title: Pocket-space maps to identify novel binding-site conformations in proteins.
abstract: The identification of novel binding-site conformations can greatly assist the progress of structure-based ligand design projects. Diverse pocket shapes drive medicinal chemistry to explore a broader chemical space and thus present additional opportunities to overcome key drug discovery issues such as potency, selectivity, toxicity, and pharmacokinetics. We report a new automated approach to diverse pocket selection, PocketAnalyzer(PCA), which applies principal component analysis and clustering to the output of a grid-based pocket detection algorithm. Since the approach works directly with pocket shape descriptors, it is free from some of the problems hampering methods that are based on proxy shape descriptors, e.g. a set of atomic positional coordinates. The approach is technically straightforward and allows simultaneous analysis of mutants, isoforms, and protein structures derived from multiple sources with different residue numbering schemes. The PocketAnalyzer(PCA) approach is illustrated by the compilation of diverse sets of pocket shapes for aldose reductase and viral neuraminidase. In both cases this allows identification of novel computationally derived binding-site conformations that are yet to be observed crystallographically. Indeed, known inhibitors capable of exploiting these novel binding-site conformations are subsequently identified, thereby demonstrating the utility of PocketAnalyzer(PCA) for rationalizing and improving the understanding of the molecular basis of protein-ligand interaction and bioactivity. A Python program implementing the PocketAnalyzer(PCA) approach is available for download under an open-source license ( http://sourceforge.net/projects/papca/  or  http://cpclab.uni-duesseldorf.de/downloads ).
authors.affiliation: Novartis Institutes for Biomedical Research, Wimblehurst Road, Horsham, West Sussex RH12 5AB, UK. ianrcraig@gmail.com.
authors.forename: Ian R
authors.initials: IR
authors.lastname: Craig
authors.forename: Christopher
authors.initials: C
authors.lastname: Pfleger
authors.forename: Holger
authors.initials: H
authors.lastname: Gohlke
authors.forename: Jonathan W
authors.initials: JW
authors.lastname: Essex
authors.forename: Katrin
authors.initials: K
authors.lastname: Spiegel
mesh_terms: D000449:Aldehyde Reductase / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D000465:Algorithms; D001665:Binding Sites; D020134:Catalytic Domain; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology; D056004:Molecular Dynamics Simulation; D009439:Neuraminidase / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D025341:Principal Component Analysis; D011506:Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D004791:Enzyme Inhibitors; D011506:Proteins; D000449:Aldehyde Reductase; D009439:Neuraminidase