Pier G. De Benedetti

Amino acids of the α1B-adrenergic receptor involved in agonist binding: differences in docking catecholamines to receptor subtypes

Site‐directed mutagenesis and molecular dynamics analysis of the 3‐D model of the α 1B ‐adrenergic receptor (AR) were combined to identify the molecular determinants of the receptor involved in catecholamine binding. Our results indicate that the three conserved serines in the fifth transmembrane domain (TMD) of the α 1B‐AR play a distinct role in catecholamine binding versus receptor activation. In addition to the amino acids D125 in TMDIII and S207 in TMDV directly involved in ligand binding, our findings identify a large number of polar residues playing an important role in the activation process of the α 1B‐AR thus providing new insights into the structure/function relationship of G protein‐coupled receptors.

Update 1 of: Computational Modeling Approaches to Structure–Function Analysis of G Protein-Coupled Receptors

Update 1 of: Computational Modeling Approaches to Structure Function Analysis of G Protein-Coupled Receptors Francesca Fanelli* and Pier G. De Benedetti DulbeccoTelethon Institute and Department ofChemistry, University ofModena and Reggio Emilia, via Campi 183, 41125Modena, Italy This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev., 2005, 105(9), 3297 3351, DOI: 10.1021/cr000095n; Published August 25, 2005. Updates to the text appear in red type.

Theoretical investigation of substrate specificity for cytochromes P450 IA2, P450 IID6 and P450 IIIA4.

Three-dimensional models of the cytochromes P450 IA2, P450 IID6 and P450 IIIA4 were built by means of comparative modeling using the X-ray crystallographic structures of P450 CAM, P450 BM-3, P450 TERP and P450 ERYF as templates. The three cytochromes were analyzed both in their intrinsic structural features and in their interaction properties with fifty specific and non-specific substrates. Substrate/enzyme complexes were obtained by means of both automated rigid and flexible body docking. The comparative analysis of the three cytochromes and the selected substrates, in their free and bound forms, allowed for the building of semi-quantitative models of substrate specificity based on both molecular and intermolecular interaction descriptors. The results of this study provide new insights into the molecular determinants of substrate specificity for the three different eukaryotic P450 isozymes and constitute a useful tool for predicting the specificity of new compounds.

Development of Quantitative Structure−Property Relationships Using Calculated Descriptors for the Prediction of the Physicochemical Properties (nD, ρ, bp, ε, η) of a Series of Organic Solvents

Quantitative structure−property relationship (QSPR) models were derived for predicting boiling point (at 760 mmHg), density (at 25 °C), viscosity (at 25 °C), static dielectric constant (at 25 °C), and refractive index (at 20 °C) of a series of pure organic solvents of structural formula X−CH2CH2−Y. A very large number of calculated molecular descriptors were derived by quantum chemical methods, molecular topology, and molecular geometry by using the CODESSA software package. A comparative analysis of the multiple linear regression techniques (heuristic and best multilinear regression) implemented in CODESSA, with the multivariate PLS/GOLPE method, has been carried out. The performance of the different regression models has been evaluated by the standard deviation of prediction errors, calculated for the compounds of both the training set (internal validation) and the test set (external validation). Satisfactory QSPR models, from both predictive and interpretative point of views, have been obtained for all...

Synthesis, Screening, and Molecular Modeling of New Potent and Selective Antagonists at the α1d Adrenergic Receptor

