2)
Na+
NH4+
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Figure 6 The antipneumonia biological pathway of luteolin-7-o-120572-D-glucoside
Ca impermeable
AMPA receptors
Glu
Adenosine aminohydrolase
DihydrooroxylinA
Inosinedeoxyinosine
Hyp
Ribose 1-phosphatedeoxyribose 1-phosphate
Pi
complex (prothrombinase)
Factor Xa
Thrombin activation
peptide
Va Xa
Na+Ca2+
Na+Ca2+
H+
Figure 7 The antipneumonia biological pathway of dihydrooroxylin A
8 The Scientific World Journal
the number of biological reactions will be more When wedefined the reactions as 15 biological network contained 5components and 9 pneumonia-related targets If the reactionwas 20 43 components and 13 targets were included in thebiological network The 4 components by contrast weremore quickly and efficiently acting on pneumonia-relatedtargets Compared with the components in SHL whichstudied frequently such as chlorogenic acid forsythin andbaicalin the content of four components within the networkwas lower but they may play the same role of pneumoniatreatment
4 Conclusion
Based on the public databases of TCM DrugBank databaseand directed TCM grammar systems we have built a PPInetwork drug target network and antipneumonia biologicalnetwork of SHL By the modules analysis we predicted thatSHL has the potential to be an antitumor candidate Thisresultmay provide a novel clue for further experimental stud-ies of SHL In future the predicted novel pharmacologicaleffects of SHL should be further validated from bench tobedside The antipneumonia biological network systemati-cally explained the reason why SHL could play the role ofantipneumonia and identified its effective components Allthese are helpful to guide the quality control and further studyof SHL
Studies have already demonstrated that SHL had thepharmacological actions of antimicrobial antiviral anti-pyretic anti-inflammatory antioxidant antiarrhythmic andenhanced immunity [16ndash19] but they only focused on indi-vidual component pharmacological action or pathway Thecomponent they studied could be extracted and was with ahigh content Compared with these studies our study couldelucidate the mechanism holistically and on the molecularlevel Meanwhile enclosing the synergistic effect of variouscomponents and the cross of pathways we not only addressedthat luteolin-7-120572-D-glucoside [20] dihydrooroxylin A [2122] and acteoside [23] played an anti-inflammatory role butalso predicted that isomenthone could act on pneumonia-related targets through biological network of SHL thusplaying the role of antipneumonia
The thought of this study accords with the networkpharmacology but the method we adopted is different fromother related works [24 25] The whole process of otherrelated works is carried out manually and the batch pro-cessing is impossible With the characteristic of flexibilitydTGS could solve these problems effectively Carrying out theTCM research under the guidance of network pharmacologyis more quick and systematic than traditional methodsMeanwhile dTGS provides a novel strategy for the study ofTCM and other complex systems
Because the research results were based on the inferenceof data included in the existing database or literature andbecause we do not take into account the quantity of compo-nents and the specific interactional environment thismethodstill has some limitations With further study of the complexsystems such as TCM formula and related disease the data
we used will be more complete and the results we got will bemore precise and integrity
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Authorsrsquo Contribution
Bai-xia Zhang Jian Li andHaoGu contributed equally to thiswork
Acknowledgments
This work was supported by National Science and Technol-ogy Major Projects for ldquomajor new drugs innovation anddevelopmentrdquo (Grant no 2011ZX09201-201-15) the NationalNatural Science Foundation of China (Grant nos 81173568and 81373985) and Program for New Century ExcellentTalents in University (Grant no NCET-11-0605)The fundershad no role in study design data collection and analysisdecision to publish or preparation of the paper
