Chemography of natural product space.

Abstract:

:We present the application of the generative topographic map algorithm to visualize the chemical space populated by natural products and synthetic drugs. Generative topographic maps may be used for nonlinear dimensionality reduction and probabilistic modeling. For compound mapping, we represented the molecules by two-dimensional pharmacophore features (chemically advanced template search descriptor). The results obtained suggest a close resemblance of synthetic drugs with natural products in terms of their pharmacophore features, despite pronounced differences in chemical structure. Generative topographic map-based cluster analysis revealed both known and new potential activities of natural products and drug-like compounds. We conclude that the generative topographic map method is suitable for inferring functional similarities between these two classes of compounds and predicting macromolecular targets of natural products.

journal_name

Planta Med

journal_title

Planta medica

authors

Miyao T,Reker D,Schneider P,Funatsu K,Schneider G

doi

10.1055/s-0034-1396322

subject

Has Abstract

pub_date

2015-04-01 00:00:00

pages

429-35

issue

6

eissn

0032-0943

issn

1439-0221

journal_volume

81

pub_type

杂志文章
  • Characterization of the Anticoagulative Constituents of Angelicae Sinensis Radix and Their Metabolites in Rats by HPLC-DAD-ESI-IT-TOF-MSn.

    abstract::Angelicae Sinensis Radix is commonly used in traditional Chinese medicine. Pharmacological studies show that Angelicae Sinensis Radix has clear anticoagulant activity. Therefore, in this study, the anticoagulant activity of crude Angelicae Sinensis Radix extracts was investigated by measuring the thrombin times of the...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-0035-1558309

    authors: Wang L,Huang S,Chen B,Zang XY,Su D,Liang J,Xu F,Liu GX,Shang MY,Cai SQ

    更新日期:2016-03-01 00:00:00

  • Molecular authentication of the traditional dai medicinal plant Croton caudatus.

    abstract::Croton caudatus is an important species in Dai folk medicine. Some other Croton species, in particular, C. kongensis, C. cascarilloides, C. crassifolius, C. lachnocarpus and C. olivaceus are often marketed as C. caudatus, and thus, the therapeutic effects of C. caudatus are not achieved. The respective morphological f...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2007-967197

    authors: Xue HG,Zhou SD,He XJ,Yu Y

    更新日期:2007-06-01 00:00:00

  • Essential oil from Myrcia ovata: chemical composition, antinociceptive and anti-inflammatory properties in mice.

    abstract::The leaves of Myrcia ovata, popularly known as "laranjinha do mato", are frequently used as an infusion in folk medicine. The essential oil obtained from these leaves is rich in citral, a mixture of neral and geranial isomers, known for its analgesic effect. Male Swiss mice (20-22 g) were tested in models of acute pai...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-0034-1383120

    authors: Dos Santos GC,Gomes GA,Gonçalves GM,de Sousa LM,Santiago GM,de Carvalho MG,Marinho BG

    更新日期:2014-11-01 00:00:00

  • Bioactive compounds from the buds of Platanus orientalis and isolation of a new kaempferol glycoside.

    abstract::A new compound kaempferol 3-O-alpha-L-(2"-E-p-coumaroyl)-rhamnopyranoside, as well as the known flavonoids, kaempferol 3-O-beta-D-(6"-E-p-coumaroyl)-glucopyranoside, kaempferol 3-O-alpha-L-(2",3"-di-E-p-coumaroyl)-rhamnopyranoside, and caffeic acid were obtained from the methanolic extract of Platanus orientalis L. bu...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2006-959751

    authors: Mitrokotsa D,Mitaku S,Demetzos C,Harvala C,Mentis A,Perez S,Kokkinopoulos D

    更新日期:1993-12-01 00:00:00

  • New Tirucallane-Type Triterpenoids from Guarea guidonia.

