Artificial neural network study on organ-targeting peptides

Journal of Computer-Aided Molecular Design

Volumn 24, Issue 1, 2010, Pages 49-56

  Jung, Eunkyoung ^a   Kim, Junhyoung ^a   Choi, Seung Hoon ^a   Kim, Minkyoung ^a   Rhee, Hokyoung ^a   Shin, Jae Min ^b   Choi, Kihang ^c   Kang, Sang Kee ^d   Lee, Nam Kyung ^d   Choi, Yun Jaie ^d   Jung, Dong Hyun ^a  

^a Insilicotech Co Ltd   (South Korea)

^b Sung Ok BD   (South Korea)

^c Korea University   (South Korea)

^d Seoul National University   (South Korea)

Author keywords

Neural network; Organ targeting peptide; ROC score; VHSE descriptor

Indexed keywords

CONTROLLED DRUG DELIVERY; NETWORK ARCHITECTURE; PEPTIDES;

CONTROL DATA; DESCRIPTORS; NEURAL-NETWORKS; ORGAN-TARGETING PEPTIDE; PEPTIDE SEQUENCES; RANDOM SEQUENCE; RECEIVER OPERATING CHARACTERISTIC SCORE; RECEIVER OPERATING CHARACTERISTICS; TARGETING PEPTIDES; VHSE DESCRIPTOR;

NEURAL NETWORKS;

PEPTIDE; PEPTIDE DERIVATIVE; PEPTIDOMIMETIC AGENT;

AMINO ACID SEQUENCE; ANIMAL EXPERIMENT; ARTICLE; ARTIFICIAL NEURAL NETWORK; CONTROLLED STUDY; DRUG SYNTHESIS; DRUG TARGETING; NONHUMAN; PHAGE DISPLAY; PREDICTION; PRIORITY JOURNAL; RAT; RECEIVER OPERATING CHARACTERISTIC; SENSITIVITY AND SPECIFICITY; STATISTICAL MODEL; STATISTICAL SIGNIFICANCE;

EID: 76449100552     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-009-9313-0     Document Type: Article

References (25)

