Guillaume Médard

Hesitant to do proteomics on bacteria? Check out this fantastic publication from Miram Abele and Christina Ludwig highlighting the possibilities and benefits as well as supplying resources to help along the way: www.mcponline.org/ar...

At EEBMB2025 conference.

My colleagues properly captured my reenactment of our surprised faces when discovering MBLAC2 as a super frequent off-target of HDAC drugs.

Aspasia Dimitriadou explaining competitive chemoproteomics assay.

Today took place the 12th Young Scientists Forum of the Hellenic Society of Biochemistry and Molecular Biology as a pre-event of the #EEBMB2025 conference. As evidenced by Aspasia Dimitriadou’s presentation, #chemoproteomics is putting down roots in Athens. And I won’t hide my pride.

We are getting our slides and posters ready! In a few days, NKUA Proteomics Core Facility goes EEBMB2025. We have from sponge proteomics to chemoproteomics for you, including multiple myeloma proteomics as well as murine multiomics.
#Chembio #Proteomics #chemoproteomics

New preprint 🚨 We systematically measured 17 million phospho-specific dose-response curves (133 kinase inhibitors × 5 cell lines) to decrypt the kinases that shape the human phosphoproteome. We show that drug perturbation potency (not effect size) links kinases to substrates while controlling FDR.

Koina: Democratizing machine learning for proteomics research - Nature Communications Koina is an open-source, online platform that simplifies access to machine learning models in proteomics, enabling easier integration into analysis tools and helping researchers adopt and reuse ML mod...

Exited to share our latest work! Out now in @natcomms.nature.com

Koina aims to transform how #proteomics uses machine learning. You no longer need to be a tech wizard to use ML and now can easily run #ML models. Integrated with FragPipe, Skyline and EncyclopeDIA!

www.nature.com/articles/s41...

Hello Toronto!🍁The Terrific TUM Team is happy to be attending #HUPO2025. Kusterlab, Wilhelmlab and Leelab have a diverse set of presentations for you that we can't wait to share 🤓.
We're excited to spend the next days reuniting with old friends and making new connections. See you there!

If you have an interest in HDAC inhibitors, do not hesitate to reach out to us to have a run through of our chemoprotemics work helped by poster P066 and P018 at #ChemBioParis2025. #ChemBio #chemoproteomics

Thanks #ChembioParis2025 for organising this nice cruise through Paris yesterday evening, following an inspiring conference day! Looking forward to another day of great #chembio today.

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Thanks to Le Studium, Loire Valley Institute for Advanced Studies, for funding this exciting consortium with great collaborators! Honoured to be involved for proteomics and chemoproteomics projects.

Back to Greece after a few intense scientific days in Tours, France, in the frame of the « Pharmacological Inhibition of Cathepsin C in Neutrophil-Mediated Inflammatory Diseases » consortium coordinated by Brice Korkmaz at the Centre of studies for Respiratory Pathologies (CEPR). 1/2

Finally the paper to convince you to toss that nanoLC off a roof? If you've ever been to this blog  before, you might have encountered the fact that I despite nanoflow liquid chromatography.  These author...

proteomicsnews.blogspot.com/2025/09/fina...

Serendipitous and Systematic Chemoproteomic Discovery of MBLAC2, HINT1, and NME1-4 Inhibitors from Histone Deacetylase-Targeting Pharmacophores Metalloenzyme inhibitors often incorporate a hydroxamic acid moiety to bind the bivalent metal ion cofactor within the enzyme’s active site. Recently, inhibitors of Zn2+-dependent histone deacetylases...

doi.org/10.1021/acsc...

Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target - Nature Chemical Biology Lechner et al. used an affinity-based chemical proteomics approach to investigate the target landscape of HDAC inhibitors, and identified an extracellular vesicle regulator MBLAC2 as a universal off-t...

doi.org/10.1038/s415...

« Médard et al. used a chemoproteomics approach to investigate the off-target effects of tubacin. They identified MBLAC2 as a novel target, and its inhibition or silencing in HEK293 cells increased EV accumulation, suggesting a regulatory role in EV secretion » .

FEBS Press The 2nd MObility for Vesicle research in Europe (MOVE) Symposium in Belgrade brought over 280 attendees from 28 countries to advance extracellular vesicle (EV) research. Featuring keynotes, presentat...

Nice to be mentioned in the recently published account of the conference!
Kudos to @sevlechner.bsky.social
#EV #chemoproteomics

febs.onlinelibrary.wiley.com/doi/full/10....

Stirring Bars are Superstition?

Do you really need to stir your reactions? How do you know?

go.bsky.app/JKJ1ZHt

Starter pack: go.bsky.app/2vBi9Ya
Let’s get this list complete !

#ChemBio #chemoproteomics @kusterlab.bsky.social

Miniaturisation of the assay allowed by mind-blowing progress in mass-spectrometry equipment and proteomics workflows is a story for another day …

For the mixing, we have to consider that less is sometimes more. Since there is little chance of achieving ideal complementary of probes with no overlaps, kinases enriched by many probes will dilute the ones enriched by only one in the mass-spec readout, eventually leading to poor quantification.

Full proteomes and transcriptomics help select biological material with good kinome diversity for our purpose … to a certain extent only, because many kinases have low abundance and because transcripts and protein levels are not always proportional.

Is kinase X nowhere in the data because no probe can fish it, or because this bugger is not expressed decently in any of the biological material we use? Do we need to test more probes or more kinome-sources? Indeed, all kinases are not expressed everywhere and all the time. Proteomes are dynamic.

Then comes the testing of individual probes. Once covalently attached to beads, they need to robustly enrich many native kinases of the human (or other) kinome in so-called pulldown experiments. And here comes the challenge and its vicious circle:

Or we can also be super pragmatic, avoid synthesis, and limit ourselves to commercial synthetic intermediates and inhibitors which already have an immobilisation handle at the right spot.

If the final molecules are already quite unselective, that is great for us. If the same molecular scaffold is used for a range of inhibitors relatively selective towards different kinase, great again. And, with those data, we can prioritise the molecules we put synthetic efforts in.

...“best” as a drug i.e. sub-optimal for us, since they achieve a certain level of selectivity. This criterium of selectivity is generally assessed for all (at best) molecules described against only one or two selected other kinases than the intended target.

We want a promiscuous probe though … do we have selectivity data in the literature? There will, in general, be panel selectivity data for one or two of the best inhibitors of a class …

Looking at X-ray co-crystal structures or docking experiments, we can see where the solvent-pointing part of the molecule is. Can we design a molecule with an immobilisation handle on this spot, that can be easily synthesized? Great. Here we go, this could be an affinity probe.