Expanding the Scope of chemical space at Novartis

Without a good library, it is difficult to find a good hit, so library design is one of the most import aspects of a screening campaign. The size of a library also impacts how it can be screened. A virtual or DNA-encoded library might be billions (or even trillions) of compounds, but for most physical screens, such huge numbers would be unfeasible. Generally, fragment screens sample more chemical space but require more resources, while screens of larger molecules can be higher throughput. In a new (open-access) J. Chem. Inf. Model. paper, Johanna Jansen, Charles Wartchow, and colleagues at Novartis describe a middle ground, the “Scope Concept.”

 

The researchers, many of whom have fragment and biophysics experience, were interested in molecules that might be larger than the rule-of-three guidelines for fragments, but still small enough to sample reasonable swaths of chemical space. To this end they developed the Scope library. To be included, compounds need to have molecular weights between 200-400, measured or calculated solubilities of at least 100 µM, at least two moieties capable of forming hydrogen bonds, and a “Scope ring system,” meaning two rings connected by a 0-3 atom linker. Additionally, undesirable substructures were removed, and in-house compounds had to pass quality control. Originally compounds were required to have log P < 5, but the solubility limit weeded these out anyway. Some warhead-containing molecules were included, though the fraction is not disclosed.

 

The Novartis compound collection was queried using these criteria to choose a 10,000-compound core Scope set as well as a 40,000-compound extension set designed for higher throughput screens. While these numbers are not large in the context of high-throughput screening libraries, they are larger than most fragment libraries according to our polls.

 

The Scope libraries proved to be popular at Novartis: 18 screens were performed in the first year across three sites. Half of these were biochemical screens. Of the rest, six used SPR, two used DSF, and one used native mass spectrometry (nMS). Most of the biochemical screens used the full 50,000 library, while the biophysical screens used the 10,000 core set and sometimes expanded to the full set. For four of five targets screened using a biochemical assay, primary hit rates were similar or slightly higher for the Scope library than a diversity library, though the Scope library was screened at a 50-100 µM concentration as opposed to 10-50 µM.

 

Three targets are discussed in some detail. The first, trypanosomal CLK1 kinase, had a freakishly high primary hit rate of 21% when screened at 100 µM, compared to 2.5% for a diversity set screened at 12.5 µM. Another kinase had an 11% hit rate, while a third had a more reasonable 1.2% hit rate when the ATP-binding site was blocked, suggesting binding to this site. The researchers now screen kinases against lower concentrations of the Scope compounds due to the high ligandability of kinases in general.

 

The chemical structures of half a dozen hits are shown, with IC₅₀ values ranging from 30 nM to 1.1 µM. Interestingly two of the molecules are covalent modifiers, and both are somewhat large for fragments, with 19 or 20 non-hydrogen atoms.

 

Another target screened was the molecular hub protein 14-3-3, which we wrote about most recently just a few months ago. A screen of the 10,000-compound Scope core set looking for stabilizers of 14-3-3σ and a peptide from the estrogen receptor yielded 86 hits, of which three were fully validated in orthogonal assays. One of these yielded a crystal structure and turned out to be a covalent modifier at a cysteine residue previously shown to be reactive. As with CLK1, the hit was on the larger side, with 22 non-hydrogen atoms. A separate publication by Colin Skepper and colleagues in ACS Med. Chem. Lett. describes this and three other covalent hits derived from diversity sets. Here too, the hits ranged from 20 to 24 non-hydrogen atoms.

 

The native mass spectrometry screen mentioned above was run against the main protease (MPro) of SARS-CoV-2. The 10,000 compound core set was screened in pools of four, with each compound at 25 µM. Of 61 primary hits, five validated with IC₅₀ values < 25 µM. In contrast to many inhibitors of this protein, these were mostly non-covalent.

 

The Scope Concept is a nice addition to the field of library design. As we noted last year, covalent fragments may need to be larger than non-covalent fragments, and it is interesting that two of the three case studies identified covalent modifiers. I hope Novartis publishes a follow-up in a few years with lessons from additional screens.