umu.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Statistical molecular design of a focused salicylidene acylhydrazide library and multivariate QSAR of inhibition of type III secretion in the Gram-negative bacterium Yersinia
Umeå University, Faculty of Science and Technology, Department of Chemistry.
Umeå University, Faculty of Science and Technology, Department of Chemistry.
Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Bacteriology.
Umeå University, Faculty of Science and Technology, Department of Chemistry.
Show others and affiliations
2010 (English)In: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, E-ISSN 1464-3391, Vol. 18, no 7, 2686-2703 p.Article in journal (Refereed) Published
Abstract [en]

A combined application of statistical molecular design (SMD), quantitative structure-activity relationship (QSAR) modeling and prediction of new active compounds was effectively used to develop salicylidene acylhydrazides as inhibitors of type III secretion (T3S) in the Gram-negative pathogen Yersinia pseudotuberculosis. SMD and subsequent synthesis furnished 50 salicylidene acylhydrazides in high purity. Based on data from biological evaluation in T3S linked assays 18 compounds were classified as active and 25 compounds showed a dose-dependent inhibition. The 25 compounds were used to compute two multivariate QSAR models and two multivariate discriminant analysis models were computed from both active and inactive compounds. Three of the models were used to predict 4416 virtual compounds in consensus and eight new compounds were selected as an external test set. Synthesis and biological evaluation of the test set in Y. pseudotuberculosis and the intracellular pathogen Chlamydia trachomatis validated the models. Y. pseudotuberculosis and C. trachomatis cell-based infection models showed that compounds identified in this study are selective and non-toxic inhibitors of T3S dependent virulence.

Place, publisher, year, edition, pages
2010. Vol. 18, no 7, 2686-2703 p.
Keyword [en]
Statistical molecular design, QSAR, Type III secretion, Bacterial virulence, Antibacterial, Yersinia, Chlamydia
National Category
Other Basic Medicine
Identifiers
URN: urn:nbn:se:umu:diva-32591DOI: 10.1016/j.bmc.2010.02.022ISI: 000276258700035PubMedID: 20219378OAI: oai:DiVA.org:umu-32591DiVA: diva2:304376
Available from: 2010-03-18 Created: 2010-03-18 Last updated: 2013-05-16Bibliographically approved
In thesis
1. Statistical molecular design, QSAR modeling, and scaffold hopping – Development of type III secretion inhibitors in Gram negative bacteria
Open this publication in new window or tab >>Statistical molecular design, QSAR modeling, and scaffold hopping – Development of type III secretion inhibitors in Gram negative bacteria
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Type III secretion is a virulence system utilized by several clinically important Gram-negative pathogens. Computational methods have been used to develop two classes of type III secretion inhibitors, the salicylidene acylhydrazides and the acetylated salicylanilides. For these classes of compounds, quantitative structure-activity relationship models have been constructed with data from focused libraries obtained by statistical molecular design. The models have been validated and shown to provide useful predictions of untested compounds belonging to these classes. Scaffold hopping of the salicylidene acylhydrazides have resulted in a number of synthetic targets that might mimic the scaffold of the compounds. The synthesis of two libraries of analogs to two of these scaffolds and the biological evaluation of them is presented.