References
[1] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[2] X Chen H Zhou Y B Liu et al ldquoDatabase of traditionalChinese medicine and its application to studies of mechanismand to prescription validationrdquo British Journal of Pharmacologyvol 149 no 8 pp 1092ndash1103 2006
[3] Z L Ji H Zhou J F Wang L Y Han C J Zheng and YZ Chen ldquoTraditional Chinese medicine information databaserdquoJournal of Ethnopharmacology vol 103 no 3 501 pages 2006
[4] J Ye X Song Z Liu et al ldquoDevelopment of an LC-MS methodfor determination of three active constituents of Shuang-huang-lian injection in rat plasma and its application to the druginteraction study of Shuang-huang-lian freeze-dried powdercombined with levofloxacin injectionrdquo Journal of Chromatog-raphy B Analytical Technologies in the Biomedical and LifeSciences vol 898 pp 130ndash135 2012
[5] H Liu Y X Qiao B Liu and J J Zhou ldquoTransformation oftraditional Chinese medicine database into data warehouserdquoChinese Pharmaceutical Journal vol 9 pp 645ndash648 2006
[6] V Law C Knox Y Djoumbou et al ldquoDrugBank 40 sheddingnew light on drug metabolismrdquo Nucleic Acids Research vol 42no 1 pp D1091ndashD1097 2014
[7] D Croft A F Mundo R Haw et al ldquoThe Reactome pathwayknowledgebaserdquoNucleic Acids Research vol 42 no 1 ppD472ndashD477 2014
[8] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[9] L Ji R L Ren H Gu et al ldquodTGSmethod for effective compo-nents identification from traditional Chinese medicine formulaand mechanism analysisrdquo Evidence-Based Complementary andAlternativeMedicine vol 2013 Article ID 840427 9 pages 2013
The Scientific World Journal 9
[10] J Yan Y Wang S-J Luo and Y-J Qiao ldquoTCM grammarsystems an approach to aid the interpretation of the molecularinteractions in Chinese herbal medicinerdquo Journal of Ethnophar-macology vol 137 no 1 pp 77ndash84 2011
[11] W Yun ldquoEntity grammar systems a grammatical tool for study-ing the hierarchal structures of biological systemsrdquo Bulletin ofMathematical Biology vol 66 no 3 pp 447ndash471 2004
[12] B Ruot I Papet F Bechereau et al ldquoIncreased albumin plasmaefflux contributes to hypoalbuminemia only during earlyphase of sepsis in ratsrdquo The American Journal of PhysiologymdashRegulatory Integrative and Comparative Physiology vol 284 no3 pp R707ndashR713 2003
[13] J U Hedlund L-O Hansson and A B Ortqvist ldquoHypoal-buminemia in hospitalized patients with community-acquiredpneumoniardquo Archives of Internal Medicine vol 155 no 13 pp1438ndash1442 1995
[14] E Persson P J Hogg and J Stenflo ldquoEffects of Ca2+ bindingon the protease module of factor Xa and its interaction withfactor Va evidence for two Gla-independent Ca2+-binding sitesin factor Xardquo The Journal of Biological Chemistry vol 268 no30 pp 22531ndash22539 1993
[15] E A Norstroslashm S Tran M Steen and B Dahlback ldquoEffectsof factor Xa and protein S on the individual activated proteinC-mediated cleavages of coagulation factor Vardquo The Journal ofBiological Chemistry vol 281 no 42 pp 31486ndash31494 2006
[16] W Zhou X X Zhu A L Yin et al ldquoEffect of various absorptionenhancers based on tight junctions on the intestinal absorptionof forsythoside A in Shuang-Huang-Lian application to itsantivirus activityrdquo Pharmacognosy Magazine vol 10 no 37 pp9ndash17 2014
[17] X Gao M Guo Q Li et al ldquoPlasma metabolomic profiling toreveal antipyretic mechanism of Shuang-Huang-Lian injectionon yeast-induced pyrexia ratsrdquo PLoS ONE vol 9 no 6 ArticleID e100017 2014
[18] R Gao Y N Lin G Liang B Yu and Y Gao ldquoComparativepharmacokinetic study of chlorogenic acid after oral admin-istration of lonicerae japonicae flos and shuang-huang-lian innormal and febrile ratsrdquo Phytotherapy Research vol 28 no 1pp 144ndash147 2014
