Biophysics and fragment-based drug discovery go together like Nutella and strawberries. Indeed, SAR by NMR ushered in the dawn of fragment-based methods two decades ago, and most fragment-based programs today make use of NMR, SPR, and/or ITC – not to mention X-ray crystallography. Interestingly, the same is not necessarily true for high-throughput screening (HTS) programs. In a recent paper in Drug Discovery Today, Rutger Folmer makes a strong case for engaging biophysics early and often in HTS. He bolsters his argument with more than 20 examples from internal programs at AstraZeneca.
The first descriptions of using NMR to profile HTS hits were not published until several years after SAR by NMR, but they were rather shocking, with up to 98% of hits failing to confirm. Nor is this merely a historical problem, as discussed here. Aggregators, redox cyclers, generically reactive covalent modifiers – all of these are problems not just in fragment screening but in HTS as well. Sometimes the most potent hits are artifacts, particularly for more difficult targets. The key to triaging out pathological actors is to assess binding and not rely solely on inhibition.
That means bringing biophysics into hit profiling at the earliest stages, before trying to optimize fruitless hits. As Rutger points out, it is often difficult to rally colleagues to look at less active molecules after they have wasted months pursuing more potent dead ends.
And biophysics can make an impact even before running screens. Profiling published tool compounds or in-licensing opportunities with biophysical techniques can reveal unwelcome surprises. Testing the output of early HTS pre-screens (7000-10,000 compounds) before a full HTS (2 million compounds at AstraZeneca) can reveal whether an assay is particularly susceptible to false positives. In some cases this can result in reconfiguring the assay, for example by choosing a different detection technology or modifying the protein construct.