Place, publisher, year, edition, pages
Umeå: VMC-KBC, 2010. 65 p.
Keyword
Statistical molecular design, QSAR, synthesis, type III secretion, virulence, scaffold hopping
National Category
Organic Chemistry
Research subject
läkemedelskemi
Identifiers
urn:nbn:se:umu:diva-32506 (URN)978-91-7264-976-7 (ISBN)
Public defence
2010-04-16, KB3B1, Umeå Universitet, kemiska Institutionen, Linaeus v., KBC, 10:00 (Swedish)
Opponent
Supervisors
Available from: 2010-03-18 Created: 2010-03-15 Last updated: 2014-03-10Bibliographically approved
2. Small Molecules as Tools in Biological Chemistry: Effects of Synthetic and Natural Products on the Type III Secretion System
Open this publication in new window or tab >>Small Molecules as Tools in Biological Chemistry: Effects of Synthetic and Natural Products on the Type III Secretion System
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The increasing use of antibiotics has led to a huge problem for society, as some bacteria have developed resistance towards many of the antibiotics currently available. To help find solutions to this problem we studied small molecules that inhibit bacterial virulence, the ability to cause disease. The type III secretion system (T3SS) is a conserved virulence system found in several gram-negative bacteria, including human and plants pathogens, such as Yersinia spp., Pseudomonas aeruginosa, Chlamydia spp., Salmonella spp., Shigella spp, enteropathogenic Escherichia coli (EPEC), enterohemorrhagic Escherichia coli (EHEC), and Erwinia spp. One class of virulence-blocking compounds is the salicylidene acylhydrazides. They were first identified in a screen towards the T3SS in Yersinia pseudotuberculosis and have since been shown to block the T3SS in a panel of gram-negative bacteria such as Chlamydia spp. Salmonella enterica, Shigella flexneri and EPEC.

We designed and synthesized a library of 58 salicylidene acylhydrazides and evaluated their activity as virulence-blocking compounds in Y. pseudotuberculosis followed by calculations of quantitative structure activity relationships (QSARs). Four QSAR models were calculated, and when used in consensus they correctly classified between five out of eight compounds for Y. pseudotuberculosis as active or inactive and six out of eight compounds for C. trachomatis.

Since the target and mode of action of the salicylidene acylhydrazides were unknown, we used solution and solid phase synthesis to synthesize three different affinity reagents. One of these affinity reagents was used in affinity chromatography experiments, where 19 putative target proteins from an E. coli O157 bacterial lysate were identified. We studied four of the proteins, Tpx, WrbA, FolX, and AdhE, in more detail in Y. pseudotuberculosis and E. coli O157. We believe that the salicylidene acylhydrazides act on multiple targets that together result in down-regulation of T3SS functions. A knockout of AdhE in E. coli O157 showed a similar phenotype as salicylidene acylhydrazide treated E. coli, suggesting that this protein may be particularly interesting as a drug target.

Many of the antibiotics used today originate form natural sources. In contrast, most virulence-blocking compounds towards the T3SS are small synthetic organic molecules. Therefore, a prefractionated natural product library with marine and terrestrial biota samples was screened towards the T3SS in Y. pseudotuberculosis. Neohopeaphenol A was identified as a hit and shown to have micromolar activity towards Y. pseudotuberculosis and P. aeruginosa in cell-based infection models. 

Abstract [sv]

Det ökande användandet av antibiotika har lett till stora problem för samhället. Många bakterier har utvecklat resistens mot de antibiotika som finns tillgängliga. För att försöka hitta en möjlig lösning på detta problem, arbetar vi med en strategi där vi med hjälp av små organiska molekyler inhiberar bakteriernas virulenssystem, deras förmåga att orsaka sjukdom. Traditionella antibiotika är antingen, bakteriocida, avdödande eller bakteriostatiska, tillväxthämmande. Bakteriernas enda sätt för att överleva antibiotikabehandlingen är att utveckla resistens. Forskarvärlden tror att molekyler som inhiberar bakteriernas virulenssystem, leder till ett minskat tryck att utveckla resistens mot dessa molekyler, eftersom de inte dödar eller hämmar bakterietillväxten, utan bara avväpnar bakterierna. Typ III sekretionssystemet är ett virulenssystem som finns i många gram-negativa bakterier, t.ex., Yersinia spp., Pseudomonas aeruginosa, Chlamydia spp., Salmonella spp., Shigella spp, enteropatogena Escherichia coli (EPEC) och Erwinia spp. Salicylidenacylhydraziderna är en substansklass virulensblockare som inhiberar typ III sekretionssystemet i de ovan nämnda bakterierna.