[19] Y Gao L Fang R Cai et al ldquoShuang-Huang-Lian exertsanti-inflammatory and anti-oxidative activities in lipopoly-saccharide-stimulated murine alveolar macrophagesrdquo Phy-tomedicine vol 21 no 4 pp 461ndash469 2014
[20] CM Park andY-S Song ldquoLuteolin and luteolin-7-O-glucosideinhibit lipopolysaccharide-induced inflammatory responsesthrough modulation of NF-120581BAp-1PI3K-AKT signaling cas-cades in RAW 2647 cellsrdquo Nutrition Research and Practice vol7 no 6 pp 423ndash429 2013
[21] H Lee Y O Kim H Kim et al ldquoFlavonoid wogonin frommedicinal herb is neuroprotective by inhibiting inflammatoryactivation of microgliardquo The FASEB Journal vol 17 no 13 pp1943ndash1944 2003
[22] Y-C Chen L-L Yang and T J-F Lee ldquoOroxylin A inhi-bition of lipopolysaccharide-induced iNOS and COX-2 geneexpression via suppression of nuclear factor-120581B activationrdquoBiochemical Pharmacology vol 59 no 11 pp 1445ndash1457 2000
[23] J He X-P Hu Y Zeng et al ldquoAdvanced research on acteosidefor chemistry and bioactivitiesrdquo Journal of Asian Natural Prod-ucts Research vol 13 no 5 pp 449ndash464 2011
[24] L An and F Feng ldquoNetwork pharmacology-based antioxi-dant effect study of Zhi-Zi-da-huang decoction for alcoholic
liver diseaserdquo Evidence-Based Complementary and AlternativeMedicine vol 2015 Article ID 492470 6 pages 2015
[25] F Zhao L Guochun Y Yang L Shi L Xu and L Yin ldquoA net-work pharmacology approach to determine active ingredientsand rationality of herb combinations of Modified-Simiaowanfor treatment of goutrdquo Journal of Ethnopharmacology vol 168pp 1ndash16 2015
The Scientific World Journal 7
AMP
PALM
L-Gln
Serum albumin
PalmitylatedN-myristoylated
eNOS
Nitricoxide
synthaseendothelial
Palmitoylatedmyristoylated
eNOS dimer
N-myristoylated eNOS (Gly2)
Na+
NH4+
Luteolinrarr7rarrOrarr ararrDrarr glucoside
Figure 6 The antipneumonia biological pathway of luteolin-7-o-120572-D-glucoside
Ca impermeable
AMPA receptors
Glu
Adenosine aminohydrolase
DihydrooroxylinA
Inosinedeoxyinosine
Hyp
Ribose 1-phosphatedeoxyribose 1-phosphate
Pi
complex (prothrombinase)
Factor Xa
Thrombin activation
peptide
Va Xa
Na+Ca2+
Na+Ca2+
H+
Figure 7 The antipneumonia biological pathway of dihydrooroxylin A
8 The Scientific World Journal
the number of biological reactions will be more When wedefined the reactions as 15 biological network contained 5components and 9 pneumonia-related targets If the reactionwas 20 43 components and 13 targets were included in thebiological network The 4 components by contrast weremore quickly and efficiently acting on pneumonia-relatedtargets Compared with the components in SHL whichstudied frequently such as chlorogenic acid forsythin andbaicalin the content of four components within the networkwas lower but they may play the same role of pneumoniatreatment
4 Conclusion
Based on the public databases of TCM DrugBank databaseand directed TCM grammar systems we have built a PPInetwork drug target network and antipneumonia biologicalnetwork of SHL By the modules analysis we predicted thatSHL has the potential to be an antitumor candidate Thisresultmay provide a novel clue for further experimental stud-ies of SHL In future the predicted novel pharmacologicaleffects of SHL should be further validated from bench tobedside The antipneumonia biological network systemati-cally explained the reason why SHL could play the role ofantipneumonia and identified its effective components Allthese are helpful to guide the quality control and further studyof SHL
Studies have already demonstrated that SHL had thepharmacological actions of antimicrobial antiviral anti-pyretic anti-inflammatory antioxidant antiarrhythmic andenhanced immunity [16ndash19] but they only focused on indi-vidual component pharmacological action or pathway Thecomponent they studied could be extracted and was with ahigh content Compared with these studies our study couldelucidate the mechanism holistically and on the molecularlevel Meanwhile enclosing the synergistic effect of variouscomponents and the cross of pathways we not only addressedthat luteolin-7-120572-D-glucoside [20] dihydrooroxylin A [2122] and acteoside [23] played an anti-inflammatory role butalso predicted that isomenthone could act on pneumonia-related targets through biological network of SHL thusplaying the role of antipneumonia