1. R Pasqualini E Ruoslahti 1996 Organ targeting in vivo using phage display peptide libraries Nature 380 364 366 10.1038/380364a0 1:CAS:528: DyaK28XhvFyrtLw%3D (Pubitemid 26097120)
2. D Rajotte W Arap M Hagedorn E Koivunen R Pasqualini E Ruoslahti 1998 Molecular heterogeneity of the vascular endothelium revealed by in vivo phage display J Clin Invest 102 430 437 10.1172/JCI3008 1:CAS:528:DyaK1cXkslOktLg%3D
3. M Trepel W Arap R Pasqualini 2000 Exploring vascular heterogeneity for gene therapy targeting Gene Ther 7 2059 2060 10.1038/sj.gt.3301361 1:CAS:528:DC%2BD3MXis1yjtw%3D%3D (Pubitemid 32118073)
4. D Rajotte E Ruoslahti 1999 Membrane dipeptidase is the receptor for a lung-targeting peptide identified by in vivo phage display J Biol Chem 274 11593 11598 10.1074/jbc.274.17.11593 1:CAS:528:DyaK1MXislGmurk%3D (Pubitemid 29197815)
5. R Pasqualini E Koivunen R Kain J Lahdenranta M Sakamoto A Stryhn RA Ashmun LH Shapiro W Arap E Ruoslahti 2000 Aminopeptidase N is a receptor for tumor-homing peptides and a target for inhibiting angiogenesis Cancer Res 60 722 727 1:CAS:528:DC%2BD3cXht1Gmtbc%3D
6. MG Kolonin R Pasqualini W Arap 2001 Molecular addresses in blood vessels as targets for therapy Curr Opin Chem Biol 5 308 313 10.1016/S1367-5931(00) 00207-6 1:CAS:528:DC%2BD3MXktlShtb8%3D (Pubitemid 32718528)
7. W Arap R Pasqualini E Ruoslahti 1998 Cancer treatment by targeted drug delivery to tumor vasculature in a mouse model Science 279 377 380 10.1126/science.279.5349.377 1:CAS:528:DyaK1cXmtl2juw%3D%3D (Pubitemid 28063372)
8. W Arap W Haedicke M Bernasconi R Kain D Rajotte S Krajewski HM Ellerby DE Bredesen R Pasqualini E Ruoslahti 2002 Targeting the prostate for destruction through a vascular address Proc Natl Acad Sci USA 99 1527 1531 10.1073/pnas.241655998 1:CAS:528:DC%2BD38Xht1ClsbY%3D (Pubitemid 34136526)
9. E Durr J Yu KM Krasinska LA Carver JR Yates JE Testa P Oh JE Schnitzer 2004 Direct proteomic mapping of the lung microvascular endothelial cell surface in vivo and in cell culture Nat Biotechnol 22 985 992 10.1038/nbt993 1:CAS:528:DC%2BD2cXmtFWrurc%3D (Pubitemid 39014475)
10. P Oh Y Li J Yu E Durr K Krasinska LA Carver JE Testa JE Schnitzer 2004 Subtractive proteomic mapping of the endothelial surface in lung and solid tumours for tissue-specific therapy Nature 429 629 635 10.1038/nature02580 1:CAS:528:DC%2BD2cXks1Kls7c%3D (Pubitemid 38812308)
11. M Trepel W Arap R Pasqualini 2002 In vivo phage display and vascular heterogeneity: implications for targeted medicine Curr Opin Chem Biol 6 399 404 10.1016/S1367-5931(02)00336-8 1:CAS:528:DC%2BD38XjvVektrY%3D (Pubitemid 34522068)
12. W Arap MG Kolonin M Trepel J Lahdenranta M Cardó-Vila RJ Giordano PJ Mintz PU Ardelt VJ Yao CI Vidal L Chen A Flamm H Valtanen LM Weavind ME Hicks RE Pollock GH Botz CD Bucana E Koivunen D Cahill P Troncoso KA Baggerly RD Pentz KA Do CJ Logothetis R Pasqualini 2002 Steps toward mapping the human vasculature by phage display Nat Med 8 121 127 10.1038/nm0202-121 1:CAS:528:DC%2BD38Xht1equrk%3D (Pubitemid 34155122)
13. E Jung J Kim M Kim DH Jung H Rhee JM Shin K Choi SK Kang MK Kim CH Yun YJ Choi SH Choi 2007 Artificial neural network models for prediction of intestinal permeability of oligopeptides BMC Bioinformatics 8 245 10.1186/1471-2105-8-245 (Pubitemid 47335050)
14. H Mei ZH Lian Y Zhou SZ Li 2005 A new set of amino acid descriptors and its application in peptide QSARs Biopolymers (Peptide Science) 80 775 786 10.1002/bip.20296 1:CAS:528:DC%2BD2MXhtlSqur%2FP (Pubitemid 43266584)
15. S Hellberg M Sjöström B Skagerberg S Wold 1987 Peptide quantitative structure-activity relationships, a multivariate approach J Med Chem 30 1126 1135 10.1021/jm00390a003 1:CAS:528:DyaL2sXktFOhsLY%3D
16. M Sandberg L Eriksson J Jonsson M Sjöströ S Wold 1998 New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids J Med Chem 41 2481 2491 10.1021/jm9700575 1:CAS:528:DyaK1cXktlShuro%3D (Pubitemid 28321898)
17. The nnet of VR 7.2 package (2004) http://www.r-project.org/, Version R 2.0.1
18. JA Hanley BJ McNeil 1982 The meaning and use of the area under a receiver operating characteristic (ROC) curve Radiology 143 29 36 1:STN:280: DyaL387ltFyksQ%3D%3D
19. C Springer H Adalsteinsson MM Young PW Kegelmeyer DC Roe 2005 PostDock: a structural, empirical approach to scoring protein ligand complexes J Med Chem 48 6821 6831 10.1021/jm0493360 1:CAS:528:DC%2BD2MXhtVGis73L (Pubitemid 41533104)
20. RD Cramer JD Bunce DE Patterson IE Frank 1988 Crossvalidation, bootstrapping, and partial least squares compared with multiple regression in conventional QSAR studies Quant Struct-Act Relat 7 18 25 10.1002/qsar. 19880070105
21. HM Ellerby W Arap LM Ellerby R Kain R Andrusiak GD Rio S Krajewski CR Lombardo R Rao E Ruoslahti DE Bredesen R Pasqualini 1999 Anti-cancer activity of targeted pro-apoptotic peptides Nat Med 5 1032 1038 10.1038/12469 1:CAS:528:DyaK1MXlslGqtLs%3D (Pubitemid 29439574)
22. Y Chen X Xu S Hong J Chen N Liu CB Underhill K Creswell L Zhang 2001 RGD-tachyplesin inhibits tumor growth Cancer Res 61 2434 2438 1:CAS:528:DC%2BD3MXisVSlu74%3D
23. Y Yoneda SC Steiniger K Capková JM Mee Y Liu GF Kaufmann KD Janda 2008 A cell-penetrating peptidic GRP78 ligand for tumor cell-specific prodrug therapy Bioorg Med Chem Lett 18 1632 1636 10.1016/j.bmcl.2008.01.060 1:CAS:528:DC%2BD1cXjt1Ckt7c%3D (Pubitemid 351318249)
24. F Curnis A Sacchi L Borgna F Magni A Gasparri A Corti 2000 Enhancement of tumor necrosis factor α antitumor immunotherapeutic properties by targeted delivery to aminopeptidase N (CD13) Nat Biotechnol 18 1185 1190 10.1038/81183 1:CAS:528:DC%2BD3cXotVSltrY%3D (Pubitemid 30823358)
25. F Curnis G Arrigoni A Sacchi L Fischetti W Arap R Pasqualini A Corti 2002 Differential binding of drugs containing the NGR motif to CD13 isoforms in tumor vessels, epithelia, and myeloid cells Cancer Res 62 867 874 1:CAS:528:DC%2BD38Xht1Kqsr8%3D