Advancing fragments without structures: NPBWR1

Last week’s post highlighted how biophysical methods, and in particular structural insights, can be critical for advancing fragments to leads. But while everyone likes a structure, one quarter of respondents to our 2017 poll said they were comfortable optimizing fragments on the basis of SAR alone. (See also a recent review.) A new example of structure-free optimization has been published in Bioorg. Med. Chem. Lett. by Remond Moningka and colleagues at Merck.

 

The researchers were interested in the GPCR neuropeptide B/W receptor subtype 1 (NPBWR1, also known as GPR7), a potential target for obesity. Although impressive advances have been made towards obtaining structural information on membrane-bound proteins such as GPCRs, especially using cryo-EM, routine structure-based design is generally not an option.

 

The researchers started with a 30,000 member library of fragments between 200-350 Da. Both the size of the library and the size of the fragments are on the large side compared to what is typically used. A cell-based screen (cAMP assay) at 100 µM yielded 500 hits that inhibited at least 30%. Counter-screening against an unrelated GPCR whittled down the number to 20, of which just 3 provided dose-responses. The low confirmed hit rate illustrates both the utility of a larger library as well as the number of false positives likely to arise in a cell assay.

 

SAR by catalog on compound 1 led to compound 2, and further SAR led to compound 3c, with low micromolar activity and good ligand efficiency. Replacing the nitro group with a more pharmaceutically acceptable trifluoromethyl group produced compound 10. It is worth noting that compound 10 is still fragment-sized yet is >300-fold more active than the initial hit. This is a useful reminder that one can often make significant improvements even before fragment growing. Finally, extensive SAR studies around the phenyl ring ultimately led to compound 21a, with low nanomolar activity.

 

The pharmacology around GPCRs can be complicated, and compound 21a turned out not to be a simple competitive (orthosteric) antagonist of NPBWR1. Rather, it seems to act as a negative allosteric modulator: it reduces the affinity of the natural ligand.

This is a concise success story of advancing a fragment in the absence of structural information. Does this mean we should not strive for structures? Heck no! Not only would structures likely facilitate faster and further improvements, they might explain the mechanism of action of the compounds. I, for one, would love to know where and how they bind.

 

But this paper is another reminder that you do not always need crystallography - or even a model -  to take a fragment to a lead.