The thought of this study accords with the networkpharmacology but the method we adopted is different fromother related works [24 25] The whole process of otherrelated works is carried out manually and the batch pro-cessing is impossible With the characteristic of flexibilitydTGS could solve these problems effectively Carrying out theTCM research under the guidance of network pharmacologyis more quick and systematic than traditional methodsMeanwhile dTGS provides a novel strategy for the study ofTCM and other complex systems
Because the research results were based on the inferenceof data included in the existing database or literature andbecause we do not take into account the quantity of compo-nents and the specific interactional environment thismethodstill has some limitations With further study of the complexsystems such as TCM formula and related disease the data
we used will be more complete and the results we got will bemore precise and integrity
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Authorsrsquo Contribution
Bai-xia Zhang Jian Li andHaoGu contributed equally to thiswork
Acknowledgments
This work was supported by National Science and Technol-ogy Major Projects for ldquomajor new drugs innovation anddevelopmentrdquo (Grant no 2011ZX09201-201-15) the NationalNatural Science Foundation of China (Grant nos 81173568and 81373985) and Program for New Century ExcellentTalents in University (Grant no NCET-11-0605)The fundershad no role in study design data collection and analysisdecision to publish or preparation of the paper
References
[1] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[2] X Chen H Zhou Y B Liu et al ldquoDatabase of traditionalChinese medicine and its application to studies of mechanismand to prescription validationrdquo British Journal of Pharmacologyvol 149 no 8 pp 1092ndash1103 2006
[3] Z L Ji H Zhou J F Wang L Y Han C J Zheng and YZ Chen ldquoTraditional Chinese medicine information databaserdquoJournal of Ethnopharmacology vol 103 no 3 501 pages 2006
[4] J Ye X Song Z Liu et al ldquoDevelopment of an LC-MS methodfor determination of three active constituents of Shuang-huang-lian injection in rat plasma and its application to the druginteraction study of Shuang-huang-lian freeze-dried powdercombined with levofloxacin injectionrdquo Journal of Chromatog-raphy B Analytical Technologies in the Biomedical and LifeSciences vol 898 pp 130ndash135 2012
[5] H Liu Y X Qiao B Liu and J J Zhou ldquoTransformation oftraditional Chinese medicine database into data warehouserdquoChinese Pharmaceutical Journal vol 9 pp 645ndash648 2006
[6] V Law C Knox Y Djoumbou et al ldquoDrugBank 40 sheddingnew light on drug metabolismrdquo Nucleic Acids Research vol 42no 1 pp D1091ndashD1097 2014
[7] D Croft A F Mundo R Haw et al ldquoThe Reactome pathwayknowledgebaserdquoNucleic Acids Research vol 42 no 1 ppD472ndashD477 2014
[8] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[9] L Ji R L Ren H Gu et al ldquodTGSmethod for effective compo-nents identification from traditional Chinese medicine formulaand mechanism analysisrdquo Evidence-Based Complementary andAlternativeMedicine vol 2013 Article ID 840427 9 pages 2013
The Scientific World Journal 9
[10] J Yan Y Wang S-J Luo and Y-J Qiao ldquoTCM grammarsystems an approach to aid the interpretation of the molecularinteractions in Chinese herbal medicinerdquo Journal of Ethnophar-macology vol 137 no 1 pp 77ndash84 2011
[11] W Yun ldquoEntity grammar systems a grammatical tool for study-ing the hierarchal structures of biological systemsrdquo Bulletin ofMathematical Biology vol 66 no 3 pp 447ndash471 2004
