Screening drug-like compounds by docking to homology models: a systematic study.
In the absence of an experimentally solved structure, a homology model of a protein target can be used instead for virtual screening of drug candidates by docking and scoring. This approach poses a number of questions regarding the choice of the template to use in constructing the model, the accuracy of the screening results, and the importance of allowing for protein flexibility. The present study addresses such questions with compound screening calculations for multiple homology models of five drug targets. A central result is that docking to homology models frequently yields enrichments of known ligands as good as that obtained by docking to a crystal structure of the actual target protein. Interestingly, however, standard measures of the similarity of the template used to build the homology model to the targeted protein show little correlation with the effectiveness of the screening calculations, and docking to the template itself often is as successful as docking to the corresponding homology model. Treating key side chains as mobile produces a modest improvement in the results. The reasons for these sometimes unexpected results, and their implications for future methodologic development, are discussed.
Kairys
Visvaldas
V
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, 20850, USA.
Fernandes
Miguel X
MX
Gilson
Michael K
MK
D003198:Computer Simulation; D051357:Cyclin-Dependent Kinase 2 / Q000378:metabolism; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000378:metabolism; D015951:Factor Xa / Q000378:metabolism; D008024:Ligands; D008958:Models, Molecular; D018583:Pliability; D011485:Protein Binding; D011487:Protein Conformation; D012984:Software; D013329:Structure-Activity Relationship
D004791:Enzyme Inhibitors; D008024:Ligands; D051357:Cyclin-Dependent Kinase 2; D015951:Factor Xa