From covalent fragment to lead against TEAD

As noted just last month, covalent fragment-based drug discovery is becoming ever more popular. However, many papers report relatively weak hits with little or no optimization. A new preprint posted to bioRxiv (HT Covalent Modifiers) by Tinghu Zhang, Nathanael Gray, and collaborators at Stanford and elsewhere describes a fragment-to-lead story for the TEAD family of transcription factors.

 

The four highly homologous members of the TEAD family play a role in the Hippo signaling pathway. When spurred by the coactivator YAP they cause gene expression that has been implicated in certain cancers, particularly mesothelioma. To bind YAP, TEAD needs to be palmitoylated on a specific cysteine residue. A covalent inhibitor that binds to this cysteine could prevent palmitoylation and thus block Hippo signaling.

 

Multiple academic and industrial groups have been pursuing this target, and one previously reported inhibitor is flufenamic acid. This molecule was used in the new paper to design a small library of analogs each functionalized with an acrylamide moiety. These were screened against TEAD2 and analyzed by mass spectrometry; MYF-01-37 modified the protein (though unfortunately time and exact concentrations are not specified). Proteolysis and tandem mass spectrometry confirmed that the molecule binds to C380, the site of palmitoylation.

 

Analysis of previously published crystal structures revealed a side pocket off the main hydrophobic channel that normally binds the palmitoyl group. The researchers created a focused library of analogs to try to access this pocket, which led to molecules such as MYF-03-69. This compound was active in a biochemical assay and showed rapid labeling of the protein as assessed by mass spectrometry. A crystal structure of the compound bound to TEAD1 confirmed the molecule forms a covalent bond to the target cysteine and does in fact bind in both pockets. 

 

MYF-03-69 inhibited palmitoylation of all four TEAD paralogs in biochemical assays. More importantly, it showed activity in several cell assays, including blocking palmitoylation and disrupting the interaction between TEAD and YAP. The molecule downregulated YAP-TEAD transcription in reporter gene assays as well as RNA sequencing assays. Finally, MYF-03-69 showed mid-nanomolar antiproliferative activity in mesothelioma cells but not in non-cancerous cell lines.

 

Despite this promising activity, MYF-03-69 lacked acceptable oral bioavailability. Further medicinal chemistry led to MYF-03-176, which has improved bioavailability and showed even better activity in reporter gene assays and better antiproliferative activity in mesothelioma cell lines. The molecule also led to tumor regression in a mouse xenograft model when dosed orally.

 

This is a nice story with lots of information, though were I a reviewer I would ask for the k_inact/K_I values for the molecules. This ratio describes the rate of covalent modification and is time and concentration independent, which makes comparisons with other molecules more straightforward (see this 2017 open-access paper for a good discussion). Since this is a preprint hopefully the final published paper will include these values. 

 

Regardless, MYF-03-176 looks like an excellent chemical probe for studying the effect of irreversible inhibition of Hippo signaling.