Kawasaki et al.
enthalpy gain. In all, the affinity of the inhibitor improves from a Kd of
11.8 to 3.45 nM. Once this transition has occurred, a further increase
in van der Waals radii brings about a monotonic improvement in both
the binding enthalpy and binding entropy. This additional entropy gain
correlates with the surface area that is buried upon binding and most
likely reflects gains in desolvation entropy. It must be emphasized
that, in this regime, no enthalpy ⁄ entropy compensation is observed
and that the binding affinity is quickly improved to 0.1 nM; i.e. two
orders of magnitude better than the parent compound. These effects
are graphically illustrated in Figure 8.
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lead optimization: a thermodynamic perspective. Chem Biol Drug
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from best in class? Drug Discov Today;13:869–874.
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Conclusions
During drug development, improving the binding affinity of a lead
compound is of paramount importance. Toward that end, it is very
important to know what the expectations for specific substitutions
are. In this article, we have considered the binding affinity gains
obtained by filling a target cavity with substitutions that only estab-
lish van der Waals interactions but no specific hydrogen or halogen
bonds. We achieve a total gain of two orders of magnitude in bind-
ing affinity or equivalently )2.68 kcal ⁄ mol. We observe that a
loosely fitting functionality is characterized by a poor interaction
enthalpy and relatively large entropy, probably because of the non-
restricted conformational degrees of freedom within the binding
pocket. The introduction of a tighter fitting functionality improves the
binding enthalpy but restricts conformational degrees of freedom,
hence a decrease in conformational entropy of the aryl ring around
the ether bond. This change appears to be rather abrupt, resembling
a transition from a disordered to an ordered state. In this particular
case, the transition occurs when the hydrogen substituents are
replaced by fluorine; however, in other situations, and depending on
the size and geometry of the cavity, the transition may occur with
substituents of different van der Waals radii. Once the transition has
occurred, additional substitutions with increasingly larger van der
Waals radii bring about progressive favorable enthalpic and also
favorable entropic changes. The improved enthalpy reflects better
van der Waals interactions while the improved entropy most likely
reflects a more favorable desolvation entropy as the solvent-buried
surface increases. Obviously, the introduction of even bulkier chemi-
cal substitutions eventually results in the complete breakdown of the
trend and a significant loss in affinity, because of a possible disrup-
tion of the structure as evidenced by an unfavorable enthalpy. These
effects observed in a binding reaction are qualitatively similar to
those observed with cavity filling mutants in protein folding (44,45).
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Acknowledgments
13. de Paulis T., Hemstapat K., Chen Y., Zhang Y., Saleh S., Alagille
D., Baldwin R.M., Tamagnan G.D., Conn P.J. (2006) Substituent
effects of N-(1,3-diphenyl-1H-pyrazol-5-yl)benzamides on positive
allosteric modulation of the metabotropic glutamate-5 receptor
in rat cortical astrocytes. J Med Chem;49:3332–3344.
This work was supported by grants from the National Institutes of
Health (GM56550 and GM57144) and the National Science Founda-
tion (MCB0641252).
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berg D.E., Freire E. (2003) High affinity inhibition of a family of
Plasmodium falciparum proteases by a designed adaptive inhibi-
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