Fragment optimization without purification

Compound purification can be a major hassle: separating the desired product from starting materials, reagents, and byproducts often takes far longer than making the compound in the first place. As we’ve previously noted, this is especially true for small, polar fragments – which are particularly attractive for drugs. Two new papers address this challenge. (Shameless plug: my company Carmot Therapeutics also has a solution to this problem.)

In J. Med. Chem., Paul Brough and Vernalis colleagues describe their discovery of inhibitors of all four isoforms of pyruvate dehydrogenase kinase (PDHK), potential targets for diabetes and oncology. The ATP-binding site of these four enzymes is similar to that of oncology target HSP90, in which Vernalis has a long-standing interest.

A screen of 1063 fragments (each at 0.5 mM) against PDHK-2 yielded 78 hits that were positive in three different NMR-based assays and also ATP-competitive. These yielded a whopping 43 structures when soaked into crystals of the related isoform PDHK-3. Compound 6 was one, and the binding mode was very similar to that previously seen for the same fragment with HSP90. Fragment growing rapidly led to molecules such as compound 8, with low micromolar potency. This compound was almost equipotent against HSP90, but modeling suggested that it might be possible to further grow this molecule in a direction that would be accommodated in the PDHKs but not in HSP90.

The next step was to make a bunch of analogs, and here's where avoiding purification becomes advantageous. Specifically, the researchers turned to off-rate screening (ORS), which entails making compounds and then testing the impure mixtures using surface plasmon resonance (SPR) to look for those which dissociate more slowly. Since off-rate is not dependent on the concentration of ligand, a low yield shouldn’t change the results of the assay.

An initial library of 56 compounds led to the discovery of compound 18, and subsequent libraries and medicinal chemistry ultimately yielded VER-246608, which is a potent pan-PDHK inhibitor. As designed, it is also completely inactive against HSP90. The molecule is described more thoroughly in this Oncotarget paper, which reveals that despite activity against PDHKs in cells, VER-246608 is not particularly effective at slowing the proliferation of cancer cells. Still, it does appear to be a useful chemical probe for further exploring the biology of the PDHKs.

Shifting methods but staying with the theme of assaying impure compounds brings us to a paper in SLAS Discovery by Sten Ohlson, Brian Dymock, and colleagues at Nanyang Technological University and the National University of Singapore. The protein tested was HSP90, and the method used was weak affinity chromatography, or WAC (see here, here, and here).

Like SPR, WAC also uses an immobilized protein. However, whereas SPR provides the (kinetic) off-rate, WAC provides the (thermodynamic) dissociation constant, which is calculated from the change in retention time of the molecule as it passes through a column containing protein-bound resin. In this case the researchers synthesized a mixture of five different compounds which varied from 7-24% of the mixture. This crude sample was analyzed by WAC, and the resulting dissociation constants, ranging from 48-147 µM, were satisfactorily similar to the values obtained using pure compounds.

Both of these approaches should accelerate screening and facilitate the analysis of complicated mixtures, such as natural product extracts. It will be fun to watch for more examples.