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Mehdi Beniddir @mehdibeni.bsky.social · 2d

Thrilled to share with you a recent work from our group: Computational Mass Spectrometry-Based Reassessment of European Amanita sect. Phalloideae Cyclopeptidome | Journal of Natural Products pubs.acs.org/doi/10.1021/... Please have a look to the associated MassQL compendium.

Computational Mass Spectrometry-Based Reassessment of European Amanita sect. Phalloideae Cyclopeptidome

An advanced metabolomic workflow featuring expert knowledge-tailored mass spectral queries and multi-informative molecular networking was applied to French DNA-barcoded collections of Amanita species ...

pubs.acs.org

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Mehdi Beniddir @mehdibeni.bsky.social · 7d

Discovery of Antivirulence ClpP Inhibitors by Self‐Resistance Gene‐Guided Mining Coupled with Dual Functional Screening - Wang - Angewandte Chemie International Edition - Wiley Online Library onlinelibrary.wiley.com/doi/10.1002/...

Discovery of Antivirulence ClpP Inhibitors by Self‐Resistance Gene‐Guided Mining Coupled with Dual Functional Screening

Streptoclipamide A, a potent ClpP inhibitor (IC50 = 480 nM), was discovered by self-resistance-guided genome mining coupled with dual functional screening. It uniquely suppresses MRSA virulence toxin...

onlinelibrary.wiley.com

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Reposted by Mehdi Beniddir

Justin J.J. van der Hooft @jjjvanderhooft.bsky.social · 29d

🚨 New Paper Alert 🚨 Great writing project with @adafede.bsky.social & Mehdi Bennidir and colleagues! @w-u-r.bsky.social
#metabolomics #CompMetabolomics #naturalproducts #discovery #libraries
pubs.rsc.org/en/content/a...

Scalability of mass spectrometry-based metabolomics for natural extracts libraries exploration: current status, challenges, and opportunities

Covering: up to 2025This review explores the potential of bioinformatics and chemoinformatics tools to advance the exploration of natural extracts libraries (NELs). Although metabolomics has become a ...

pubs.rsc.org

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Reposted by Mehdi Beniddir

Adriano Rutz @adafede.bsky.social · 24d

@mehdibeni.bsky.social drove it forward, and it was a pleasure to contribute with @robinschmid.bsky.social, @Wout Bittremieux, @Olivier Cailloux, and @jjjvanderhooft.bsky.social.
It places the scalability of MS-based metabolomics for natural extracts as a central challenge rather than a side issue.

Justin J.J. van der Hooft @jjjvanderhooft.bsky.social · 29d

🚨 New Paper Alert 🚨 Great writing project with @adafede.bsky.social & Mehdi Bennidir and colleagues! @w-u-r.bsky.social
#metabolomics #CompMetabolomics #naturalproducts #discovery #libraries
pubs.rsc.org/en/content/a...

Scalability of mass spectrometry-based metabolomics for natural extracts libraries exploration: current status, challenges, and opportunities

Covering: up to 2025This review explores the potential of bioinformatics and chemoinformatics tools to advance the exploration of natural extracts libraries (NELs). Although metabolomics has become a ...

pubs.rsc.org

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Mehdi Beniddir @mehdibeni.bsky.social · Sep 11

What a relief! Finally, MS2DECIDE is no longer a preprint
@chemrxiv.org It has just been published @ChemistryMethods chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/...
@BioCIS @univparissaclay.bsky.social @lamsade.bsky.social @univdauphine.bsky.social
@cnrs-paris-saclay.bsky.social @cnrs.fr

MS2DECIDE: Aggregating Multiannotated Tandem Mass Spectrometry Data with Decision Theory Enhances Natural Products Prioritization

Tandem mass spectrum to decision (MS2DECIDE) leverages decision theory and expert knowledge to aggregate the outputs of three widely used annotation tools (GNPS, Sirius, and ISDB-LOTUS) and compute a...

chemistry-europe.onlinelibrary.wiley.com

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Mehdi Beniddir @mehdibeni.bsky.social · Aug 27

Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI | Analytical Chemistry pubs.acs.org/doi/10.1021/...

Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI

A significant bottleneck in metabolomics data interpretation is the effective use of domain knowledge to assign structural information based on fragmentation patterns. The mass spectrometry query lang...

pubs.acs.org

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Reposted by Mehdi Beniddir

Mitja M. Zdouc @mmzdouc.bsky.social · Aug 21

Into natural product biosynthesis & tailoring enzymes? Frustrated by the lack of a dedicated resource to explore their functions? Tired of endless literature searches for reaction info? Meet the MITE database, freely available at mite.bioinformatics.nl. Preprint: doi.org/10.26434/che... (1/8)

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Reposted by Mehdi Beniddir

Hatzios Lab @hatzioslab.bsky.social · Aug 4

Congrats to postdoc Zhe Zhou on her paper out today in @cp-cellhostmicrobe.bsky.social showing that gut bacteria cross-feed a common dietary antioxidant to produce energy under anaerobic conditions. Thanks to collaborators Angela Jiang and Xiaofang Jiang at NIH.
www.sciencedirect.com/science/arti...

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Mehdi Beniddir @mehdibeni.bsky.social · Aug 19

Have a look to our just accepted manuscript @orgchemfront.rsc.org We bypassed the Abnormal Chichibabin reaction and accessed to pre-haouamine thank you @univparissaclay.bsky.social for gold open access @BioCIS
pubs.rsc.org/en/content/a...

Bypassing the Abnormal Chichibabin Reaction Dead-End Provides a Biomimetic Access to Pre-Haouamine

Haouamines are highly constrained marine alkaloids possessing a unique in nature skeleton. The high degree of complexity of such alkaloids raises questions about their chemical assembly. This is addre...

pubs.rsc.org

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Reposted by Mehdi Beniddir

Carl Zimmer @carlzimmer.com · Jul 24

After a new space telescope scan, signs of life on the exoplanet K2-18b remain elusive. It's even left scientists questioning what it will take to recognize life beyond our solar system. My story [gift link] nyti.ms/4o32ZH1

Hints of Life on Exoplanet K2-18b Recede Even Further

New observations fail to confirm signs of life in the atmosphere of the distant planet K2-18b. They also raise questions about what it will take to detect biology light-years away.

nyti.ms

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Mehdi Beniddir @mehdibeni.bsky.social · Jul 22

Multilaboratory Untargeted Mass Spectrometry Metabolomics Collaboration to Identify Bottlenecks and Comprehensively Annotate A Single Dataset | Analytical Chemistry pubs.acs.org/doi/10.1021/...

Multilaboratory Untargeted Mass Spectrometry Metabolomics Collaboration to Identify Bottlenecks and Comprehensively Annotate A Single Dataset

Annotation is the process of assigning features in mass spectrometry metabolomics data sets to putative chemical structures or “analytes.” The purpose of this study was to identify challenges in the a...

pubs.acs.org

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Mehdi Beniddir @mehdibeni.bsky.social · Jul 8

Time for Bordeaux wine tasting @isvv-bordeaux.bsky.social under the guidance of Axel Marchal. @aferp.bsky.social

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Reposted by Mehdi Beniddir

Royal Society of Chemistry @rsc.org · Jul 8

Directing Biosynthesis has been connecting #Biosynthesis researchers for over a decade – and the next conference takes place from 29 June – 1 July 2026. It’s a key opportunity to connect with colleagues across all career levels.

Will you be joining us? rsc.li/dbviii #DBVIII #SkyChem

Promotional image for the Royal Society of Chemistry event titled 'Directing Biosynthesis VIII' scheduled for 29 June to 1 July 2026 in Manchester, UK. The graphic features a vibrant green plant sprouting, symbolizing growth, against a geometric background, with details to save the date.

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Mehdi Beniddir @mehdibeni.bsky.social · Jul 7

Enjoying #AFERP-STOLON symposium in Bordeaux for the three next coming days. Happy to meet old friends of the NP Chemistry community.

