Thermodynamics of Fragment
Binding
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Abstract
The ligand binding pockets of proteins have preponderance
of hydrophobic
amino acids and are typically within the apolar interior of the protein;
nevertheless, they are able to bind low complexity, polar, water-soluble
fragments. In order to understand this phenomenon, we analyzed high
resolution X-ray data of protein–ligand complexes from the
Protein Data Bank and found that fragments bind to proteins with two
near optimal geometry H-bonds on average. The linear extent of the
fragment binding site was found not to be larger than 10 Å, and
the H-bonding region was found to be restricted to about 5 Å
on average. The number of conserved H-bonds in proteins cocrystallized
with multiple different fragments is also near to 2. These fragment
binding sites that are able to form limited number of strong H-bonds
in a hydrophobic environment are identified as hot spots. An estimate
of the free-energy gain of H-bond formation versus apolar desolvation
supports that fragment sized compounds need H-bonds to achieve detectable
binding. This suggests that fragment binding is mostly enthalpic that
is in line with their observed binding thermodynamics documented in
Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic
rationale
for fragment based approaches. The binding of larger compounds tends
to more rely on apolar desolvation with a corresponding increase of
the entropy content of their binding free-energy. These findings explain
the reported size-dependence of maximal available affinity and ligand
efficiency both behaving differently in the small molecule region
featured by strong H-bond formation and in the larger molecule region
featured by apolar desolvation