[12] B Ruot I Papet F Bechereau et al ldquoIncreased albumin plasmaefflux contributes to hypoalbuminemia only during earlyphase of sepsis in ratsrdquo The American Journal of PhysiologymdashRegulatory Integrative and Comparative Physiology vol 284 no3 pp R707ndashR713 2003
[13] J U Hedlund L-O Hansson and A B Ortqvist ldquoHypoal-buminemia in hospitalized patients with community-acquiredpneumoniardquo Archives of Internal Medicine vol 155 no 13 pp1438ndash1442 1995
[14] E Persson P J Hogg and J Stenflo ldquoEffects of Ca2+ bindingon the protease module of factor Xa and its interaction withfactor Va evidence for two Gla-independent Ca2+-binding sitesin factor Xardquo The Journal of Biological Chemistry vol 268 no30 pp 22531ndash22539 1993
[15] E A Norstroslashm S Tran M Steen and B Dahlback ldquoEffectsof factor Xa and protein S on the individual activated proteinC-mediated cleavages of coagulation factor Vardquo The Journal ofBiological Chemistry vol 281 no 42 pp 31486ndash31494 2006
[16] W Zhou X X Zhu A L Yin et al ldquoEffect of various absorptionenhancers based on tight junctions on the intestinal absorptionof forsythoside A in Shuang-Huang-Lian application to itsantivirus activityrdquo Pharmacognosy Magazine vol 10 no 37 pp9ndash17 2014
[17] X Gao M Guo Q Li et al ldquoPlasma metabolomic profiling toreveal antipyretic mechanism of Shuang-Huang-Lian injectionon yeast-induced pyrexia ratsrdquo PLoS ONE vol 9 no 6 ArticleID e100017 2014
[18] R Gao Y N Lin G Liang B Yu and Y Gao ldquoComparativepharmacokinetic study of chlorogenic acid after oral admin-istration of lonicerae japonicae flos and shuang-huang-lian innormal and febrile ratsrdquo Phytotherapy Research vol 28 no 1pp 144ndash147 2014
[19] Y Gao L Fang R Cai et al ldquoShuang-Huang-Lian exertsanti-inflammatory and anti-oxidative activities in lipopoly-saccharide-stimulated murine alveolar macrophagesrdquo Phy-tomedicine vol 21 no 4 pp 461ndash469 2014
[20] CM Park andY-S Song ldquoLuteolin and luteolin-7-O-glucosideinhibit lipopolysaccharide-induced inflammatory responsesthrough modulation of NF-120581BAp-1PI3K-AKT signaling cas-cades in RAW 2647 cellsrdquo Nutrition Research and Practice vol7 no 6 pp 423ndash429 2013
[21] H Lee Y O Kim H Kim et al ldquoFlavonoid wogonin frommedicinal herb is neuroprotective by inhibiting inflammatoryactivation of microgliardquo The FASEB Journal vol 17 no 13 pp1943ndash1944 2003
[22] Y-C Chen L-L Yang and T J-F Lee ldquoOroxylin A inhi-bition of lipopolysaccharide-induced iNOS and COX-2 geneexpression via suppression of nuclear factor-120581B activationrdquoBiochemical Pharmacology vol 59 no 11 pp 1445ndash1457 2000
[23] J He X-P Hu Y Zeng et al ldquoAdvanced research on acteosidefor chemistry and bioactivitiesrdquo Journal of Asian Natural Prod-ucts Research vol 13 no 5 pp 449ndash464 2011
[24] L An and F Feng ldquoNetwork pharmacology-based antioxi-dant effect study of Zhi-Zi-da-huang decoction for alcoholic
liver diseaserdquo Evidence-Based Complementary and AlternativeMedicine vol 2015 Article ID 492470 6 pages 2015
[25] F Zhao L Guochun Y Yang L Shi L Xu and L Yin ldquoA net-work pharmacology approach to determine active ingredientsand rationality of herb combinations of Modified-Simiaowanfor treatment of goutrdquo Journal of Ethnopharmacology vol 168pp 1ndash16 2015
8 The Scientific World Journal
the number of biological reactions will be more When wedefined the reactions as 15 biological network contained 5components and 9 pneumonia-related targets If the reactionwas 20 43 components and 13 targets were included in thebiological network The 4 components by contrast weremore quickly and efficiently acting on pneumonia-relatedtargets Compared with the components in SHL whichstudied frequently such as chlorogenic acid forsythin andbaicalin the content of four components within the networkwas lower but they may play the same role of pneumoniatreatment
4 Conclusion
