Fragments in the clinic: VVD-214

Just over two years ago we highlighted a new clinical candidate targeting WRN, a covalent inhibitor then called VVD-133214. An open-access paper published near the end of last year in J. Med. Chem. from Shota Kikuchi, David Weinstein, and colleagues at Vividion describes in detail the optimization of the covalent fragment hit to the clinical compound. (Shota presented some of this work at the 2024 DDC meeting.) This paper is also an interesting contrast to non-covalent fragment-finding approaches against this target we wrote about earlier this month.

 

The 2024 post described the chemoproteomic screening that identified compound 1a, which covalently binds to C727 in WRN. An early observation was that some molecules were cooperative with ATP while others were competitive. Given the high concentration of ATP in cells, the researchers prioritized the former category, which led to compound 1f. (Note that while I’m showing only the k_inact/K_I values, the researchers used biochemical and cell-based assays to drive SAR).

 

The vinyl sulfone warhead is unusual amongst covalent clinical compounds, so the researchers sought to characterize it. The rate of reaction with glutathione for compound 1f is comparable to the approved drug osimertinib: reactive, though acceptable. To try to lower the reactivity and also prevent isomerization of the double bond, the researchers introduced a methyl group. Compound 2a not only showed increased stability but also improved activity against WRN and sub-micromolar activity in a cell-based assay. A crystal structure of a later molecule revealed interactions with a hydrophobic patch on the protein, explaining the improvement in potency. Importantly, the other enantiomer was much less potent.

 

Other rings were tried, unsuccessfully, to replace the pyrimidine and the phenyl moieties. However, changing the cyclopentyl ring to a tert-butyl moiety (compound 5d) further improved the potency to the point where the compound could be tested in vivo, where it proved to be active in a mouse xenograft study. Mass spectrometry experiments revealed prolonged occupancy of C727 out to 24 hours after compound dosing even though the compound itself had been cleared, consistent with a long half-life of the WRN protein. The researchers note that high target engagement (TE) at 24 hours was predictive of tumor growth inhibition, which streamlines optimization since it is easier to run a one-day TE experiment than a multi-week efficacy study.

 

Further optimization of ADME properties ultimately led to VVD-214, which was active in a mouse xenograft study and showed good oral bioavailability and pharmacokinetics in mouse, rat, dog, and monkey. This compound was also profiled in a chemoproteomic assay and found to be quite selective for the C727 of WRN.

 

There are several important lessons in this paper. First, the initial fragment is larger than prescribed by the rule of three, consistent with an analysis of covalent inhibitors last year. Second, much of the SAR was empirical; crystallography was not used until relatively late in the campaign. When a crystal structure was finally solved of VVD-214 bound to WRN it revealed no polar contacts between the ligand and the protein, only hydrophobic interactions, which is rare for fragments, let alone drugs. Perhaps because of the lack of polar interactions, it was impossible to measure the inhibition constant (K_I), and saturating the warhead to make it unreactive completely abolished activity. In other words, the binding is largely driven by reactivity, but specific reactivity for WRN rather than generic chemical reactivity.

 

In 2024 just two WRN inhibitors had entered the clinic, the other being a noncovalent molecule called HRO761. We quoted the Vividion team as saying that “this presents a rare opportunity to compare two small molecule oncology drugs targeting the same protein by different mechanisms.” Since then, HRO761 has been quietly discontinued, as has another noncovalent drug, IDE275. Meanwhile, development of VVD-214 is ongoing, and another covalent compound, MOMA-341, which we mentioned here, has also begun human testing. (To be fair, so has yet another non-covalent molecule NDI-219216. And the binding mechanism of a sixth WRN drug, EIK1005, is undisclosed.) While it’s still early in the match, covalent drugs seem to be punching above their weight. May the best drug(s) prevail - Practical Fragments is rooting for them all.