    abstract::The aerial parts of Guarea guidonia afforded three new tirucallane-type triterpenoids: 3,4-seco-tirucalla-4(28),8(9),24(25)-trien-7α,11α-dihydroxy-21,23-epoxy-3,11-olide, named guareolide (1: ), 3,4-seco-tirucalla-4(28),7(8),24(25)-trien-21-hydroxy-21,23-epoxy-3-oic acid, named guareoic acid A (2: ), and 3,4-seco-tiru...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-0044-100524

    authors: Hernandez V,De Leo M,Cotugno R,Braca A,De Tommasi N,Severino L

    更新日期:2018-07-01 00:00:00

  • Medicinal Plants in the Treatment of Colitis: Evidence from Preclinical Studies.

    abstract::Ulcerative colitis is a chronic inflammatory condition whose treatment includes aminosalicylates, corticosteroids, and immunomodulators. Medicinal plants seem to be an important alternative treatment for this condition. They have been the subject of a great number of studies in recent years. This study was conducted t...

    journal_title:Planta medica

    pub_type: 杂志文章,评审

    doi:10.1055/s-0043-104933

    authors: Santana MT,Cercato LM,Oliveira JP,Camargo EA

    更新日期:2017-05-01 00:00:00

  • A new cytotoxic trichothecene macrolide from the endophyte Myrothecium roridum.

    abstract::A new cytotoxic roridin-type trichothecene macrolide named roritoxin E(1) was characterized from the solid culture of Myrothecium roridum IFB-E091 (residing originally inside Artemisia annua root), together with the known compounds lumichrome (2), (22 E,24 S)-cerevisterol (3), and (22 E,24 R)-6 beta-methoxy-ergosta-7,...

    journal_title:Planta medica

    pub_type: 信件

    doi:10.1055/s-0029-1240897

    authors: Shen L,Wang JS,Shen HJ,Song YC,Tan RX

    更新日期:2010-07-01 00:00:00

  • Polyacetylenverbindungen aus Jungia seleriana.

    abstract::The aerial parts of JUNGIA SETERIANA afforded in addition to known compounds two pairs of isomeric C (17)-acetylenes which differ in the number of triple bonds and in the configuration of the 9,10-double bond. The structures and configurations followed from the UV and the (1)H-NMR spectra, especially from those of the...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2007-969670

    authors: Bohlmann F,Zdero C,King RM,Robinson H

    更新日期:1984-04-01 00:00:00

  • Assessment of cannabinoids content in micropropagated plants of Cannabis sativa and their comparison with conventionally propagated plants and mother plant during developmental stages of growth.

    abstract::Gas chromatography-flame ionization detection (GC-FID) was used to assess the chemical profile and quantification of cannabinoids to identify the differences, if existing, in the chemical constituents of in vitro propagated plants (IVP), conventionally grown plants (VP) and indoor grown mother plants (MP-Indoor) of a ...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-0029-1240628

    authors: Chandra S,Lata H,Mehmedic Z,Khan IA,ElSohly MA

    更新日期:2010-05-01 00:00:00

  • Leaf alkaloid contents of Tabernaemontana pachysiphon as influenced by endogenous and environmental factors in the natural habitat.

    abstract::Indole alkaloid contents were investigated in leaves of Tabernaemontana pachysiphon (Apocynaceae) trees in the natural habitat, Shimba Hills National Reserve, Kenya. The contents of the major alkaloids apparicine, tubotaiwine, tubotaiwine- N-oxide, and isovoacangine varied with site, leaf age, leaf growth form, positi...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2006-957393

    authors: Höft M,Verpoorte R,Beck E

    更新日期:1998-03-01 00:00:00

  • The alkaloid 4-methylaaptamine isolated from the sponge Aaptos aaptos impairs Herpes simplex virus type 1 penetration and immediate-early protein synthesis.

    abstract::We describe in this paper that the alkaloid 4-methylaaptamine, isolated from the marine sponge Aaptos aaptos, inhibited HSV-1 infection. We initially observed that 4-methylaaptamine inhibited HSV-1 replication in Vero cells in a dose-dependent manner with an EC50 value of 2.4 microM. Moreover, the concentration requir...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2007-967109

    authors: Souza TM,Abrantes JL,de A Epifanio R,Leite Fontes CF,Frugulhetti IC

    更新日期:2007-03-01 00:00:00

  • Mechanisms of hypoglycemic activity of ganoderan B: a glycan of Ganoderma lucidum fruit bodies.

