title: On-the-Fly Integration of Data from a Spin-Diffusion-Based NMR Experiment into Protein-Ligand Docking.
abstract: INPHARMA (interligand nuclear Overhauser enhancement for pharmacophore mapping) determines the relative orientation of two competitive ligands in the protein binding pocket. It is based on the observation of interligand transferred NOEs mediated by spin diffusion through protons of the protein and is, therefore, sensitive to the specific interactions of each of the two ligands with the protein. We show how this information can be directly included into a protein-ligand docking program to guide the prediction of the complex structures. Agreement between the experimental and back-calculated spectra based on the full relaxation matrix approach is translated into a score contribution that is combined with the scoring function ChemPLP of our docking tool PLANTS. This combined score is then used to predict the poses of five weakly bound cAMP-dependent protein kinase (PKA) ligands. After optimizing the setup, which finally also included trNOE data and optimized protonation states, very good success rates were obtained for all combinations of three ligands. For one additional ligand, no conclusive results could be obtained due to the ambiguous electron density of the ligand in the X-ray structure, which does not disprove alternative ligand poses. The failures of the remaining ligand are caused by suboptimal locations of specific protein side chains. Therefore, side-chain flexibility should be included in an improved INPHARMA-PLANTS version. This will reduce the strong dependence on the used protein input structure leading to improved scores overall, not only for this last ligand.
authors.affiliation: Institute of Pharmacy, Eberhard Karls Universität Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.|Department of Chemistry and Zukunftskolleg, Universität Konstanz , 78457 Konstanz, Germany.
authors.forename: Ionut
authors.initials: I
authors.lastname: Onila
authors.affiliation: Department of Chemistry and Zukunftskolleg, Universität Konstanz , 78457 Konstanz, Germany.
authors.forename: Tim
authors.initials: T
authors.lastname: ten Brink
authors.affiliation: Institute of Pharmacy, Eberhard Karls Universität Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.|Department of Chemistry and Zukunftskolleg, Universität Konstanz , 78457 Konstanz, Germany.
authors.forename: Kai
authors.initials: K
authors.lastname: Fredriksson
authors.affiliation: Structural and Computational Biology Unit, EMBL , Meyerhofstrasse 1, 69117 Heidelberg, Germany.
authors.forename: Luca
authors.initials: L
authors.lastname: Codutti
authors.affiliation: Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Adam
authors.initials: A
authors.lastname: Mazur
authors.affiliation: Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Griesinger
authors.affiliation: Structural and Computational Biology Unit, EMBL , Meyerhofstrasse 1, 69117 Heidelberg, Germany.|Helmholtz Centre for Infection Research , Inhoffenstraße 7, 38124 Braunschweig, Germany.
authors.forename: Teresa
authors.initials: T
authors.lastname: Carlomagno
authors.affiliation: Institute of Pharmacy, Eberhard Karls Universität Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.|Department of Chemistry and Zukunftskolleg, Universität Konstanz , 78457 Konstanz, Germany.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Exner
mesh_terms: D008024:Ligands; D008279:Magnetic Resonance Imaging; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D011494:Protein Kinases / Q000737:chemistry; D011506:Proteins / Q000737:chemistry*
chemical_list: D008024:Ligands; D011506:Proteins; D011494:Protein Kinases