New probes of ligand flexibility in drug design: transferred (13)C CSA-dipolar cross-correlated relaxation at natural abundance.
Understanding the impact of molecular flexibility remains an important outstanding problem in rational drug design. Toward this end, we present new NMR relaxation methods that describe ligand flexibility at the atomic level. Specifically, we measure natural abundance (13)C cross-correlated relaxation parameters for ligands in rapid exchange between the free and receptor-bound states. The rapid exchange transfers the bound state relaxation parameters to the free state, such that a comparison of relaxation rates in the absence and presence of protein receptor yields site-specific information concerning the bound ligand flexibility. We perform these measurements for aromatic carbons, which are highly prevalent in drug-like molecules and demonstrate significant cross-correlated relaxation between the (13)C-(1)H dipole-dipole (DD) and (13)C chemical shift anisotropy (CSA) relaxation mechanisms. Our use of natural abundance measurements addresses the practical difficulties of obtaining isotope-labeled ligands in pharmaceutical research settings. We demonstrate our methods on a small ligand of the 42 kDa kinase domain of the p38 MAP kinase. We show that exchange-transferred cross-correlated relaxation measurements are not only sensitive probes of bound ligand flexibility but also offer complementary advantages over standard R(1) = 1/T(1) and R(2) = 1/T(2) measurements. The ligand flexibility profiles obtained from the relaxation data can help assess the influence of dynamics on ligand potency or pharmacokinetic properties or both, and thereby include inherent molecular flexibility in drug design.
Peng
Jeffrey W
JW
Vertex Pharmaceuticals, Inc, 130 Waverly Street, Cambridge, Massachusetts 02139, USA. Jeffrey.W.Peng.6@nd.edu
D016880:Anisotropy; D001565:Benzoates / Q000737:chemistry / Q000378:metabolism; D002247:Carbon Isotopes; D015195:Drug Design; D007700:Kinetics; D008024:Ligands; D020928:Mitogen-Activated Protein Kinases / Q000737:chemistry / Q000378:metabolism; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D048051:p38 Mitogen-Activated Protein Kinases
D001565:Benzoates; D002247:Carbon Isotopes; D008024:Ligands; D020928:Mitogen-Activated Protein Kinases; D048051:p38 Mitogen-Activated Protein Kinases