Simon Sieber

We built GenoPHI: a machine learning workflow that predicts phage-host interactions at strain level. This could help rapidly select phages to treat drug-resistant bacterial infections or for microbiome engineering without exhaustive lab testing.

www.biorxiv.org/content/10.1...

Aaand it's out! Meet MITE - the natural product tailoring enzyme database, just published in @narjournal.bsky.social! MITE DB captures the substrate- and reaction-specificity of tailoring enzymes, allowing to capture this information in a human- and machine-readable way! doi.org/10.1093/nar/...

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)

We are looking for a 3-year postdoc to work with Daniel Probst, Justin van der Hooft and myself on an exciting project involving federated learning and integrative omics for discovery of new antibiotics from natural products.
Apply here: www.wur.nl/en/vacancy/p...
Please share!

Thank you !!

Genomic and chemical characterization of cytotoxic Ahp-cyclodepsipeptides from Phormidium using Thamnocephalus platyurus bioassay Toxic benthic cyanobacterial mats have been identified globally as a potential health hazard since they can produce potent cyanotoxins. Such mats have…

Thrilled to see our study on novel toxins from cyanobacteria blooms in #Fribourg in STOTEN! Our results indicate that Phormidium is the producer of cyanopeptolins, whose side chains are crucial for their activity.

Great collaboration with Pilar Junier

www.sciencedirect.com/science/arti...

Thanks to the organisers for a fantastic #ICTC13 and to all the participants for the super fruitful discussions. It was my first ICTC and I had such a wonderful experience 🤩. I'm so looking forward to ICTC14 👀

@ictc13.bsky.social

Many thanks to the @ictc13.bsky.social organizers for this excellently organized and inspiring conference and the always friendly, welcoming + enthusiastic atmosphere 💙💚

Our group photo ❤️. Big thanks to all participants for their contributions.

Amazing keynote talk by Elke Dittmann @dittmannelke.bsky.social "Dissecting the Role of #Microcystin on the Carbon Concentrating Mechanism of #Microcystis aeruginosa".

A great start to the 13th International Conference on Toxic Cyanobacteria at a beautiful venue in Crete with more than 290 participants! Fantastic work from the organizing committee !! @ictc13.bsky.social #cyanobacteria

Peptide catalysis: Trends and opportunities Peptides are highly selective organocatalysts, with intrinsic modularity allowing precise control over structure and function. Advances in peptide synthesis, biotechnology, and cheminformatics will en...

🎉 Big day for our group: our first publication is out!
Tom did a fantastic job highlighting current trends & opportunities in peptide catalysis — now published in Chem Catalysis (open access). Huge congrats, Tom!
www.cell.com/chem-catalys...

AI-guided Antibiotic Discovery Pipeline from Target Selection to Compound Identification Antibiotic resistance presents a growing global health crisis, demanding new therapeutic strategies that target novel bacterial mechanisms. Recent advances in protein structure prediction and machine ...

Excited to share our new preprint: AI-guided Antibiotic Discovery Pipeline from Target Selection to Compound Identification!
It includes a comprehensive benchmark of structure-based drug design (SBDD) methods and presents a full, practical pipeline for antibiotic discovery.
arxiv.org/abs/2504.11091

MDN-0057 to MDN-0060, a Family of Broad-Spectrum Antibiotics against Gram-Negative Pathogens Produced by Ophiosphaerella korrae A novel family of antibiotics, MDN-0057 to MDN-0060 (1–4), was isolated from liquid cultures of the fungus Ophiosphaerella korrae. These compounds incorporate two isocyanide groups in their complex structures that were elucidated by extensive spectroscopic analyses, including HRESIMS, and 1D and 2D NMR experiments. The relative configurations were determined by using J-based configuration analyses and the interpretation of key NOESY correlations consistent with the existence of a major conformation in solution. Mosher ester derivatization analysis allowed the establishment of their absolute configurations. All four compounds displayed in vitro antibacterial activity with a broad spectrum against Gram-negative pathogens.

A new research article from @medinadiscovery.bsky.social is now out in Journal of Natural Products. It describes the discovery of a novel family of isocyanide antibiotics with broad spectrum activity against Gram negative bacteria.
pubs.acs.org/doi/10.1021/...

Multiplexed cytometry for single cell chemical biology Flow cytometry has great potential for screening in translational research areas due to its deep quantification of cellular features, ability to colle…

We put together this protocol in part to encourage broader adoption of Multiplexed Activity Metabolomics, an engine for functional metabolomics of all types including specialized metabolite discovery.

We enjoy knowing if metabolite is active before isolating it, and so should you! #natprod

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...

