Important notice

These pages present the Plasmodesma serveur which is currently under continuous development.

The service provided on internet is meant to be improved regularly, both by the extension of the analytical methods and addition of new methods, but also by input from the users of the service, and in articular from remarks that will be discussed during the Faraday meeting.

Welcome

This Web service allows to use the *Plasmodesma* server freely

When using this service, please refer to:

for this interactive site:
Margueritte, L., Duciel, L., Bourjot, M., Vonthron-Sénécheau, C., & Delsuc, M. A. "Automatised Pharmacophoric Deconvolution of Plant Extracts, application to Cinchona bark crude extract." Faraday Discussions (2019).
for the analytical method itself (Plasmodesma):
L. Margueritte, P. Markov, L. Chiron, J.-P. Starck, C. Vonthron-Sénécheau, M. Bourjot & M.-A. Delsuc, "Automatic differential analysis of NMR experiments in complex samples." Magn. Reson. Chem., (2018), 56, 469–479.

This site is associated to the work:

Automatised Pharmacophoric Deconvolution of Plant Extracts, application to Cinchona bark crude extract

Laure Margueritte^a‡, Laura Duciel^b,c‡, Mélanie Bourjot^d, Catherine Vonthron-Sénécheau^a, and Marc-André Delsuc^∗b

a. Laboratoire d’Innovation Thérapeutique (LIT) UMR CNRS 7200, LabEx Medalis, Faculté de Pharmacie, Université de Strasbourg, Illkirch-Graffenstaden, France
b. CASC4DE Le Lodge, 20, Avenue du Neuhof, 67100 Strasbourg, France
c. Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U596, CNRS UMR 7104, Université de Strasbourg, Illkirch-Graffenstaden, France
d. Institut Pluridisciplinaire Hubert Curien (IPHC) UMR CNRS 7178, Faculté de Pharmacie, Université de Strasbourg, Illkirch-Graffenstaden, France.

‡ These two authors contributed equally

Faraday Discuss., 2019, Accepted Manuscript | 10.1039/C8FD00242H

Abstract

We present a development of the *Plasmodesma* dereplication method [Margueritte et al., Magn. Reson. Chem., 2018 56, 469]. This method is based on the automatic acquisition of a standard set of NMR experiments from a medium size set of samples differing by their bioactivity. From this raw data, an analysis pipeline is run and the data is analysed by leveraging machine learning approaches in order to extract the spectral fingerprints of the active compounds. The optimal conditions for the analysis are determined, and tested on two different system, a synthetic sample where a single active molecule is to be isolated and characterized, and a complex bioactive matrix with synergetic interactions between the components. The method allows the identification of the active compounds and performs a pharmacophoric deconvolution.

The program is made available on internet, with an interactive visualisation of the statistical analysis, at https://plasmodesma.igbmc.science.

To process a data-set

Start with a set of samples with a quantitative measurement (activity, IC50,...)
Acquire a set of 2D NMR experiments (the program actually handles COSY, TOCSY, HSQC, HMBC, DOSY). It is important that
- all samples are acquired with exactly the same set-up, ideally in automation
- create a Bruker experiment for each sample
- the same expno are used all along the different experiments
Create a zip archive of the Bruker experiements, no need to process them
Go to the page "Data Processing" to send your job - this will start the processing job on our server. You will receive a mail when the processing is finished. (processing time may depend on the server load).
This mail will contain a link pointing to the site where you can be look at the results of the analysis

Program

This program is available here: https://github.com/delsuc/plasmodesma

Acknowledgements

This sever is made possible thanks to the help of many people and organisations.

We thanks

The CASC4DE company for the code of the web server
The IGBMC for access to CPU time
J. Seiler and the IGBMC IT team for the support of the server