title: Charges Shift Protonation: Neutron Diffraction Reveals that Aniline and 2-Aminopyridine Become Protonated Upon Binding to Trypsin.
abstract: Hydrogen atoms play a key role in protein-ligand recognition. They determine the quality of established H-bonding networks and define the protonation of bound ligands. Structural visualization of H atoms by X-ray crystallography is rarely possible. We used neutron diffraction to determine the positions of the hydrogen atoms in the ligands aniline and 2-aminopyridine bound to the archetypical serine protease trypsin. The resulting structures show the best resolution so far achieved for proteins larger than 100 residues and allow an accurate description of the protonation states and interactions with nearby water molecules. Despite its low pKaof 4.6 and a large distance of 3.6 Å to the charged Asp189 at the bottom of the S1 pocket, the amino group of aniline becomes protonated, whereas in 2-aminopyridine, the pyridine nitrogen picks up the proton although its amino group is 1.6 Å closer to Asp189. Therefore, apart from charge-charge distances, tautomer stability is decisive for the resulting binding poses, an aspect that is pivotal for predicting correct binding.
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.|CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.
authors.forename: Johannes
authors.initials: J
authors.lastname: Schiebel
authors.affiliation: CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.
authors.forename: Roberto
authors.initials: R
authors.lastname: Gaspari
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Sandner
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
authors.forename: Khang
authors.initials: K
authors.lastname: Ngo
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
authors.forename: Hans-Dieter
authors.initials: HD
authors.lastname: Gerber
authors.affiliation: CompuNet, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genova, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Cavalli
authors.affiliation: Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstraße 1, 85748, Garching, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Ostermann
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Heine
authors.affiliation: Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
authors.forename: Gerhard
authors.identifier: 0000-0002-4913-390X
authors.initials: G
authors.lastname: Klebe
mesh_terms: D000631:Aminopyridines / Q000737:chemistry* / Q000494:pharmacology*; D000814:Aniline Compounds / Q000737:chemistry* / Q000494:pharmacology*; D055808:Drug Discovery; D006801:Humans; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D033363:Neutron Diffraction; D011522:Protons; D014357:Trypsin / Q000737:chemistry / Q000378:metabolism*; D014361:Trypsin Inhibitors / Q000737:chemistry / Q000494:pharmacology
chemical_list: D000631:Aminopyridines; D000814:Aniline Compounds; D008024:Ligands; D011522:Protons; D014361:Trypsin Inhibitors; D014357:Trypsin; C023650:aniline; C032439:alpha-aminopyridine
keywords: biophysics; drug discovery; medicinal chemistry; neutron crystallography; protonation state