Based on the public databases of TCM DrugBank databaseand directed TCM grammar systems we have built a PPInetwork drug target network and antipneumonia biologicalnetwork of SHL By the modules analysis we predicted thatSHL has the potential to be an antitumor candidate Thisresultmay provide a novel clue for further experimental stud-ies of SHL In future the predicted novel pharmacologicaleffects of SHL should be further validated from bench tobedside The antipneumonia biological network systemati-cally explained the reason why SHL could play the role ofantipneumonia and identified its effective components Allthese are helpful to guide the quality control and further studyof SHL
Studies have already demonstrated that SHL had thepharmacological actions of antimicrobial antiviral anti-pyretic anti-inflammatory antioxidant antiarrhythmic andenhanced immunity [16ndash19] but they only focused on indi-vidual component pharmacological action or pathway Thecomponent they studied could be extracted and was with ahigh content Compared with these studies our study couldelucidate the mechanism holistically and on the molecularlevel Meanwhile enclosing the synergistic effect of variouscomponents and the cross of pathways we not only addressedthat luteolin-7-120572-D-glucoside [20] dihydrooroxylin A [2122] and acteoside [23] played an anti-inflammatory role butalso predicted that isomenthone could act on pneumonia-related targets through biological network of SHL thusplaying the role of antipneumonia
The thought of this study accords with the networkpharmacology but the method we adopted is different fromother related works [24 25] The whole process of otherrelated works is carried out manually and the batch pro-cessing is impossible With the characteristic of flexibilitydTGS could solve these problems effectively Carrying out theTCM research under the guidance of network pharmacologyis more quick and systematic than traditional methodsMeanwhile dTGS provides a novel strategy for the study ofTCM and other complex systems
Because the research results were based on the inferenceof data included in the existing database or literature andbecause we do not take into account the quantity of compo-nents and the specific interactional environment thismethodstill has some limitations With further study of the complexsystems such as TCM formula and related disease the data
we used will be more complete and the results we got will bemore precise and integrity
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Authorsrsquo Contribution
Bai-xia Zhang Jian Li andHaoGu contributed equally to thiswork
Acknowledgments
This work was supported by National Science and Technol-ogy Major Projects for ldquomajor new drugs innovation anddevelopmentrdquo (Grant no 2011ZX09201-201-15) the NationalNatural Science Foundation of China (Grant nos 81173568and 81373985) and Program for New Century ExcellentTalents in University (Grant no NCET-11-0605)The fundershad no role in study design data collection and analysisdecision to publish or preparation of the paper
References
[1] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[2] X Chen H Zhou Y B Liu et al ldquoDatabase of traditionalChinese medicine and its application to studies of mechanismand to prescription validationrdquo British Journal of Pharmacologyvol 149 no 8 pp 1092ndash1103 2006
[3] Z L Ji H Zhou J F Wang L Y Han C J Zheng and YZ Chen ldquoTraditional Chinese medicine information databaserdquoJournal of Ethnopharmacology vol 103 no 3 501 pages 2006
[4] J Ye X Song Z Liu et al ldquoDevelopment of an LC-MS methodfor determination of three active constituents of Shuang-huang-lian injection in rat plasma and its application to the druginteraction study of Shuang-huang-lian freeze-dried powdercombined with levofloxacin injectionrdquo Journal of Chromatog-raphy B Analytical Technologies in the Biomedical and LifeSciences vol 898 pp 130ndash135 2012
[5] H Liu Y X Qiao B Liu and J J Zhou ldquoTransformation oftraditional Chinese medicine database into data warehouserdquoChinese Pharmaceutical Journal vol 9 pp 645ndash648 2006
[6] V Law C Knox Y Djoumbou et al ldquoDrugBank 40 sheddingnew light on drug metabolismrdquo Nucleic Acids Research vol 42no 1 pp D1091ndashD1097 2014