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Reposted by Mehdi Beniddir

Natural Product Reports @natprodreports.rsc.org · Jul 3

🔓Check out this #OpenAccess review in our MS Metabolomics themed collection by Charlotte Simmler & co @cnrs.fr describing the complex chemistry of benthic seawater from exometabolite sampling strategies to MS-based metabolomics #natprod

Read it in full on our website👇

Describing the complex chemistry of benthic seawater: from exometabolite sampling strategies to MS-based metabolomics

Covering: 1982 up to the end of 2024 Marine exometabolites (EMs) are small molecules released by marine (micro)organisms into the seawater. Collectively, all of the released EMs contribute to the…

pubs.rsc.org

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Mehdi Beniddir @mehdibeni.bsky.social · Jun 5

Microcrystal Electron Diffraction-Guided Discovery of Fungal Metabolites | Journal of the American Chemical Society pubs.acs.org/doi/10.1021/...

Microcrystal Electron Diffraction-Guided Discovery of Fungal Metabolites

Nature remains a vast repository of complex and functional metabolites whose structural characterization continues to drive innovations in pharmaceuticals, agrochemicals, and materials science. The cr...

pubs.acs.org

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Mehdi Beniddir @mehdibeni.bsky.social · May 4

Design and Biosynthesis of Ornithine 8-Containing Semaglutide Variants with a Click Chemistry-Modifiable Position 26 | ACS Synthetic Biology pubs.acs.org/doi/full/10....

Design and Biosynthesis of Ornithine 8-Containing Semaglutide Variants with a Click Chemistry-Modifiable Position 26

Semaglutide, a glucagon-like peptide-1 (GLP-1) receptor agonist, constitutes an effective and widely used treatment for type 2 diabetes and obesity. However, challenges such as insufficient oral bioav...

pubs.acs.org

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Mehdi Beniddir @mehdibeni.bsky.social · May 4

A heme-dependent enzyme forms the hydrazine in the antibiotic negamycin
www.nature.com/articles/s41...

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Reposted by Mehdi Beniddir

christoph_STCmicrobeblog @christophstc.bsky.social · May 3

thx @shyznogd.bsky.social for posting 🙏 I immediately joined the virtual strawberry party (couldn't jump straight to madrid, unfortunately)

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Reposted by Mehdi Beniddir

Eric Topol @erictopol.bsky.social · May 1

New @science.org
An innovative way to deliver drugs to the gut at low doses to suppress inflammation
www.science.org/doi/10.1126/...

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Reposted by Mehdi Beniddir

Nature @nature.com · Mar 19

Nature research paper: A polyene macrolide targeting phospholipids in the fungal cell membrane ttps://www.nature.com/articles/s41586-025-08678-9

A polyene macrolide targeting phospholipids in the fungal cell membrane - Nature

Mandimycin, a polyene macrolide, exhibits strong antifungal activity and possesses a mode of action that is distinct from other compounds of this class.

go.nature.com

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Reposted by Mehdi Beniddir

Nature @nature.com · Mar 26

Nature research paper: A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome

https://go.nature.com/4iECjJz

A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome - Nature

A new lasso peptide antibiotic exhibits broad-spectrum activity against Gram-negative and Gram-positive bacteria by interfering with bacterial protein synthesis, is unaffected by common resistance mechanisms and shows no toxicity towards human cells.

go.nature.com

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Mehdi Beniddir @mehdibeni.bsky.social · May 1

Félicitations

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Mehdi Beniddir @mehdibeni.bsky.social · Apr 30

It would be great to see whether our approach could help you to generate oxylipins mass spectral signatures.

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Reposted by Mehdi Beniddir

Kyo Bin Kang @kyobinkang.bsky.social · Apr 29

Thanks to the KR-FR STARS grant, we could meet up with each other in Paris and Seoul in 2023, which brought us to the others of each one's local socities (KSP and AFERP). Congratulations everyone, especially Sarah, @mehdibeni.bsky.social and @adafede.bsky.social 🎉

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