I denna avhandling har vi designat och syntetiserat ett bibliotek med 58 salicylidenacylhydrazider och utvärderat deras biologiska aktivitet som virulensblockare i Y. pseudotuberculosis. Vi relaterade den biologiska aktiviteten till de kemiska egenskaperna hos salicylidenacylhydraziderna i kvantitativa strukturaktivitetssamband. Med hjälp av dessa samband kunde vi prediktera och validera aktiviteten till aktiv eller inaktiv för fem av åtta nya salicylidenacylhydrazider i Y. pseudotuberculosis och sex av åtta i C. trachomatis.

Eftersom verkningsmekanismen för salicylidenacylhydraziderna var okänd, så syntetiserade vi tre olika affinitetsmolekyler med kombinerad lösnings- och fastfas-syntes. En av affinitetsmolekylerna användes sedan för att ”fiska ut” och identifiera 19 potentiella målproteiner i ett bakterielysat från E. coli. Fyra av dessa proteiner, TpX, WrbA, FolX och AdhE har vi studerat vidare i Y. pseudotuberculosis och E. coli. Utifrån resultaten tror vi att salicylidenacylhydraziderna interagerar med flera proteiner som tillsammans resulterar i en nedreglering av type III sekretionssystemen. Vår samarbetspartner, Andrew Roe och hans forskargrupp (Universitetet i Glasgow), har studerat AdhE i E. coli.  De har visat att E. coli som saknar genen för proteinet AdhE, har samma fenotyp som E. coli behandlad med salicylidenacylhydraziderna, d.v.s. ett nedreglerat T3SS, vilket gör AdhE till ett speciellt intressant målprotein.

I jämförelse med många av våra nuvarande antibiotika som har ett naturligt ursprung så är de flesta studerade virulensblockare små syntetiska organiska molekyler. Därför testades en stor kollektion av naturprodukter från marina och landlevande växter och invertebrater från Sydostasien, för att hitta nya inhibitorer mot typ III sekretionssystemet i Y. pseudotuberculosis. Neohopeaphenol A som kommer från barken på Hopea hainanensis, ett träd som växer i sydostasiens regnskogar, identifierades som en ny virulensblockare. Neohopeaphenol A visade sig vara en potent virulensblockare i in vitro infektionsförsök med Y. psudotuberkulosis eller Pseudomonas aeruginosa.

Forskningen i denna avhandling visar att virulensblockare kan hjälpa oss att förstå hur bakterier orsakar sjukdom. Förhoppningsvis kan det i framtiden leda till nya typer av läkemedel mot infektionssjukdomar. 

Place, publisher, year, edition, pages
Umeå: Umeå universitet, 2013. 75 p.
Keyword
Type III secretion, salicylidene acylhydrazide, virulence-blocker, virulence, inhibitor, target identification, neohopeaphenol A, Yersinia pseudotuberculosis, Pseudomonas aeruginosa, Escherichia coli
National Category
Chemical Sciences
Research subject
biological chemistry
Identifiers
urn:nbn:se:umu:diva-70281 (URN)978-91-7459-671-7 (ISBN)978-91-7459-672-4 (ISBN)
Public defence
2013-06-07, KBC-huset, KB3B1, Umeå universitet, Umeå, 10:00 (English)
Opponent
Supervisors
Available from: 2013-05-17 Created: 2013-05-13 Last updated: 2013-05-16Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Authority records BETA

Dahlgren, Markus KZetterström, Caroline EGylfe, ÅsaLinusson, AnnaElofsson, Mikael

Search in DiVA

By author/editor
Dahlgren, Markus KZetterström, Caroline EGylfe, ÅsaLinusson, AnnaElofsson, Mikael
By organisation
Department of ChemistryClinical BacteriologyUmeå Centre for Microbial Research (UCMR)
In the same journal
Bioorganic & Medicinal Chemistry
Other Basic Medicine

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 341 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf