Research Article Treatment of Acute Lymphoblastic Leukemia...

Research ArticleTreatment of Acute Lymphoblastic Leukemia fromTraditional Chinese Medicine

Ya-Li Hsiao1 Pei-Chun Chang1 Hung-Jin Huang2

Chia-Chen Kuo1 and Calvin Yu-Chian Chen12

1 Department of Biomedical Informatics Asia University Taichung 41354 Taiwan2 School of Medicine College of Medicine China Medical University Taichung 40402 Taiwan

Correspondence should be addressed to Calvin Yu-Chian Chen ycc929MITedu

Received 3 January 2014 Accepted 7 January 2014 Published 22 May 2014

Academic Editor Fuu-Jen Tsai

Copyright copy 2014 Ya-Li Hsiao 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

Acute lymphoblastic leukemia (ALL) is a cancer that immature white blood cells continuously overproduce in the bone marrowThese cells crowd out normal cells in the bone marrow bringing damage and death Methotrexate (MTX) is a drug used inthe treatment of various cancer and autoimmune diseases In particular for the treatment of childhood acute lymphoblasticleukemia it had significant effect MTX competitively inhibits dihydrofolate reductase (DHFR) an enzyme that participates in thetetrahydrofolate synthesis so as to inhibit purine synthesis In addition its downstream metabolite methotrexate polyglutamates(MTX-PGs) inhibit the thymidylate synthase (TS) Therefore MTX can inhibit the synthesis of DNA However MTX hascytotoxicity and neurotoxinmay causemultiple organ injury and is potentially lethalThus the lower toxicity drugs are necessary tobe developed Recently diseases treatments with Traditional Chinese Medicine (TCM) as complements are getting more and moreattention In this study we attempted to discover the compounds with drug-like potential for ALL treatment from the componentsin TCM We applied virtual screen and QSAR models based on structure-based and ligand-based studies to identify the potentialTCM component compounds Our results show that the TCM compounds adenosine triphosphate manninotriose raffinose andstachyose could have potential to improve the side effects of MTX for ALL treatment

1 Introduction

Dihydrofolate reductase (DHFR) is essential in cellularmetabolism and cell growth It catalyzes the conversion ofdihydrofolate into tetrahydrofolate which is a carrier for themethyl group The methyl group carried by tetrahydrofolateis required for de novo synthesis of varieties of essentialmetabolites including amino acids lipids pyrimidines andpurines Methotrexate (MTX) a folate antagonist arrests cellgrowth by competitively binding to DHFR thereby blockingde novo synthesis of nucleotide precursors and inhibitingDNA synthesis [1] MTX has been found to be useful asan antineoplastic and immunosuppressive agent because itinhibits the proliferation of rapidly dividing malignant [2]

MTX tightly binding on DHFR is one of the most widelyused drugs in cancer treatment and is especially effective

in the treatment of acute lymphocytic leukemia [3] Inaddition its folate analogue is widely used in the treatment ofacute lymphoblastic leukemia (ALL) [4] ovarian cancer [5]osteosarcoma [6] rheumatoid arthritis [7] psoriasis [8] andinflammatory bowel disease [9] and for prevention of graft-versus-host disease after transplantation [10]

In the cells MTX acts by inhibiting two enzymes First asan analog of folate MTX is a powerful competitive inhibitorwith 1000-fold more potent than the natural substrate ofDHFR DHFR is responsible for converting dihydrofolate(FH2) to their active form tetrahydrofolate (FH4) which isa substrate of thymidylate synthase (TS) Second MTX isconverted to activemethotrexate polyglutamates (MTX-PGs)by folylpolyglutamate synthase [11 12] The polyglutamatedforms of MTX inhibit TS directly Due to these inhibitions

Hindawi Publishing CorporationEvidence-Based Complementary and Alternative MedicineVolume 2014 Article ID 601064 21 pageshttpdxdoiorg1011552014601064

2 Evidence-Based Complementary and Alternative Medicine

Table 1 Experimental pIC50 values for DHFR inhibitors [40]

Name R1 R2 X R3 pIC501 CH3 CH3 CH2 H 4712 CH3 CH3 CH2 41015840-CH3 460913lowast CH3 CH3 CH2 41015840-OCH3 423064 CH3 CH3 CH2 41015840-F 466155lowast CH3 CH3 CH2 41015840-Cl 452436 CH3 CH3 CH2 3101584041015840-diCl 489287lowast CH3 CH3 ndashO-CH2ndash H 716128 CH3 C2H5 ndashO-CH2ndash H 680979lowast H c-Pr ndashO-CH2ndash H 6261210 ndash(CH2)3ndash ndashO-CH2ndash H 6872911 ndash (CH2)4ndash ndashO-CH2ndash H 676212 ndash (CH2)5ndash ndashO-CH2ndash H 5747113 ndash (CH2)6ndash ndashO-CH2ndash H 5273314 ndash (CH2)4ndash ndashO-CH2CH2ndash H 7508615 ndash (CH2)5ndash ndashO-CH2CH2ndash H 8045816 ndash (CH2)4ndash ndashO-(CH2)3-Ondash H 769917 ndash (CH2)5ndash ndashO-(CH2)3-Ondash H 7494918 CH3 CH3 ndashO-(CH2)3-Ondash H 8221819 CH3 CH3 ndashO-(CH2)4-Ondash H 7568620 CH3 C2H5 ndashO-(CH2)3-Ondash H 8096921 H c-Pr ndashO-(CH2)3-Ondash H 8154922 ndash (CH2)4ndash ndashO-(CH2)3-Ondash H 869923lowast ndash (CH2)4ndash ndashO-(CH2)4-Ondash H 7376824 ndash (CH2)5ndash ndashO-(CH2)3-Ondash H 8154925 ndash (CH2)5ndash ndashO-(CH2)4-Ondash H 6806926 ndash(CH2)6ndash ndashO-(CH2)3-Ondash H 7958627 ndash(CH2)5ndash ndashO-(CH2)3-Ondash F 7823928 ndash(CH2)5ndash ndashO-(CH2)3-Ondash Cl 7853929 ndash(CH2)5ndash ndashO-(CH2)3-Ondash NO2 7823930 ndash(CH2)5ndash ndashO-(CH2)3-Ondash Me 7744731 ndash(CH2)5ndash ndashO-(CH2)3-Ondash t-Bu 7657632 ndash(CH2)5ndash ndashO-(CH2)3-Ondash OMe 8221833lowast ndash(CH2)5ndash ndashO-(CH2)3-Ondash CN 834 ndash(CH2)5ndash ndashO-(CH2)3-Ondash COCH3 7886135 ndash(CH2)5ndash ndashO-(CH2)3-Ondash SO2NH2 8221836lowast ndash(CH2)4ndash ndashO-(CH2)3-Ondash F 837 ndash(CH2)4ndash ndashO-(CH2)3-Ondash Cl 8154938 ndash(CH2)4ndash ndashO-(CH2)3-Ondash NO2 8096939lowast ndash(CH2)4ndash ndashO-(CH2)3-Ondash Me 840 ndash(CH2)4ndash ndashO-(CH2)3-Ondash t-Bu 7769641 ndash(CH2)4ndash ndashO-(CH2)3-Ondash OMe 7958642 ndash(CH2)4ndash ndashO-(CH2)3-Ondash CN 8096943 ndash(CH2)4ndash ndashO-(CH2)3-Ondash COCH3 8045844lowast ndash(CH2)4ndash ndashO-(CH2)3-N(Me)ndash H 7387245 ndash(CH2)4ndash ndashO-(CH2)3ndash H 74949MTX 85229lowasttest set

the cells will not be capable of de novo synthesis of purinesand thymidylate and thus DNA synthesis will be inhibited[13]

MTX

MTXIntracellularly

FH4

FH2

Purine synthesisDNA synthesis

NADPHSerine

Glycine

SHMT

dUMP

dTMP

MTX mechanism for intracellularly

FPGS

Methionin

MTRR

Homocysteine

Methyl-THF

Methylene-THF

DHFR

TS

H+

NADP+

MTX-PGs

+

Cell membraneinhibition mechanism of MTX in DNA synthesis pathway

Figure 1 Inhibitionmechanism ofMTX inDNA synthesis pathwayMTX methotrexate FPGS folylpolyglutamate synthetase MTX-PGs methotrexate polyglutamates DHFR dihydrofolate reduc-tase TS thymidylate synthase FH4 tetrahydrofolate FH2 dihy-drofolateMethylene-THF 510-methylenetetrahydrofolateMethyl-THF 5-methyltetrahydrofolate dUMP deoxyurindine-51015840-mon-ophosphate dTMP deoxythymidine-51015840-monophosphate MTRRmethionine synthase reductase SHMT serine hydroxymethyltrans-ferase

The primary action of MTX is inhibition of the enzymeDHFR which converts dihydrofolate (FH2) to tetrahydro-folate (FH4) [11 14] MTX-PGs exert a stronger inhibitionof DHFR and TS [15ndash17] Thus through direct inhibitionby MTX and due to lack of FH4 and accumulation ofFH2 deoxythymidine monophosphate synthesis and purinede novo synthesis is blocked which eventually lead toleukemic cell death bone marrow suppression gastroin-testinal mucositis liver toxicity and rarely alopecia [1415 18 19] In fact both MTX and natural folates undergopolyglutamylation catalyzed by the enzyme folylpolyglutamylsynthase The MTX-PGs ensure intracellular retention andfurthermore increase the affinity for the MTX-sensitiveenzymes [16 18 20] (Figure 1)

However MTX may lead to acute renal cytotoxicity [21]which is serious and potentially fatal in the spinal canal andmay occur after the administration of neurotoxicity [22ndash25]and hematological toxicity [26] caused by animal somaticcells and human bone marrow chromosomal lesions [27]which led to the hematopoietic system abnormalities [28]gastrointestinal toxicity [29] made multiorgan dysfunction[30] nephrotoxicity [31] made renal failure [31 32] andhepatotoxicitymade liver fibrosis [33] Higher concentrationsof long-chain MTX-PGs have been in the risk of gastroin-testinal and hepatic toxicity [12 34 35] Thus the lowertoxicity drugs are necessary to be developed Recently theincreasing numbers of mechanisms of different diseases havebeen clarified to detect the helpful target protein for diseasestreatment [36ndash49] and diseases treatments with traditionalChinese medicine (TCM) as complements are getting moreand more attention The compounds extracted from tradi-tional Chinese medicine have displayed their potential as

Evidence-Based Complementary and Alternative Medicine 3

Table 2 DHFR and TS docking score of TCM candidates

Index TCM candidate DHFR docking score TS docking score1 Adenosine triphosphate 2266790 18621702 Methyl 6-O-digalloyl-beta-D-glucopyranoside (II) 1626260 15417303 Methyl 46-di-O-galloyl-beta-D-glucopyranoside 1537500 14828804 Methyl 6-O-digalloyl-beta-D-glucopyranoside 1517650 15803505 Manninotriose 1297870 11460306 Forsythiaside 1296030 2799407 Isoacteoside 1245900 3061908 Rehmannioside B 1199930 7929209 Rehmannioside A 1164330 71397010 Raffinose 1154940 134212011 Cistanoside C 1124270 mdash12 Methyl 336-tri-O-galloyl-beta-D-glucopyranoside 1099470 20783013 Stachyose 1070940 8576014 Chlorogenic acid 1038080 mdash15 Jionoside D 1035050 39343016 Isochlorogenic acid 1029470 mdash17 Jionoside C 1023940 mdash18 Rutin 1011310 78816lowast MTX 970960 mdashlowastlowast MTX-PGs mdash 69671lowastcontrollowastlowastMethotrexate polyglutamate

Table 3 Predicted pharmacokinetic properties of TCM candidates and MTX

Index TCM candidate Pharmacokinetic propertiesAbsorption Solubility Hepatotoxicity PPB

1 Adenosine triphosphate 3 2 1 02 Chlorogenic acid 3 4 1 03 Cistanoside C 3 2 1 24 Forsythiaside 3 2 1 05 Isoacteoside 3 2 1 06 Isochlorogenic acid 3 4 1 07 Jionoside C 3 3 1 28 Jionoside D 3 2 1 29 Manninotriose 3 3 0 010 Methyl 46-di-O-galloyl-beta-D-glucopyranoside 3 2 1 011 Methyl 6-O-digalloyl-beta-D-glucopyranoside 3 2 1 012 Methyl 6-O-digalloyl-beta-D-glucopyranoside (II) 3 2 1 013 Methyl 336-tri-O-galloyl-beta-D-glucopyranoside 3 0 1 014 Raffinose 3 3 0 015 Rehmannioside A 3 4 1 016 Rehmannioside B 3 4 1 017 Rutin 3 1 1 218 Stachyose 3 1 0 0Control MTX 3 3 1 11Absorption (Human intestinal absorption) there are four prediction levels 0 (good absorption) 1 (moderate absorption) 2 (poor absorption) 3 (very poorabsorption)2Solubility there are gour prediction levels 0 (extremely low) 1 (very low but possible) 2 (low) 3 (good) 4 (optimal) 5 (too soluble) 6 (warning)3Hepatotoxicity there are four prediction levels 0 (nontoxic) 1 (toxic)4PPB (Plasma protein binding) there are there prediction levels 0 (binding is lt90) 1 (binding is gt90) 2 (binding gt95)


Table 4 Partial Least Square (PLS) analysis for CoMFA and CoMSIA models

Cross Validation Non-cross Validtion FractionONC 119902

21199032 SEE 119865 S E H D A

CoMFA7 05250 09630 02590 1362760 07970 02030 mdash mdash mdash

CoMSIAS 36 06350 09890 03040 196900 10000 00000 00000 00000 00000E mdash mdash mdash mdash mdash mdash mdash mdash mdash mdashH 2 06130 07760 05940 727070 00000 00000 10000 00000 00000D 7 04180 07160 07130 133480 00000 00000 00000 10000 00000A 1 00810 01600 11380 81640 00000 00000 00000 00000 10000SE 37 06050 09890 03250 167260 09980 00200 00000 00000 00000SH 2 05970 07790 05910 739120 03880 00000 06120 00000 00000SD 36 06670 09890 03020 199580 06350 00000 00000 03650 00000SA 30 07020 09890 02340 397820 07480 00000 00000 00000 02520EH 7 06270 09540 02860 1104680 00000 00500 09500 00000 00000ED 7 04130 07090 07210 129020 00000 00180 00000 09820 00000EA 2 00760 01830 11350 46860 00000 02000 00000 00000 08000HD 2 05780 07940 05690 811680 00000 00000 07220 02780 00000HA 2 05890 07910 05740 795410 00000 00000 07450 00000 02550DA 9 04300 07290 07160 104430 00000 00000 00000 07800 02200SHE 8 05850 09690 02400 1395820 03570 00440 06000 00000 00000SED 38 06500 09890 03490 141810 06340 00010 00000 03650 00000SEA 31 07030 09880 02430 357980 07420 00110 00000 00000 02470SHD 22 05780 09890 01830 893410 03070 00000 04490 02430 00000SHA 2 05800 07950 05680 814850 03130 00000 04980 00000 01900SDA 30 07170 09890 02320 403890 05640 00000 00000 02910 01450EDA 11 04240 07380 07250 84650 00000 00200 00000 07640 02150EHAlowast 11 05770 09800 01990 1489890 00000 00630 06910 00000 02460HAD 2 05550 08020 05580 852150 00000 00000 06150 02080 01770SEHD 23 05970 09890 01870 811730 02940 00230 04520 02310 00000SEHA 23 05970 09800 01880 804080 03000 00420 04620 00000 01960SEDA 31 07110 09890 02420 361870 05640 00050 00000 02840 01470SHDA 5 05630 09290 03470 1023970 02600 00000 03980 01920 01510EHDAlowast 12 06070 09820 01940 1435670 00000 00500 05880 02040 01580SEHDA 23 06120 09890 01880 803300 02690 00340 04020 01630 01330OCN Optimal number of componentsSEE Standard error of estimateF F-test valuelowastPrediction modelS StericH HydrophobicD Hydrogen bond donorA Hydrogen bone acceptorE Electrostatic

lead compounds against tumors [50ndash54] stroke [55ndash58] viralinfection [59ndash63] metabolic syndrome [64ndash66] diabetes[67] inflammation [62] and other diseases [68 69] For thistrend we attempted to discover the compounds with drug-like potential and lower toxicity for ALL treatment from thecomponents in traditional Chinese medicine

2 Materials and Methods

21 Virtual Screening The receptors human dihydrofolatereductase (DHFR) and human thymidylate synthase (TS)proteins were downloaded from Protein Data Bank of 1U72(PDB ID 1U72) [70] and 1HVY (PDB ID 1HVY) [71]


Table 5 Experimental and predicted pIC50 values of 45 DHFR inhibitors using the constructed CoMFA and CoMSIA models

DHFR inhibitors no Experimental pIC50 CoMFA CoMSIA EHDA CoMSIA EHAPredicted Residual Predicted Residual Predicted Residual

1 4710 4652 00580 4481 0229 4532 01782 4609 4606 00031 4635 minus0026 4662 minus00533lowast 4231 4576 minus03454 4333 minus0102 4407 minus01764 4662 5027 minus03655 4698 minus0037 4701 minus00395lowast 4524 4571 minus00467 4807 minus0283 4797 minus02736 4893 4476 04168 4723 0170 4651 02427lowast 7161 6810 03512 7287 minus0126 7359 minus01988 6810 6529 02807 6722 0088 6723 00879lowast 6261 6495 minus02338 6270 minus0009 6240 002110 6873 6648 02249 6808 0065 6832 004111 6762 6793 minus00310 6686 0076 6645 011712 5747 5749 minus00019 5767 minus0020 5705 004213 5273 5346 minus00727 5245 0028 5279 minus000614 7509 7454 00546 7494 0015 7522 minus001315 8046 8322 minus02762 8056 minus0010 8052 minus000616 7699 8127 minus04280 8130 minus0431 8110 minus041117 7495 7670 minus01751 7871 minus0376 7820 minus032518 8222 8079 01428 8130 0092 8105 011719 7569 7561 00076 7581 minus0012 7609 minus004020 8097 8207 minus01101 8105 minus0008 8240 minus014321 8155 8007 01479 8242 minus0087 8215 minus006022 8699 8127 05720 8130 0569 8110 058923lowast 7377 7636 minus02592 7325 0052 7318 005924 8155 7670 04849 7871 0284 7820 033525 6807 7113 minus03061 6902 minus0095 6824 minus001726 7959 7987 minus00284 7887 0072 7975 minus001627 7824 7763 00609 7981 minus0157 7955 minus013128 7854 7839 00149 7906 minus0052 7850 000429 7824 7843 minus00191 7824 0000 7827 minus000330 7745 7914 minus01693 7736 0009 7733 001231 7658 8069 minus04114 7665 minus0007 7654 000432 8222 8005 02168 7848 0374 7814 040833lowast 8000 8100 minus01000 7978 0022 8010 minus001034 7886 7455 04311 7947 minus0061 7811 007535 8222 7981 02408 8208 0014 8237 minus001536lowast 8000 8173 minus01730 8130 minus0130 8139 minus013937 8155 8180 minus00251 8170 minus0015 8187 minus003238 8097 8122 minus00251 8097 0000 8097 000039lowast 8000 7990 00100 8007 minus0007 8054 minus005440 7770 7683 00866 7832 minus0062 7697 007341 7959 8223 minus02644 7883 0076 7907 005242 8097 7974 01229 8040 0057 8150 minus005343 8046 7996 00498 8052 minus0006 8061 minus001544lowast 7387 7542 minus01548 7567 minus0180 7590 minus020345 7495 7449 00459 7484 0011 7516 minus0021lowasttest set


