Fragments from DOS, advanced

DOS – diversity-oriented synthesis – intentionally generates a disparate set of compounds from a small number of starting materials in just a few synthetic steps. The idea is that if any of these turn out to be hits, it will be straightforward to make analogs. Since figuring out what to do with a fragment is a common bottleneck, DOS-derived fragments could help. An open-access paper published in Chem. Sci. by David Spring (University of Cambridge) and collaborators from several institutions demonstrates how to use DOS to move fragment hits forward.

 

The researchers had previously disclosed (also open access) a rule-of-three-compliant DOS library of 40 compounds derived from racemic α-methyl propargylglycine. In the current paper, these molecules were screened crystallographically at 500 mM on the Diamond Light Source XChem platform against three protein targets.

 

The first, penicillin binding protein 3 (PBP3) from P. aeruginosa, is a classic antibiotic target. A single hit, compound 1, was identified. Interestingly, this turned out to be a covalent modifier, with the catalytic serine opening up the lactone. The researchers made 10 analogs exploring four different vectors, each in five synthetic steps using cheap reagents (< £3 per gram). These were screened crystallographically and six bound; one example is compound 6.

 

 

The next protein screened, cleavage factor 25kDa (CFI₂₅), is a subunit of the pre-mRNA cleavage factor Im. (No, I hadn’t heard of it either.) A crystallographic screen yielded two hits, one of which – compound 19 – was elaborated into 14 analogs. This provided some preliminary SAR around the phenyl ring as well as a surprise: compound 31 bound to a different region of the protein.

 

Finally, the researchers screened activin A, a member of the transforming growth factor β superfamily. Compound 40 was elaborated into 14 analogs exploring four vectors, and compound 42 was found to bind in a similar manner.

 

There are several take-aways from this paper. First, DOS libraries can be remarkably diverse: compounds 1, 19, and 40 are all quite different from one another. Second, although I hesitate to discuss hit rates from such a small library, it is encouraging that hits were found at all even from fairly shapely fragments. These are also the first reported small molecule binders for CFI₂₅ and activin A. Laudably, all the structures have been deposited in the protein data bank, extensive details are provided in 185 pages of supplementary material, and the library itself is available for screening at XChem.

 

One downside to crystallographic screening is that affinities are not part of the package, and some hits may be so weak as to be difficult to advance. But the researchers note they are further characterizing the compounds in the hope of producing more potent analogs. Although Teddy’s deadline for demonstrating a highly ligand-efficient molecule from DOS has long passed, hopefully the Safran Zunft Challenge will soon be met.