Mehdi Beniddir

Rethinking Natural Product Discovery: A Complex Epistemological Approach Linking Chemical Ecology and Pharmacognosy Global challenges such as health crises, biodiversity loss, and climate change demand a rethinking of natural product discovery. Despite advances in dereplication, metabolomics, and genomic sequencing...

Rethinking Natural Product Discovery: A Complex Epistemological Approach Linking Chemical Ecology and Pharmacognosy | Journal of Natural Products pubs.acs.org/doi/10.1021/...

Quinoline tag helps vancomycin breach gram-negative defenses The work reveals how tiny structural shifts can deliver outsize biological effects

Chemists have found that attaching a small quinoline group to vancomycin lets it slip inside the bacteria and reach its target. cen.acs.org/pharmaceutic... #chemsky 🧪

Thrilled to see MS2DECIDE featured in the front cover of the latest issue of @chemistryeurope.bsky.social Chemistry-Methods
@cnrs-paris-saclay.bsky.social @univparissaclay.bsky.social @univdauphine.bsky.social

And you, have you considered 5o decipher your k(α) ?

So happy to see MS2DECIDE highlighted by @cnrs-paris-saclay.bsky.social

Stereochemistry-aware string-based molecular generation Abstract. This study investigates the impact of incorporating stereochemical information, a crucial aspect of computational drug discovery and materials de

Stereochemistry-aware string-based molecular generation url: academic.oup.com/pnasnexus/ar...

Discovery of Late Intermediates in Methylenomycin Biosynthesis Active against Drug-Resistant Gram-Positive Bacterial Pathogens The methylenomycins are highly functionalized cyclopentanone antibiotics produced by Streptomyces coelicolor A3(2). A biosynthetic pathway to the methylenomycins has been proposed based on sequence analysis of the proteins encoded by the methylenomycin biosynthetic gene cluster and the incorporation of labeled precursors. However, the roles played by putative biosynthetic enzymes remain experimentally uninvestigated. Here, the biosynthetic functions of enzymes encoded by mmyD, mmyO, mmyF, and mmyE were investigated by creating in-frame deletions in each gene and investigating the effect on methylenomycin production. No methylenomycin-related metabolites were produced by the mmyD mutant, consistent with the proposed role of MmyD in an early biosynthetic step. The production of methylenomycin A, but not methylenomycin C, was abolished in the mmyF and mmyO mutants, consistent with the corresponding enzymes catalyzing the epoxidation of methylenomycin C, as previously proposed. Expression of mmyF and mmyO in a S. coelicolor M145 derivative engineered to express mmr, which confers methylenomycin resistance, enabled the resulting strain to convert methylenomycin C to methylenomycin A, confirming this hypothesis. A novel metabolite (premethylenomycin C), which readily cyclizes to form the corresponding butanolide (premethylenomycin C lactone), accumulated in the mmyE mutant, indicating the corresponding enzyme is involved in introducing the exomethylene group into methylenomycin C. Remarkably, both premethylenomycin C and its lactone precursor were one to two orders of magnitude more active against various Gram-positive bacteria, including antibiotic-resistant Staphylococcus aureus and Enterococcus faecium isolates, than methylenomycins A and C, providing a promising starting point for the development of novel antibiotics to combat antimicrobial resistance.

Discovery of Late Intermediates in Methylenomycin Biosynthesis Active against Drug-Resistant Gram-Positive Bacterial Pathogens | Journal of the American Chemical Society pubs.acs.org/doi/10.1021/...

Stereochemistry-aware string-based molecular generation Abstract. This study investigates the impact of incorporating stereochemical information, a crucial aspect of computational drug discovery and materials de

Stereochemistry-aware string-based molecular generation url: academic.oup.com/pnasnexus/ar...

New Analytical Methodology to Reveal Biosignatures on Mars and Ocean Worlds Terrestrial analog environments and their microbial communities are key elements to prepare for the exploration of extraterrestrial planetary environments that potentially sustained, or even may still...

New Analytical Methodology to Reveal Biosignatures on Mars and Ocean Worlds #AC #MassSpec pubs.acs.org/doi/10.1021/...

Why Do Filamentous Actinomycetota Produce Such a Vast Array of Specialized Metabolites? Bacteria of the phylum Actinomycetota are extremely diverse: They inhabit niches ranging from soils and ocean sediments to the normal human microbiota, and they cause tuberculosis, one of the most pre...

Why Do Filamentous Actinomycetota Produce Such a Vast Array of Specialized Metabolites?
www.annualreviews.org/content/jour...

Discovery and Biosynthetic Interrogation of a Cobalt-Containing Terpene-Polyketide-Nonribosomal Peptide Tribrid with Anticoronavirus Activity The structural complexity of natural products arises from the complexity of their biosynthetic pathways and directly contributes to their biological activities. Guided by this principle, we screened 5...

Discovery and Biosynthetic Interrogation of a Cobalt-Containing Terpene-Polyketide-Nonribosomal Peptide Tribrid with Anticoronavirus Activity | Journal of the American Chemical Society pubs.acs.org/doi/abs/10.1...

NMRMind: A Transformer-Based Model Enabling the Elucidation from Multidimensional NMR to Structures Nuclear magnetic resonance (NMR) data provides rich quantum information on molecular structure, which is closely related to chemical structure and widely used for structural characterization in chemic...

NMRMind: A Transformer-Based Model Enabling the Elucidation from Multidimensional NMR to Structures | Analytical Chemistry pubs.acs.org/doi/abs/10.1...

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 ...

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.

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...

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/...

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 ...

🚨 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...

@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.

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...

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

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...

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

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)

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...

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...

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.

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

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...

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

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

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.

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

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

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…

🔓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👇

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...

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

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...

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....

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

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