Table 6 Predicted bioactivity (pIC50) of MTX and TCM candidates using MLR Bayesian SVM CoMFA and CoMSIA models

Name MLR Bayesian SVM CoMFA CoMSIA EHDAlowast CoMSIA EHAlowastlowast

Adenosine triphosphate 64559 58145 87175 79640 78600 78350Methyl 6-O-digalloyl-beta-D-glucopyranoside (II) 275044 51810 80157 69800 66030 55170Methyl 46-di-O-galloyl-beta-D-glucopyranoside 277317 54868 84131 75490 65980 59300Methyl 6-O-digalloyl-beta-D-glucopyranoside 267188 52477 78936 68980 66620 56840Manninotriose 291034 51934 59247 76470 62450 53700Forsythiaside 299821 53595 85713 77140 80830 78950Isoacteoside 276319 63265 81255 76550 77990 75430Rehmannioside B 267291 43032 73293 69990 68000 58300Rehmannioside A 303632 44182 93324 67480 58070 46750Raffinose 328592 51647 84766 69350 59620 42830Cistanoside C 261802 57174 82029 76060 80200 79640Methyl 336-tri-O-galloyl-beta-D-glucopyranoside 307405 60369 83193 67670 63240 66300Stachyose 405491 59779 85055 74300 56830 44510Chlorogenic acid 173951 42335 78897 78080 79640 77680Jionoside D 260421 55238 82089 75080 74900 72820Isochlorogenic acid 161484 44196 74839 71990 63590 64480Jionoside C 237203 56640 82741 77600 70800 69110Rutin 303096 56910 82465 65720 80190 76830The pIC50 experimental values of MTX was 85229lowastEHDA model of CoMSIAlowastlowastEHA model of CoMSIA

We adopted the traditional Chinese medicine formulas thattreat acute lymphoblastic leukemia from database ldquoShanghaiInnovative ResearchCenter of Traditional ChineseMedicinerdquo(httpwwwsirc-tcmshcnenindexhtml) [72]The compo-nent compounds of these formulas were integrated with theherbs data from the TCMDatabaseTaiwan [73] and becamethe ALL disease-specific compound library Virtual screeningof candidates from the compound library was conductedusing the LigandFit Module of DS 25 under the Chemistryat HARvard Macromolecular Mechanics (CHARMm) forcefield DockScore was selected as output values Candidateswere ranked according to DockScore and pharmacokineticcharacteristics including absorption solubility blood brainbarrier (BBB) and plasma protein binding (PPB) werepredicted by ADMET protocols for each candidate

22 2D-Quantitative Structure Activity Relationship (2D-QSAR) Models In this study 45 candidates (Figure 2) withknown experimental pIC50 values [74] that have inhibitoryactivities toward DHFR were used in the QSAR studies(Table 1) The 45 known inhibitors were randomly dividedinto a training set of 36 candidates and a test set of 9 candi-datesThe chemical structures of these candidateswere drawnby ChemDraw Ultra 100 (CambridgeSoft Inc USA) andtransformed to 3D molecule models by Chem3D Ultra 100(CambridgeSoft Inc USA) Molecular descriptors for eachcandidate were calculated using the DS 25 CalculateMolecu-lar Property Module Genetic function approximation (GFA)model was used to select representative descriptors thatcorrelated (119903

2gt 08) to bioactivity (pIC50) which were used

N

N

NX

NH2

H2NR1

R2

R3

N

N

N

NN

NH2

H2N

O

COOH

COOH

H

MTX structure

Dihydrotriazine and spiro derivatives

Figure 2 Chemical structure of DHFR inhibitors [40]

to construct 2D-QSAR models The training set was used toconstruct multiple linear regression (MLR) support vectormachine (SVM) and Bayesian network (BN)modelsThe testset was used to test the accuracy of these models

221 Multiple Linear Regression (MLR) Model Multiplelinear regression [75] attempts to model the relationshipbetween two or more explanatory variables and a response


SIRC TCM

Virtual screening and dockingwith DHFR

Pharmacokinetic propertiesand ldquodrug-likerdquo potential

Literature search for DHFR inhibitors with pIC50

Virtual screening and docking with TS

Virtual screening and dockingOverall assessment of ldquodrug-likerdquo potential

Ligand-based bioactivity modeling

BNTMLR SVM CoMFA CoMSIA

Figure 3 The experimental flowchart

variable by fitting a linear equation to observed data Themodel was built in the form of equation as follows

pIC50

= 1198860+ 11988611199091+ 11988621199092+ sdot sdot sdot + 119886

119899119909119899 (1)

where 119909119894represents the 119894th molecular descriptor and 119886

119894is its

fitting coefficient The generated MLR model was validatedwith test dataset The square correlation coefficients (119877

2)

between predicted and actual pIC50 of the training set wasused to verify accuracy of themodelThis buildingmodel wasapplied to predict the pIC50 values of the TCM candidates

222 Support Vector Machine (SVM) Model SVM imple-ment classification or regression analysis with linear or non-linear algorithms [76] The algorithm identifies a maximum-margin hyper-plane to discriminate two class training sam-ples Samples on the margin are called the support vectorsLagrange multipliers and kernels were introduced to formthe final pattern separating regression model In this studyLibSVM [77ndash79] package was selected to build our regressionSVMmodelThe selected kernel was theGaussian radial basisfunction kernel equation

119870(119909119894 119909119896) = exp[

1003817100381710038171003817119909119894minus 119909119896

1003817100381710038171003817

2

21205902

] (2)

Cross-validation of the SVM model was also conductedfollowing the default settings in LibSVM [80] The generatedregression SVM model was validated with test dataset Thesquare correlation coefficients (119877

2) between predicted and

actual pIC50 of the training set was used to verify accuracyof the model This building model was applied to predict thepIC50 values of the TCM candidates

223 Bayesian Network Model We used the Bayes NetToolbox (BNT) inMatlab (httpscodegooglecompbnt) tocreate Bayesian network model [81] by the training data setAfter data discretization we applied linear regression analysis

for each pIC50 category in the training dataset For the 119894thpIC50 category with 119899 candidates let 119910

119894119895and 119909

119894119895119901represent

the pIC50 value and the 119901th descriptor value in the 119895thligand respectively The regression model of the data sets119910119894119895 1199091198941198951 119909

119894119895119901119899

119895=1is formulated as

119910119894= 119883119894120573119894+ 120576119894 (3)

where

119910119894=

[

[

[

[

[

1199101198941

1199101198942

119910119894119899

]

]

]

]

]

119883119894=

[

[

[

[

[

11990911989411

sdot sdot sdot 1199091198941119901

11990911989421

sdot sdot sdot 1199091198942119901

1199091198941198991

sdot sdot sdot 119909119894119899119901

]

]

]

]

]

(4)

and 120573119894and 120576119894are the regression coefficients and error term

in the 119894th pIC50 category We used ordinary least squares toestimate the unknown regression coefficient 120573

119894

120573119894= (119883119879

119894119883119894)

minus1

119883119879

119894119910119894 (5)

The Banjo (Bayesian network inference with Java objects)is software for structure learning of static Bayesian networks(BN) [82] It is implemented in JavaWe used training datasetto discover the relationships in the BN structure among thedescriptors and the pIC50 by the Banjo package After thatwe used test data to assess the accuracy of our algorithm Forthe test data 119863 the pIC50 category (119896) is predicted by thefollowing formula

119896 =

119899arg max119894=1

119875 (119894 | 119863) (6)

where 119894 represented the 119894th category of pIC50 and 119899 repre-sented the total number of the pIC50 categoriesThemarginalprobability 119875(119894 | 119863) can be calculated by BNT moduleFinally the pIC50 value is calculated as follows

pIC50 = 119883119896

120573119896 (7)


(1)

H2N

NN

NN

HO

HOP

P

P

O

O

OOO

O

OH

OH

OH

OH

(4)

HO

HO

HO

OO

O

O

O

O

OHOH

OH

OHHO

(2)

HO

HO

HO

OO

OO

O

O

OH

OH

OH

OH

OH

(3)

HO

HO

HO

HO

O

O

O

O

O

O

OH

OH

OH

OH

(5)

HO

HO

HOHO

HO

HO

OO

O

OO

OH

OH

OH

OH

OH

(9)

OO

OOOO

HO

HO

HO

HO

OH

OH

OHOH

OH

(7)

O

O

O

O O

OHO

HO

HO

OH OH

OH

OH

OH

OH

(6)HO

HO

HOOH

OH

OHOH OH

OHO O O O

O

O

(8)

HO

HO

HO

OHOH

OH

OH

O

OO

OOH

O

O

OH

(10)

OHOH

OH

OH

OHOH

HO

HO HO

HO

HO

O OO

OO

(a)

Figure 4 Continued


HO

HO

HO

HO

HO

HO

OO

O

O

O

O

O

OH

OH

(11)

(13) HOHO

HO HOOH OH

OH OHOH

OH

OHO O

O

O OO

O

OH

HO

HO

(15)

HO

O

O

O

OHO

O

OH

OH

OH

OHOH

OHO

O

(17)

HO

O

O

O

OOH OH

OHOH

OH

OH

O

O

MTX

O

OO

OH

OH

NN

NN

HN

H2N

2NH

O

O

(18)

OHOH

OH

OH

OH

OH

HO

HO

HO

HO

OO O

O

HNN

NN

N

MTX-PGs OH

OHNO

O

OH2N

2NH

O

(16)

OHOH

OHOO

HO

HO

HO

(14)

OH

OH

OH

OH

OO

O

HO

HO

(12)

O

OO

OO

OO

O

OHOH

OH

HOHO

HO

HOHO

HO

HO

(b)

Figure 4 (a)-(b) The chemical scaffolds of MTX MTX-PGs and TCM candidates for acute lymphoblastic leukemia treatment


O29 O30

O32Gln35

Glu30

NDP187

N1

Arg70

Lys68

(a)

O28O30

Gln35Glu30

NDP187

N9 Arg70

(b)

NDP187

O10

Arg70

(c)

O34

O12

NDP187

Asn64

(d)

O45O23

O34

O44

Asn64

NDP187

H86Lys68

Lys63

(e)

O27

UMP314

O28 Arg50

(f)

Asn112

UMP314

O28

O29O30

H43

Arg50

(g)

UMP314

O31

O32Arg50

(h)

Figure 5 Continued


UMP314

O30Met309

(i)

UMP314O33

O44H11

O42

Arg50

Asn112

Met309

Met311

(j)

Figure 5 Docking pose of MTX and TCM candidates with DHFR for (a) (b) (c) (d) and (e) Docking pose of MTX-PGs with TS for (f)(g) (h) (i) and (j) TCM candidates are shown in cyanThe cofactors are shown in purple In H-bond interactions nitrogen atoms are shownin blue hydrogen atoms are shown in gray oxygen atoms are shown in magenta hydrogen bonds are shown in red dotted line pi bonds areshown in orange solid line (a)MTX (b) and (g) adenosine triphosphate (c) and (h)manninotriose (d) and (i) raffinose (e) and (j) stachyoseand (f) MTX-PGs

The square correlation coefficients (1198772) between pre-dicted and actual pIC50 of the training set were used to verifyaccuracy of the model This building model was applied topredict the pIC50 values of the TCM candidates

23 3D-Quantitative Structure Activity Relationship (3D-QSAR) Models Comparative molecular field analysis(CoMFA) and comparative molecular similarity indicesanalysis (CoMSIA) were performed by Sybyl-X 111 (TriposInc St Louis MO USA) for DHFR inhibitors Lennard-Jones potential and Coulomb potential were employedto calculate steric and electrostatic interaction energiesThe two 3D-QSAR models were further evaluated by cross-validated correlation coefficient (1199022) and non-cross-validatedcorrelation coefficient (1199032) The correlation between the forcefield and biological activities was calculated by partial leastsquares (PLSs) method

The flowchart for the entire experimental procedure forTCM candidates screening is illustrated in Figure 3

3 Results and Discussion

31 Virtual Screening The virtual screening was performedby the LigandFitModule ofDS 25 in force field of CHARMmThe receptor binding sites were defined by the binding posi-tion ofMTX onDHFR protein and by the binding position ofMTX-PGs on TS protein The compounds from our librarywere docked into the two receptors In this protocol thereceptors were fixed and the ligands that complement thebinding sites were flexible in energy minimization processThe control compound used in this study was MTX whichcontains aromatic and heterocyclic rings (Figure 4)

The top eighteen results from DHFR docking score aretabulated in Table 2 The TS docking score for the eighteencandidates are also tabulated in Table 2 All the eighteenTCM candidates had higher Dock Scores than the controlmethotrexate (MTX) and MTX-PGs Chemical scaffolds ofMTX MTX-PGs and the eighteen TCM candidates areshown in Figure 4 Adsorption solubility hepatotoxicity andplasma protein binding were assessed to evaluate pharma-cokinetic properties of the selected candidates (Table 3)Considering the factor of hepatotoxicity we selected theTCM compounds adenosine triphosphate manninotrioseraffinose and stachyose for advanced study MTX and TCMcandidates had very poor absorption for human intestineBinding strength of the ligands to carrier proteins in the bloodstream is indicated by the plasma protein binding (PPB)value [21] MTX has more than 90 for PPB but adenosinetriphosphate manninotriose raffinose and stachyose wereless than 90 for PPB

Ligand-receptor interactions during docking are shownin Figures 5 and 6 MTX docked on DHFR (Figure 5(a))through four hydrogen bondings of Glu30 Gln35 Lys68and Arg70 Adenosne triphosphate formed three H-bondswith Glu30 Gln35 and Arg70 (Figure 5(b)) Manninotrioseformed H-bond with Arg28 (Figure 5(c)) Raffinose formedH-bonds with Asn64 and NDP (Figure 5(d)) Stachyoseformed H-bonds with Lys63 Asn64 and Lys68 (Figure 5(e))MTX-PGs docked on TS (Figure 5(f)) by single H-bondwith Arg50 Adenosne triphosphate manninotriose andstachyose docked onTS (Figures 5(g) 5(h) and 5(j)) by singleH-bond with Arg50 Raffinose docked on TS by single H-bond with Met309 (Figure 5(i))


254

276286

307

333

N1

C2

C3

C4C5

C6

N7

N8

N9

C10 C11

N12C13

N14 C15

C16C17

C18

C19 C20

C21

C22

O23N24

C25

C26

C27

C28

O29

O30

C31

O32

O33MTX

Phe34

Phe31

N

CA CB

CG

CD

CE NZ

C

O

Lys68

N

CA CB

CG

CD

NE CZ

NH1

NH2

C

OArg70

Asn64

N

CA

CB

CGCD

OE1OE2

C OGlu30

NCA

CB CGCD

OE1 NE2

C

O

Gln35

Ndp187

Val8

Ala9

Val115Ile7

Pro61

Leu67

Thr56

Ile60

(a)

276

264

N1C2

N3

C4

C5C6

N7

C8

N9

N10

C11

C12

C13

C14

O15

C16O17

O18

O19

P20O21

O22

O23

P24O25

O26

P27

O28

O29O30

Adenosine triphosphate

Phe34

Ndp187

NCA

CBCG

CD

OE1 NE2

C

O

Gln35

Asn64

Val8

NCA

CB

CG

CD

NECZ

NH1

NH2C

O

Arg70

Leu67

Phe31

Ile60

Ile7

Ala9Glu30

Thr56Val115

Leu22

Pro61

Tyr121

(b)

295

C1 C2

C3

C4O5

C6C7

O8

O9O10

O11

O12

C13

C14 C15

C16

C17C18

O19

O20

O21

O22 O23C24

C25

C26C27

C28

C29

O30

O31

O32

O33

O34

Manninotriose

Phe34

NCA

CB

CG

CD

NE

CZNH1

NH2

CO

Arg28

Phe31

Asn64

Ile60

Pro61

Pro26

Leu67

Ser59

Ndp187

Ligand bondNonligand bondHydrogen bond and

Nonligand residues involved

Corresponding atoms involvedin hydrophobic contact(s)

in hydrophobic contact(s)its length30

His53

(c)

274

280295

265311

317

C1

C2C3

C4

C5O6

O7 O8

C9

O10

O11

O12

C13C14

C15C16

C17C18

O19O20

O21

O22 O23

C24 C25

C26

C27O28

C29O30 O31

C32O33

O34

Raffinose

PA O1A

O2A

O5BC5B

C4BO4B

C3B

O3B

C2B

O2BC1B

N9A C8AN7A

C5AC6A

N6AN1A

C2A

N3A C4A

O3PN

O1N

O2N O5D C5D

C4D

O4DC3DO3D

C2DO2D

C1D

N1N C2NC3N C7N

O7N

N7NC4NC5NC6N

P2B

O1X

O2XO3X

Ndp187

N

CA

CB

CGOD1

ND2C

O

Asn64

Phe31

N

CA

CB OG

CO

Ser59

N CA

CBCG

CDNECZ

NH1 NH2

C

O

Arg28

Ile60

Phe34

Pro61Leu67

Leu22

Pro26





His53

(d)

Figure 6 Continued


247

319

303

279

261

C1

C2

C3C4

O5 C6C7

C8C9

C10

O11

C12

C13C14

C15

C16O17

C18

C19

C20

C21

C22

O23

C24

O25

O26

C27

O28

O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39

O40C41

O42

O43

O44

O45

Stachyose

N

CACB

CGOD1ND2

C

O

Asn64Phe31

N

CA

CB

CG

CD

CE

NZC

OLys68

N

CACB

CGCD

CE

NZ

C

O

Lys63

Pro61

Phe34

Gln35

Leu67

Pro26

Ile60

(e)