In the present study, more than 75 compounds structurally related to BMY 7378 have been designed and synthesized. Structural variations of each part of the reference molecule have been introduced, obtaining highly selective ligands for the alpha(1d) adrenergic receptor. The molecular determinants for selectivity at this receptor are essentially held by the phenyl substituent in the phenylpiperazine moiety. The integration of an extensive SAR analysis with docking simulations using the rhodopsin-based models of the three alpha(1)-AR subtypes and of the 5-HT(1A) receptor provides significant insights into the characterization of the receptor binding sites as well as into the molecular determinants of ligand selectivity at the alpha(1d)-AR and the 5-HT(1A) receptors. The results of multiple copies simultaneous search (MCSS) on the substituted phenylpiperazines together with those of manual docking of compounds BMY 7378 and 69 into the putative binding sites of the alpha(1a)-AR, alpha(1b)-AR, alpha(1d)-AR, and the 5-HT(1A) receptors suggest that the phenylpiperazine moiety would dock into a site formed by amino acids in helices 3, 4, 5, 6 and extracellular loop 2 (E2), whereas the spirocyclic ring of the ligand docks into a site formed by amino acids of helices 1, 2, 3, and 7. This docking mode is consistent with the SAR data produced in this work. Furthermore, the binding site of the imide moiety does not allow for the simultaneous involvement of the two carbonyl oxygen atoms in H-bonding interactions, consistent with the SAR data, in particular with the results obtained with the lactam derivative 128. The results of docking simulations also suggest that the second and third extracellular loops may act as selectivity filters for the substituted phenylpiperazines. The most potent and selective compounds for alpha(1d) adrenergic receptor, i.e., 69 (Rec 26D/038) and 128 (Rec 26D/073), are characterized by the presence of the 2,5-dichlorophenylpiperazine moiety.

Theoretical study of the electrostatically driven step of receptor-G protein recognition

This study proposes a theoretical model describing the electrostatically driven step of the α1b‐adrenergic receptor (AR)‐G protein recognition. The comparative analysis of the structural‐dynamics features of functionally different receptor forms, i.e., the wild type (ground state) and its constitutively active mutants D142A and A293E, was instrumental to gain insight on the receptor‐G protein electrostatic and steric complementarity. Rigid body docking simulations between the different forms of the α1b‐AR and the heterotrimeric Gαq, Gαs, Gαi1, and Gαt suggest that the cytosolic crevice shared by the active receptor and including the second and the third intracellular loops as well as the cytosolic extension of helices 5 and 6, represents the receptor surface with docking complementarity with the G protein. On the other hand, the G protein solvent‐exposed portions that recognize the intracellular loops of the activated receptors are the N‐terminal portion of α3, αG, the αG/α4 loop, α4, the α4/β6 loop, α5, and the C‐terminus. Docking simulations suggest that the two constitutively active mutants D142A and A293E recognize different G proteins with similar selectivity orders, i.e., Gαq  ≈= Gαs > Gαi > > Gαt. The theoretical models herein proposed might provide useful suggestions for new experiments aiming at exploring the receptor‐G protein interface. Proteins 1999;37:145–156. ©1999 Wiley‐Liss, Inc.

Mechanisms of Inter- and Intramolecular Communication in GPCRs and G Proteins

This study represents the first attempt to couple, by computational experiments, the mechanisms of intramolecular and intermolecular communication concerning a guanidine nucleotide exchange factor (GEF), the thromboxane A2 receptor (TXA2R), and the cognate G protein (Gq) in its heterotrimeric GDP-bound state. Two-way pathways mediate the communication between the receptor-G protein interface and both the agonist binding site of the receptor and the nucleotide binding site of the G protein. The increase in solvent accessibility in the neighborhoods of the highly conserved E/DRY receptor motif, in response to agonist binding, is instrumental in favoring the penetration of the C-terminus of Gqalpha in between the cytosolic ends of H3, H5, and H6. The arginine of the E/DRY motif is predicted to be an important mediator of the intramolecular and intermolecular communication involving the TXA2R. The receptor-G protein interface is predicted to involve multiple regions from the receptor and the G protein alpha-subunit. However, receptor contacts with the C-terminus of the alpha5-helix seem to be the major players in the receptor-catalyzed motion of the alpha-helical domain with respect to the Ras-like domain and in the formation of a nucleotide exit route in between the alphaF-helix and beta6/alpha5 loop of Gqalpha. The inferences from this study are of wide interest, as they are expected to apply to the whole rhodopsin family, given also the considerable G protein promiscuity.