The latest discovery from the lab and great colleagues at McMaster and U Illinois, Chicago. Lariocidin, a new lasso peptide antibiotic that inhibits the ribosome. rdcu.be/efdha

Why could a new class of antibiotics really make a difference? The discovery of penicillin dates back to 1928. And since then, antibiotics have contributed to saving millions of lives all over the world, extending the average duration of human life by 23 years. I...

The newly discovered lariocidine has shown promise against AMR bacteria by targeting ribosomes with a novel mechanism of action. While still years away from market approval, its potential to combat #AMR infections offers hope in addressing the global AMR crisis.

www.thevermilion.com/why-could-a-...

Dereplication of secondary metabolites from Sophora flavescens using an LC–MS/MS-based molecular networking strategy - Scientific Reports Scientific Reports - Dereplication of secondary metabolites from Sophora flavescens using an LC–MS/MS-based molecular networking strategy

Dereplication of secondary metabolites from Sophora flavescens using an LC–MS/MS-based molecular networking strategy #SciRep www.nature.com/articles/s41...

chemistry.unwrapped @uzhchemistry.bsky.social

It's a fantastic feeling: Alfred Werner Legat has accepted our research grant, which focuses on developing a chemoselective approach to targeting natural products! Thank you for your support! @uzhchemistry.bsky.social

The results published in Redox Biology by @locbp.bsky.social @uzhchemistry.bsky.social fill an important gap in the knowledge of redox homeostasis in subcellular organelles.

This study from the Tilley Lab @uzhchemistry.bsky.social highlights the significance of morphology control in optimizing Sb₂Se₃ photocathodes, providing insights for future material and device design. pubs.rsc.org/en/content/a...

MS-RT: A Method for Evaluating MS/MS Clustering Performance for Metabolomics Data The clustering of tandem mass spectra (MS/MS) is a crucial computational step to deduplicate repeated acquisitions in data-dependent experiments. This technique is essential in untargeted metabolomics, particularly with high-throughput mass spectrometers capable of generating hundreds of MS/MS spectra per second. Despite advancements in MS/MS clustering algorithms in proteomics, their performance in metabolomics has not been extensively evaluated due to the lack of database search tools with false discovery rate control for molecule identification. To bridge this gap, this study introduces the MS1-retention time (MS-RT) method to assess MS/MS clustering performance in metabolomics data sets. Here, we validate MS-RT by comparing MS-RT to established proteomics clustering evaluation approaches that utilize database search identifications. Additionally, we evaluate the performance of several MS/MS clustering tools on metabolomics data sets, highlighting their advantages and drawbacks. This MS-RT method and the MS/MS clustering tool benchmarking will provide valuable real world practical recommendations for tools and set the stage for future advancements in metabolomics MS/MS clustering.

I am excited to share this new paper out in JPR - "MS-RT: A Method for Evaluating MS/MS Clustering Performance for Metabolomics Data." This work introduces the MS-RT method to assess MS/MS clustering accuracy on metabolomics data.

doi.org/10.1021/acs....

Today we launched a new project – chemistry.unwrapped which we were working on over the last year. If you are interested, follow us on Instagram, TikTok or YouTube! :)

@uzhchemistry.bsky.social @juriceklab.bsky.social #pisky #chemsky #chemistryisfun #funexperiments

It's a fantastic feeling: Alfred Werner Legat has accepted our research grant, which focuses on developing a chemoselective approach to targeting natural products! Thank you for your support! @uzhchemistry.bsky.social

Unusual heterocycles and biosynthesis of natural products, published today in Communications Chemistry 🧵

Congratulations Véronique Mathys on the successful defence of your bachelor thesis 👏👏👏 very nice work under the supervision of Noah Rychener ✨ @juriceklab.bsky.social @uzhchemistry.bsky.social #chemsky

LLM-assisted tool generation is awesome. To extend the HRMS checker (doi.org/10.1021/acs....) to automated experimental checking, a peptide sequence parser function (ca. 200 lines of code) was generated in under 2 hours. #ChemSky

Dearomative Diels-Alder reactions are currently hot in total synthesis. They go back to Peter Yates (who trained my mentor Sam Danishefsky). And the Wessely reaction was also discovered in Vienna :)

Unlocking hidden treasures: the evolution of high-throughput mass spectrometry in screening for cryptic natural products Covering: 1994 to 2024Historically, microbial natural product discovery has been predominantly guided by biological activity from crude microbial extracts with metabolite characterization proceeding o...

Unlocking hidden treasures: the evolution of high-throughput mass spectrometry in screening for cryptic natural products

Brett Covington & Mohammad Seyedsayamdost

@natprodreports.bsky.social

pubs.rsc.org/en/content/a...