Surface-plasmon resonance (SPR) is among the most popular methods for finding fragments. However, as we have noted, SPR can be very prone to operator error and misinterpretation. In a recent (open access) SLAS Discovery paper, U. Helena Danielson (Uppsala University) and a who’s-who team of biophysicists from across Europe provide experimental strategies for screening difficult proteins.
The researchers chose five different proteins, some of which were screened in two or three different forms for a total of nine protein constructs. Six of these were screened against their FL1056 library, a custom-built 1056-member library which include molecules from the FragNet program. The library includes a number of “three dimensional” molecules as assessed by principal moment of inertia (PMI). The other library, FL90, is a small set of commercially available fragments we highlighted here.
Before screening compounds against proteins, the researchers conducted a “clean screen.” This involved injecting fragments (at 500 µM each) over the sensor surface using the same buffer that would be used in the actual screen to pre-identify fragments that stick to the surface. This typically disqualified about 1% of fragments, though for one set of conditions the number was closer to 3%.
That work done, the researchers turned to the actual screens. After proteins were immobilized on the sensor chips, the fragments were typically screened at a single concentration of 250 µM each. The threshold for the initial hit cutoff was set low, often around 10% of the library, to minimize false negatives. Subsequent follow-up studies at varying concentrations were used for confirmation. This led to a significant winnowing, with the final number of confirmed hits between 0.5 and 7% of the library.
The proteins themselves were intentionally chosen to present various difficulties. Acetylcholine binding protein (AChBP, which we wrote about here) forms a large (125 kDa) pentameric complex with multiple binding sites. Lysine demethylase 1 (LSD1) is a multidomain, cofactor-dependent protein that requires a partner protein, CoREST, for activity. LSD1 was screened in the presence or absence of CoREST. Farnesyl pyrophosphate synthase (FPPS, which we wrote about here) is a target for cancer and osteoporosis, and the microbial forms are targets for trypanosomiasis drugs. Human as well as Trypanosoma cruzi and Trypanosoma brucei proteins were screened. Protein tyrosine phosphatase 1B (PTP1B, which we recently wrote about here) is a difficult enzyme with a couple allosteric sites. The C-terminal region is intrinsically disordered, and the protein was screened with or without this region. Finally, human tau is both intrinsically disordered and prone to aggregation. As we noted earlier this year it is of interest due to its potential role in Alzheimer’s disease.
Happily, hits were identified against all the proteins, some with ligand efficiency values above 0.5 kcal/mol per heavy atom. The chemical structures for selected hits are shown, and the researchers do appropriately caution that validating them using orthogonal (non-SPR) methods is essential before further studies.
I do wish the researchers had noted whether shapely hits were enriched or depleted among the confirmed hits. To my eye most seemed fairly flat, and some seemed dubiously PAINS-like, including an eyebrow-raising dinitro-catechol. Nonetheless, the paper is a nice summary of multiple SPR campaigns. If you’re about to embark on one yourself, it is worth carefully perusing.