Fragments vs IP6K1 without using structural information

The three members of the inositol hexakisphophate kinase family are potential targets for a wide range of diseases, from Alzheimer’s to cancer to metabolic disease. However, current inhibitors are not specific for individual isoforms. Also, the most potent compounds contain a carboxylic acid moiety, which is usually at odds with brain penetration. In a new ACS Med. Chem. Lett. paper, James Barrow and collaborators at Johns Hopkins School of Medicine, the Lieber Institute for Brain Development, and AstraZeneca describe neutral, selective inhibitors.

 

The researchers started with a high-throughput biochemical screen of 17,000 fragments, each at 100 µM, against IP6K1. The library itself is available here. After dose-response follow-up studies, 90 hits confirmed, with IC₅₀ values as good as 2 µM. Most of the hits contained carboxylic acids, but compound 5 did not, and also had good ligand efficiency.

 

No crystal structures of IP6K1 have been reported, so the researchers used an AlphaFold model for docking compound 5. This suggested a fragment growing approach. A variety of replacements for the pyrrolidine were attempted, and while some of these had improved activity many also proved to be chemically unstable. Removing the nitrogen and growing led to compound 24, which was both chemically stable and had sub-micromolar activity.

 

The quinazolinone core itself was associated with poor solubility, and the researchers made multiple attempts to modify it, such as introducing additional nitrogen atoms or methylating to remove a hydrogen-bond donor. Unfortunately, all these modifications led to significant losses in potency.

 

Compound 24 is highly selective for IP6K1 over IP6K2 and somewhat selective over IP6K3. Unfortunately, it showed no cellular activity, possibly due to modest biochemical potency and solubility. Nonetheless, this brief paper illustrates that starting with a larger than normal fragment library can lead to new chemotypes. Screening the larger library gave the researchers more chances to find fragments that did not contain carboxylic acids. Indeed, the difficulty of modifying the quinazolinone moiety demonstrates the utility of screening more molecules. Had the closely related molecules been in the library, they might not have turned up as hits, but their presence would suggest that relevant chemical space had been interrogated.

 

The paper is also a nice example of optimizing hits in the absence of structural information. Although much needs to be done to turn compound 24 into a chemical probe, the fact that it is still so small (almost rule-of-three compliant) provides hope that this can be done.