Magnet for the Needle in Haystack: “Crystal Structure First” Fragment Hits Unlock Active Chemical Matter Using Targeted Exploration of Vast Chemical Spaces

Fragment-based
drug discovery (FBDD) has successfully
led to approved
therapeutics for challenging and “undruggable” targets.
In the context of FBDD, we introduce a novel, multidisciplinary method
to identify active molecules from purchasable chemical space. Starting
from four small-molecule fragment complexes of protein kinase A (PKA),
a template-based docking screen using Enamine’s multibillion
REAL Space was performed. A total of 93 molecules out of 106 selected
compounds were successfully synthesized. Forty compounds were active
in at least one validation assay with the most active follow-up having
a 13,500-fold gain in affinity. Crystal structures for six of the
most promising binders were rapidly obtained, verifying the binding
mode. The overall success rate for this novel fragment-to-hit approach
was 40%, accomplished in only 9 weeks. The results challenge the established
fragment prescreening paradigm since the standard industrial filters
for fragment hit identification in a thermal shift assay would have
missed the initial fragments.