Halo Library, a Tool for Rapid Identification of Ligand Binding Sites on Proteins Using Crystallographic Fragment Screening

X-ray crystallographic fragment screening (XCFS) uses
fragment-sized
molecules (∼60 to 300 Da) to access binding sites on proteins
that may be inaccessible to larger drug-like molecules (>300 Da).
Previous studies have shown that fragments containing halogen atoms
bind more often to proteins than non-halogenated fragments. Here,
we designed the Halo Library containing 46 halogenated fragments (including
the “universal fragment” 4-bromopyrazole), a majority
of which have been reported to bind to or inhibit one or more targets.
The library was screened against the crystals of HIV-1 reverse transcriptase
with the drug rilpivirine, yielding an overall hit rate of 26%. Two
new binding sites were discovered, and several hot spots were identified.
This small library may thus provide a convenient tool for rapidly
assessing the feasibility of a target for XCFS, mapping hot spots
and cryptic sites, as well as finding fragment binders that can be
useful for developing drug leads.