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1.  IDSite: An accurate approach to predict P450-mediated drug metabolism 
Accurate prediction of drug metabolism is crucial for drug design. Since a large majority of drugs metabolism involves P450 enzymes, we herein describe a computational approach, IDSite, to predict P450-mediated drug metabolism. To model induced-fit effects, IDSite samples the conformational space with flexible docking in Glide followed by two refinement stages using the Protein Local Optimization Program (PLOP). Sites of metabolism (SOMs) are predicted according to a physical-based score that evaluates the potential of atoms to react with the catalytic iron center. As a preliminary test, we present in this paper the prediction of hydroxylation and O-dealkylation sites mediated by CYP2D6 using two different models: a physical-based simulation model, and a modification of this model in which a small number of parameters are fit to a training set. Without fitting any parameters to experimental data, the Physical IDSite scoring recovers 83% of the experimental observations for 56 compounds with a very low false positive rate. With only 4 fitted parameters, the Fitted IDSite was trained with the subset of 36 compounds and successfully applied to the other 20 compounds, recovering 94% of the experimental observations with high sensitivity and specificity for both sets.
doi:10.1021/ct200462q
PMCID: PMC3254112  PMID: 22247702
2.  Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX  
All-atom models derived from moderate-resolution protein crystal structures contain a high frequency of close nonbonded contacts, independent of the major refinement program used for structure determination. All-atom refinement with PrimeX corrects many of these problematic interactions, producing models that are better suited for use in computational chemistry and related applications.
All-atom models are essential for many applications in molecular modeling and computational chemistry. Non­bonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5–2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R free values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-­fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein–ligand interactions.
doi:10.1107/S0907444912017453
PMCID: PMC3413210  PMID: 22868759
H atoms; van der Waals radii; restraints; nonbonded contacts; clashes; molecular geometry; model quality; force fields; refinement; riding H atoms; electrostatics; hydrogen bonds
3.  A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A2A Adenosine Receptor 
Structure (London, England : 1993)  2009;17(12):1660-1668.
SUMMARY
The function of G-protein coupled receptors is tightly modulated by the lipid environment. Long timescale molecular dynamics simulations (totaling ~3 microsec) of the A2A receptor in cholesterol-free bilayers, with and without the antagonist ZM241385 bound, demonstrate an instability of helix II in the apo receptor in cholesterol-poor membrane regions. We directly observe that the effect of cholesterol binding is to stabilize helix II against a buckling type deformation, perhaps rationalizing the observation that the A2A receptor couples to G-protein only in the presence of cholesterol (Zezula and Freissmuth, 2008). The results suggest a mechanism by which the A2A receptor may function as a coincidence detector, activating only in the presence of both cholesterol and agonist. We also observed a previously hypothesized conformation of the tryptophan “rotameric switch” on helix VI in which a phenylalanine on helix V positions the tryptophan out of the ligand binding pocket.
doi:10.1016/j.str.2009.10.010
PMCID: PMC2796422  PMID: 20004169
4.  The role of the active site solvent in the thermodynamics of factor Xa-ligand binding 
Understanding the underlying physics of the binding of small molecule ligands to protein active sites is a key objective of computational chemistry and biology. It is widely believed that displacement of water molecules from the active site by the ligand is a principal (if not the dominant) source of binding free energy. Although continuum theories of hydration are routinely used to describe the contributions of the solvent to the binding affinity of the complex, it is still an unsettled question as to whether or not these continuum solvation theories describe the underlying molecular physics with sufficient accuracy to reliably rank the binding affinities of a set of ligands for a given protein. Here we develop a novel, computationally efficient, descriptor of the contribution of the solvent to the binding free energy of a small molecule and its associated receptor that captures the effects of the ligand displacing the solvent from the protein active site with atomic detail. This descriptor quantitatively predicts (R2=0.81) the binding free energy differences between congeneric ligand pairs for the test system factor Xa, elucidates physical properties of the active site solvent that appear to be missing in most continuum theories of hydration, and identifies several features of the hydration of the factor Xa active site relevant to the structure-activity-relationship of its inhibitors.
doi:10.1021/ja0771033
PMCID: PMC2761766  PMID: 18266362
5.  Integrated Modeling Program, Applied Chemical Theory (IMPACT) 
Journal of computational chemistry  2005;26(16):1752-1780.
We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed charge and polarizable force fields that can be used with the program and illustrate how the force fields, when used together with new atom typing and parameter assignment modules, have greatly expanded the coverage of organic compounds and medicinally relevant ligands. As we discuss in this review, explicit solvent simulations have been used to guide our design of implicit solvent models based on the generalized Born framework and a novel nonpolar estimator that have recently been incorporated into the program. With IMPACT it is possible to use several different advanced conformational sampling algorithms based on combining features of molecular dynamics and Monte Carlo simulations. The program includes two specialized molecular mechanics modules: Glide, a high-throughput docking program, and QSite, a mixed quantum mechanics/molecular mechanics module. These modules employ the IMPACT infrastructure as a starting point for the construction of the protein model and assignment of molecular mechanics parameters, but have then been developed to meet specialized objectives with respect to sampling and the energy function.
doi:10.1002/jcc.20292
PMCID: PMC2742605  PMID: 16211539
IMPACT; Monte Carlo simulation; QM/MM applications

Results 1-5 (5)