[7] D Croft A F Mundo R Haw et al ldquoThe Reactome pathwayknowledgebaserdquoNucleic Acids Research vol 42 no 1 ppD472ndashD477 2014
[8] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[9] L Ji R L Ren H Gu et al ldquodTGSmethod for effective compo-nents identification from traditional Chinese medicine formulaand mechanism analysisrdquo Evidence-Based Complementary andAlternativeMedicine vol 2013 Article ID 840427 9 pages 2013
The Scientific World Journal 9
[10] J Yan Y Wang S-J Luo and Y-J Qiao ldquoTCM grammarsystems an approach to aid the interpretation of the molecularinteractions in Chinese herbal medicinerdquo Journal of Ethnophar-macology vol 137 no 1 pp 77ndash84 2011
[11] W Yun ldquoEntity grammar systems a grammatical tool for study-ing the hierarchal structures of biological systemsrdquo Bulletin ofMathematical Biology vol 66 no 3 pp 447ndash471 2004
[12] B Ruot I Papet F Bechereau et al ldquoIncreased albumin plasmaefflux contributes to hypoalbuminemia only during earlyphase of sepsis in ratsrdquo The American Journal of PhysiologymdashRegulatory Integrative and Comparative Physiology vol 284 no3 pp R707ndashR713 2003
[13] J U Hedlund L-O Hansson and A B Ortqvist ldquoHypoal-buminemia in hospitalized patients with community-acquiredpneumoniardquo Archives of Internal Medicine vol 155 no 13 pp1438ndash1442 1995
[14] E Persson P J Hogg and J Stenflo ldquoEffects of Ca2+ bindingon the protease module of factor Xa and its interaction withfactor Va evidence for two Gla-independent Ca2+-binding sitesin factor Xardquo The Journal of Biological Chemistry vol 268 no30 pp 22531ndash22539 1993
[15] E A Norstroslashm S Tran M Steen and B Dahlback ldquoEffectsof factor Xa and protein S on the individual activated proteinC-mediated cleavages of coagulation factor Vardquo The Journal ofBiological Chemistry vol 281 no 42 pp 31486ndash31494 2006
[16] W Zhou X X Zhu A L Yin et al ldquoEffect of various absorptionenhancers based on tight junctions on the intestinal absorptionof forsythoside A in Shuang-Huang-Lian application to itsantivirus activityrdquo Pharmacognosy Magazine vol 10 no 37 pp9ndash17 2014
[17] X Gao M Guo Q Li et al ldquoPlasma metabolomic profiling toreveal antipyretic mechanism of Shuang-Huang-Lian injectionon yeast-induced pyrexia ratsrdquo PLoS ONE vol 9 no 6 ArticleID e100017 2014
[18] R Gao Y N Lin G Liang B Yu and Y Gao ldquoComparativepharmacokinetic study of chlorogenic acid after oral admin-istration of lonicerae japonicae flos and shuang-huang-lian innormal and febrile ratsrdquo Phytotherapy Research vol 28 no 1pp 144ndash147 2014
[19] Y Gao L Fang R Cai et al ldquoShuang-Huang-Lian exertsanti-inflammatory and anti-oxidative activities in lipopoly-saccharide-stimulated murine alveolar macrophagesrdquo Phy-tomedicine vol 21 no 4 pp 461ndash469 2014
[20] CM Park andY-S Song ldquoLuteolin and luteolin-7-O-glucosideinhibit lipopolysaccharide-induced inflammatory responsesthrough modulation of NF-120581BAp-1PI3K-AKT signaling cas-cades in RAW 2647 cellsrdquo Nutrition Research and Practice vol7 no 6 pp 423ndash429 2013
[21] H Lee Y O Kim H Kim et al ldquoFlavonoid wogonin frommedicinal herb is neuroprotective by inhibiting inflammatoryactivation of microgliardquo The FASEB Journal vol 17 no 13 pp1943ndash1944 2003
[22] Y-C Chen L-L Yang and T J-F Lee ldquoOroxylin A inhi-bition of lipopolysaccharide-induced iNOS and COX-2 geneexpression via suppression of nuclear factor-120581B activationrdquoBiochemical Pharmacology vol 59 no 11 pp 1445ndash1457 2000
[23] J He X-P Hu Y Zeng et al ldquoAdvanced research on acteosidefor chemistry and bioactivitiesrdquo Journal of Asian Natural Prod-ucts Research vol 13 no 5 pp 449ndash464 2011
[24] L An and F Feng ldquoNetwork pharmacology-based antioxi-dant effect study of Zhi-Zi-da-huang decoction for alcoholic
liver diseaserdquo Evidence-Based Complementary and AlternativeMedicine vol 2015 Article ID 492470 6 pages 2015
