Mehdi Beniddir
@mehdibeni.bsky.social
📤 755
📥 475
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Professor of Natural Products Chemistry Université Paris-Saclay. Exobiology lover.
Why Do Filamentous Actinomycetota Produce Such a Vast Array of Specialized Metabolites?
www.annualreviews.org/content/jour...
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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...
https://www.annualreviews.org/content/journals/10.1146/annurev-micro-060424-051257
about 15 hours ago
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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...
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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...
https://pubs.acs.org/doi/abs/10.1021/jacs.5c16450
about 16 hours ago
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NMRMind: A Transformer-Based Model Enabling the Elucidation from Multidimensional NMR to Structures | Analytical Chemistry
pubs.acs.org/doi/abs/10.1...
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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...
https://pubs.acs.org/doi/abs/10.1021/acs.analchem.5c03783
1 day ago
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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.
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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 ...
https://pubs.acs.org/doi/10.1021/acs.jnatprod.5c00820
5 days ago
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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/...
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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...
https://onlinelibrary.wiley.com/doi/10.1002/anie.202514683
10 days ago
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Mehdi Beniddir
Justin J.J. van der Hooft
about 1 month ago
🚨 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...
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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 ...
https://pubs.rsc.org/en/content/articlelanding/2025/np/d5np00034c
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Adriano Rutz
26 days ago
@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.
add a skeleton here at some point
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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
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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...
https://chemistry-europe.onlinelibrary.wiley.com/doi/10.1002/cmtd.202400088#
about 1 month ago
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Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI | Analytical Chemistry
pubs.acs.org/doi/10.1021/...
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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...
https://pubs.acs.org/doi/10.1021/acs.analchem.5c02591
about 2 months ago
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Mehdi Beniddir
Mitja M. Zdouc
about 2 months ago
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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Hatzios Lab
2 months ago
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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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...
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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...
https://pubs.rsc.org/en/content/articlelanding/2025/qo/d5qo01111f
about 2 months ago
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Mehdi Beniddir
Carl Zimmer
3 months ago
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
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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.
https://nyti.ms/4o32ZH1
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Multilaboratory Untargeted Mass Spectrometry Metabolomics Collaboration to Identify Bottlenecks and Comprehensively Annotate A Single Dataset | Analytical Chemistry
pubs.acs.org/doi/10.1021/...
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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...
https://pubs.acs.org/doi/10.1021/acs.analchem.4c05577
3 months ago
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Time for Bordeaux wine tasting
@isvv-bordeaux.bsky.social
under the guidance of Axel Marchal.
@aferp.bsky.social
3 months ago
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Mehdi Beniddir
Royal Society of Chemistry
3 months ago
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
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Enjoying
#AFERP-STOLON
symposium in Bordeaux for the three next coming days. Happy to meet old friends of the NP Chemistry community.
3 months ago
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Mehdi Beniddir
Natural Product Reports
4 months ago
🔓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👇
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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…
https://pubs.rsc.org/en/content/articlelanding/2025/np/d4np00064a
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Microcrystal Electron Diffraction-Guided Discovery of Fungal Metabolites | Journal of the American Chemical Society
pubs.acs.org/doi/10.1021/...
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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...
https://pubs.acs.org/doi/10.1021/jacs.5c01466
4 months ago
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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....
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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...
https://pubs.acs.org/doi/full/10.1021/acssynbio.5c00132
6 months ago
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A heme-dependent enzyme forms the hydrazine in the antibiotic negamycin
www.nature.com/articles/s41...
