Covalent fragments in the clinic: VVD-133214

Back in 2016 we highlighted a paper describing chemoproteomic screening of covalent fragments. That technology formed the basis of Vividion, which was acquired by Bayer in 2021. Now, a paper just published in Nature by Matthew Patricelli, Todd Kinsella, and collaborators at Vividion, Roche, and Universitat Autònoma de Barcelona describes one of the fruits to come from this platform.

 

The work stems from another promising recent approach to find oncology targets, synthetic lethality: searching for proteins that are essential in certain types of cancer cells but dispensable for normal cells, which might mean reduced toxicity. WRN is a DNA helicase that can clean up secondary DNA structures caused by expanded TA-dinucleotide repeats found in cancer cells with microsatellite instability (MSI), which is caused by mutations in DNA repair genes. Previous research had shown that knocking out WRN caused double-stranded DNA breaks and cell death in MSI-high (MSI-H) cancer cells but not normal cells, which do not have so many expanded TA-dinucleotide repeats. This has set off an industry-wide search for WRN inhibitors.

 

The researchers screened several thousand fragment electrophiles against cell lysates and found that some, such as VVD-109063, modified C727 of WRN. Although this cysteine is located some distance from the ATP binding site, functional activity studies with the pure protein found that the molecule was an inhibitor.

 

Optimization of VVD-109063 and related molecules found inconsistencies between results in lysates and intact cells. Some engaged C727 better in intact cells than lysates, others worse. Differences in cell permeability were ruled out by the fact that a cysteine on an unrelated protein was liganded to a similar extent in cell lysates and intact cells. The researchers speculated that, because cell lysates are diluted, they have lower ATP concentrations, and sure enough some molecules were less active in the presence of ATP while others were more active.

 

The team decided to focus on the second class. Optimization ultimately resulted in the clinical candidate VVD-133214. (Unfortunately details are not given; the paper does say these will be provided elsewhere).

 

A crystal structure of VVD-133214 confirmed covalent binding to C727, with the molecule in a hydrophobic pocket in a flexible “hinge region” of the protein. This causes a conformational rearrangement into a “closed” form, which presumably affects the catalytic activity of the helicase. Surprisingly, there are no hydrogen bonds between WRN and VVD-133214. This is highly unusual: a paper we discussed in 2021 found >90% of fragment-derived leads had at least one polar contact.

 

The k_inact/K_i value is reported as being 4848 M^-1s^-1, which is on the low side for clinical-stage irreversible inhibitors. Like sotorasib, its potency seems driven by k_inact, with the K_i being greater than > 15 µM. Consistent with this low inherent affinity, the molecule was inactive against the C727A mutant enzyme.

 

Much of the paper focuses on the biology, which is interesting but beyond the scope of this post. Suffice it to say that VVD-133214 is cytotoxic in MSI-H cells, where it causes G2 arrest and DNA damage, but inactive in microsatellite stable (MSS) cells. Oral dosing led to tumor regression in several MSI-H mouse models, including patient-derived xenografts.

 

This is a nice paper, though I look forward to a full account of the medicinal chemistry. In particular, vinyl sulfones are generally considered quite reactive, and I know of only one other clinical-stage molecule with this warhead. Presumably the cyclopropyl substituent was added at least in part to sterically block access to the electrophile.

 

Also, while the paper refers to VVD-133214 as “clinical-stage,” it appears neither on clinicaltrials.gov nor on Vividion’s website. The Roche website lists RG6457 as a phase 1 WRN covalent inhibitor partnered with Vividion, so perhaps this is the same molecule.

 

The paper ends by mentioning another clinical-stage WRN inhibitor from a different company, this one noncovalent. It notes that “this presents a rare opportunity to compare two small molecule oncology drugs targeting the same protein by different mechanisms,” and that using both could be useful in combating resistance. Practical Fragments wishes luck to these – and other drugs targeting WRN – helping patients quickly.