255

C1 N2

C3

C4

C5

N6

N7

C8

C9

N10N11

N12

C13

N14 C15

C16

C17

C18

C19

C20

C21

C22

N23

O24C25

C26 O27

O28

C29C30C31

O32O33

MTX-PGs

Met311

NCA

CB

CG

CD

NECZ

NH1NH2

CO

Arg50

Ile108Phe117

Ala111

Asn112

Leu221

Ump314

Thr51

Phe225

Ala312

Trp109

(f)

269

284

303279

283

280330

N1

C2

N3

C4

C5C6

N7C8

N9

N10

C11C12

C13

C14

O15

C16O17

O18

O19

P20 O21

O22

O23

P24O25

O26

P27

O28

O29

O30


N1

C2

N3C4

C5

C6 O2

O4

P

OP1OP2

OP3UMP314

N

CA

CB

CG

CD1

CD2

C

O

Leu221

Phe225

N

CACB

CGOD1

ND2

C

O

Asn112

N CA

CB

CG

CDNE

CZ

NH1NH2

C

OArg50

Ile108

Met311

N

CACB

CG

CDOE1

OE2

C

O

Glu87

Leu192

Trp109

Gly222

C1998400

O4998400 C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(g)

325

304

258

284

324

294

271

285

C1C2

C3

C4 O5C6 C7

O8

O9O10

O11

O12

C13

C14C15

C16

C17 C18

O19

O20

O21

O22O23

C24

C25C26

C27

C28C29

O30

O31

O32O33

O34Manninotriose

N1

C2

N3C4

C5C6

O2

O4P

OP1

OP2OP3

UMP314N CA

CB

CG

OD1

OD2

CO

Asp218

N

CA CB

CG

CD

NECZ

NH1

NH2

C

O

Arg50

Phe225

N

CACB

CGCD

OE1

OE2

CO

Glu87

Met311

Phe117

Val313

Asn112

Leu221

NCA

CB

CG

OD1

ND2

CO Asn226

Ile108

Ala312

Thr51

Trp109

Ala111

Leu192

Tyr258

C1998400

O4998400

C2998400

C3998400

C4998400

O5998400

O3998400

C5998400





His53

(h)

Figure 6 Continued


288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)

Figure 6 The Ligplot analysis of hydrophobic interactions between DHFR and TCM candidates and between TS and TCM candidates (a)MTXwith DHFR (b) and (g) adenosine triphosphate with DHFR and TS (c) and (h) manninotriose with DHFR and TS (d) and (i) raffinosewith DHFR and TS (e) and (j) stachyose with DHFR and TS and (f) MTX-PGs with DHFR and TS Bonds ligand bonds nonligand bondshydrogen bonds and hydrophobic are shown in purple orange olive green and brick red respectively Atoms nitrogen oxygen carbon andsulfur are shown in blue red black and yellow respectively

Analysis of hydrophobic interactions showed that MTXdocking onDHFRwasmore stable than the TCM candidatesComparing with chemical structures of the TCM candidatesit could be attributed to the larger size for MTX docking onDHFR (Figures 6(a) 6(b) 6(c) 6(d) and 6(e)) However theTCM candidates docking on TS weremore stable thanMTX-PGs due to hydrophobic interactions (Figures 6(f) 6(g) 6(h)6(i) and 6(j))

32 Bioactivity Prediction Using QSAR Models QSAR mod-els were constructed using known DHFR inhibitors [40]and applied for predicting molecular properties of theTCM ligands Molecular descriptors associated with bioac-tivity including BD Count Num RotatableBonds CHI V 1IAC Mean JX JY SC 3 C Jurs FNSA 1 Jurs RPCS JursSASA and Shadow Xlength were used to construct MLRmodel SVMmodel and Bayesian network model

Our MLR model was as followsGFATempModel 1 = 31623 + 25173 lowast HBD Count minus

047471lowastNum RotatableBonds minus 17664lowastCHI V 1minus 12997lowast IAC Mean minus 45669 lowast JX + 3662 lowast JY + 011612 lowast SC 3 C +18941 lowast Jurs FNSA 1 minus 48012 lowast Jurs RPCS + 0029451 lowast

Jurs SASA minus 0084377 lowast Shadow XlengthIn CoMFAmodel the steric fields were the primary con-

tributing factor In CoMSIA various factors were consideredand modeled The optimum CoMSIA models were ldquoEHAmodelrdquo and ldquoEHDA modelrdquo based on high 119902

2 high 1199032 and

low SEE values (Table 4) The ldquoEHA modelrdquo was consistingof electrostatic field and hydrophobic and hydrogen bondacceptor The ldquoEHDA modelrdquo was consisting of electrostaticfield and hydrophobic and hydrogen bond donor and hydro-gen bond acceptor The CoMFA model and CoMSIA modelof EHDA and of EHA were with ONC of 7 11 and 12respectively


MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

Training set R2= 0936

(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)

Figure 7 Correlation of observed and predicted activity (pIC50) using 2D-QSAR models and 3D-QSAR models MLR Bayesian networkand SVM were 2D-QSAR model CoMFA CoMSIA EHDA and CoMSIA EHA were 3D-QSAR model


(a) (b)

(c) (d)

(e)

Figure 8 The CoMFA contour maps for DHFR (a) MTX (b) adenosine triphosphate (c) manninotriose (d) raffinose and (e) stachyoseGreen and yellow contours denote regions favoring and disfavoring steric fields respectively Blue and red contours denote regions favoringand disfavoring electrostatic fields respectively

Experimental and predicted pIC50 values of 45 DHFRinhibitors using CoMFA and CoMSIA models are shown inTable 5 Residuals calculated from the differences betweenobserved and predicted pIC50 values ranged betweenminus03655 and 04311 for the CoMFA between minus0411 and 0589for the CoMSIA with ldquoEHA modelrdquo and between minus0431 and0569 for CoMSIA with ldquoEHDA modelrdquo

The correlations between the predicted and actual bioac-tivity for DHFR inhibitors are shown in Figure 7 The 119877

2

values are 0936 for MLR 0734 for Bayesian network 0884

for SVM 0957 for CoMFA 0977 for CoMSIA with EHAmodel and 0978 for CoMSIA with EHDA model implicatehigh correlation High correlation coefficients validated thereliability of the constructed CoMFA and CoMSIA modelsThe predicted bioactivity values of TCM candidates by 2D-QSAR and 3D-QSAR models are listed in Table 6

33 The Contour Maps of CoMFA and CoMSIA ModelsLigand activities of MTX and the TCM candidates can be


(a) (b)

(c) (d)

(e)

Figure 9 The CoMSIA contour maps of EHA model for DHFR (a) MTX (b) adenosine triphosphate (c) manninotriose (d) raffinose and(e) stachyose Blue and orange contours denote regions favoring and disfavoring electrostatic fields respectively Yellow and white contoursdenote regions favoring and disfavoring hydrophobic fields respectively Green and red contours denote regions favoring and disfavoringH-bond acceptor fields respectively

predicted based on the 3D-QSAR contour map includ-ing features in steric field hydrophobic field and H-bonddonoracceptor characteristics MTX and the TCM candi-dates contoured well to the steric features of the CoMFAin Figure 8 CoMSIA map provides more information withregard to bioactivity differences for ldquoEHA modelrdquo andldquoEHDA modelrdquo in Figures 9 and 10 respectively From theconsistent results observed among the 3D-QSAR modelsvalidations we inferred that adenosine triphosphate man-ninotriose raffinose and stachyose of TCMcandidatesmighthave good biological activity for DHFR

Contour to steric favoring and hydrophobic favoringregions was observed for adenosine triphosphate man-ninotriose raffinose and stachyose Consistent with thedocking pose contour (Figures 8 9 and 10) we propose thatthe four TCM candidates maymaintain bioactivity for DHFRunder dynamic conditions in physiological environments

4 Conclusion

DHFR andTS proteins are key regulators in de novo synthesisof purines and thymidylate Inhibiton of these proteinshas the potential for treating acute lymphoblastic leukemia


(a) (b)

(c) (d)

(e)

Figure 10TheCoMSIA contourmaps of EHDAmodel for DHFR (a)MTX (b) adenosine triphosphate (c)manninotriose (d) raffinose and(e) stachyose Blue and orange contours denote regions favoring and disfavoring electrostatic fields respectively Yellow and white contoursdenote regions favoring and disfavoring hydrophobic fields respectively Green and red contours denote regions favoring and disfavoringH-bond acceptor fields respectively Cyan and purple contours denote regions favoring and disfavoring H-bond donor fields respectively

In this study we applied virtual screen and QSAR modelsbased on structure-based and ligand-based methods in orderto identify the potential TCM compounds The TCM com-pounds adenosine triphosphate manninotriose raffinoseand stachyose could bind on DHFR and TS specifically andhad lowhepatotoxicityTheseTCMcompounds had potentialto improve the side effects of MTX for ALL treatment

Conflict of InterestsThe authors declare that they have no conflict of interestsregarding the publication of this paper

Acknowledgments

The research was supported by Grants from the NationalScience Council of Taiwan (NSC102-2632-E-468-001-MY3NSC102-2325-B039-001 and NSC102-2221-E-468-027-) AsiaUniversity (101-ASIA-24 101-ASIA-59 ASIA100-CMU-2 andASIA101-CMU-2) and China Medical University Hos-pital (DMR-103-001 DMR-103-058 and DMR-103-096)This study is also supported in part by Taiwan Depart-ment of Health Clinical Trial and Research Center ofExcellence (DOH102-TD-B-111-004) and Taiwan Depart-ment of Health Cancer Research Center of Excellence


(MOHW103-TD-B-111-03) and CMU under the Aim forTop University Plan of the Ministry of Education Tai-wan

References

[1] L H Hartwell andM B Kastan ldquoCell cycle control and cancerrdquoScience vol 266 no 5192 pp 1821ndash1828 1994

[2] M J Chen T Shimada and A D Moulton ldquoThe functionalhuman dihydrofolate reductase generdquo Journal of BiologicalChemistry vol 259 no 6 pp 3933ndash3943 1984

[3] Y C Hsieh P Tedeschi R A Lawal et al ldquoEnhanced degra-dation of dihydrofolate reductase through inhibition of NADkinase by nicotinamide analogsrdquoMolecular Pharmacology vol83 no 2 pp 339ndash353 2013

[4] M Krajinovic and A Moghrabi ldquoPharmacogenetics ofmethotrexaterdquo Pharmacogenomics vol 5 no 7 pp 819ndash8342004

[5] G Toffoli A Russo F Innocenti et al ldquoEffect of methylenete-trahydrofolate reductase 677CrarrT polymorphism on toxicityand homocysteine plasma level after chronic methotrexatetreatment of ovarian cancer patientsrdquo International Journal ofCancer vol 103 no 3 pp 294ndash299 2003

[6] A Patino-Garcıa M Zalacaın LMarrodanM San-Julian andL Sierrasesumaga ldquoMethotrexate in pediatric osteosarcomaresponse and toxicity in relation to genetic polymorphisms anddihydrofolate reductase and reduced folate carrier 1 expressionrdquoJournal of Pediatrics vol 154 no 5 pp 688ndash693 2009

[7] P Ranganathan ldquoAn update onmethotrexate pharmacogeneticsin rheumatoid arthritisrdquo Pharmacogenomics vol 9 no 4 pp439ndash451 2008

[8] E Campalani M Arenas A M Marinaki C M LewisJ N W N Barker and C H Smith ldquoPolymorphisms infolate pyrimidine and purine metabolism are associated withefficacy and toxicity of methotrexate in psoriasisrdquo Journal ofInvestigative Dermatology vol 127 no 8 pp 1860ndash1867 2007

[9] K R Herrlinger J R F Cummings M C N M Barnardo MSchwab T Ahmad and D P Jewell ldquoThe pharmacogenetics ofmethotrexate in inflammatory bowel diseaserdquo Pharmacogenet-ics and Genomics vol 15 no 10 pp 705ndash711 2005

[10] C M Ulrich Y Yasui R Storb et al ldquoPharmacogenetics ofmethotrexate toxicity among marrow transplantation patientsvaries with the methylenetetrahydrofolate reductase C677Tpolymorphismrdquo Blood vol 98 no 1 pp 231ndash234 2001

[11] T S Mikkelsen C F Thorn J J Yang et al ldquoPharmGKB sum-mary methotrexate pathwayrdquo Pharmacogenetics and Genomicsvol 21 no 10 pp 679ndash686 2011

[12] J C Barredo T W Synold J Laver et al ldquoDifferences in con-stitutive and post-methotrexate folylpolyglutamate synthetaseactivity in B-lineage and T-lineage leukemiardquo Blood vol 84 no2 pp 564ndash569 1994

[13] L Huang W J E Tissing R de Jonge B D van Zelst andR Pieters ldquoPolymorphisms in folate-related genes associationwith side effects of high-dose methotrexate in childhood acutelymphoblastic leukemiardquo Leukemia vol 22 no 9 pp 1798ndash1800 2008

[14] R Gorlick E Goker T Trippett et al ldquoIntrinsic and acquiredresistance to methotrexate in acute leukemiardquo New EnglandJournal of Medicine vol 335 no 14 pp 1041ndash1048 1996

[15] B A Chabner C J Allegra and G A Curt ldquoPolyglutamationof methotrexate is Methotrexate a prodrugrdquo Journal of ClinicalInvestigation vol 76 no 3 pp 907ndash912 1985

[16] K Schmiegelow ldquoAdvances in individual prediction ofmethotrexate toxicity a reviewrdquo British Journal of Haematologyvol 146 no 5 pp 489ndash503 2009

[17] S A Jacobs RHAdamson andBA Chabner ldquoStoichiometricinhibition of mammalian dihydrofolate reductase by the 120574

glutamyl metabolite of methotrexate 4 amino 4 deoxy N10methylpteroylglutamyl 120574 glutamaterdquo Biochemical and Biophysi-cal Research Communications vol 63 no 3 pp 692ndash698 1975

[18] A K Fotoohi and F Albertioni ldquoMechanisms of antifolate resis-tance and methotrexate efficacy in leukemia cellsrdquo Leukemiaand Lymphoma vol 49 no 3 pp 410ndash426 2008

[19] J C White and I D Goldman ldquoMechanism of action ofmethotrexate IV Free intracellular methotrexate required tosuppress dihydrofolate reduction to tetrahydrofolate by Ehrlichascites tumor cells in vitrordquoMolecular Pharmacology vol 12 no5 pp 711ndash719 1976

[20] CM Baugh C L Krumdieck andMGNair ldquoPolygammaglu-tamylmetabolites ofmethotrexaterdquoBiochemical andBiophysicalResearch Communications vol 52 no 1 pp 27ndash34 1973

[21] I C Hung S S Chang P C Chang C C Lee and CY C Chen ldquoMemory enhancement by traditional Chinesemedicinerdquo Journal of Biomolecular Structure amp Dynamics vol31 no 12 pp 1411ndash1439 2013

[22] S Kishi J Griener C Cheng et al ldquoHomocysteine pharmaco-genetics and neurotoxicity in children with leukemiardquo Journalof Clinical Oncology vol 21 no 16 pp 3084ndash3091 2003

[23] D H Mahoney Jr J J Shuster R Nitschke et al ldquoAcuteneurotoxicity in children with B-precursor acute lymphoidleukemia an association with intermediate-dose intravenousmethotrexate and intrathecal triple therapymdasha pediatric oncol-ogy group studyrdquo Journal of Clinical Oncology vol 16 no 5 pp1712ndash1722 1998

[24] G Osterlundh I Kjellmer B Lannering L Rosengren UA Nilsson and I Marky ldquoNeurochemical markers of braindamage in cerebrospinal fluid during induction treatment ofacute lymphoblastic leukemia in childrenrdquo Pediatric Blood andCancer vol 50 no 4 pp 793ndash798 2008

[25] A Shuper B Stark L Kornreich I J Cohen G Avrahami andI Yaniv ldquoMethotrexate-related neurotoxicity in the treatmentof childhood acute lymphoblastic leukemiardquoThe Israel MedicalAssociation Journal vol 4 no 11 pp 1050ndash1053 2002

[26] I Costea A Moghrabi C Laverdiere A Graziani and MKrajinovic ldquoFolate cycle gene variants and chemotherapy tox-icity in pediatric patients with acute lymphoblastic leukemiardquoHaematologica vol 91 no 8 pp 1113ndash1116 2006

[27] R C Choudhury S K Ghosh and A K Palo ldquoCytogenetictoxicity ofmethotrexate inmouse bonemarrowrdquoEnvironmentalToxicology and Pharmacology vol 8 no 3 pp 191ndash196 2000

[28] L R Belur R I James C May et al ldquoMethotrexate precondi-tioning allows sufficient engraftment to confer drug resistancein mice transplanted with marrow expressing drug-resistantdihydrofolate reductase activityrdquo Journal of Pharmacology andExperimental Therapeutics vol 314 no 2 pp 668ndash674 2005

[29] S L Whittle and R A Hughes ldquoFolate supplementationand methotrexate treatment in rheumatoid arthritis a reviewrdquoRheumatology vol 43 no 3 pp 267ndash271 2004

[30] S Saigal R K Singh and B Poddar ldquoAcute methotrexatetoxicity presenting asmultiorgan failure and acute pneumonitisa rare case reportrdquo Indian Journal of Critical Care Medicine vol16 no 4 pp 225ndash227 2012


[31] B C Widemann and P C Adamson ldquoUnderstanding andmanaging methotrexate nephrotoxicityrdquo Oncologist vol 11 no6 pp 694ndash703 2006

[32] S G Yarlagadda and M A Perazella ldquoDrug-induced crystalnephropathy an updaterdquo Expert Opinion on Drug Safety vol7 no 2 pp 147ndash158 2008

[33] PHalonen JMattila T RuuskaMK Salo andAMakipernaaldquoLiver histology after current intensified therapy for childhoodacute lymphoblastic leukemia microvesicular fatty change andsiderosis are themain findingsrdquoMedical and Pediatric Oncologyvol 40 no 3 pp 148ndash154 2003

[34] T Dervieux D Furst D O Lein et al ldquoPolyglutamationof methotrexate with common polymorphisms in reducedfolate carrier aminoimidazole carboxamide ribonucleotidetransformylase and thymidylate synthase are associated withmethotrexate effects in rheumatoid arthritisrdquo Arthritis andRheumatism vol 50 no 9 pp 2766ndash2774 2004

