Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?
An application of the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) protocol to the prediction of protein kinase inhibitor selectivity is presented. Six different inhibitors are placed in equivalent orientations in each of six different receptors. Fully solvated molecular dynamics is then run for 1 ns on each of the 36 complexes, and the resulting trajectories scored, using the implicit solvent model. The results show some correlation with experimentally-determined specificities; anomalies may be attributed to a variety of causes, including difficulties in quantifying induced fit penalties and variabilities in normal modes calculations. Decomposing interaction energies on a per-residue basis yields more useful insights into the natures of the binding modes and suggests that the real value of such calculations lies in understanding interactions rather than outright prediction.
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Christopher S
CS
Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London, GB-WC2A 3PX, United Kingdom.
Bates
Paul A
PA
D000595:Amino Acid Sequence; D001665:Binding Sites; D003198:Computer Simulation; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D047428:Protein Kinase Inhibitors / Q000737:chemistry*; D011494:Protein Kinases / Q000737:chemistry*; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D013237:Stereoisomerism; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
D008024:Ligands; D047428:Protein Kinase Inhibitors; D011494:Protein Kinases