Novel Potent 5-HT3 Receptor Ligands Based on the Pyrrolidone Structure: Synthesis, Biological Evaluation, and Computational Rationalization of the Ligand–Receptor Interaction Modalities

Novel conformationally constrained derivatives of classical 5-HT(3) receptor antagonists were designed and synthesized with the aim of probing the central 5-HT(3) receptor recognition site in a systematic way. The newly-synthesized compounds were tested for their potential ability to inhibit [(3)H]granisetron specific binding to 5-HT(3) receptor in rat cortical membranes. These studies revealed subnanomolar affinity in some of the compounds under study. The most potent ligand in this series was found to be quinuclidine derivative (S)-7i, which showed an affinity comparable with that of the reference ligand granisetron. The potential 5-HT(3) agonist/antagonist activity of some selected compounds was assessed in vitro on the 5-HT(3) receptor-dependent [(14)C]guanidinium uptake in NG 108-15 cells. Both of the tropane derivatives tested in this functional assay (7a and 9a) showed antagonist properties, while the quinuclidine derivatives studied [the enantiomers of compounds 7i, 8g, and 9g, and compound (R)-8h] showed a full range of intrinsic efficacies. Therefore, the functional behavior of these 5-HT(3) receptor ligands appears to be affected by the structural features of both the azabicyclo moiety and the heteroaromatic portion. In agreement with the data obtained on NG 108-15 cells, investigations on the 5-HT(3) receptor-dependent Bezold-Jarisch reflex in urethane-anaesthetized rats confirmed the 5-HT(3) receptor antagonist properties of compounds 7a and (S)-7i showing for these compounds ID(50) values of 2.8 and 181 microg/kg, respectively. Finally, compounds 7a, (S)-7i and 9a (at the doses of 0.01, 1.0, and 0.01 mg/kg ip, respectively) prevented scopolamine-induced amnesia in the mouse passive avoidance test suggestive of a potential usefulness in cognitive disorders for these compounds. Qualitative and quantitative structure-affinity relationship studies were carried out by means of theoretical descriptors derived on a single structure and ad-hoc defined size and shape descriptors (indirect approach). The results showed to be useful in capturing information relevant to ligand-receptor interaction. Additional information derived by the analysis of the energy minimized 3-D structures of the ligand-receptor complexes (direct approach) suggested interesting mechanistic and methodological considerations on the binding mode multiplicity at the 5-HT(3) receptors and on the degree of tolerance allowed in the alignment of molecules for the indirect approach, respectively.

Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling.

Herein we make an overview of the results of our computational experiments aimed at gaining insight into the molecular mechanisms of GPCR functioning either in their normal conditions or when hit by gain-of-function or loss-of-function mutations. Molecular simulations of a number of GPCRs in their wild type and mutated as well as free and ligand-bound forms were instrumental in inferring the structural features, which differentiate the mutation- and ligand-induced active from the inactive states. These features essentially reside in the interaction pattern of the E/DRY arginine and in the degree of solvent exposure of selected cytosolic domains. Indeed, the active states differ from the inactive ones in the weakening of the interactions made by the highly conserved arginine and in the increase in solvent accessibility of the cytosolic interface between helices 3 and 6. Where possible, the structural hallmarks of the active and inactive receptor states are translated into molecular descriptors useful for in silico functional screening of novel receptor mutants or ligands. Computational modeling of the supramolecular organization of GPCRs and their intracellular partners is the current challenge toward a deep understanding of their functioning mechanisms.

The Interactions of the 5-HT3 Receptor with Arylpiperazine, Tropane, and Quinuclidine Ligands

The serotonin 5-HT(3) receptor subtype is unique among the receptors for this neurotransmitter because it has been demonstrated to be a ligand-gated ion channel capable of mediating rapid intercellular communication. This review covers the authors work performed during more than a decade in the development of 5-HT(3) receptor ligands belonging to the classes of arylpiperazines, tropanes, and quinuclidine derivatives. The discussion is focused mainly on what the authors have learned about the interaction of these structurally different ligands with their receptor and shows the way their ideas evolved along with the progress of the project. Furthermore, a summary of the most significant structure-affinity relationships, derived from the original work, is reported to support the discussion.