Journal Club

Predicting Substrates by Docking High-Energy Intermediates to Enzyme Structures. Hermann JC, Ghanem E, Li Y, Raushel FM, Irwin JJ, Shoichet BK. J Am Chem Soc 2006 Dec 13;128(49):15882-15891.
Enzymes have evolved to catalyze reactions, not merely to bind substrates. Catalysis can be thought of as effective binding of transition states, where this favorable binding energy drives the reaction forward. Thus, to predict what reaction is catalyzed by an enzyme, it may be smarter to dock structures that resemble transition states than to dock substrates.

Docking to predict function has previously used databases of metabolites representing possible substrates and products. Docking transition states is probably not a new idea (considering that catalytic antibodies are generated with transition state analogs), but there are confounding issues.

The issues have not been solved here, but reasonable approaches have been used. A limited reaction space is involved, and the authors have been careful to use terms like high-energy intermediate and transition state analog as opposed to just transition state.

Receptor structures:
"Ligand" databases:
Docking setup and parameters:
Retrospective docking (validation):

For 5/7 amidohydrolase structures, docking the high-energy states outperformed docking the ground states. For dihydroorotase and adenosine deaminase (Fig. 5, below) both approaches worked well, with negligible differences. Enhancement seemed to be more pronounced for apo structures (those crystallized without ligand).

Results for D-hydantoinase, 14 known substrates in database (Fig 1):

high-energy vs. ground state docking
solid bars for catalytically competent poses
lower bars better

Does no bar mean not in top 1000?

Does the enrichment plot include both types of poses?
(brown line suggests it does, seems to end higher than 4/14)

[ Not shown here: Stereoviews of 5-hydroxyethyl-hydantoin docked (Fig 2). ]
[ Not shown here: Results for iso-aspartyl-dipeptidase, 37 substrates (Fig 3). ]
Results for phosphotriesterase, 11 substrates (Fig 4):
What's up with the curves?? Smoothing gone overboard?

Fig 4B must not include both types of poses. Otherwise, both curves would be at 100% for 25% of the database docked and the brown curve would be above the blue curve. Upon careful re-examination, the descriptions of Figs. 3 and 4B hint at this rather obliquely.

Results for the other four, with relatively few substrates (Fig 5):
[ Not shown here: Stereoviews of cytosine docked (Fig 6). ]
Prospective docking (prediction):

Five mutant phosphotriesterases (mutations at 1–3 active-site residues) were modeled by simply replacing the affected side chains. Stereoisomers of four potential new substrates (Chart 1) were docked into the wild-type and mutant receptors. The compounds were synthesized and tested "in real life." Of 24 possible predictions of enantioselectivity (6 receptors x 4 substrates), no predictions were made for 3 combinations because no catalytically competent pose was obtained. 19/21 predictions were qualitatively verified, two were wrong.

As far as I could tell, this part of the paper did not involve docking of high-energy intermediates.