6 months ago
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Mehdi Beniddir
christoph_STCmicrobeblog
6 months ago
thx
@shyznogd.bsky.social
for posting 🙏 I immediately joined the virtual strawberry party (couldn't jump straight to madrid, unfortunately)
add a skeleton here at some point
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Mehdi Beniddir
Eric Topol
6 months ago
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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Mehdi Beniddir
Nature
7 months ago
Nature research paper: A polyene macrolide targeting phospholipids in the fungal cell membrane ttps://www.nature.com/articles/s41586-025-08678-9
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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.
https://go.nature.com/4iVlPww
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Mehdi Beniddir
Nature
7 months ago
Nature research paper: A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome
https://go.nature.com/4iECjJz
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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.
https://go.nature.com/4iECjJz
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Kyo Bin Kang
6 months ago
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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Mehdi Beniddir
Kyo Bin Kang
6 months ago
It was so fun to be a part of this project. Updating MIADB, we also retrieved MS/MS spectral features specific to each MIA subclasses, which can be applied to MassQL for subclass-level annotation.
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It is with tremendous emotion that I share with you our recent work
@jcheminf.bsky.social
rb.gy/gynwlf
that resulted in the update of the MIADB and the generation of valuable spectrometric signatures that could be used as
#MassQL
queries 🙏 S. Szwarc
@univparissaclay.bsky.social
@adafede.bsky.social
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Translating community-wide spectral library into actionable chemical knowledge: a proof of concept with monoterpene indole alkaloids - Journal of Cheminformatics
With over 3000 representatives, the monoterpene indole alkaloids (MIAs) class is among the most diverse families of plant natural products. The MS/MS spectral space exploration of these complex compou...
https://rb.gy/gynwlf
6 months ago
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Mehdi Beniddir
CNRS
6 months ago
#CNRSfellows
🚩 Neuf nouvelles figures prestigieuses rejoignent le programme "fellows-ambassadeurs" du CNRS. Ces chercheurs s'engagent pour trois ans au service de la recherche française 🇫🇷🔬
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Neuf nouveaux fellows-ambassadeurs au CNRS
https://www.cnrs.fr/fr/actualite/neuf-nouveaux-fellows-ambassadeurs-au-cnrs?utm_medium=Social&utm_source=Bluesky#Echobox=1745837368
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Mehdi Beniddir
Natural Product Reports
7 months ago
🔓Check out this
#OpenAccess
review by Lindsay Caesar & co. at
@unm.edu
& James Madison University, part of our Emerging Investigators collection, on natural product discovery from microbial communities in caves & underground mines
#natprod
#microsky
Read in full here🔽
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Subterranean marvels: microbial communities in caves and underground mines and their promise for natural product discovery
Covering: 2014 to 2024 Since the dawn of human history, caves have played an intimate role in our existence. From our earliest ancestors seeking shelter from the elements to more recent generations…
https://pubs.rsc.org/en/content/articlelanding/2025/np/d4np00055b
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Mehdi Beniddir
ᐯIᑕTOᖇ ᑎIᘔET, ᗰᗪ
6 months ago
Pleased to share our new paper out in 𝘑𝘰𝘶𝘳𝘯𝘢𝘭 𝘰𝘧 𝘊𝘭𝘪𝘯𝘪𝘤𝘢𝘭 𝘐𝘯𝘷𝘦𝘴𝘵𝘪𝘨𝘢𝘵𝘪𝘰𝘯 led by Monika Kumaraswamy, MD, now Chief of Infectious Diseases UTexas-Tyler Is minimimum inhibitory concentration (MIC) testing the gold standard for antibiotic-resistant superbugs? 🦠 🧫 🧵 1/6
www.jci.org/articles/vie...
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Machine Learning-Based Bioactivity Classification of Natural Products Using LC-MS/MS Metabolomics | Journal of Natural Products
pubs.acs.org/doi/10.1021/...
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https://pubs-acs-org.inc.bib.cnrs.fr/doi/10.1021/acs.jnatprod.4c01123
6 months ago
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Rationally minimizing natural product libraries using mass spectrometry | mSystems
journals.asm.org/doi/10.1128/...
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Rationally minimizing natural product libraries using mass spectrometry | mSystems
Natural product libraries are large collections of extracts derived from fungi, plants, bacteria, or any other natural sources. These libraries play an important role in the initial phases of drug dis...
https://journals.asm.org/doi/10.1128/msystems.00844-24
8 months ago
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Toward an integrated omics approach for plant biosynthetic pathway discovery in the age of AI: Trends in Biochemical Sciences
www.cell.com/trends/bioch...
