Mapping and Fitting the Peripheral Benzodiazepine Receptor Binding Site by Carboxamide Derivatives. Comparison of Different Approaches to Quantitative Ligand-Receptor Interaction Modeling Maurizio Anzini,* ,§ Andrea Cappelli,* ,‡ Salvatore Vomero, ‡ Michele Seeber, $ Maria Cristina Menziani, $ Thierry Langer, † Bertram Hagen, † Cristina Manzoni, # and Jean-Jacques Bourguignon ∧ Dipartimento di Scienze Farmacobiologiche, Universita ` degli Studi “Magna Graecia” di Catanzaro, Complesso “Ninı ` Barbieri”, 88021 Roccelletta di Borgia, Catanzaro, Italy, Dipartimento Farmaco Chimico Tecnologico, Universita ` di Siena, Via A. Moro, 53100 Siena, Italy, Dipartimento di Chimica, Universita ` degli Studi di Modena, Via Campi 183, 41100 Modena, Italy, Institute of Pharmaceutical Chemistry, University of Innsbruck, Innrain 52A, A-6020, Innsbruck, Austria, Istituto di Ricerche Farmacologiche “Mario Negri”, Via Eritrea, 62, 20157 Milano, Italy, and Laboratoire de Pharmacochimie de la Communication Cellulaire (UMR 7081), Universite ´ Louis Pasteur, 74 Route du Rhin, 67401 Illkirch Cedex, France Received April 28, 2000 The synthetic-computational approach to the study of the binding site of peripheral benzodi- azepine receptor (PBR) ligands related to 1-(2-chlorophenyl)-N-methyl-N-(1-methylpropyl)-3- isoquinolinecarboxamide (PK11195, 1) within their receptor (Cappelli et al. J. Med. Chem. 1997, 40, 2910-2921) has been extended. A series of carboxamide derivatives endowed with differently substituted planar aromatic or heteroaromatic systems was designed with the aim of getting further information on the topological requisites of the carbonyl and aromatic moieties for interaction with the PBR binding site. The synthesis of most of these compounds involves Weinreb amidation of the appropriate lactone as the key step. The most potent compound, among the newly synthesized ones, shows a nanomolar PBR affinity similar to that shown by 1 and the presence of a basic N-ethyl-N-benzylaminomethyl group in 3-position of the quinoline nucleus. Thus, it may be considered the first example of a new class of water soluble derivatives of 1. Several computational methods were used to furnish descriptors of the isolated ligands (indirect approaches) able to rationalize the variation in the binding affinity of the enlarged series of compounds. Sound QSAR models are obtained by size and shape descriptors (volume approach) which codify for the short-range contributions to ligand-receptor interactions. Molecular descriptors which explicitly account for the electrostatic contribution to the interaction (CoMFA, CoMSIA, and surface approaches) perform well, but they do not improve the quantitative models. Moreover, useful hints for the identification of the antagonist binding site in the three-dimensional modeling of the receptor (direct approach) were provided by the receptor hypothesis derived by the pharmacophoric approach. The ligand-receptor complexes obtained provided a detailed description of the modalities of the interaction and interesting suggestions for further experiments. Introduction After the discovery of benzodiazepine binding sites in the periphery (peripheral benzodiazepine receptor, PBR), intensive research devoted to the characterization of this receptor has been undertaken. 1 PBR has been primarily found on the mitochondrial outer membrane even if a nonmitochondrial localization in some cells has been suggested. Although the physiological role of PBR is still unclear, a wide range of pharmacological activities, such as anticonvulsant, anxiolytic, immunomodulating, and cardiovascular, has been related to its activation. 2 In particular, this receptor appears to be involved in steroidogenesis, the regulation of which represents a potential clinical application of PBR ligands. 3 Human, bovine, rat, and murine PBR have been isolated, cloned, and sequenced. 4 However, the crystal- lographic structure is not yet available, since its close association to the membrane makes this protein difficult to isolate, purify, and crystallize in its native form. Models of the secondary 5 and tertiary 6 structure of the PBR available in the literature are essentially concerned with the transmembrane region (TM), which consists of five R-helices composed of 21 hydrophobic residues. The N-terminus of the sequence is located in the mitochondrial domain, while the C-terminus is exposed to the cytoplasm. The transmembrane regions are connected by loops rich in hydrophilic residues. Furthermore, recently reported site-directed mutagen- esis studies demonstrated that the portion of the recep- tor involved in the interaction with the ligands mainly consists of the first cytoplasmic loop and that agonists and antagonists bind the receptor in different, albeit partly overlapping, sites. 7 * To whom correspondence should be addressed. Anzini, M. Tel: +39 961 391157. Fax: +39 961 391490. E-mail: anzini@unicz.it. Cappelli, A. Tel: +39 577 234320. Fax: +39 577 234333. E-mail: cappelli@unisi.it. § Dipartimento di Scienze Farmacobiologiche, Universita ` “Magna Graecia” di Catanzaro. ‡ Dipartimento Farmaco Chimico Tecnologico, Universita ` di Siena. $ Dipartimento di Chimica, Universita ` degli Studi di Modena. † Institute of Pharmaceutical Chemistry, University of Innsbruck. # Istituto di Ricerche Farmacologiche “Mario Negri”. ∧ Laboratoire de Pharmacochimie de la Communication Celluleire, Universite ´ Louis Pasteur. 1134 J. Med. Chem. 2001, 44, 1134-1150 10.1021/jm0009742 CCC: $20.00 © 2001 American Chemical Society Published on Web 03/20/2001