[35] M L Becker R Gaedigk L Van Haandel et al ldquoThe effect ofgenotype on methotrexate polyglutamate variability in juvenileidiopathic arthritis and association with drug responserdquoArthri-tis and Rheumatism vol 63 no 1 pp 276ndash285 2011

[36] C-H Wang W-D Lin D-T Bau et al ldquoAppearance ofacanthosis nigricansmay precede obesity an involvement of theinsulinIGF receptor signaling pathwayrdquoBioMedicine vol 3 no2 pp 82ndash87 2013

[37] M-C Lin S-Y Tsai F-Y Wang et al ldquoLeptin induces cellinvasion and the upregulation of matrilysin in human coloncancer cellsrdquo BioMedicine vol 3 no 4 pp 174ndash180 2013

[38] I C Chou W-D Lin C-H Wang et al ldquoAssociation analysisbetween Tourettersquos syndrome and two dopamine genes (DAT1DBH) in Taiwanese childrenrdquo BioMedicine vol 3 no 2 pp 88ndash91 2013

[39] T Yamamoto W-C Hung T Takano and A NishiyamaldquoGenetic nature and virulence of community-associatedmethicillin-resistant Staphylococcus aureusrdquo BioMedicine vol3 no 1 pp 2ndash18 2013

[40] Y-M Chang B K Velmurugan W W Kuo et al ldquoInhibitoryeffect of alpinate Oxyphyllae fructus extracts on Ang II-induced cardiac pathological remodeling-related pathways inH9c2 cardiomyoblast cellsrdquo BioMedicine vol 3 no 4 pp 148ndash152 2013

[41] S P Mahamuni R D Khose F Menaa and S L BadoleldquoTherapeutic approaches to drug targets in hyperlipidemiardquoBioMedicine vol 2 no 4 pp 137ndash146 2012

[42] Y-T Chang W-D Lin Z-N Chin et al ldquoNonketotic hyper-glycinemia a case report and brief reviewrdquo BioMedicine vol 2no 2 pp 80ndash82 2012

[43] W-Y LinH-P Liu J-S Chang et al ldquoGenetic variationswithinthe PSORS1 region affect Kawasaki disease development andcoronary artery aneurysm formationrdquo BioMedicine vol 3 no2 pp 73ndash81 2013

[44] I C Chou W-D Lin C-H Wang et al ldquoMobius syndrome ina male with XXXY mosaicismrdquo BioMedicine vol 3 no 2 pp102ndash104 2013

[45] D-Y Lin F-J Tsai C-H Tsai and C-Y Huang ldquoMechanismsgoverning the protective effect of 17120573-estradiol and estrogenreceptors against cardiomyocyte injuryrdquo BioMedicine vol 1 no1 pp 21ndash28 2011

[46] C-H Wang W-D Lin and F-J Tsai ldquoCraniofacial dysmor-phism what is your diagnosisrdquo BioMedicine vol 2 no 2 pp49ndash50 2012

[47] C C Lee C-H Tsai L Wan et al ldquoIncreased incidence ofParkinsonism among Chinese with 120573-glucosidase mutation incentral Taiwanrdquo BioMedicine3 no 2 pp 92ndash94 2013

[48] F-J Tsai ldquoBiomedicine brings the future nearerrdquo BioMedicinevol 1 no 1 p 1 2011

[49] F-J Tsai ldquoRare diseases a mysterious puzzlerdquo BioMedicine vol3 no 2 p 65 2013

[50] Y A Tsou K C Chen S S Chang Y R Wen and CY Chen ldquoA possible strategy against head and neck cancerin silico investigation of three-in-one inhibitorsrdquo Journal ofBiomolecular Structure amp Dynamics vol 31 no 12 pp 1358ndash1369 2013

[51] Y A Tsou K C Chen H C Lin S S Chang and C Y CChen ldquoUroporphyrinogen decarboxylase as a potential targetfor specific components of traditional Chinese Medicine avirtual screening and molecular dynamics studyrdquo PLoS ONEvol 7 no 11 2012

[52] S C Yang S S Chang H Y Chen and C Y C ChenldquoIdentification of Potent EGFR Inhibitors from TCMDatabaseTaiwanrdquo PLoS Computational Biology vol 7no 10 2011

[53] C-Y Chen and C Y-C Chen ldquoInsights into designing thedual-targeted HER2HSP90 inhibitorsrdquo Journal of MolecularGraphics and Modelling vol 29 no 1 pp 21ndash31 2010

[54] H-J Huang K-J Lee H W Yu et al ldquoStructure-based andligand-based drug design for HER 2 receptorrdquo Journal ofBiomolecular Structure amp Dynamics vol 28 no 1 pp 23ndash372010

[55] W Ieongtou S S Chang D Wu et al ldquoMolecular levelactivation insights from a NR2ANR2B agonistrdquo Journal ofBiomolecular Structure amp Dynamics 2013

[56] K-C Chen and C Yu-Chian Chen ldquoStroke prevention bytraditional Chinese medicine A genetic algorithm supportvectormachine andmolecular dynamics approachrdquo SoftMattervol 7 no 8 pp 4001ndash4008 2011

[57] K-C Chen K-W Chang H-Y Chen and C Y-C ChenldquoTraditional Chinese medicine a solution for reducing dualstroke risk factors at oncerdquo Molecular BioSystems vol 7 no 9pp 2711ndash2719 2011

[58] T-T Chang K-C Chen K-W Chang et al ldquoIn silico phar-macology suggests ginger extracts may reduce stroke risksrdquoMolecular BioSystems vol 7 no 9 pp 2702ndash2710 2011

[59] H J Huang Y R Jian and C Y Chen ldquoTraditional Chinesemedicine application in HIV an in silico studyrdquo Journal ofBiomolecular Structure ampDynamics vol 32 no 1 pp 1ndash12 2014

[60] C-H Lin T-T Chang M-F Sun et al ldquoPotent inhibitordesign against H1N1 swine influenza structure-based andmolecular dynamics analysis for M2 inhibitors from traditionalChinese medicine databaserdquo Journal of Biomolecular Structureamp Dynamics vol 28 no 4 pp 471ndash482 2011

[61] T-T Chang M-F Sun H-Y Chen et al ldquoScreening from theworldrsquos largest TCM database against H1N1 virusrdquo Journal ofBiomolecular Structure amp Dynamics vol 28 no 5 pp 773ndash7862011

[62] S-S Chang H-J Huang and C Y-C Chen ldquoTwo birdswith one stone Possible dual-targeting H1N1 inhibitors fromtraditional Chinese medicinerdquo PLoS Computational Biologyvol 7 no 12 Article ID e1002315 2011

[63] C Y Chen Y H Chang D T Bau et al ldquoLigand-based dualtarget drug design for H1N1 swine flumdasha preliminary firststudyrdquo Journal of Biomolecular Structure amp Dynamics vol 27no 2 pp 171ndash178 2009


[64] K C Chen S S Chang H J Huang et al ldquoThree-in-oneagonists for PPAR-alpha PPAR-gamma and PPAR-delta fromtraditional Chinesemedicinerdquo Journal of Biomolecular Structureamp Dynamics vol 30 no 6 pp 662ndash683 2012

[65] P-C Chang J-D Wang M-M Lee et al ldquoLose weight withtraditional Chinese medicine Potential suppression of fatmass and obesity-associated proteinrdquo Journal of BiomolecularStructure amp Dynamics vol 29 no 3 pp 471ndash483 2011

[66] H J Huang K J Lee H W Yu et al ldquoA novel strategy fordesigning the selective PPAR agonist by the ldquoSum of Activityrdquomodelrdquo Journal of Biomolecular Structure amp Dynamics vol 28no 2 pp 187ndash200 2010

[67] K C Chen S S Chang F J Tsai and C Y Chen ldquoHanethnicity-specific type 2 diabetic treatment from traditionalChinese medicinerdquo Journal of Biomolecular Structure ampDynamics vol 31 no 11 pp 1219ndash1235 2013

[68] W I Tou S S Chang C C Lee and C Y Chen ldquoDrugdesign for neuropathic pain regulation from traditional Chinesemedicinerdquo Scientific Reports vol 3 p 844 2013

[69] K C Chen Y R Jian M F Sun et al ldquoInvestigation of silentinformation regulator 1 (Sirt1) agonists from Traditional Chi-nese Medicinerdquo Journal of Biomolecular Structure amp Dynamicsvol 31 no 11 pp 1207ndash1218 2013

[70] V Cody J R Luft andW Pangborn ldquoUnderstanding the role ofLeu22 variants in methotrexate resistance comparison of wild-type and Leu22Arg variant mouse and human dihydrofolatereductase ternary crystal complexes with methotrexate andNADPHrdquo Acta Crystallographica Section D Biological Crystal-lography vol 61 no 2 pp 147ndash155 2005

[71] J Phan S Koli W Minor R B Dunlap S H Berger andL Lebioda ldquoHuman thymidylate synthase is in the closedconformation when complexed with dUMP and raltitrexed anantifolate drugrdquo Biochemistry vol 40 no 7 pp 1897ndash1902 2001

[72] Shanghai Innovative Research Center of Traditional ChineseMedicine (SIRCTCM) SIRCoTCM AddNo1 Building439 Chunxiao RoadZhangjiang Hi-tech ParkShanghai 2012

[73] C Y-C Chen ldquoTCM DatabaseTaiwan the worldrsquos largesttraditional Chinese medicine database for drug screening InSilicordquo PLoS ONE vol 6 no 1 Article ID e15939 2011

[74] X Ma G Xiang C-W Yap and W-K Chui ldquo3D-QSAR Studyon dihydro-135-triazines and their spiro derivatives as DHFRinhibitors by comparative molecular field analysis (CoMFA)rdquoBioorganic and Medicinal Chemistry Letters vol 22 no 9 pp3194ndash3197 2012

[75] B K Slinker and S A Glantz ldquoMultiple linear regressionaccounting formultiple simultaneous determinants of a contin-uous dependent variablerdquo Circulation vol 117 no 13 pp 1732ndash1737 2008

[76] V Vapnik ldquoPattern recognition using generalized portraitmethodrdquo Automation and Remote Control vol 24 pp 774ndash7801963

[77] O Ivanciuc ldquoApplications of support vector machines in chem-istryrdquoReviews in Computational Chemistry vol 23 pp 291ndash4002007

[78] V Vapnik The Nature of Statistical Learning Theory Springer1995

[79] C-C Chang and C-J Lin ldquoLIBSVM a Library for supportvector machinesrdquo ACM Transactions on Intelligent Systems andTechnology vol 2 no 3 article 27 2011

[80] R Burbidge M Trotter B Buxton and S Holden ldquoDrugdesign by machine learning support vector machines for

pharmaceutical data analysisrdquo Computers and Chemistry vol26 no 1 pp 5ndash14 2001

[81] J Yu V A Smith P P Wang A J Hartemink and E D JarvisldquoAdvances to Bayesian network inference for generating causalnetworks from observational biological datardquo Bioinformaticsvol 20 no 18 pp 3594ndash3603 2004

[82] N Friedman M Linial I Nachman and D Persquoer ldquoUsingBayesian networks to analyze expression datardquo Journal ofComputational Biology vol 7 no 3-4 pp 601ndash620 2000

Submit your manuscripts athttpwwwhindawicom

Stem CellsInternational

Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014


MEDIATORSINFLAMMATION

of


Behavioural Neurology

EndocrinologyInternational Journal of



Disease Markers


BioMed Research International

OncologyJournal of



Oxidative Medicine and Cellular Longevity


PPAR Research

The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014

Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014

Journal of

ObesityJournal of



Computational and Mathematical Methods in Medicine

OphthalmologyJournal of


Diabetes ResearchJournal of



Research and TreatmentAIDS


Gastroenterology Research and Practice


Parkinsonrsquos Disease

Evidence-Based Complementary and Alternative Medicine

Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom


Table 1 Experimental pIC50 values for DHFR inhibitors [40]

Name R1 R2 X R3 pIC501 CH3 CH3 CH2 H 4712 CH3 CH3 CH2 41015840-CH3 460913lowast CH3 CH3 CH2 41015840-OCH3 423064 CH3 CH3 CH2 41015840-F 466155lowast CH3 CH3 CH2 41015840-Cl 452436 CH3 CH3 CH2 3101584041015840-diCl 489287lowast CH3 CH3 ndashO-CH2ndash H 716128 CH3 C2H5 ndashO-CH2ndash H 680979lowast H c-Pr ndashO-CH2ndash H 6261210 ndash(CH2)3ndash ndashO-CH2ndash H 6872911 ndash (CH2)4ndash ndashO-CH2ndash H 676212 ndash (CH2)5ndash ndashO-CH2ndash H 5747113 ndash (CH2)6ndash ndashO-CH2ndash H 5273314 ndash (CH2)4ndash ndashO-CH2CH2ndash H 7508615 ndash (CH2)5ndash ndashO-CH2CH2ndash H 8045816 ndash (CH2)4ndash ndashO-(CH2)3-Ondash H 769917 ndash (CH2)5ndash ndashO-(CH2)3-Ondash H 7494918 CH3 CH3 ndashO-(CH2)3-Ondash H 8221819 CH3 CH3 ndashO-(CH2)4-Ondash H 7568620 CH3 C2H5 ndashO-(CH2)3-Ondash H 8096921 H c-Pr ndashO-(CH2)3-Ondash H 8154922 ndash (CH2)4ndash ndashO-(CH2)3-Ondash H 869923lowast ndash (CH2)4ndash ndashO-(CH2)4-Ondash H 7376824 ndash (CH2)5ndash ndashO-(CH2)3-Ondash H 8154925 ndash (CH2)5ndash ndashO-(CH2)4-Ondash H 6806926 ndash(CH2)6ndash ndashO-(CH2)3-Ondash H 7958627 ndash(CH2)5ndash ndashO-(CH2)3-Ondash F 7823928 ndash(CH2)5ndash ndashO-(CH2)3-Ondash Cl 7853929 ndash(CH2)5ndash ndashO-(CH2)3-Ondash NO2 7823930 ndash(CH2)5ndash ndashO-(CH2)3-Ondash Me 7744731 ndash(CH2)5ndash ndashO-(CH2)3-Ondash t-Bu 7657632 ndash(CH2)5ndash ndashO-(CH2)3-Ondash OMe 8221833lowast ndash(CH2)5ndash ndashO-(CH2)3-Ondash CN 834 ndash(CH2)5ndash ndashO-(CH2)3-Ondash COCH3 7886135 ndash(CH2)5ndash ndashO-(CH2)3-Ondash SO2NH2 8221836lowast ndash(CH2)4ndash ndashO-(CH2)3-Ondash F 837 ndash(CH2)4ndash ndashO-(CH2)3-Ondash Cl 8154938 ndash(CH2)4ndash ndashO-(CH2)3-Ondash NO2 8096939lowast ndash(CH2)4ndash ndashO-(CH2)3-Ondash Me 840 ndash(CH2)4ndash ndashO-(CH2)3-Ondash t-Bu 7769641 ndash(CH2)4ndash ndashO-(CH2)3-Ondash OMe 7958642 ndash(CH2)4ndash ndashO-(CH2)3-Ondash CN 8096943 ndash(CH2)4ndash ndashO-(CH2)3-Ondash COCH3 8045844lowast ndash(CH2)4ndash ndashO-(CH2)3-N(Me)ndash H 7387245 ndash(CH2)4ndash ndashO-(CH2)3ndash H 74949MTX 85229lowasttest set

the cells will not be capable of de novo synthesis of purinesand thymidylate and thus DNA synthesis will be inhibited[13]

MTX

MTXIntracellularly

FH4

FH2

Purine synthesisDNA synthesis

NADPHSerine

Glycine

SHMT

dUMP

dTMP

MTX mechanism for intracellularly

FPGS

Methionin

MTRR

Homocysteine

Methyl-THF

Methylene-THF

DHFR

TS

H+

NADP+

MTX-PGs

+

Cell membraneinhibition mechanism of MTX in DNA synthesis pathway

Figure 1 Inhibitionmechanism ofMTX inDNA synthesis pathwayMTX methotrexate FPGS folylpolyglutamate synthetase MTX-PGs methotrexate polyglutamates DHFR dihydrofolate reduc-tase TS thymidylate synthase FH4 tetrahydrofolate FH2 dihy-drofolateMethylene-THF 510-methylenetetrahydrofolateMethyl-THF 5-methyltetrahydrofolate dUMP deoxyurindine-51015840-mon-ophosphate dTMP deoxythymidine-51015840-monophosphate MTRRmethionine synthase reductase SHMT serine hydroxymethyltrans-ferase

The primary action of MTX is inhibition of the enzymeDHFR which converts dihydrofolate (FH2) to tetrahydro-folate (FH4) [11 14] MTX-PGs exert a stronger inhibitionof DHFR and TS [15ndash17] Thus through direct inhibitionby MTX and due to lack of FH4 and accumulation ofFH2 deoxythymidine monophosphate synthesis and purinede novo synthesis is blocked which eventually lead toleukemic cell death bone marrow suppression gastroin-testinal mucositis liver toxicity and rarely alopecia [1415 18 19] In fact both MTX and natural folates undergopolyglutamylation catalyzed by the enzyme folylpolyglutamylsynthase The MTX-PGs ensure intracellular retention andfurthermore increase the affinity for the MTX-sensitiveenzymes [16 18 20] (Figure 1)

However MTX may lead to acute renal cytotoxicity [21]which is serious and potentially fatal in the spinal canal andmay occur after the administration of neurotoxicity [22ndash25]and hematological toxicity [26] caused by animal somaticcells and human bone marrow chromosomal lesions [27]which led to the hematopoietic system abnormalities [28]gastrointestinal toxicity [29] made multiorgan dysfunction[30] nephrotoxicity [31] made renal failure [31 32] andhepatotoxicitymade liver fibrosis [33] Higher concentrationsof long-chain MTX-PGs have been in the risk of gastroin-testinal and hepatic toxicity [12 34 35] Thus the lowertoxicity drugs are necessary to be developed Recently theincreasing numbers of mechanisms of different diseases havebeen clarified to detect the helpful target protein for diseasestreatment [36ndash49] and diseases treatments with traditionalChinese medicine (TCM) as complements are getting moreand more attention The compounds extracted from tradi-tional Chinese medicine have displayed their potential as










21199032 SEE 119865 S E H D A

















N

N

NX

NH2

H2NR1

R2

R3

N

N

N

NN

NH2

H2N

O

COOH

COOH

H

MTX structure






SIRC TCM










pIC50

= 1198860+ 11988611199091+ 11988621199092+ sdot sdot sdot + 119886

119899119909119899 (1)


119894is its


2)