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https://www-cell-com.inc.bib.cnrs.fr/trends/biochemical-sciences/fulltext/S0968-0004%2825%2900025-8
8 months ago
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Mehdi Beniddir
BioMassSpec
8 months ago
Machine Learning-Based Bioactivity Classification of Natural Products Using LC-MS/MS Metabolomics
#JNatProd
pubs.acs.org/doi/10.1021/...
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Machine Learning-Based Bioactivity Classification of Natural Products Using LC-MS/MS Metabolomics
The rediscovery of known drug classes represents a major challenge in natural products drug discovery. Compound rediscovery inhibits the ability of researchers to explore novel natural products and wa...
https://pubs.acs.org/doi/10.1021/acs.jnatprod.4c01123
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Although a little different from my
#DREAMOLECULES
, excited to share our recent group's work on the discovery of otitiglycomycins A and B, Glycolipids from Nocardia otitidiscavarum with Zika Virus Antiviral Activity
@icsnlab.bsky.social
@univparissaclay.bsky.social
pubs.acs.org/doi/full/10....
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Otitiglycomycins A and B: Glycolipids from the Strain Nocardia otitidiscavarum 20S-13 with Antiviral Activity against Zika Virus
The Zika virus (ZIKV), an emerging orthoflavivirus, presents a significant public health threat due to its rapid dissemination and association with severe neurological complications. The urgent need f...
https://pubs.acs.org/doi/full/10.1021/acs.jnatprod.4c01302
9 months ago
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Mehdi Beniddir
Jorge Navarro
10 months ago
Happy to announce the beta release of
#BiGSCAPE2
! This is the result of a great effort by Arjan Draisma, Catarina Loureiro and Nico Louwen, who worked tirelessly to improve the code from the ground up! Also major kudos to
@marnixmedema.bsky.social
for his leadership 💪
github.com/medema-group...
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GitHub - medema-group/BiG-SCAPE: Similarity networks of biosynthetic gene clusters
Similarity networks of biosynthetic gene clusters. Contribute to medema-group/BiG-SCAPE development by creating an account on GitHub.
https://github.com/medema-group/BiG-SCAPE
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Mehdi Beniddir
The New York Times
10 months ago
Google said its quantum computer needed less than five minutes to perform a mathematical calculation that one of the world’s most powerful supercomputers could not complete in 10 septillion years, a length of time that exceeds the age of the known universe.
nyti.ms/3DaZFH5
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Mehdi Beniddir
ICSN lab
11 months ago
Great news: ICSN lab is now on Bluesky !
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Mehdi Beniddir
Microbial Biotechnology (MBT)
11 months ago
Janevska
@slavi-jan.bsky.social
et al engineered an Aspergillus nidulans chassis for psilocybin production by repressing L-tryptophan catabolism. Deleting aminotransferase genes aroH1 and aroH2 led to a 10-fold increase in psilocybin yield. Read ➡️
https://buff.ly/4g8VutI
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Mehdi Beniddir
Russell Cox Chem
11 months ago
Title: Engineered and total biosynthesis of fungal specialized metabolites Article link:
www.nature.com/articles/s41...
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Engineered and total biosynthesis of fungal specialized metabolites - Nature Reviews Chemistry
The total biosynthesis and engineering of complex natural products is now routinely achieved in filamentous fungal host organisms. This technology offers substantial advantages over traditional total ...
https://www.nature.com/articles/s41570-023-00564-0
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Mehdi Beniddir
Dirk Trauner
11 months ago
Check out our first foray into the fascinating world of isosteroidal alkaloids, arguably one of Nature’s most diverse natural product family:
chemrxiv.org/engage/chemr...
