title: Multipolar interactions in the D pocket of thrombin: large differences between tricyclic imide and lactam inhibitors.
abstract: Two series of tricyclic inhibitors of the serine protease thrombin, imides (+/-)-1-(+/-)-8 and lactams (+/-)-9-(+/-)-13, were analysed to evaluate contributions of orthogonal multipolar interactions with the backbone C=O moiety of Asn98 to the free enthalpy of protein-ligand complexation. The lactam derivatives are much more potent and more selective inhibitors (K(i) values between 0.065 and 0.005 microM, selectivity for thrombin over trypsin between 361- and 1609-fold) than the imide compounds (Ki values between 0.057 and 23.7 microM, selectivity for thrombin over trypsin between 3- and 67-fold). The increase in potency and selectivity is explained by the favorable occupancy of the P-pocket of thrombin by the additional isopropyl substituent in the lactam derivatives. The nature of the substituent on the benzyl ring filling the D pocket strongly influences binding potency in the imide series, with Ki values increasing in the sequence: F < OCH2O < Cl < H < OMe < OH < N(pyr)<< Br. This sequence can be explained by both steric fit and the occurrence of orthogonal multipolar interactions with the backbone C[double bond, length as m-dash]O moiety of Asn98. In contrast, the substituent on the benzyl ring hardly affects the ligand potency in the lactam series. This discrepancy was clarified by the comparison of X-ray structures solved for co-crystals of thrombin with imide and lactam ligands. Whereas the benzyl substituents in the imide inhibitors are sufficiently close (< or =3.5 Angstroms) to the C=O group of Asn98 to allow for attractive orthogonal multipolar interactions, the distances in the lactam series are too large (> or =4 Angstroms) for attractive dipolar contacts to be effective.
authors.affiliation: Laboratorium für Organische Chemie, ETH-Zürich, Hönggerberg HCI, Switzerland.
authors.forename: Eliane
authors.initials: E
authors.lastname: Schweizer
authors.forename: Anja
authors.initials: A
authors.lastname: Hoffmann-Röder
authors.forename: Jacob A
authors.initials: JA
authors.lastname: Olsen
authors.forename: Paul
authors.initials: P
authors.lastname: Seiler
authors.forename: Ulrike
authors.initials: U
authors.lastname: Obst-Sander
authors.forename: Björn
authors.initials: B
authors.lastname: Wagner
authors.forename: Manfred
authors.initials: M
authors.lastname: Kansy
authors.forename: David W
authors.initials: DW
authors.lastname: Banner
authors.forename: François
authors.initials: F
authors.lastname: Diederich
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D003500:Cyclization; D007094:Imides / Q000737:chemistry* / Q000494:pharmacology; D007700:Kinetics; D007769:Lactams / Q000737:chemistry* / Q000494:pharmacology; D008956:Models, Chemical; D011485:Protein Binding; D015842:Serine Proteinase Inhibitors / Q000737:chemistry* / Q000494:pharmacology; D013917:Thrombin / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism
chemical_list: D007094:Imides; D007769:Lactams; D015842:Serine Proteinase Inhibitors; D013917:Thrombin