119870(119909119894 119909119896) = exp[

1003817100381710038171003817119909119894minus 119909119896

1003817100381710038171003817

2

21205902

] (2)






119894119895and 119909

119894119895119901represent


119894119895119901119899


119910119894= 119883119894120573119894+ 120576119894 (3)

where

119910119894=

[

[

[

[

[

1199101198941

1199101198942

119910119894119899

]

]

]

]

]

119883119894=

[

[

[

[

[

11990911989411

sdot sdot sdot 1199091198941119901

11990911989421

sdot sdot sdot 1199091198942119901

1199091198941198991

sdot sdot sdot 119909119894119899119901

]

]

]

]

]

(4)



119894

120573119894= (119883119879

119894119883119894)

minus1

119883119879

119894119910119894 (5)


119896 =

119899arg max119894=1

119875 (119894 | 119863) (6)


pIC50 = 119883119896

120573119896 (7)


(1)

H2N

NN

NN

HO

HOP

P

P

O

O

OOO

O

OH

OH

OH

OH

(4)

HO

HO

HO

OO

O

O

O

O

OHOH

OH

OHHO

(2)

HO

HO

HO

OO

OO

O

O

OH

OH

OH

OH

OH

(3)

HO

HO

HO

HO

O

O

O

O

O

O

OH

OH

OH

OH

(5)

HO

HO

HOHO

HO

HO

OO

O

OO

OH

OH

OH

OH

OH

(9)

OO

OOOO

HO

HO

HO

HO

OH

OH

OHOH

OH

(7)

O

O

O

O O

OHO

HO

HO

OH OH

OH

OH

OH

OH

(6)HO

HO

HOOH

OH

OHOH OH

OHO O O O

O

O

(8)

HO

HO

HO

OHOH

OH

OH

O

OO

OOH

O

O

OH

(10)

OHOH

OH

OH

OHOH

HO

HO HO

HO

HO

O OO

OO

(a)

Figure 4 Continued


HO

HO

HO

HO

HO

HO

OO

O

O

O

O

O

OH

OH

(11)

(13) HOHO

HO HOOH OH

OH OHOH

OH

OHO O

O

O OO

O

OH

HO

HO

(15)

HO

O

O

O

OHO

O

OH

OH

OH

OHOH

OHO

O

(17)

HO

O

O

O

OOH OH

OHOH

OH

OH

O

O

MTX

O

OO

OH

OH

NN

NN

HN

H2N

2NH

O

O

(18)

OHOH

OH

OH

OH

OH

HO

HO

HO

HO

OO O

O

HNN

NN

N

MTX-PGs OH

OHNO

O

OH2N

2NH

O

(16)

OHOH

OHOO

HO

HO

HO

(14)

OH

OH

OH

OH

OO

O

HO

HO

(12)

O

OO

OO

OO

O

OHOH

OH

HOHO

HO

HOHO

HO

HO

(b)



O29 O30

O32Gln35

Glu30

NDP187

N1

Arg70

Lys68

(a)

O28O30

Gln35Glu30

NDP187

N9 Arg70

(b)

NDP187

O10

Arg70

(c)

O34

O12

NDP187

Asn64

(d)

O45O23

O34

O44

Asn64

NDP187

H86Lys68

Lys63

(e)

O27

UMP314

O28 Arg50

(f)

Asn112

UMP314

O28

O29O30

H43

Arg50

(g)

UMP314

O31

O32Arg50

(h)

Figure 5 Continued


UMP314

O30Met309

(i)

UMP314O33

O44H11

O42

Arg50

Asn112

Met309

Met311

(j)










254

276286

307

333

N1

C2

C3

C4C5

C6

N7

N8

N9

C10 C11

N12C13

N14 C15

C16C17

C18

C19 C20

C21

C22

O23N24

C25

C26

C27

C28

O29

O30

C31

O32

O33MTX

Phe34

Phe31

N

CA CB

CG

CD

CE NZ

C

O

Lys68

N

CA CB

CG

CD

NE CZ

NH1

NH2

C

OArg70

Asn64

N

CA

CB

CGCD

OE1OE2

C OGlu30

NCA

CB CGCD

OE1 NE2

C

O

Gln35

Ndp187

Val8

Ala9

Val115Ile7

Pro61

Leu67

Thr56

Ile60

(a)

276

264

N1C2

N3

C4

C5C6

N7

C8

N9

N10

C11

C12

C13

C14

O15

C16O17

O18

O19

P20O21

O22

O23

P24O25

O26

P27

O28

O29O30


Phe34

Ndp187

NCA

CBCG

CD

OE1 NE2

C

O

Gln35

Asn64

Val8

NCA

CB

CG

CD

NECZ

NH1

NH2C

O

Arg70

Leu67

Phe31

Ile60

Ile7

Ala9Glu30

Thr56Val115

Leu22

Pro61

Tyr121

(b)

295

C1 C2

C3

C4O5

C6C7

O8

O9O10

O11

O12

C13

C14 C15

C16

C17C18

O19

O20

O21

O22 O23C24

C25

C26C27

C28

C29

O30

O31

O32

O33

O34

Manninotriose

Phe34

NCA

CB

CG

CD

NE

CZNH1

NH2

CO

Arg28

Phe31

Asn64

Ile60

Pro61

Pro26

Leu67

Ser59

Ndp187





His53

(c)

274

280295

265311

317

C1

C2C3

C4

C5O6

O7 O8

C9

O10

O11

O12

C13C14

C15C16

C17C18

O19O20

O21

O22 O23

C24 C25

C26

C27O28

C29O30 O31

C32O33

O34

Raffinose

PA O1A

O2A

O5BC5B

C4BO4B

C3B

O3B

C2B

O2BC1B

N9A C8AN7A

C5AC6A

N6AN1A

C2A

N3A C4A

O3PN

O1N

O2N O5D C5D

C4D

O4DC3DO3D

C2DO2D

C1D

N1N C2NC3N C7N

O7N

N7NC4NC5NC6N

P2B

O1X

O2XO3X

Ndp187

N

CA

CB

CGOD1

ND2C

O

Asn64

Phe31

N

CA

CB OG

CO

Ser59

N CA

CBCG

CDNECZ

NH1 NH2

C

O

Arg28

Ile60

Phe34

Pro61Leu67

Leu22

Pro26





His53

(d)

Figure 6 Continued


247

319

303

279

261

C1

C2

C3C4

O5 C6C7

C8C9

C10

O11

C12

C13C14

C15

C16O17

C18

C19

C20

C21

C22

O23

C24

O25

O26

C27

O28

O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39

O40C41

O42

O43

O44

O45

Stachyose

N

CACB

CGOD1ND2

C

O

Asn64Phe31

N

CA

CB

CG

CD

CE

NZC

OLys68

N

CACB

CGCD

CE

NZ

C

O

Lys63

Pro61

Phe34

Gln35

Leu67

Pro26

Ile60

(e)

255

C1 N2

C3

C4

C5

N6

N7

C8

C9

N10N11

N12

C13

N14 C15

C16

C17

C18

C19

C20

C21

C22

N23

O24C25

C26 O27

O28

C29C30C31

O32O33

MTX-PGs

Met311

NCA

CB

CG

CD

NECZ

NH1NH2

CO

Arg50

Ile108Phe117

Ala111

Asn112

Leu221

Ump314

Thr51

Phe225

Ala312

Trp109

(f)

269

284

303279

283

280330

N1

C2

N3

C4

C5C6

N7C8

N9

N10

C11C12

C13

C14

O15

C16O17

O18

O19

P20 O21

O22

O23

P24O25

O26

P27

O28

O29

O30


N1

C2

N3C4

C5

C6 O2

O4

P

OP1OP2

OP3UMP314

N

CA

CB

CG

CD1

CD2

C

O

Leu221

Phe225

N

CACB

CGOD1

ND2

C

O

Asn112

N CA

CB

CG

CDNE

CZ

NH1NH2

C

OArg50

Ile108

Met311

N

CACB

CG

CDOE1

OE2

C

O

Glu87

Leu192

Trp109

Gly222

C1998400

O4998400 C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(g)

325

304

258

284

324

294

271

285

C1C2

C3

C4 O5C6 C7

O8

O9O10

O11

O12

C13

C14C15

C16

C17 C18

O19

O20

O21

O22O23

C24

C25C26

C27

C28C29

O30

O31

O32O33

O34Manninotriose

N1

C2

N3C4

C5C6

O2

O4P

OP1

OP2OP3

UMP314N CA

CB

CG

OD1

OD2

CO

Asp218

N

CA CB

CG

CD

NECZ

NH1

NH2

C

O

Arg50

Phe225

N

CACB

CGCD

OE1

OE2

CO

Glu87

Met311

Phe117

Val313

Asn112

Leu221

NCA

CB

CG

OD1

ND2

CO Asn226

Ile108

Ala312

Thr51

Trp109

Ala111

Leu192

Tyr258

C1998400

O4998400

C2998400

C3998400

C4998400

O5998400

O3998400

C5998400





His53

(h)

Figure 6 Continued


288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)








2 high 1199032 and



MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

























21199032 SEE 119865 S E H D A

















N

N

NX

NH2

H2NR1

R2

R3

N

N

N

NN

NH2

H2N

O

COOH

COOH

H

MTX structure






SIRC TCM










pIC50

= 1198860+ 11988611199091+ 11988621199092+ sdot sdot sdot + 119886

119899119909119899 (1)


119894is its


2)



119870(119909119894 119909119896) = exp[

1003817100381710038171003817119909119894minus 119909119896

1003817100381710038171003817

2

21205902

] (2)






119894119895and 119909

119894119895119901represent


119894119895119901119899


119910119894= 119883119894120573119894+ 120576119894 (3)

where

119910119894=

[

[

[

[

[

1199101198941

1199101198942

119910119894119899

]

]

]

]

]

119883119894=

[

[

[

[

[

11990911989411

sdot sdot sdot 1199091198941119901

11990911989421

sdot sdot sdot 1199091198942119901

1199091198941198991

sdot sdot sdot 119909119894119899119901

]

]

]

]

]

(4)



119894

120573119894= (119883119879

119894119883119894)

minus1

119883119879

119894119910119894 (5)


119896 =

119899arg max119894=1

119875 (119894 | 119863) (6)


pIC50 = 119883119896

120573119896 (7)


(1)

H2N

NN

NN

HO

HOP

P

P

O

O

OOO

O

OH

OH

OH

OH

(4)

HO

HO

HO

OO

O

O

O

O

OHOH

OH

OHHO

(2)

HO

HO

HO

OO

OO

O

O

OH

OH

OH

OH

OH

(3)

HO

HO

HO

HO

O

O

O

O

O

O

OH

OH

OH

OH

(5)

HO

HO

HOHO

HO

HO

OO

O

OO

OH

OH

OH

OH

OH

(9)

OO

OOOO

HO

HO

HO

HO

OH

OH

OHOH

OH

(7)

O

O

O

O O

OHO

HO

HO

OH OH

OH

OH

OH

OH

(6)HO

HO

HOOH

OH

OHOH OH

OHO O O O

O

O

(8)

HO

HO

HO

OHOH

OH

OH

O

OO

OOH

O

O

OH

(10)

OHOH

OH

OH

OHOH

HO

HO HO

HO

HO

O OO

OO

(a)

Figure 4 Continued


HO

HO

HO

HO

HO

HO

OO

O

O

O

O

O

OH

OH

(11)

(13) HOHO

HO HOOH OH

OH OHOH

OH

OHO O

O

O OO

O

OH

HO

HO

(15)

HO

O

O

O

OHO

O

OH

OH

OH

OHOH

OHO

O

(17)

HO

O

O

O

OOH OH

OHOH

OH

OH

O

O

MTX

O

OO

OH

OH

NN

NN

HN

H2N

2NH

O

O

(18)

OHOH

OH

OH

OH

OH

HO

HO

HO

HO

OO O

O

HNN

NN

N

MTX-PGs OH

OHNO

O

OH2N

2NH

O

(16)

OHOH

OHOO

HO

HO

HO

(14)

OH

OH

OH

OH

OO

O

HO

HO

(12)

O

OO

OO

OO

O

OHOH

OH

HOHO

HO

HOHO

HO

HO

(b)



O29 O30

O32Gln35

Glu30

NDP187

N1

Arg70

Lys68

(a)

O28O30

Gln35Glu30

NDP187

N9 Arg70

(b)

NDP187

O10

Arg70

(c)

O34

O12

NDP187

Asn64

(d)

O45O23

O34

O44

Asn64

NDP187

H86Lys68

Lys63

(e)

O27

UMP314

O28 Arg50

(f)

Asn112

UMP314

O28

O29O30

H43

Arg50

(g)

UMP314

O31

O32Arg50

(h)

Figure 5 Continued


UMP314

O30Met309

(i)

UMP314O33

O44H11

O42

Arg50

Asn112

Met309

Met311

(j)










254

276286

307

333

N1

C2

C3

C4C5

C6

N7

N8

N9

C10 C11

N12C13

N14 C15

C16C17

C18

C19 C20

C21

C22

O23N24

C25

C26

C27

C28

O29

O30

C31

O32

O33MTX

Phe34

Phe31

N

CA CB

CG

CD

CE NZ

C

O

Lys68

N

CA CB

CG

CD

NE CZ

NH1

NH2

C

OArg70

Asn64

N

CA

CB

CGCD

OE1OE2

C OGlu30

NCA

CB CGCD

OE1 NE2

C

O

Gln35

Ndp187

Val8

Ala9

Val115Ile7

Pro61

Leu67

Thr56

Ile60

(a)

276

264

N1C2

N3

C4

C5C6

N7

C8

N9

N10

C11

C12

C13

C14

O15

C16O17

O18

O19

P20O21

O22

O23

P24O25

O26

P27

O28

O29O30


Phe34

Ndp187

NCA

CBCG

CD

OE1 NE2

C

O

Gln35

Asn64

Val8

NCA

CB

CG

CD

NECZ

NH1

NH2C

O

Arg70

Leu67

Phe31

Ile60

Ile7

Ala9Glu30

Thr56Val115

Leu22

Pro61

Tyr121

(b)

295

C1 C2

C3

C4O5

C6C7

O8

O9O10

O11

O12

C13

C14 C15

C16

C17C18

O19

O20

O21

O22 O23C24

C25

C26C27

C28

C29

O30

O31

O32

O33

O34

Manninotriose

Phe34

NCA

CB

CG

CD

NE

CZNH1

NH2

CO

Arg28

Phe31

Asn64

Ile60

Pro61

Pro26

Leu67

Ser59

Ndp187





His53

(c)

274

280295

265311

317

C1

C2C3

C4

C5O6

O7 O8

C9

O10

O11

O12

C13C14

C15C16

C17C18

O19O20

O21

O22 O23

C24 C25

C26

C27O28

C29O30 O31

C32O33

O34

Raffinose

PA O1A

O2A

O5BC5B

C4BO4B

C3B

O3B

C2B

O2BC1B

N9A C8AN7A

C5AC6A

N6AN1A

C2A

N3A C4A

O3PN

O1N

O2N O5D C5D

C4D

O4DC3DO3D

C2DO2D

C1D

N1N C2NC3N C7N

O7N

N7NC4NC5NC6N

P2B

O1X

O2XO3X

Ndp187

N

CA

CB

CGOD1

ND2C

O

Asn64

Phe31

N

CA

CB OG

CO

Ser59

N CA

CBCG

CDNECZ

NH1 NH2

C

O

Arg28

Ile60

Phe34

Pro61Leu67

Leu22

Pro26





His53

(d)

Figure 6 Continued


247

319

303

279

261

C1

C2

C3C4

O5 C6C7

C8C9

C10

O11

C12

C13C14

C15

C16O17

C18

C19

C20

C21

C22

O23

C24

O25

O26

C27

O28

O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39

O40C41

O42

O43

O44

O45

Stachyose

N

CACB

CGOD1ND2

C

O

Asn64Phe31

N

CA

CB

CG

CD

CE

NZC

OLys68

N

CACB

CGCD

CE

NZ

C

O

Lys63

Pro61

Phe34

Gln35

Leu67

Pro26

Ile60

(e)

255

C1 N2

C3

C4

C5

N6

N7

C8

C9

N10N11

N12

C13

N14 C15

C16

C17

C18

C19

C20

C21

C22

N23

O24C25

C26 O27

O28

C29C30C31

O32O33

MTX-PGs

Met311

NCA

CB

CG

CD

NECZ

NH1NH2

CO

Arg50

Ile108Phe117

Ala111

Asn112

Leu221

Ump314

Thr51

Phe225

Ala312

Trp109

(f)

269

284

303279

283

280330

N1

C2

N3

C4

C5C6

N7C8

N9

N10

C11C12

C13

C14

O15

C16O17

O18

O19

P20 O21

O22

O23

P24O25

O26

P27

O28

O29

O30


N1

C2

N3C4

C5

C6 O2

O4

P

OP1OP2

OP3UMP314

N

CA

CB

CG

CD1

CD2

C

O

Leu221

Phe225

N

CACB

CGOD1

ND2

C

O

Asn112

N CA

CB

CG

CDNE

CZ

NH1NH2

C

OArg50

Ile108

Met311

N

CACB

CG

CDOE1

OE2

C

O

Glu87

Leu192

Trp109

Gly222

C1998400

O4998400 C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(g)

325

304

258

284

324

294

271

285

C1C2

C3

C4 O5C6 C7

O8

O9O10

O11

O12

C13

C14C15

C16

C17 C18

O19

O20

O21

O22O23

C24

C25C26

C27

C28C29

O30

O31

O32O33

O34Manninotriose

N1

C2

N3C4

C5C6

O2

O4P

OP1

OP2OP3

UMP314N CA

CB

CG

OD1

OD2

CO

Asp218

N

CA CB

CG

CD

NECZ

NH1

NH2

C

O

Arg50

Phe225

N

CACB

CGCD

OE1

OE2

CO

Glu87

Met311

Phe117

Val313

Asn112

Leu221

NCA

CB

CG

OD1

ND2

CO Asn226

Ile108

Ala312

Thr51

Trp109

Ala111

Leu192

Tyr258

C1998400

O4998400

C2998400

C3998400

C4998400

O5998400

O3998400

C5998400





His53

(h)

Figure 6 Continued


288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)








2 high 1199032 and



MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of



























N

N

NX

NH2

H2NR1

R2

R3

N

N

N

NN

NH2

H2N

O

COOH

COOH

H

MTX structure






SIRC TCM










pIC50

= 1198860+ 11988611199091+ 11988621199092+ sdot sdot sdot + 119886

119899119909119899 (1)


119894is its


2)