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Concise Synthesis of (–)-Veratramine and (–)-20-epi-Veratramine via Aromative Diels-Alder Reaction
A concise and convergent synthesis of the isosteroidal alkaloids veratramine and 20-epi-veratramine has been accom-plished. A Horner-Wadsworth-Emmons olefination joins two chiral building blocks of ap...
https://chemrxiv.org/engage/chemrxiv/article-details/67448fe17be152b1d0b7bfdc
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Mehdi Beniddir
bioRxiv Microbiology
11 months ago
A generative artificial intelligence approach for antibiotic optimization https://www.biorxiv.org/content/10.1101/2024.11.27.625757v1
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A generative artificial intelligence approach for antibiotic optimization https://www.biorxiv.org/content/10.1101/2024.11.27.625757v1
Antimicrobial resistance (AMR) poses a critical global health threat, underscoring the urgent need f
https://www.biorxiv.org/content/10.1101/2024.11.27.625757v1
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Very happy to introduce MS2DECIDE, a decision theory-based cheminformatics tools for NP prioritization from multiannotated MS/MS data. Have a look at our preprint @ChemRxiv
rb.gy/1qn6c6
@LAMSADEDauphine @Paris_Dauphine @BioCIS @UnivParisSaclay
@cnrs.bsky.social
11 months ago
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Mehdi Beniddir
Russell Cox Chem
11 months ago
Title: Comparing total chemical synthesis and total biosynthesis routes to fungal specialized metabolites
pubs.rsc.org/en/content/a...
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Comparing total chemical synthesis and total biosynthesis routes to fungal specialized metabolites
Covering the period 1965–2024Total synthesis has been defined as the art and science of making the molecules of living Nature in the laboratory, and by extension, their analogues. At the extremes, spe...
https://pubs.rsc.org/en/content/articlelanding/2024/np/d4np00015c
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NP-MRD
11 months ago
Learn all about the latest developments in NP-MRD: The Natural Products Magnetic Resonance Database (NP-MRD) for 2025
#NMR
#NMRchat
academic.oup.com/nar/article/...
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The Natural Products Magnetic Resonance Database (NP-MRD) for 2025
Abstract. The Natural Products Magnetic Resonance Database (NP-MRD; https://np-mrd.org) is a comprehensive, freely accessible, web-based resource for the d
https://academic.oup.com/nar/article/doi/10.1093/nar/gkae1067/7906838
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Mehdi Beniddir
ActinoBase
11 months ago
The chemical ecology and physiological functions of type I polyketide natural products: the emerging picture
pubs.rsc.org/en/content/a...
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The chemical ecology and physiological functions of type I polyketide natural products: the emerging picture
Covering: up to 2024.For many years, the value of complex polyketides lay in their medical properties, including their antibiotic and antifungal activities, with little consideration paid to their nat...
https://pubs.rsc.org/en/content/articlelanding/2024/np/d4np00046c
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New drug discovery and development from natural products: Advances and...
www.sciencedirect.com/science/arti...
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New drug discovery and development from natural products: Advances and strategies
Natural products (NPs) have a long history as sources for drug discovery, more than half of approved drugs are related to NPs, which also exhibit mult…
https://www.sciencedirect.com/science/article/pii/S0163725824001724
11 months ago
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Mehdi Beniddir
Pieter Dorrestein
11 months ago
This will me my fist blueet! Microbial N-Acyl lipids have been shown to regulate glucose, pain etc among other things. Therefore Helena, Vincent and Martijn asked the question - are there more and if so what types? And boy did they find some
www.biorxiv.org/content/10.1...
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The microbiome diversifies N-acyl lipid pools - including short-chain fatty acid-derived compounds
N -acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N -acyl lipids with untargeted mass spectrometry-based...
https://www.biorxiv.org/content/10.1101/2024.10.31.621412v1
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Very excited to share with you the discovery of trirosaline, our recent
#DREAMOLECULE
. We used a Combination of Machine Learning and Empirical NMR Computation @JOC_OL @SzwarcSarah @ElKalamouni @miacyc_anr @UnivParisSaclay @BioCIS @ICSN_lab
pubs.acs.org/doi/10.1021/...
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https://pubs.acs.org/doi/10.1021/acs.orglett.3c03972?ref=pdf
almost 2 years ago
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