Our work on macrocyclic HDAC11 inhibitors is now out in JACS Au! pubs.acs.org/doi/10.1021/...
#openaccess #chemsky

#SIRT7 is a histone deacetylase with highly specific activity on #chromatin substrates.
We just published mechanism-based #cryoEM structures of #SIRT7 on nucleosomes to understand its activity 👇
www.nature.com/articles/s41...
(1/8) #ChemBio #ChemSky

The macrocycle is therefore fully validated as a potent, selective and cell-permeable probe of HDAC11. We hope that it can shed some light on HDAC11 biology of which we still understand very little. Huge thanks to all the co-authors, this project was a great collaborative effort.

Finally, @tnhansen.bsky.social tested the macrocycle for the downstream effects of HDAC11 inhibition. YAP1 and SOX2, which are both regulated by HDAC11, were significantly depleted following the treatment with the macrocycles.

We next turned the macrocycle into a cell permeability probe by a single atom H --> Cl change on the N-hexyl Asuha. It was then employed in chloroalkane penetration assay by Christian Bartling from the Strømgaard lab. The data shows that the macrocycle is highly cell penetrable with CP50 of 43nM.

Excitingly, the macrocycles inhibit demyristoylation, but not deacetylation in HDAC11-expressing breast cancer cell lysates. Marie Hesse, a great MSc student, then turned the inhibitor into a pulldown probe and succeeded at pulling down HDAC11 together with its only known interaction partner HDAC6.

Through SAR study on the zinc-binding moiety, we confirmed it was the N-alkylation that was driving the selectivity towards HDAC11 , as the non-alkylated analogue was a potent broad-spectrum HDAC inhibitor. Meanwhile, C6 and C14 analogues showed minimal activity against remaining 10 HDAC isozymes.

Somewhat surprisingly, considering all compounds contained a zinc-binding group, only 12 HDAC11 inhibitors (out of 4608!) were identified in the screening. 7 hits were resynthesized and 6/7 showed selectivity for HDAC11 over HDAC1. Our lead 420-L4, in particular, showed high potency (Ki of 40nM).

@alexanderln.bsky.social, a former colleague from @ucph.bsky.social and then a postdoc in the Heinis lab synthesized and screened the library, employing their state-of-art automated and high-throughput SPPS and macrocyclization: doi.org/10.1002/anie...

Inspired by natural product(like) macrocyclic inhibitors of class I HDACs, we aimed to discover HDAC11-selective macrocyclic inhibitors. We designed a biased peptide macrocyclic library (>4600 members) carrying N-alkylated hydroxamic acid moiety to mimic the natural substrate of HDAC11.

HDAC11 is an understudied, highly tissue-specific HDAC isozyme with unusual enzymatic activity (doi.org/10.1016/j.ch...). It removes long fatty acid chains (C14) from the side chain of lysine, as reported by our lab and others in 2018.

Happy to share the latest preprint from my PhD studies on the discovery of de novo macrocyclic inhibitors of HDAC11. This was a great collaboration between @christianaolsen.bsky.social lab (@carlosmyruela.bsky.social, @tnhansen.bsky.social) and Christian Heinis lab (@alexanderln.bsky.social).