New chemistries for covalent fragments

Good things come in threes, and since our last two posts have covered covalent fragments, we thought we’d continue the theme with two more papers on the topic.

The first, in MedChemComm by György Keserű and colleagues at the Hungarian Academy of Sciences, is actually a companion to a paper we covered at the end of last year. The researchers were interested in electrophilic heterocycles, and assembled a library of 84, of which 57 were commercial and the rest were synthesized. In their previous paper, the researchers focused on reactivity against proteins. This paper is focused more on aqueous stability and intrinsic reactivity with glutathione, a biologically important thiol. The paper includes handy figures and tables summarizing reactivity rate constants and half-lives (at pH 7.4). These should be useful for selecting warheads that are sufficiently reactive as to be able to label proteins, but not so reactive as to label many proteins nonselectively.

The researchers also did computational studies to try to understand different trends in reactivity. And if you’re interested in testing the compounds yourself, they note that the “library is available for screening against relevant targets upon request from the authors.”

The second paper, by Philippe Roche, Xavier Morelli, and collaborators at Aix-Marseille University, was published in J. Chem. Inf. Model. Last year we highlighted their diversity-oriented target-focused synthesis (DOTS) approach, which combines virtual screening with automated synthesis to rapidly generate new compounds for testing. They have now expanded this approach (called CovaDOTS) to focus on covalent modifiers.

Conceptually, CovaDOTS is akin to fragment linking, in which one of the “fragments” is the nucleophilic residue in the target protein. The process starts with a known noncovalent ligand which is computationally grown by attaching it to commercially available building blocks that contain reactive warheads. These new molecules are then linked with the side chain of an amino acid (cysteine and serine in the paper), and the assemblies are docked against the protein to find molecules that fit well. Ultimately, the best would be resynthesized and tested.

The researchers applied CovaDOTS to three proteins for which covalent and non-covalent ligands had been previously characterized crystallographically. In the case of two kinases, EGFR and ERK2, the program performed well, with the “correct” (i.e., published) ligand observed in the top 14% and 4.4% of hits. For the serine peptidase PREP, the published ligand was the top hit of 303 molecules scored. In all three cases, the predicted binding mode also closely resembled the experimentally determined structure.

One limitation of CovaDOTS is that, as currently implemented, it considers only commercially available building blocks that also “possess both a warhead and an activated function compatible with the selected chemical reaction(s).” It would be interesting to combine the approach with the “make-on-demand” molecules we discussed a few months ago. And of course, it will be interesting to see real-world examples of how the program performs, in addition to these retrospective case studies.

This ends the June 2019 covalent fragment trilogy, but I think it’s fair to say that covalent fragments have a bright future. Look forward to many sequels!