119870(119909119894 119909119896) = exp[

1003817100381710038171003817119909119894minus 119909119896

1003817100381710038171003817

2

21205902

] (2)






119894119895and 119909

119894119895119901represent


119894119895119901119899


119910119894= 119883119894120573119894+ 120576119894 (3)

where

119910119894=

[

[

[

[

[

1199101198941

1199101198942

119910119894119899

]

]

]

]

]

119883119894=

[

[

[

[

[

11990911989411

sdot sdot sdot 1199091198941119901

11990911989421

sdot sdot sdot 1199091198942119901

1199091198941198991

sdot sdot sdot 119909119894119899119901

]

]

]

]

]

(4)



119894

120573119894= (119883119879

119894119883119894)

minus1

119883119879

119894119910119894 (5)


119896 =

119899arg max119894=1

119875 (119894 | 119863) (6)


pIC50 = 119883119896

120573119896 (7)


(1)

H2N

NN

NN

HO

HOP

P

P

O

O

OOO

O

OH

OH

OH

OH

(4)

HO

HO

HO

OO

O

O

O

O

OHOH

OH

OHHO

(2)

HO

HO

HO

OO

OO

O

O

OH

OH

OH

OH

OH

(3)

HO

HO

HO

HO

O

O

O

O

O

O

OH

OH

OH

OH

(5)

HO

HO

HOHO

HO

HO

OO

O

OO

OH

OH

OH

OH

OH

(9)

OO

OOOO

HO

HO

HO

HO

OH

OH

OHOH

OH

(7)

O

O

O

O O

OHO

HO

HO

OH OH

OH

OH

OH

OH

(6)HO

HO

HOOH

OH

OHOH OH

OHO O O O

O

O

(8)

HO

HO

HO

OHOH

OH

OH

O

OO

OOH

O

O

OH

(10)

OHOH

OH

OH

OHOH

HO

HO HO

HO

HO

O OO

OO

(a)

Figure 4 Continued


HO

HO

HO

HO

HO

HO

OO

O

O

O

O

O

OH

OH

(11)

(13) HOHO

HO HOOH OH

OH OHOH

OH

OHO O

O

O OO

O

OH

HO

HO

(15)

HO

O

O

O

OHO

O

OH

OH

OH

OHOH

OHO

O

(17)

HO

O

O

O

OOH OH

OHOH

OH

OH

O

O

MTX

O

OO

OH

OH

NN

NN

HN

H2N

2NH

O

O

(18)

OHOH

OH

OH

OH

OH

HO

HO

HO

HO

OO O

O

HNN

NN

N

MTX-PGs OH

OHNO

O

OH2N

2NH

O

(16)

OHOH

OHOO

HO

HO

HO

(14)

OH

OH

OH

OH

OO

O

HO

HO

(12)

O

OO

OO

OO

O

OHOH

OH

HOHO

HO

HOHO

HO

HO

(b)



O29 O30

O32Gln35

Glu30

NDP187

N1

Arg70

Lys68

(a)

O28O30

Gln35Glu30

NDP187

N9 Arg70

(b)

NDP187

O10

Arg70

(c)

O34

O12

NDP187

Asn64

(d)

O45O23

O34

O44

Asn64

NDP187

H86Lys68

Lys63

(e)

O27

UMP314

O28 Arg50

(f)

Asn112

UMP314

O28

O29O30

H43

Arg50

(g)

UMP314

O31

O32Arg50

(h)

Figure 5 Continued


UMP314

O30Met309

(i)

UMP314O33

O44H11

O42

Arg50

Asn112

Met309

Met311

(j)










254

276286

307

333

N1

C2

C3

C4C5

C6

N7

N8

N9

C10 C11

N12C13

N14 C15

C16C17

C18

C19 C20

C21

C22

O23N24

C25

C26

C27

C28

O29

O30

C31

O32

O33MTX

Phe34

Phe31

N

CA CB

CG

CD

CE NZ

C

O

Lys68

N

CA CB

CG

CD

NE CZ

NH1

NH2

C

OArg70

Asn64

N

CA

CB

CGCD

OE1OE2

C OGlu30

NCA

CB CGCD

OE1 NE2

C

O

Gln35

Ndp187

Val8

Ala9

Val115Ile7

Pro61

Leu67

Thr56

Ile60

(a)

276

264

N1C2

N3

C4

C5C6

N7

C8

N9

N10

C11

C12

C13

C14

O15

C16O17

O18

O19

P20O21

O22

O23

P24O25

O26

P27

O28

O29O30


Phe34

Ndp187

NCA

CBCG

CD

OE1 NE2

C

O

Gln35

Asn64

Val8

NCA

CB

CG

CD

NECZ

NH1

NH2C

O

Arg70

Leu67

Phe31

Ile60

Ile7

Ala9Glu30

Thr56Val115

Leu22

Pro61

Tyr121

(b)

295

C1 C2

C3

C4O5

C6C7

O8

O9O10

O11

O12

C13

C14 C15

C16

C17C18

O19

O20

O21

O22 O23C24

C25

C26C27

C28

C29

O30

O31

O32

O33

O34

Manninotriose

Phe34

NCA

CB

CG

CD

NE

CZNH1

NH2

CO

Arg28

Phe31

Asn64

Ile60

Pro61

Pro26

Leu67

Ser59

Ndp187





His53

(c)

274

280295

265311

317

C1

C2C3

C4

C5O6

O7 O8

C9

O10

O11

O12

C13C14

C15C16

C17C18

O19O20

O21

O22 O23

C24 C25

C26

C27O28

C29O30 O31

C32O33

O34

Raffinose

PA O1A

O2A

O5BC5B

C4BO4B

C3B

O3B

C2B

O2BC1B

N9A C8AN7A

C5AC6A

N6AN1A

C2A

N3A C4A

O3PN

O1N

O2N O5D C5D

C4D

O4DC3DO3D

C2DO2D

C1D

N1N C2NC3N C7N

O7N

N7NC4NC5NC6N

P2B

O1X

O2XO3X

Ndp187

N

CA

CB

CGOD1

ND2C

O

Asn64

Phe31

N

CA

CB OG

CO

Ser59

N CA

CBCG

CDNECZ

NH1 NH2

C

O

Arg28

Ile60

Phe34

Pro61Leu67

Leu22

Pro26





His53

(d)

Figure 6 Continued


247

319

303

279

261

C1

C2

C3C4

O5 C6C7

C8C9

C10

O11

C12

C13C14

C15

C16O17

C18

C19

C20

C21

C22

O23

C24

O25

O26

C27

O28

O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39

O40C41

O42

O43

O44

O45

Stachyose

N

CACB

CGOD1ND2

C

O

Asn64Phe31

N

CA

CB

CG

CD

CE

NZC

OLys68

N

CACB

CGCD

CE

NZ

C

O

Lys63

Pro61

Phe34

Gln35

Leu67

Pro26

Ile60

(e)

255

C1 N2

C3

C4

C5

N6

N7

C8

C9

N10N11

N12

C13

N14 C15

C16

C17

C18

C19

C20

C21

C22

N23

O24C25

C26 O27

O28

C29C30C31

O32O33

MTX-PGs

Met311

NCA

CB

CG

CD

NECZ

NH1NH2

CO

Arg50

Ile108Phe117

Ala111

Asn112

Leu221

Ump314

Thr51

Phe225

Ala312

Trp109

(f)

269

284

303279

283

280330

N1

C2

N3

C4

C5C6

N7C8

N9

N10

C11C12

C13

C14

O15

C16O17

O18

O19

P20 O21

O22

O23

P24O25

O26

P27

O28

O29

O30


N1

C2

N3C4

C5

C6 O2

O4

P

OP1OP2

OP3UMP314

N

CA

CB

CG

CD1

CD2

C

O

Leu221

Phe225

N

CACB

CGOD1

ND2

C

O

Asn112

N CA

CB

CG

CDNE

CZ

NH1NH2

C

OArg50

Ile108

Met311

N

CACB

CG

CDOE1

OE2

C

O

Glu87

Leu192

Trp109

Gly222

C1998400

O4998400 C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(g)

325

304

258

284

324

294

271

285

C1C2

C3

C4 O5C6 C7

O8

O9O10

O11

O12

C13

C14C15

C16

C17 C18

O19

O20

O21

O22O23

C24

C25C26

C27

C28C29

O30

O31

O32O33

O34Manninotriose

N1

C2

N3C4

C5C6

O2

O4P

OP1

OP2OP3

UMP314N CA

CB

CG

OD1

OD2

CO

Asp218

N

CA CB

CG

CD

NECZ

NH1

NH2

C

O

Arg50

Phe225

N

CACB

CGCD

OE1

OE2

CO

Glu87

Met311

Phe117

Val313

Asn112

Leu221

NCA

CB

CG

OD1

ND2

CO Asn226

Ile108

Ala312

Thr51

Trp109

Ala111

Leu192

Tyr258

C1998400

O4998400

C2998400

C3998400

C4998400

O5998400

O3998400

C5998400





His53

(h)

Figure 6 Continued


288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)








2 high 1199032 and



MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















SIRC TCM










pIC50

= 1198860+ 11988611199091+ 11988621199092+ sdot sdot sdot + 119886

119899119909119899 (1)


119894is its


2)



119870(119909119894 119909119896) = exp[

1003817100381710038171003817119909119894minus 119909119896

1003817100381710038171003817

2

21205902

] (2)






119894119895and 119909

119894119895119901represent


119894119895119901119899


119910119894= 119883119894120573119894+ 120576119894 (3)

where

119910119894=

[

[

[

[

[

1199101198941

1199101198942

119910119894119899

]

]

]

]

]

119883119894=

[

[

[

[

[

11990911989411

sdot sdot sdot 1199091198941119901

11990911989421

sdot sdot sdot 1199091198942119901

1199091198941198991

sdot sdot sdot 119909119894119899119901

]

]

]

]

]

(4)



119894

120573119894= (119883119879

119894119883119894)

minus1

119883119879

119894119910119894 (5)


119896 =

119899arg max119894=1

119875 (119894 | 119863) (6)


pIC50 = 119883119896

120573119896 (7)


(1)

H2N

NN

NN

HO

HOP

P

P

O

O

OOO

O

OH

OH

OH

OH

(4)

HO

HO

HO

OO

O

O

O

O

OHOH

OH

OHHO

(2)

HO

HO

HO

OO

OO

O

O

OH

OH

OH

OH

OH

(3)

HO

HO

HO

HO

O

O

O

O

O

O

OH

OH

OH

OH

(5)

HO

HO

HOHO

HO

HO

OO

O

OO

OH

OH

OH

OH

OH

(9)

OO

OOOO

HO

HO

HO

HO

OH

OH

OHOH

OH

(7)

O

O

O

O O

OHO

HO

HO

OH OH

OH

OH

OH

OH

(6)HO

HO

HOOH

OH

OHOH OH

OHO O O O

O

O

(8)

HO

HO

HO

OHOH

OH

OH

O

OO

OOH

O

O

OH

(10)

OHOH

OH

OH

OHOH

HO

HO HO

HO

HO

O OO

OO

(a)

Figure 4 Continued


HO

HO

HO

HO

HO

HO

OO

O

O

O

O

O

OH

OH

(11)

(13) HOHO

HO HOOH OH

OH OHOH

OH

OHO O

O

O OO

O

OH

HO

HO

(15)

HO

O

O

O

OHO

O

OH

OH

OH

OHOH

OHO

O

(17)

HO

O

O

O

OOH OH

OHOH

OH

OH

O

O

MTX

O

OO

OH

OH

NN

NN

HN

H2N

2NH

O

O

(18)

OHOH

OH

OH

OH

OH

HO

HO

HO

HO

OO O

O

HNN

NN

N

MTX-PGs OH

OHNO

O

OH2N

2NH

O

(16)

OHOH

OHOO

HO

HO

HO

(14)

OH

OH

OH

OH

OO

O

HO

HO

(12)

O

OO

OO

OO

O

OHOH

OH

HOHO

HO

HOHO

HO

HO

(b)



O29 O30

O32Gln35

Glu30

NDP187

N1

Arg70

Lys68

(a)

O28O30

Gln35Glu30

NDP187

N9 Arg70

(b)

NDP187

O10

Arg70

(c)

O34

O12

NDP187

Asn64

(d)

O45O23

O34

O44

Asn64

NDP187

H86Lys68

Lys63

(e)

O27

UMP314

O28 Arg50

(f)

Asn112

UMP314

O28

O29O30

H43

Arg50

(g)

UMP314

O31

O32Arg50

(h)

Figure 5 Continued


UMP314

O30Met309

(i)

UMP314O33

O44H11

O42

Arg50

Asn112

Met309

Met311

(j)










254

276286

307

333

N1

C2

C3

C4C5

C6

N7

N8

N9

C10 C11

N12C13

N14 C15

C16C17

C18

C19 C20

C21

C22

O23N24

C25

C26

C27

C28

O29

O30

C31

O32

O33MTX

Phe34

Phe31

N

CA CB

CG

CD

CE NZ

C

O

Lys68

N

CA CB

CG

CD

NE CZ

NH1

NH2

C

OArg70

Asn64

N

CA

CB

CGCD

OE1OE2

C OGlu30

NCA

CB CGCD

OE1 NE2

C

O

Gln35

Ndp187

Val8

Ala9

Val115Ile7

Pro61

Leu67

Thr56

Ile60

(a)

276

264

N1C2

N3

C4

C5C6

N7

C8

N9

N10

C11

C12

C13

C14

O15

C16O17

O18

O19

P20O21

O22

O23

P24O25

O26

P27

O28

O29O30


Phe34

Ndp187

NCA

CBCG

CD

OE1 NE2

C

O

Gln35

Asn64

Val8

NCA

CB

CG

CD

NECZ

NH1

NH2C

O

Arg70

Leu67

Phe31

Ile60

Ile7

Ala9Glu30

Thr56Val115

Leu22

Pro61

Tyr121

(b)

295

C1 C2

C3

C4O5

C6C7

O8

O9O10

O11

O12

C13

C14 C15

C16

C17C18

O19

O20

O21

O22 O23C24

C25

C26C27

C28

C29

O30

O31

O32

O33

O34

Manninotriose

Phe34

NCA

CB

CG

CD

NE

CZNH1

NH2

CO

Arg28

Phe31

Asn64

Ile60

Pro61

Pro26

Leu67

Ser59

Ndp187





His53

(c)

274

280295

265311

317

C1

C2C3

C4

C5O6

O7 O8

C9

O10

O11

O12

C13C14

C15C16

C17C18

O19O20

O21

O22 O23

C24 C25

C26

C27O28

C29O30 O31

C32O33

O34

Raffinose

PA O1A

O2A

O5BC5B

C4BO4B

C3B

O3B

C2B

O2BC1B

N9A C8AN7A

C5AC6A

N6AN1A

C2A

N3A C4A

O3PN

O1N

O2N O5D C5D

C4D

O4DC3DO3D

C2DO2D

C1D

N1N C2NC3N C7N

O7N

N7NC4NC5NC6N

P2B

O1X

O2XO3X

Ndp187

N

CA

CB

CGOD1

ND2C

O

Asn64

Phe31

N

CA

CB OG

CO

Ser59

N CA

CBCG

CDNECZ

NH1 NH2

C

O

Arg28

Ile60

Phe34

Pro61Leu67

Leu22

Pro26





His53

(d)

Figure 6 Continued


247

319

303

279

261

C1

C2

C3C4

O5 C6C7

C8C9

C10

O11

C12

C13C14

C15

C16O17

C18

C19

C20

C21

C22

O23

C24

O25

O26

C27

O28

O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39

O40C41

O42

O43

O44

O45

Stachyose

N

CACB

CGOD1ND2

C

O

Asn64Phe31

N

CA

CB

CG

CD

CE

NZC

OLys68

N

CACB

CGCD

CE

NZ

C

O

Lys63

Pro61

Phe34

Gln35

Leu67

Pro26

Ile60

(e)

255

C1 N2

C3

C4

C5

N6

N7

C8

C9

N10N11

N12

C13

N14 C15

C16

C17

C18

C19

C20

C21

C22

N23

O24C25

C26 O27

O28

C29C30C31

O32O33

MTX-PGs

Met311

NCA

CB

CG

CD

NECZ

NH1NH2

CO

Arg50

Ile108Phe117

Ala111

Asn112

Leu221

Ump314

Thr51

Phe225

Ala312

Trp109

(f)

269

284

303279

283

280330

N1

C2

N3

C4

C5C6

N7C8

N9

N10

C11C12

C13

C14

O15

C16O17

O18

O19

P20 O21

O22

O23

P24O25

O26

P27

O28

O29

O30


N1

C2

N3C4

C5

C6 O2

O4

P

OP1OP2

OP3UMP314

N

CA

CB

CG

CD1

CD2

C

O

Leu221

Phe225

N

CACB

CGOD1

ND2

C

O

Asn112

N CA

CB

CG

CDNE

CZ

NH1NH2

C

OArg50

Ile108

Met311

N

CACB

CG

CDOE1

OE2

C

O

Glu87

Leu192

Trp109

Gly222

C1998400

O4998400 C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(g)

325

304

258

284

324

294

271

285

C1C2

C3

C4 O5C6 C7

O8

O9O10

O11

O12

C13

C14C15

C16

C17 C18

O19

O20

O21

O22O23

C24

C25C26

C27

C28C29

O30

O31

O32O33

O34Manninotriose

N1

C2

N3C4

C5C6

O2

O4P

OP1

OP2OP3

UMP314N CA

CB

CG

OD1

OD2

CO

Asp218

N

CA CB

CG

CD

NECZ

NH1

NH2

C

O

Arg50

Phe225

N

CACB

CGCD

OE1

OE2

CO

Glu87

Met311

Phe117

Val313

Asn112

Leu221

NCA

CB

CG

OD1

ND2

CO Asn226

Ile108

Ala312

Thr51

Trp109

Ala111

Leu192

Tyr258

C1998400

O4998400

C2998400

C3998400

C4998400

O5998400

O3998400

C5998400





His53

(h)

Figure 6 Continued


288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)








2 high 1199032 and



MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















(1)

H2N

NN

NN

HO

HOP

P

P

O

O

OOO

O

OH

OH

OH

OH

(4)

HO

HO

HO

OO

O

O

O

O

OHOH

OH

OHHO

(2)

HO

HO

HO

OO

OO

O

O

OH

OH

OH

OH

OH

(3)

HO

HO

HO

HO

O

O

O

O

O

O

OH

OH

OH

OH

(5)

HO

HO

HOHO

HO

HO

OO

O

OO

OH

OH

OH

OH

OH

(9)