    abstract::Ganoderan B increased the plasma insulin level in normal and glucose-loaded mice but elicited no effect on insulin binding to isolated adipocytes. Administration of ganoderan B elicited significant increases of the activities of hepatic glucokinase, phosphofructokinase and glucose-6-phosphate dehydrogenase, decreased ...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2006-962057

    authors: Hikino H,Ishiyama M,Suzuki Y,Konno C

    更新日期:1989-10-01 00:00:00

  • Growth inhibition and G1 cell cycle arrest mediated by 25-methoxyhispidol A, a novel triterpenoid, isolated from the fruit of Poncirus trifoliata in human hepatocellular carcinoma cells.

    abstract::Poncirus trifoliata (Rutaceae) extracts have been known to possess anti-allergic, anti-inflammatory and antiviral activities. However, other biological activities, especially, the anticancer potential of extracts of P. trifoliata or its constituents, have not been fully investigated yet. In this study, we have evaluat...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2008-1034286

    authors: Hong J,Min HY,Xu GH,Lee JG,Lee SH,Kim YS,Kang SS,Lee SK

    更新日期:2008-02-01 00:00:00

  • Polyclonal antibody against a complement-activating pectin from the roots of Angelica acutiloba.

    abstract::Anti-sera against a complement-activating pectin (AR-2IIb), which was purified from the roots of Angelica acutiloba Kitagawa, were obtained by immunization of rabbits, and a polyclonal anti-AR-2IIb antibody of the IgG class was purified by affinity chromatography on AR-2IIb-immobilized Sepharose and Protein G-Sepharos...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2006-959524

    authors: Wang NL,Kiyohara H,Matsumoto T,Otsuka H,Hirano M,Yamada H

    更新日期:1994-10-01 00:00:00

  • Extracellular polysaccharides produced by suspension-cultured cells from Digitalis lanata.

    abstract::Extracellular polysaccharides (ECP) were isolated in yields of up to 4 mg/ml from the culture media of suspension-cultured cells from Digitalis lanata Ehrh. ECP content was increasing continuously over the first ten days of cultivation and then stayed constant until day 20. ECP were fractionated by ion-exchange chroma...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2006-957730

    authors: Hensel A,Schmidgall J,Kreis W

    更新日期:1997-10-01 00:00:00

  • An approach to the antiinflammatory activity of borjatriol.

    abstract::The antiinflammatory activity of borjatriol (a diterpenoid isolated from SIDERITIS MUGRONENSIS Borja) was tested using the cotton pellet-granuloma assay. The compound inhibited the granuloma weight and the serum lysozyme activity in a dose-dependently way. The determination of this enzyme has allowed us to distinguish...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2007-969630

    authors: Villar A,Salom R,Alcaraz MJ

    更新日期:1984-02-01 00:00:00

  • Benzophenanthridine alkaloids of Chelidonium majus; I. Inhibition of 5- and 12-lipoxygenase by a non-redox mechanism.

    abstract::The benzophenanthridine alkaloids sanguinarine and chelerythrine of Chelidonium majus, L. (Papaveraceae), are potent inhibitors of 5-lipoxygenase in polymorphonuclear leukocytes and 12-lipoxygenase in mouse epidermis, while the activity of soybean lipoxygenase is not influenced. The extract of the herb of Ch.majus als...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2006-957924

    authors: Vavrecková C,Gawlik I,Müller K

    更新日期:1996-10-01 00:00:00

  • Two New Glucosides from Hypoxis obtusa: Obtuside A and Obtuside B1,5.

    abstract::From the rhizomes of HYPOXIS OBTUSA two monoglucosides having the same aglycone as hypoxoside, 1-(3',4'- dihydroxyphenyl)-5-(3'',4''-dihydroxyphenyl)-1-pen-ten-4-yne, have been obtained. By methylation followed by hydrogenation they have been transformed into the same compound, 1-(3'-methoxy-4'- O-beta- D-glucopyranos...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2006-962019

    authors: Galeffi C,Multari G,De Vicente Y,Messana I,Nicoletti M,Marini-Bettolo GB

