There are many ways to screen for fragments. One of the really emerging areas uses mass spec detection: WAC, native mass spec, HDX, and ligand-observed MS. The group that we highlighted back in March has a new paper where they look at the method in terms of accuracy of Kd determination and compare the results to other biophysical methods.
Their previous work they looked at relative affinity ranking of bound fragments. In this study, they compared the accuracy of Kd determination in this method to ITC. First they used a pool of 3 or 4 known CAI inhibitors and a pool of 50 fragments (from their collection). The conditions were defined:
The hCAI protein was incubated with each inhibitor mixture in the binding buffer with a total volume of 50 mLat room temperature for 40 min. The protein concentration was maintained at 25 mM and the inhibitor concentration increased from 1 mM to 50 mM. The control was prepared by using the binding buffer substitute for hCAI during incubation. The incubation solution was then filtered through a 10 kDa MW cutoff ultrafiltration membrane by centrifugation at 13,000 g for 10 min at 4 C followed by a quickwash with 10mM ammonium acetate (pH 8.0) to remove the unbound compounds.
Two different methods were used to calculate Kd: 1. saturation curves and 2. measuring the unbound fraction of ligand . Method 1 was deemed unsuitable for determining Kds for ligands with largely different Kds. Method 2 did not depend on saturation curve fitting, instead using a calibration curve and did not observe any fragment competition at higher P:L ratios (6:1 or 8:1). This approach also improved the sensitivity of the assay allowing better detection of lower affinity ligands. Kds determined using this method matched those determined by ITC.
To further test the method, they ran a pool of 50 fragments against HCV RNA polymerase NS5B. This gave, as expected, a complicated chromatographic baseline. To exclude promiscuous binders, they ran against BSA in parallel. Eight fragments in the mixed pool showed selective binding to NS5B using unbound fraction analysis vs. 2 from the bound fraction analysis. 7 of 8 fragments were confirmed by SPR (ITC could not be used). The 1 BFA fragment to be analyzed by SPR showed that it was a very weak binder.
This sort of work makes me happy. Methods always need to be pushed and evaluated. When evaluating methods, if this sort of cross validation hasn't been done, question as to why not?
I guess I was a little less sanguine about the technique after reading this paper. The weakest fragment validated by ITC was still quite strong, with a dissociation constant of 37 micromolar.
Worse, depending on the assay conditions, dissociation constants measured for the same ligand could vary by more than an order of magnitude. If experts in the technique find this much variation with a well-characterized protein such as carbonic anhydrase, it may prove troublesome in less experienced hands for more difficult targets.
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