OO

OOOO

HO

HO

HO

HO

OH

OH

OHOH

OH

(7)

O

O

O

O O

OHO

HO

HO

OH OH

OH

OH

OH

OH

(6)HO

HO

HOOH

OH

OHOH OH

OHO O O O

O

O

(8)

HO

HO

HO

OHOH

OH

OH

O

OO

OOH

O

O

OH

(10)

OHOH

OH

OH

OHOH

HO

HO HO

HO

HO

O OO

OO

(a)

Figure 4 Continued


HO

HO

HO

HO

HO

HO

OO

O

O

O

O

O

OH

OH

(11)

(13) HOHO

HO HOOH OH

OH OHOH

OH

OHO O

O

O OO

O

OH

HO

HO

(15)

HO

O

O

O

OHO

O

OH

OH

OH

OHOH

OHO

O

(17)

HO

O

O

O

OOH OH

OHOH

OH

OH

O

O

MTX

O

OO

OH

OH

NN

NN

HN

H2N

2NH

O

O

(18)

OHOH

OH

OH

OH

OH

HO

HO

HO

HO

OO O

O

HNN

NN

N

MTX-PGs OH

OHNO

O

OH2N

2NH

O

(16)

OHOH

OHOO

HO

HO

HO

(14)

OH

OH

OH

OH

OO

O

HO

HO

(12)

O

OO

OO

OO

O

OHOH

OH

HOHO

HO

HOHO

HO

HO

(b)



O29 O30

O32Gln35

Glu30

NDP187

N1

Arg70

Lys68

(a)

O28O30

Gln35Glu30

NDP187

N9 Arg70

(b)

NDP187

O10

Arg70

(c)

O34

O12

NDP187

Asn64

(d)

O45O23

O34

O44

Asn64

NDP187

H86Lys68

Lys63

(e)

O27

UMP314

O28 Arg50

(f)

Asn112

UMP314

O28

O29O30

H43

Arg50

(g)

UMP314

O31

O32Arg50

(h)

Figure 5 Continued


UMP314

O30Met309

(i)

UMP314O33

O44H11

O42

Arg50

Asn112

Met309

Met311

(j)










254

276286

307

333

N1

C2

C3

C4C5

C6

N7

N8

N9

C10 C11

N12C13

N14 C15

C16C17

C18

C19 C20

C21

C22

O23N24

C25

C26

C27

C28

O29

O30

C31

O32

O33MTX

Phe34

Phe31

N

CA CB

CG

CD

CE NZ

C

O

Lys68

N

CA CB

CG

CD

NE CZ

NH1

NH2

C

OArg70

Asn64

N

CA

CB

CGCD

OE1OE2

C OGlu30

NCA

CB CGCD

OE1 NE2

C

O

Gln35

Ndp187

Val8

Ala9

Val115Ile7

Pro61

Leu67

Thr56

Ile60

(a)

276

264

N1C2

N3

C4

C5C6

N7

C8

N9

N10

C11

C12

C13

C14

O15

C16O17

O18

O19

P20O21

O22

O23

P24O25

O26

P27

O28

O29O30


Phe34

Ndp187

NCA

CBCG

CD

OE1 NE2

C

O

Gln35

Asn64

Val8

NCA

CB

CG

CD

NECZ

NH1

NH2C

O

Arg70

Leu67

Phe31

Ile60

Ile7

Ala9Glu30

Thr56Val115

Leu22

Pro61

Tyr121

(b)

295

C1 C2

C3

C4O5

C6C7

O8

O9O10

O11

O12

C13

C14 C15

C16

C17C18

O19

O20

O21

O22 O23C24

C25

C26C27

C28

C29

O30

O31

O32

O33

O34

Manninotriose

Phe34

NCA

CB

CG

CD

NE

CZNH1

NH2

CO

Arg28

Phe31

Asn64

Ile60

Pro61

Pro26

Leu67

Ser59

Ndp187





His53

(c)

274

280295

265311

317

C1

C2C3

C4

C5O6

O7 O8

C9

O10

O11

O12

C13C14

C15C16

C17C18

O19O20

O21

O22 O23

C24 C25

C26

C27O28

C29O30 O31

C32O33

O34

Raffinose

PA O1A

O2A

O5BC5B

C4BO4B

C3B

O3B

C2B

O2BC1B

N9A C8AN7A

C5AC6A

N6AN1A

C2A

N3A C4A

O3PN

O1N

O2N O5D C5D

C4D

O4DC3DO3D

C2DO2D

C1D

N1N C2NC3N C7N

O7N

N7NC4NC5NC6N

P2B

O1X

O2XO3X

Ndp187

N

CA

CB

CGOD1

ND2C

O

Asn64

Phe31

N

CA

CB OG

CO

Ser59

N CA

CBCG

CDNECZ

NH1 NH2

C

O

Arg28

Ile60

Phe34

Pro61Leu67

Leu22

Pro26





His53

(d)

Figure 6 Continued


247

319

303

279

261

C1

C2

C3C4

O5 C6C7

C8C9

C10

O11

C12

C13C14

C15

C16O17

C18

C19

C20

C21

C22

O23

C24

O25

O26

C27

O28

O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39

O40C41

O42

O43

O44

O45

Stachyose

N

CACB

CGOD1ND2

C

O

Asn64Phe31

N

CA

CB

CG

CD

CE

NZC

OLys68

N

CACB

CGCD

CE

NZ

C

O

Lys63

Pro61

Phe34

Gln35

Leu67

Pro26

Ile60

(e)

255

C1 N2

C3

C4

C5

N6

N7

C8

C9

N10N11

N12

C13

N14 C15

C16

C17

C18

C19

C20

C21

C22

N23

O24C25

C26 O27

O28

C29C30C31

O32O33

MTX-PGs

Met311

NCA

CB

CG

CD

NECZ

NH1NH2

CO

Arg50

Ile108Phe117

Ala111

Asn112

Leu221

Ump314

Thr51

Phe225

Ala312

Trp109

(f)

269

284

303279

283

280330

N1

C2

N3

C4

C5C6

N7C8

N9

N10

C11C12

C13

C14

O15

C16O17

O18

O19

P20 O21

O22

O23

P24O25

O26

P27

O28

O29

O30


N1

C2

N3C4

C5

C6 O2

O4

P

OP1OP2

OP3UMP314

N

CA

CB

CG

CD1

CD2

C

O

Leu221

Phe225

N

CACB

CGOD1

ND2

C

O

Asn112

N CA

CB

CG

CDNE

CZ

NH1NH2

C

OArg50

Ile108

Met311

N

CACB

CG

CDOE1

OE2

C

O

Glu87

Leu192

Trp109

Gly222

C1998400

O4998400 C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(g)

325

304

258

284

324

294

271

285

C1C2

C3

C4 O5C6 C7

O8

O9O10

O11

O12

C13

C14C15

C16

C17 C18

O19

O20

O21

O22O23

C24

C25C26

C27

C28C29

O30

O31

O32O33

O34Manninotriose

N1

C2

N3C4

C5C6

O2

O4P

OP1

OP2OP3

UMP314N CA

CB

CG

OD1

OD2

CO

Asp218

N

CA CB

CG

CD

NECZ

NH1

NH2

C

O

Arg50

Phe225

N

CACB

CGCD

OE1

OE2

CO

Glu87

Met311

Phe117

Val313

Asn112

Leu221

NCA

CB

CG

OD1

ND2

CO Asn226

Ile108

Ala312

Thr51

Trp109

Ala111

Leu192

Tyr258

C1998400

O4998400

C2998400

C3998400

C4998400

O5998400

O3998400

C5998400





His53

(h)

Figure 6 Continued


288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)








2 high 1199032 and



MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















HO

HO

HO

HO

HO

HO

OO

O

O

O

O

O

OH

OH

(11)

(13) HOHO

HO HOOH OH

OH OHOH

OH

OHO O

O

O OO

O

OH

HO

HO

(15)

HO

O

O

O

OHO

O

OH

OH

OH

OHOH

OHO

O

(17)

HO

O

O

O

OOH OH

OHOH

OH

OH

O

O

MTX

O

OO

OH

OH

NN

NN

HN

H2N

2NH

O

O

(18)

OHOH

OH

OH

OH

OH

HO

HO

HO

HO

OO O

O

HNN

NN

N

MTX-PGs OH

OHNO

O

OH2N

2NH

O

(16)

OHOH

OHOO

HO

HO

HO

(14)

OH

OH

OH

OH

OO

O

HO

HO

(12)

O

OO

OO

OO

O

OHOH

OH

HOHO

HO

HOHO

HO

HO

(b)



O29 O30

O32Gln35

Glu30

NDP187

N1

Arg70

Lys68

(a)

O28O30

Gln35Glu30

NDP187

N9 Arg70

(b)

NDP187

O10

Arg70

(c)

O34

O12

NDP187

Asn64

(d)

O45O23

O34

O44

Asn64

NDP187

H86Lys68

Lys63

(e)

O27

UMP314

O28 Arg50

(f)

Asn112

UMP314

O28

O29O30

H43

Arg50

(g)

UMP314

O31

O32Arg50

(h)

Figure 5 Continued


UMP314

O30Met309

(i)

UMP314O33

O44H11

O42

Arg50

Asn112

Met309

Met311

(j)










254

276286

307

333

N1

C2

C3

C4C5

C6

N7

N8

N9

C10 C11

N12C13

N14 C15

C16C17

C18

C19 C20

C21

C22

O23N24

C25

C26

C27

C28

O29

O30

C31

O32

O33MTX

Phe34

Phe31

N

CA CB

CG

CD

CE NZ

C

O

Lys68

N

CA CB

CG

CD

NE CZ

NH1

NH2

C

OArg70

Asn64

N

CA

CB

CGCD

OE1OE2

C OGlu30

NCA

CB CGCD

OE1 NE2

C

O

Gln35

Ndp187

Val8

Ala9

Val115Ile7

Pro61

Leu67

Thr56

Ile60

(a)

276

264

N1C2

N3

C4

C5C6

N7

C8

N9

N10

C11

C12

C13

C14

O15

C16O17

O18

O19

P20O21

O22

O23

P24O25

O26

P27

O28

O29O30


Phe34

Ndp187

NCA

CBCG

CD

OE1 NE2

C

O

Gln35

Asn64

Val8

NCA

CB

CG

CD

NECZ

NH1

NH2C

O

Arg70

Leu67

Phe31

Ile60

Ile7

Ala9Glu30

Thr56Val115

Leu22

Pro61

Tyr121

(b)

295

C1 C2

C3

C4O5

C6C7

O8

O9O10

O11

O12

C13

C14 C15

C16

C17C18

O19

O20

O21

O22 O23C24

C25

C26C27

C28

C29

O30

O31

O32

O33

O34

Manninotriose

Phe34

NCA

CB

CG

CD

NE

CZNH1

NH2

CO

Arg28

Phe31

Asn64

Ile60

Pro61

Pro26

Leu67

Ser59

Ndp187





His53

(c)

274

280295

265311

317

C1

C2C3

C4

C5O6

O7 O8

C9

O10

O11

O12

C13C14

C15C16

C17C18

O19O20

O21

O22 O23

C24 C25

C26

C27O28

C29O30 O31

C32O33

O34

Raffinose

PA O1A

O2A

O5BC5B

C4BO4B

C3B

O3B

C2B

O2BC1B

N9A C8AN7A

C5AC6A

N6AN1A

C2A

N3A C4A

O3PN

O1N

O2N O5D C5D

C4D

O4DC3DO3D

C2DO2D

C1D

N1N C2NC3N C7N

O7N

N7NC4NC5NC6N

P2B

O1X

O2XO3X

Ndp187

N

CA

CB

CGOD1

ND2C

O

Asn64

Phe31

N

CA

CB OG

CO

Ser59

N CA

CBCG

CDNECZ

NH1 NH2

C

O

Arg28

Ile60

Phe34

Pro61Leu67

Leu22

Pro26





His53

(d)

Figure 6 Continued


247

319

303

279

261

C1

C2

C3C4

O5 C6C7

C8C9

C10

O11

C12

C13C14

C15

C16O17

C18

C19

C20

C21

C22

O23

C24

O25

O26

C27

O28

O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39

O40C41

O42

O43

O44

O45

Stachyose

N

CACB

CGOD1ND2

C

O

Asn64Phe31

N

CA

CB

CG

CD

CE

NZC

OLys68

N

CACB

CGCD

CE

NZ

C

O

Lys63

Pro61

Phe34

Gln35

Leu67

Pro26

Ile60

(e)

255

C1 N2

C3

C4

C5

N6

N7

C8

C9

N10N11

N12

C13

N14 C15

C16

C17

C18

C19

C20

C21

C22

N23

O24C25

C26 O27

O28

C29C30C31

O32O33

MTX-PGs

Met311

NCA

CB

CG

CD

NECZ

NH1NH2

CO

Arg50

Ile108Phe117

Ala111

Asn112

Leu221

Ump314

Thr51

Phe225

Ala312

Trp109

(f)

269

284

303279

283

280330

N1

C2

N3

C4

C5C6

N7C8

N9

N10

C11C12

C13

C14

O15

C16O17

O18

O19

P20 O21

O22

O23

P24O25

O26

P27

O28

O29

O30


N1

C2

N3C4

C5

C6 O2

O4

P

OP1OP2

OP3UMP314

N

CA

CB

CG

CD1

CD2

C

O

Leu221

Phe225

N

CACB

CGOD1

ND2

C

O

Asn112

N CA

CB

CG

CDNE

CZ

NH1NH2

C

OArg50

Ile108

Met311

N

CACB

CG

CDOE1

OE2

C

O

Glu87

Leu192

Trp109

Gly222

C1998400

O4998400 C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(g)

325

304

258

284

324

294

271

285

C1C2

C3

C4 O5C6 C7

O8

O9O10

O11

O12

C13

C14C15

C16

C17 C18

O19

O20

O21

O22O23

C24

C25C26

C27

C28C29

O30

O31

O32O33

O34Manninotriose

N1

C2

N3C4

C5C6

O2

O4P

OP1

OP2OP3

UMP314N CA

CB

CG

OD1

OD2

CO

Asp218

N

CA CB

CG

CD

NECZ

NH1

NH2

C

O

Arg50

Phe225

N

CACB

CGCD

OE1

OE2

CO

Glu87

Met311

Phe117

Val313

Asn112

Leu221

NCA

CB

CG

OD1

ND2

CO Asn226

Ile108

Ala312

Thr51

Trp109

Ala111

Leu192

Tyr258

C1998400

O4998400

C2998400

C3998400

C4998400

O5998400

O3998400

C5998400





His53

(h)

Figure 6 Continued


288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)








2 high 1199032 and



MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















O29 O30

O32Gln35

Glu30

NDP187

N1

Arg70

Lys68

(a)

O28O30

Gln35Glu30

NDP187

N9 Arg70

(b)

NDP187

O10

Arg70

(c)

O34

O12

NDP187

Asn64

(d)

O45O23

O34

O44

Asn64

NDP187

H86Lys68

Lys63

(e)

O27

UMP314

O28 Arg50

(f)

Asn112

UMP314

O28

O29O30

H43

Arg50

(g)

UMP314

O31

O32Arg50

(h)

Figure 5 Continued


UMP314

O30Met309

(i)

UMP314O33

O44H11

O42

Arg50

Asn112

Met309

Met311

(j)










254

276286

307

333

N1

C2

C3

C4C5

C6

N7

N8

N9

C10 C11

N12C13

N14 C15

C16C17

C18

C19 C20

C21

C22

O23N24

C25

C26

C27

C28

O29

O30

C31

O32

O33MTX

Phe34

Phe31

N

CA CB

CG

CD

CE NZ

C

O

Lys68

N

CA CB

CG

CD

NE CZ

NH1

NH2

C

OArg70

Asn64

N

CA

CB

CGCD

OE1OE2

C OGlu30

NCA

CB CGCD

OE1 NE2

C

O

Gln35

Ndp187

Val8

Ala9

Val115Ile7

Pro61

Leu67

Thr56

Ile60

(a)

276

264

N1C2

N3

C4

C5C6

N7

C8

N9

N10

C11

C12

C13

C14

O15

C16O17

O18

O19

P20O21

O22

O23

P24O25

O26

P27

O28

O29O30


Phe34

Ndp187

NCA

CBCG

CD

OE1 NE2

C

O

Gln35

Asn64

Val8

NCA

CB

CG

CD

NECZ

NH1

NH2C

O

Arg70

Leu67

Phe31

Ile60

Ile7

Ala9Glu30

Thr56Val115

Leu22

Pro61

Tyr121

(b)

295

C1 C2

C3

C4O5

C6C7

O8

O9O10

O11

O12

C13

C14 C15

C16

C17C18

O19

O20

O21

O22 O23C24

C25

C26C27

C28

C29

O30

O31

O32

O33

O34

Manninotriose

Phe34

NCA

CB

CG

CD

NE

CZNH1

NH2

CO

Arg28

Phe31

Asn64

Ile60

Pro61

Pro26

Leu67

Ser59

Ndp187





His53

(c)

274

280295

265311

317

C1

C2C3

C4

C5O6

O7 O8

C9

O10

O11

O12

C13C14

C15C16

C17C18

O19O20

O21

O22 O23

C24 C25

C26

C27O28

C29O30 O31

C32O33

O34

Raffinose

PA O1A

O2A

O5BC5B

C4BO4B

C3B

O3B

C2B

O2BC1B

N9A C8AN7A

C5AC6A

N6AN1A

C2A

N3A C4A

O3PN

O1N

O2N O5D C5D

C4D

O4DC3DO3D

C2DO2D

C1D

N1N C2NC3N C7N

O7N

N7NC4NC5NC6N

P2B

O1X

O2XO3X

Ndp187

N

CA

CB

CGOD1

ND2C

O

Asn64

Phe31

N

CA

CB OG

CO

Ser59

N CA

CBCG

CDNECZ

NH1 NH2

C

O

Arg28

Ile60

Phe34

Pro61Leu67

Leu22

Pro26





His53

(d)

Figure 6 Continued


247

319

303

279

261

C1

C2

C3C4

O5 C6C7

C8C9

C10

O11

C12

C13C14

C15

C16O17

C18

C19

C20

C21

C22

O23

C24

O25

O26

C27

O28

O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39

O40C41

O42

O43

O44

O45

Stachyose

N

CACB

CGOD1ND2

C

O

Asn64Phe31

N

CA

CB

CG

CD

CE

NZC

OLys68

N

CACB

CGCD

CE

NZ

C

O

Lys63

Pro61

Phe34

Gln35

Leu67

Pro26

Ile60

(e)