    更新日期:1989-06-01 00:00:00

  • Composition and antimicrobial activity of the essential oil of Peumus boldus leaves.

    abstract::The composition and the antimicrobial activity of the essential oil from the leaves of Peumus boldus is investigated. Analyses of the oil obtained by hydrodistillation were carried out by GC and GC-MS using columns of two different stationary phases. Fractionation of the essential oil by column chromatography on silic...

    journal_title:Planta medica

    pub_type: 信件

    doi:10.1055/s-2006-960461

    authors: Vila R,Valenzuela L,Bello H,Cañigueral S,Montes M,Adzet T

    更新日期:1999-03-01 00:00:00

  • Saucernetin-7 and saucernetin-8 isolated from Saururus chinensis inhibit the LPS-induced production of nitric oxide and prostaglandin E2 in macrophage RAW264.7 cells.

    abstract::In the present study, we demonstrate that saucernetin-8 ( 1) and saucernetin-7 ( 2), isolated from the underground parts of Saururus chinensis (Saururaceae), exerted potent inhibitory effects on LPS-induced nitric oxide (NO) and prostaglandin E (2) (PGE (2)) production in RAW 264.7 cells. Both compounds 1 and 2, known...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2003-45106

    authors: Park HJ,Kim RG,Seo BR,Ha J,Ahn BT,Bok SH,Lee YS,Kim HJ,Lee KT

    更新日期:2003-10-01 00:00:00

  • [About major alkaloids of Strychnos scheffleri from Zaire].

    abstract::Leaves and stem barks of S. scheffleri Gilg afforded eight dihydroindole alkaloids. Four tertiary monomers (O-methyl Na-acetylstrychnosplendine, Na-acetylstrychnosplendine, strychnobrasiline and strychnofendlerine) have been isolated from leaf material while stem barks yielded one tertiary monomer (desacetylisoretulin...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2007-971656

    authors: Caprasse M,Angenot L

    更新日期:1981-08-01 00:00:00

  • Polyacetylenic compounds and butanol fraction from Bidens pilosa can modulate the differentiation of helper T cells and prevent autoimmune diabetes in non-obese diabetic mice.

    abstract::Compelling evidence suggests that infiltrating CD4+ type I helper T (Th1) cells in the pancreatic islets play a pivotal role in the progression of diabetes in non-obese diabetic (NOD) mice. We demonstrate in the present report that a butanol fraction of B. pilosa suppressed the development of diabetes, helped maintain...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2004-832645

    authors: Chang SL,Chang CL,Chiang YM,Hsieh RH,Tzeng CR,Wu TK,Sytwu HK,Shyur LF,Yang WC

    更新日期:2004-11-01 00:00:00

  • Antiulcer action of Styrax camporum and Caesalpinia ferrea in rats. '.

    abstract::Stem extracts of Styrax camporum Pohl and Caesalpinia ferrea Martius were administered orally and intraperitoneally to rats and effected a decrease in the acute ulceration number. The volume, pH, and hydrochloric acid concentration of gastric secretions were measured after administration of both extracts, atropine, an...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2006-959430

    authors: Bacchi EM,Sertié JA

    更新日期:1994-04-01 00:00:00

  • An anti-inflammatory ent-kaurane from the stems of Annona squamosa that inhibits various human neutrophil functions.

    abstract::We have previously shown that 11 ent-kauranes isolated from the stems of Annona squamosa exhibited immunomodulating effects in leukocytes. In this study, a cellular model using isolated human neutrophils, which are important in the pathogenesis of rheumatoid arthritis, ischemia-reperfusion injury, chronic obstructive ...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2005-871234

    authors: Yeh SH,Chang FR,Wu YC,Yang YL,Zhuo SK,Hwang TL

    更新日期:2005-10-01 00:00:00

  • Inhibition of rat adjuvant-induced arthritis by ginkgetin, a biflavone from ginkgo biloba leaves.

