Electrophilic MiniFrags vs HDAC8

In fragment-based lead discovery, small is good – at least down to a certain point. While most fragments consist of between 7 and 20 non-hydrogen atoms, some investigators have built libraries of much smaller fragments with at most 7 or 8 heavy atoms. We’ve written about MiniFrags and MicroFrags, which are typically screened crystallographically at high concentrations to find hot spots. In a new open-access J. Med. Chem. paper, Franz-Josef Meyer-Almes, György Keserű, and collaborators at the Budapest University of Technology and Economics, the University of Applied Sciences Darmstadt, and the University of Veterinary Medicine Vienna have applied the concept to covalent fragments.

 

The researchers started with a set of 84 fragments, all heterocycles functionalized with one of six warheads, which we wrote about here. They systematically methylated nitrogen atoms on some of these to generate 58 more fragments containing obligate positive charges, such as compound B6+ below. The intrinsic reactivity of the fragments was assessed by reacting them with the biologically relevant thiol glutathione (GSH).

 

Methylating the heterocycles made them more electrophilic and thus more reactive. For example, only 16 of the 84 non-methylated fragments had a half-life (t_1/2) < 48 hours against GSH, in contrast with 30 of the 58 methylated fragments. In fact, 17 of the methylated fragments had t_1/2 < 10 minutes.

 

Next, all 142 fragments were screened at 250 µM for 2 hours at 30 ºC in a biochemical assay against histone deacetylase 8 (HDAC8), an enzyme important for cell cycle progression. Hits were confirmed in dose-response experiments after 1 hour pre-incubation. Consistent with the glutathione data, only 12 of the non-methylated compounds showed IC₅₀ < 50 µM, while 54 of the 58 methylated compounds were active. One of the fragments, B6+, had a k_inact/K_I value of 4006 M^-1s^-1, not far from that found in approved covalent drugs.

 

HDAC8 contains ten cysteine residues, and sites of modification were determined using both site-directed mutagenesis as well as tryptic digestion followed by mass spectrometry. In total, seven residues could be labeled by one or more fragments. The most reactive cysteine, C153, is close to the binding site of a previously reported inhibitor (compound 1), and the researchers tried merging reactive fragments such as B6+ onto this molecule. The best molecule, compound 3, had a k_inact/K_I value of 1566 M^-1s^-1. However, the drop from B6+ alone suggests that the non-covalent affinity component of compound 1 may have been lost.

 

This is an interesting approach, and as the researchers note, activity assays available for covalent fragments are higher-throughput than the crystallographic screens required for MiniFrags and MicroFrags. On the other hand, there are limitations. For one thing, the obligate positive charge on the methylated fragments could overwhelm other properties, and could even lead to denaturation of proteins at high concentrations, rendering screens uninformative. These fragments are also less likely to be cell permeable.

 

Finally, as we wrote ten years ago, characterizing irreversible covalent fragments presents a challenge in deconvoluting intrinsic reactivity from specific binding. Computational mapping of hot spots on HDAC8 using FTMap revealed that some correlate with modified cysteine residues. But other modified cysteine residues are in surface-exposed flexible loops with no nearby pockets, and hits against these are likely not advanceable. The fact that some of the fragments modify as many as five cysteine residues on HDAC8 suggests they may be too reactive.

 

Still, the systematic characterization of this library is useful experimentally and for training models. It will be interesting to see it deployed against additional protein targets.