255

C1 N2

C3

C4

C5

N6

N7

C8

C9

N10N11

N12

C13

N14 C15

C16

C17

C18

C19

C20

C21

C22

N23

O24C25

C26 O27

O28

C29C30C31

O32O33

MTX-PGs

Met311

NCA

CB

CG

CD

NECZ

NH1NH2

CO

Arg50

Ile108Phe117

Ala111

Asn112

Leu221

Ump314

Thr51

Phe225

Ala312

Trp109

(f)

269

284

303279

283

280330

N1

C2

N3

C4

C5C6

N7C8

N9

N10

C11C12

C13

C14

O15

C16O17

O18

O19

P20 O21

O22

O23

P24O25

O26

P27

O28

O29

O30


N1

C2

N3C4

C5

C6 O2

O4

P

OP1OP2

OP3UMP314

N

CA

CB

CG

CD1

CD2

C

O

Leu221

Phe225

N

CACB

CGOD1

ND2

C

O

Asn112

N CA

CB

CG

CDNE

CZ

NH1NH2

C

OArg50

Ile108

Met311

N

CACB

CG

CDOE1

OE2

C

O

Glu87

Leu192

Trp109

Gly222

C1998400

O4998400 C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(g)

325

304

258

284

324

294

271

285

C1C2

C3

C4 O5C6 C7

O8

O9O10

O11

O12

C13

C14C15

C16

C17 C18

O19

O20

O21

O22O23

C24

C25C26

C27

C28C29

O30

O31

O32O33

O34Manninotriose

N1

C2

N3C4

C5C6

O2

O4P

OP1

OP2OP3

UMP314N CA

CB

CG

OD1

OD2

CO

Asp218

N

CA CB

CG

CD

NECZ

NH1

NH2

C

O

Arg50

Phe225

N

CACB

CGCD

OE1

OE2

CO

Glu87

Met311

Phe117

Val313

Asn112

Leu221

NCA

CB

CG

OD1

ND2

CO Asn226

Ile108

Ala312

Thr51

Trp109

Ala111

Leu192

Tyr258

C1998400

O4998400

C2998400

C3998400

C4998400

O5998400

O3998400

C5998400





His53

(h)

Figure 6 Continued


288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)








2 high 1199032 and



MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















UMP314

O30Met309

(i)

UMP314O33

O44H11

O42

Arg50

Asn112

Met309

Met311

(j)










254

276286

307

333

N1

C2

C3

C4C5

C6

N7

N8

N9

C10 C11

N12C13

N14 C15

C16C17

C18

C19 C20

C21

C22

O23N24

C25

C26

C27

C28

O29

O30

C31

O32

O33MTX

Phe34

Phe31

N

CA CB

CG

CD

CE NZ

C

O

Lys68

N

CA CB

CG

CD

NE CZ

NH1

NH2

C

OArg70

Asn64

N

CA

CB

CGCD

OE1OE2

C OGlu30

NCA

CB CGCD

OE1 NE2

C

O

Gln35

Ndp187

Val8

Ala9

Val115Ile7

Pro61

Leu67

Thr56

Ile60

(a)

276

264

N1C2

N3

C4

C5C6

N7

C8

N9

N10

C11

C12

C13

C14

O15

C16O17

O18

O19

P20O21

O22

O23

P24O25

O26

P27

O28

O29O30


Phe34

Ndp187

NCA

CBCG

CD

OE1 NE2

C

O

Gln35

Asn64

Val8

NCA

CB

CG

CD

NECZ

NH1

NH2C

O

Arg70

Leu67

Phe31

Ile60

Ile7

Ala9Glu30

Thr56Val115

Leu22

Pro61

Tyr121

(b)

295

C1 C2

C3

C4O5

C6C7

O8

O9O10

O11

O12

C13

C14 C15

C16

C17C18

O19

O20

O21

O22 O23C24

C25

C26C27

C28

C29

O30

O31

O32

O33

O34

Manninotriose

Phe34

NCA

CB

CG

CD

NE

CZNH1

NH2

CO

Arg28

Phe31

Asn64

Ile60

Pro61

Pro26

Leu67

Ser59

Ndp187





His53

(c)

274

280295

265311

317

C1

C2C3

C4

C5O6

O7 O8

C9

O10

O11

O12

C13C14

C15C16

C17C18

O19O20

O21

O22 O23

C24 C25

C26

C27O28

C29O30 O31

C32O33

O34

Raffinose

PA O1A

O2A

O5BC5B

C4BO4B

C3B

O3B

C2B

O2BC1B

N9A C8AN7A

C5AC6A

N6AN1A

C2A

N3A C4A

O3PN

O1N

O2N O5D C5D

C4D

O4DC3DO3D

C2DO2D

C1D

N1N C2NC3N C7N

O7N

N7NC4NC5NC6N

P2B

O1X

O2XO3X

Ndp187

N

CA

CB

CGOD1

ND2C

O

Asn64

Phe31

N

CA

CB OG

CO

Ser59

N CA

CBCG

CDNECZ

NH1 NH2

C

O

Arg28

Ile60

Phe34

Pro61Leu67

Leu22

Pro26





His53

(d)

Figure 6 Continued


247

319

303

279

261

C1

C2

C3C4

O5 C6C7

C8C9

C10

O11

C12

C13C14

C15

C16O17

C18

C19

C20

C21

C22

O23

C24

O25

O26

C27

O28

O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39

O40C41

O42

O43

O44

O45

Stachyose

N

CACB

CGOD1ND2

C

O

Asn64Phe31

N

CA

CB

CG

CD

CE

NZC

OLys68

N

CACB

CGCD

CE

NZ

C

O

Lys63

Pro61

Phe34

Gln35

Leu67

Pro26

Ile60

(e)

255

C1 N2

C3

C4

C5

N6

N7

C8

C9

N10N11

N12

C13

N14 C15

C16

C17

C18

C19

C20

C21

C22

N23

O24C25

C26 O27

O28

C29C30C31

O32O33

MTX-PGs

Met311

NCA

CB

CG

CD

NECZ

NH1NH2

CO

Arg50

Ile108Phe117

Ala111

Asn112

Leu221

Ump314

Thr51

Phe225

Ala312

Trp109

(f)

269

284

303279

283

280330

N1

C2

N3

C4

C5C6

N7C8

N9

N10

C11C12

C13

C14

O15

C16O17

O18

O19

P20 O21

O22

O23

P24O25

O26

P27

O28

O29

O30


N1

C2

N3C4

C5

C6 O2

O4

P

OP1OP2

OP3UMP314

N

CA

CB

CG

CD1

CD2

C

O

Leu221

Phe225

N

CACB

CGOD1

ND2

C

O

Asn112

N CA

CB

CG

CDNE

CZ

NH1NH2

C

OArg50

Ile108

Met311

N

CACB

CG

CDOE1

OE2

C

O

Glu87

Leu192

Trp109

Gly222

C1998400

O4998400 C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(g)

325

304

258

284

324

294

271

285

C1C2

C3

C4 O5C6 C7

O8

O9O10

O11

O12

C13

C14C15

C16

C17 C18

O19

O20

O21

O22O23

C24

C25C26

C27

C28C29

O30

O31

O32O33

O34Manninotriose

N1

C2

N3C4

C5C6

O2

O4P

OP1

OP2OP3

UMP314N CA

CB

CG

OD1

OD2

CO

Asp218

N

CA CB

CG

CD

NECZ

NH1

NH2

C

O

Arg50

Phe225

N

CACB

CGCD

OE1

OE2

CO

Glu87

Met311

Phe117

Val313

Asn112

Leu221

NCA

CB

CG

OD1

ND2

CO Asn226

Ile108

Ala312

Thr51

Trp109

Ala111

Leu192

Tyr258

C1998400

O4998400

C2998400

C3998400

C4998400

O5998400

O3998400

C5998400





His53

(h)

Figure 6 Continued


288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)








2 high 1199032 and



MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















254

276286

307

333

N1

C2

C3

C4C5

C6

N7

N8

N9

C10 C11

N12C13

N14 C15

C16C17

C18

C19 C20

C21

C22

O23N24

C25

C26

C27

C28

O29

O30

C31

O32

O33MTX

Phe34

Phe31

N

CA CB

CG

CD

CE NZ

C

O

Lys68

N

CA CB

CG

CD

NE CZ

NH1

NH2

C

OArg70

Asn64

N

CA

CB

CGCD

OE1OE2

C OGlu30

NCA

CB CGCD

OE1 NE2

C

O

Gln35

Ndp187

Val8

Ala9

Val115Ile7

Pro61

Leu67

Thr56

Ile60

(a)

276

264

N1C2

N3

C4

C5C6

N7

C8

N9

N10

C11

C12

C13

C14

O15

C16O17

O18

O19

P20O21

O22

O23

P24O25

O26

P27

O28

O29O30


Phe34

Ndp187

NCA

CBCG

CD

OE1 NE2

C

O

Gln35

Asn64

Val8

NCA

CB

CG

CD

NECZ

NH1

NH2C

O

Arg70

Leu67

Phe31

Ile60

Ile7

Ala9Glu30

Thr56Val115

Leu22

Pro61

Tyr121

(b)

295

C1 C2

C3

C4O5

C6C7

O8

O9O10

O11

O12

C13

C14 C15

C16

C17C18

O19

O20

O21

O22 O23C24

C25

C26C27

C28

C29

O30

O31

O32

O33

O34

Manninotriose

Phe34

NCA

CB

CG

CD

NE

CZNH1

NH2

CO

Arg28

Phe31

Asn64

Ile60

Pro61

Pro26

Leu67

Ser59

Ndp187





His53

(c)

274

280295

265311

317

C1

C2C3

C4

C5O6

O7 O8

C9

O10

O11

O12

C13C14

C15C16

C17C18

O19O20

O21

O22 O23

C24 C25

C26

C27O28

C29O30 O31

C32O33

O34

Raffinose

PA O1A

O2A

O5BC5B

C4BO4B

C3B

O3B

C2B

O2BC1B

N9A C8AN7A

C5AC6A

N6AN1A

C2A

N3A C4A

O3PN

O1N

O2N O5D C5D

C4D

O4DC3DO3D

C2DO2D

C1D

N1N C2NC3N C7N

O7N

N7NC4NC5NC6N

P2B

O1X

O2XO3X

Ndp187

N

CA

CB

CGOD1

ND2C

O

Asn64

Phe31

N

CA

CB OG

CO

Ser59

N CA

CBCG

CDNECZ

NH1 NH2

C

O

Arg28

Ile60

Phe34

Pro61Leu67

Leu22

Pro26





His53

(d)

Figure 6 Continued


247

319

303

279

261

C1

C2

C3C4

O5 C6C7

C8C9

C10

O11

C12

C13C14

C15

C16O17

C18

C19

C20

C21

C22

O23

C24

O25

O26

C27

O28

O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39

O40C41

O42

O43

O44

O45

Stachyose

N

CACB

CGOD1ND2

C

O

Asn64Phe31

N

CA

CB

CG

CD

CE

NZC

OLys68

N

CACB

CGCD

CE

NZ

C

O

Lys63

Pro61

Phe34

Gln35

Leu67

Pro26

Ile60

(e)

255

C1 N2

C3

C4

C5

N6

N7

C8

C9

N10N11

N12

C13

N14 C15

C16

C17

C18

C19

C20

C21

C22

N23

O24C25

C26 O27

O28

C29C30C31

O32O33

MTX-PGs

Met311

NCA

CB

CG

CD

NECZ

NH1NH2

CO

Arg50

Ile108Phe117

Ala111

Asn112

Leu221

Ump314

Thr51

Phe225

Ala312

Trp109

(f)

269

284

303279

283

280330

N1

C2

N3

C4

C5C6

N7C8

N9

N10

C11C12

C13

C14

O15

C16O17

O18

O19

P20 O21

O22

O23

P24O25

O26

P27

O28

O29

O30


N1

C2

N3C4

C5

C6 O2

O4

P

OP1OP2

OP3UMP314

N

CA

CB

CG

CD1

CD2

C

O

Leu221

Phe225

N

CACB

CGOD1

ND2

C

O

Asn112

N CA

CB

CG

CDNE

CZ

NH1NH2

C

OArg50

Ile108

Met311

N

CACB

CG

CDOE1

OE2

C

O

Glu87

Leu192

Trp109

Gly222

C1998400

O4998400 C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(g)

325

304

258

284

324

294

271

285

C1C2

C3

C4 O5C6 C7

O8

O9O10

O11

O12

C13

C14C15

C16

C17 C18

O19

O20

O21

O22O23

C24

C25C26

C27

C28C29

O30

O31

O32O33

O34Manninotriose

N1

C2

N3C4

C5C6

O2

O4P

OP1

OP2OP3

UMP314N CA

CB

CG

OD1

OD2

CO

Asp218

N

CA CB

CG

CD

NECZ

NH1

NH2

C

O

Arg50

Phe225

N

CACB

CGCD

OE1

OE2

CO

Glu87

Met311

Phe117

Val313

Asn112

Leu221

NCA

CB

CG

OD1

ND2

CO Asn226

Ile108

Ala312

Thr51

Trp109

Ala111

Leu192

Tyr258

C1998400

O4998400

C2998400

C3998400

C4998400

O5998400

O3998400

C5998400





His53

(h)

Figure 6 Continued


288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)








2 high 1199032 and



MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















247

319

303

279

261

C1

C2

C3C4

O5 C6C7

C8C9

C10

O11

C12

C13C14

C15

C16O17

C18

C19

C20

C21

C22

O23

C24

O25

O26

C27

O28

O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39

O40C41

O42

O43

O44

O45

Stachyose

N

CACB

CGOD1ND2

C

O

Asn64Phe31

N

CA

CB

CG

CD

CE

NZC

OLys68

N

CACB

CGCD

CE

NZ

C

O

Lys63

Pro61

Phe34

Gln35

Leu67

Pro26

Ile60

(e)

255

C1 N2

C3

C4

C5

N6

N7

C8

C9

N10N11

N12

C13

N14 C15

C16

C17

C18

C19

C20

C21

C22

N23

O24C25

C26 O27

O28

C29C30C31

O32O33

MTX-PGs

Met311

NCA

CB

CG

CD

NECZ

NH1NH2

CO

Arg50

Ile108Phe117

Ala111

Asn112

Leu221

Ump314

Thr51

Phe225

Ala312

Trp109

(f)

269

284

303279

283

280330

N1

C2

N3

C4

C5C6

N7C8

N9

N10

C11C12

C13

C14

O15

C16O17

O18

O19

P20 O21

O22

O23

P24O25

O26

P27

O28

O29

O30


N1

C2

N3C4

C5

C6 O2

O4

P

OP1OP2

OP3UMP314

N

CA

CB

CG

CD1

CD2

C

O

Leu221

Phe225

N

CACB

CGOD1

ND2

C

O

Asn112

N CA

CB

CG

CDNE

CZ

NH1NH2

C

OArg50

Ile108

Met311

N

CACB

CG

CDOE1

OE2

C

O

Glu87

Leu192

Trp109

Gly222

C1998400

O4998400 C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(g)

325

304

258

284

324

294

271

285

C1C2

C3

C4 O5C6 C7

O8

O9O10

O11

O12

C13

C14C15

C16

C17 C18

O19

O20

O21

O22O23

C24

C25C26

C27

C28C29

O30

O31

O32O33

O34Manninotriose

N1

C2

N3C4

C5C6

O2

O4P

OP1

OP2OP3

UMP314N CA

CB

CG

OD1

OD2

CO

Asp218

N

CA CB

CG

CD

NECZ

NH1

NH2

C

O

Arg50

Phe225

N

CACB

CGCD

OE1

OE2

CO

Glu87

Met311

Phe117

Val313

Asn112

Leu221

NCA

CB

CG

OD1

ND2

CO Asn226

Ile108

Ala312

Thr51

Trp109

Ala111

Leu192

Tyr258

C1998400

O4998400

C2998400

C3998400

C4998400

O5998400

O3998400

C5998400





His53

(h)

Figure 6 Continued


288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)








2 high 1199032 and



MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















288326

308

281C1

C2

C3C4

C5

O6

O7O8

C9

O10

O11

O12

C13

C14

C15C16

C17

C18

O19

O20

O21

O22 O23

C24C25

C26

C27

O28

C29

O30O31

C32O33

O34

Raffinose

N1

C2

N3

C4

C5

C6

O2

O4

P

OP1

OP2

OP3

UMP314

N

CA

CBCG

OD1

OD2

C

OAsp218

Leu221

N

CACB

CG2 CG1

CD1

CO

Ile108

Met309 Met311

Lys308

Trp109

Phe225

Gly222

Glu310

C1998400O4998400

C2998400C3998400

C4998400

O5998400

O3998400

C5998400





His53

(i)

304

282

329

308291

311

259

260

254 274

C1C2

C3

C4

O5 C6

C7

C8C9

C10

O11C12

C13C14

C15

C16

O17

C18

C19

C20

C21

C22O23

C24

O25

O26

C27

O28O29

C30

O31

C32

O33

O34

O35

O36

O37

O38

O39O40

C41

O42

O43

O44

O45

Stachyose

N1

C2N3

C4

C5 C6

O2

O4

POP1

OP2OP3

UMP314

N

CA

CBCG

SDCE

C

OMet311

N

CA

CBCG

SD CE

CO

Met309

NCA

CB

CG

CDNE

CZ

NH1NH2

C O

Arg50

N

CA

CB CG

OD1

ND2

C

OAsn112

Leu221

NCA

CB

C

OAla312

NCA

CB

CGOD1

OD2

CO

Asp218

Ile108

Phe225

Tyr258

Thr51

Leu192

Lys308

Trp109

Gly222

Glu310

C1998400

O4998400

C2998400

C3998400C4998400

O5998400

O3998400

C5998400





His53

(j)








2 high 1199032 and



MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















MLR

45

5

55

6

65

7

75

8

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity


(a)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 09572

(b)

Bayesian

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0734

(c)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHDAR2= 0978

(d)

SVM

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

R2= 0884

Train setTest set

(e)

45

50

55

60

65

70

75

80

85

45 50 55 60 65 70 75 80 85

Pred

icte

d ac

tivity

Observed activity

CoMSIA EHAR2= 0977

Train setTest set

(f)



(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















(a) (b)

(c) (d)

(e)




2





(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















(a) (b)

(c) (d)

(e)




4 Conclusion



(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















(a) (b)

(c) (d)

(e)




Acknowledgments




References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of


















References




























































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of












































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of
















Research Article Treatment of Acute Lymphoblastic Leukemia...

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