[25] F Zhao L Guochun Y Yang L Shi L Xu and L Yin ldquoA net-work pharmacology approach to determine active ingredientsand rationality of herb combinations of Modified-Simiaowanfor treatment of goutrdquo Journal of Ethnopharmacology vol 168pp 1ndash16 2015
The Scientific World Journal 9
[10] J Yan Y Wang S-J Luo and Y-J Qiao ldquoTCM grammarsystems an approach to aid the interpretation of the molecularinteractions in Chinese herbal medicinerdquo Journal of Ethnophar-macology vol 137 no 1 pp 77ndash84 2011
[11] W Yun ldquoEntity grammar systems a grammatical tool for study-ing the hierarchal structures of biological systemsrdquo Bulletin ofMathematical Biology vol 66 no 3 pp 447ndash471 2004
[12] B Ruot I Papet F Bechereau et al ldquoIncreased albumin plasmaefflux contributes to hypoalbuminemia only during earlyphase of sepsis in ratsrdquo The American Journal of PhysiologymdashRegulatory Integrative and Comparative Physiology vol 284 no3 pp R707ndashR713 2003
[13] J U Hedlund L-O Hansson and A B Ortqvist ldquoHypoal-buminemia in hospitalized patients with community-acquiredpneumoniardquo Archives of Internal Medicine vol 155 no 13 pp1438ndash1442 1995
[14] E Persson P J Hogg and J Stenflo ldquoEffects of Ca2+ bindingon the protease module of factor Xa and its interaction withfactor Va evidence for two Gla-independent Ca2+-binding sitesin factor Xardquo The Journal of Biological Chemistry vol 268 no30 pp 22531ndash22539 1993
[15] E A Norstroslashm S Tran M Steen and B Dahlback ldquoEffectsof factor Xa and protein S on the individual activated proteinC-mediated cleavages of coagulation factor Vardquo The Journal ofBiological Chemistry vol 281 no 42 pp 31486ndash31494 2006
[16] W Zhou X X Zhu A L Yin et al ldquoEffect of various absorptionenhancers based on tight junctions on the intestinal absorptionof forsythoside A in Shuang-Huang-Lian application to itsantivirus activityrdquo Pharmacognosy Magazine vol 10 no 37 pp9ndash17 2014
[17] X Gao M Guo Q Li et al ldquoPlasma metabolomic profiling toreveal antipyretic mechanism of Shuang-Huang-Lian injectionon yeast-induced pyrexia ratsrdquo PLoS ONE vol 9 no 6 ArticleID e100017 2014
[18] R Gao Y N Lin G Liang B Yu and Y Gao ldquoComparativepharmacokinetic study of chlorogenic acid after oral admin-istration of lonicerae japonicae flos and shuang-huang-lian innormal and febrile ratsrdquo Phytotherapy Research vol 28 no 1pp 144ndash147 2014
[19] Y Gao L Fang R Cai et al ldquoShuang-Huang-Lian exertsanti-inflammatory and anti-oxidative activities in lipopoly-saccharide-stimulated murine alveolar macrophagesrdquo Phy-tomedicine vol 21 no 4 pp 461ndash469 2014
[20] CM Park andY-S Song ldquoLuteolin and luteolin-7-O-glucosideinhibit lipopolysaccharide-induced inflammatory responsesthrough modulation of NF-120581BAp-1PI3K-AKT signaling cas-cades in RAW 2647 cellsrdquo Nutrition Research and Practice vol7 no 6 pp 423ndash429 2013
[21] H Lee Y O Kim H Kim et al ldquoFlavonoid wogonin frommedicinal herb is neuroprotective by inhibiting inflammatoryactivation of microgliardquo The FASEB Journal vol 17 no 13 pp1943ndash1944 2003
[22] Y-C Chen L-L Yang and T J-F Lee ldquoOroxylin A inhi-bition of lipopolysaccharide-induced iNOS and COX-2 geneexpression via suppression of nuclear factor-120581B activationrdquoBiochemical Pharmacology vol 59 no 11 pp 1445ndash1457 2000
[23] J He X-P Hu Y Zeng et al ldquoAdvanced research on acteosidefor chemistry and bioactivitiesrdquo Journal of Asian Natural Prod-ucts Research vol 13 no 5 pp 449ndash464 2011
[24] L An and F Feng ldquoNetwork pharmacology-based antioxi-dant effect study of Zhi-Zi-da-huang decoction for alcoholic
liver diseaserdquo Evidence-Based Complementary and AlternativeMedicine vol 2015 Article ID 492470 6 pages 2015
[25] F Zhao L Guochun Y Yang L Shi L Xu and L Yin ldquoA net-work pharmacology approach to determine active ingredientsand rationality of herb combinations of Modified-Simiaowanfor treatment of goutrdquo Journal of Ethnopharmacology vol 168pp 1ndash16 2015
