netLibrary - eBook Summary Structure-based Drug Design by ...

Document
This method was used to screen a significant portion of the contents of the Cambridge Structural
Database [45] against the ALR2 holoenzyme binding site (D.K. Wilson, J. M. Petrash, and F. A.
Quiocho, unpublished data). Among the approximately 30 highest scoring compounds were several
aromatic aldoximes that had inhibition constants in the micromolar range. These were similar to
aldoximes such as benzaldoxime, which has been previously observed to have similar inhibition
constants [46].
Page 242
A disappointing result was that this search did not “rediscover” any of the known high-affinity ALR2
inhibitors that were contained in the search library. Before the determination of the ternary complex of
the enzyme with zopolrestat, this was interpreted as meaning that these compounds bound to the enzyme
in a conformation somewhat different than the one adopted in the crystal structure used for the search.
The structure of the ternary complex showed this to be a wrong assumption; it was the protein that
changed conformation upon inhibitor binding, creating a pocket that did not exist in the holoenzyme
structure. When bound to the protein, zopolrestat is actually quite similar in conformation to its small
molecule x-ray structure. It is therefore very possible that different ALR2 inhibitors and substrates may
cause the enzyme to flex in different ways, creating binding sites that may be different in size and
chemical nature.
B. Computational Thermodynamic Perturbation
Computational thermodynamic perturbation is a powerful, albeit computationally expensive, group of
techniques that are designed to estimate relative binding affinities of two closely related drugs, given the
structure of at least one of them complexed with the target protein [44]. This approach has the potential
to assay candidate compounds in the computer for improvements in inhibitor binding, thereby removing
the necessity to sythesize and assay these compounds in the lab.
For a number of reasons, ALR2 promises to be a good system for the application of this technique and
the experimental verification of the results. The structure is very well determined in complex with
zopolrestat, a high-affinity inhibitor. A number of zopolrestat derivatives with various functional groups
decorating the compound have been sythesized and partially characterized with respect to ALR2
inhibition [13,47]. These compounds could serve as a sort of basis set of controls for the theoretical
calculations. If parameters used in these calculations can be selected such that the computationally
derived binding energies agree even qualitatively with the experimentally determined binding energies,
serious consideration should be given to new compounds that are predicted to bind with enhanced
affinity. Since ALR2 is crystallizable with zopolrestat bound, there is every reason to believe that
crystals of the enzyme complexed with similar compounds will be obtainable. Such structures could
provide the basis for further rounds of drug improvement.
http://legacy.netlibrary.com/nlreader/nlReader.dll?bookid=12640&filename=Page_242.html [4/5/2004 5:09:26 PM]