    abstract::Ginkgetin, a biflavone isolated from Ginkgo biloba leaves, was previously reported as an inhibitor of group II phospholipase A2. In this study, ginkgetin was evaluated for in vivo antiarthritic and analgesic activities. Ginkgetin (10-20 mg/kg/day) strongly reduced arthritic inflammation in an animal model of rat adjuv...

    journal_title:Planta medica

    pub_type: 信件

    doi:10.1055/s-2006-960815

    authors: Kim HK,Son KH,Chang HW,Kang SS,Kim HP

    更新日期:1999-06-01 00:00:00

  • Bioactive Isocedrenes from Perezia multiflora.

    abstract::Four isocedrenes (1:  - 4: ), including one new compound (2: ), were isolated from an ethanolic extract of the aerial parts of Perezia multiflora by bioactivity-guided fractionation. For compounds 1: and 3: , a revised stereochemical assignment is proposed based on molecular modeling studies using DFT-NMR calculations...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/a-1298-4706

    authors: Bourgeade-Delmas S,André-Barrès C,Lucas J,Trinel M,Castillo Pareja D,Jullian V

    更新日期:2020-11-23 00:00:00

  • New aspects of DNA-based authentication of Chinese medicinal plants by molecular biological techniques.

    abstract::DNA technology provides a powerful tool to complement chemical analyses for authentication of Chinese medicinal plants and to ensure that herbal materials are not contaminated with ineffective or potentially harmful substitutes or adulterants. In the last two decades molecular biotechnology has provided sophisticated ...

    journal_title:Planta medica

    pub_type: 杂志文章,评审

    doi:10.1055/s-0030-1250519

    authors: Heubl G

    更新日期:2010-12-01 00:00:00

  • Phytochemical analysis and cytotoxicity towards multidrug-resistant leukemia cells of essential oils derived from Lebanese medicinal plants.

    abstract::Juniperus excelsa fruit essential oil as well as J. oxycedrus, Cedrus libani, and Pinus pinea wood essential oils have been obtained with yields between 2.2 ± 0.3 % to 3.4 ± 0.5 % and analyzed by gas chromatography. Sesquiterpenes mainly characterized C. libani and J. oxycedrus essential oils, while in P. pinea and J....

    journal_title:Planta medica

    pub_type: 信件

    doi:10.1055/s-0032-1327896

    authors: Saab AM,Guerrini A,Sacchetti G,Maietti S,Zeino M,Arend J,Gambari R,Bernardi F,Efferth T

    更新日期:2012-12-01 00:00:00

  • Antifungal activity from Alpinia galanga and the competition for incorporation of unsaturated fatty acids in cell growth.

    abstract::An antimicrobial diterpene was isolated from Alpinia galanga in the screening for potentiators of phytochemical antibiotic action. The structure was elucidated by spectral data and identified as (E)-8 beta, 17-epoxylabd-12-ene-15, 16-dial (1). Diterpene 1 synergistically enhanced the antifungal activity of quercetin a...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-2006-957890

    authors: Haraguchi H,Kuwata Y,Inada K,Shingu K,Miyahara K,Nagao M,Yagi A

    更新日期:1996-08-01 00:00:00

  • New cytotoxic lupane triterpenes from Perrottetia arisanensis.

    abstract::Eight new lupane triterpenes, including 7beta-cis-coumaroylbetulinic acid (1), 7beta-trans-coumaroylbetulinic acid (2), 7beta-cis-coumaroyl-3-epi-betulinic acid (3), 7beta-trans-coumaroyl-3-epi-betulinic acid (4), 7beta-cis-coumaroylbetulonic acid (5), 7beta-trans-coumaroylbetulonic acid (6), 7beta-hydroxybetulinaldeh...

    journal_title:Planta medica

    pub_type: 杂志文章

    doi:10.1055/s-0029-1185438

    authors: Du YC,Lin AS,Wu CC,Hsieh PW,Chen YH,Chen IH,Chen SL,Yen HF,Lübken T,Chang FR,Wu YC

    更新日期:2009-06-01 00:00:00