Modeling the binding affinity of p38α MAP kinase inhibitors by partial least squares regression.

The p38 mitogen-activated protein kinase is activated by environmental stress and cytokines and plays a role in transcriptional regulation and inflammatory responses. Factors influencing the activity and selectivity of the p38α mitogen-activated protein kinase inhibitors have been investigated in this paper by inspecting the binding orientation and the possible residue-inhibitor interactions in the binding site. The binding pattern of a set of 45 different inhibitors against p38α mitogen-activated protein kinase was studied through Molecular Dynamic Simulations of the protein-inhibitor complexes. Further, Partial Least Squares regression was used to develop a Quantitative Structure Activity Relationship model to predict the binding affinities of ligands. The selected model successfully predicted the test set with a Root Mean Square Error of Prediction of 1.36. The regression coefficients and the Variable Importance in Projection plots highlighted the residue-inhibitor interactions which exhibited the largest absolute effect on the ligand binding, such as the van der Waals interaction with LYS50, ILE81, ASP165; electrostatic interactions with SER29, LEU164; hydrogen bonds with MET106; and total energy interaction with SER29 and LEU83.

Bivalent Ligands for the Serotonin 5-HT3 Receptor.

The serotonin 5-HT3 receptor is a ligand-gated ion channel, which by virtue of its pentameric architecture, can be considered to be an intriguing example of intrinsically multivalent biological receptors. This paper describes a general design approach to the study of multivalency in this multimeric ion channel. Bivalent ligands for 5-HT3 receptor have been designed by linking an arylpiperazine moiety to probes showing different functional features. Both homobivalent and heterobivalent ligands have shown 5-HT3 receptor affinity in the nanomolar range, providing evidence for the viability of our design approach. Moreover, the high affinity shown by homobivalent ligands suggests that bivalency is a promising approach in 5-HT3 receptor modulation and provides the rational basis for applying the concepts of multivalency to the study of 5-HT3 receptor function.

Insights into MAPK p38alpha DFG flip mechanism by accelerated molecular dynamics.

The DFG motif at the beginning of the activation loop of the MAPK p38alpha undergoes a local structural reorganization upon binding of allosteric type-II and type-III inhibitors, which causes the residue F169 to move from a buried conformation (defined as DFG-in) to a solvent exposed conformation (defined as DFG-out). Although both experimental and computer simulation studies had been performed with the aim of unveiling the details of the DFG-in to DFG-out transition, the molecular mechanism is still far from being unequivocally depicted. Here, the accelerated molecular dynamics (AMD) technique has been applied to model the active loop flexibility of p38alpha and sample special protein conformations which can be accessible only in some conditions or time periods. Starting from the assumption of an experimentally known initial and final state of the protein, the study allowed the description of the interaction network and the structural intermediates which lead the protein to change its loop conformation and active site accessibility. Besides a few important hydrogen bond interactions, a primary role seems to be played by cation-pi interactions, involving the DFG-loop residue F(169), which participate in the stabilization of an intermediate conformation and in its consequent transition to the DFG-out conformation. From this study, insights which may prove useful for inhibitor design and/or site directed mutagenesis studies are derived.

A new self-consistent empirical interatomic potential model for oxides, silicates, and silica-based glasses.

A new empirical pairwise potential model for ionic and semi-ionic oxides has been developed. Its transferability and reliability have been demonstrated by testing the potentials toward the prediction of structural and mechanical properties of a wide range of silicates of technological and geological importance. The partial ionic charge model with a Morse function is used, and it allows the modeling of the quenching of melts, silicate glasses, and inorganic crystals at high-pressure and high-temperature conditions. The results obtained by molecular dynamics and free energy calculations are discussed in relation to the prediction of structural and mechanical properties of a series of soda lime silicate glasses.

A computational protocol to probe the role of solvation effects on the reduction potential of azurin mutants.

Semiquantitative relationships between thermodynamic parameters of Cu2+ reduction experimentally measured for a series of azurin mutants and the solvation free energy of the oxidized state of the proteins were derived. Solvation free energy calculations were carried out within an ONIOM/PCM scheme specifically adapted to this protein series. The method proved to be able to capture the main determinants of the measured reduction parameters, providing satisfactory predictions of the E degrees '.

Further studies on the interaction of the 5-hydroxytryptamine3 (5-HT3) receptor with arylpiperazine ligands. development of a new 5-HT3 receptor ligand showing potent acetylcholinesterase inhibitory properties.

Novel arylpiperazine derivatives bearing lipophilic probes were designed, synthesized, and evaluated for their potential ability to interact with the 5-hydroxytryptamine(3) (5-HT(3)) receptor. Most of the new compounds show subnanomolar 5-HT(3) receptor affinity. Ester 6bc showing a picomolar K(i) value is one of the most potent 5-HT(3) receptor ligands so far synthesized. The structure-affinity relationship study suggests the existence of a certain degree of conformational freedom of the amino acid residues interacting with the substituents in positions 3 and 4 of the quipazine quinoline nucleus. Thus, the tacrine-related heterobivalent ligand 6o was designed in an attempt to capitalize on the evidence of such a steric tolerance. Compound 6o shows a nanomolar potency for both the 5-HT(3) receptor and the human AChE and represents the first example of a rationally designed high-affinity 5-HT(3) receptor ligand showing nanomolar AChE inhibitory activity. Finally, the computational analysis performed on compound 6o allowed the rationalization of the structure-energy determinants for AChE versus BuChE selectivity and revealed the existence of a subsite at the boundary of the 5-HT(3) receptor extracellular domain, which could represent a "peripheral" site similar to that evidenced in the AChE gorge.

A computational tool for the prediction of crystalline phases obtained from controlled crystallization of glasses.

An automatic tool (named CLUSTER) for the prediction of the most probable crystal phases that can separate from glasses has been developed. The program analyzes the output of molecular dynamics simulations of glasses or glass ceramics, systematically sampling the ratios of the ions in different portions of the simulation box and comparing them to the stoichiometric ratio of compositionally equivalent crystalline phases retrieved from a crystal structure database. The efficacy of the similarity index elaborated has been judged by comparing the results obtained with the crystal phases identified by XRD analysis after thermal treatment in a series of multicomponent potential bioactive glasses and glass ceramics for which the advantages of rational-designed erosion-controlled release is straightforward.

Qualitative and quantitative structure-property relationships analysis of multicomponent potential bioglasses.

The results of a qualitative and quantitative structure-property relationships analysis of multicomponent potential bioglasses of composition (2 - y) SiO2 x 1 Na2O x 1.1 CaO x y P2O5 x x ZnO (x = 0, 0.16, 0.35, 0.78 and y = 0.10, 0.20, 0.36) are presented. Quantitative models are obtained by means of structural descriptors derived by molecular dynamics simulations and experimental data measured for density, thermal analysis, 29Si and 31P magic angle spinning NMR, and chemical durability in water. Analysis of the crystal species obtained upon glass crystallization helped in the rationalization of the structural role of the different components. Finally, glass surface characterization with scanning electron microscopy, transmission electron microscopy, and X-ray diffraction after soaking in acellular simulated body fluid demonstrated the in vitro bioactivity of the newly obtained 1.80 SiO2 x 1 Na2O x 1.1 Ca x 0.20 P2O5 x 0.16 ZnO (HP5Z5) glass, corresponding to x = 0.16 and y = 0.20.

Design, synthesis, structural studies, biological evaluation, and computational simulations of novel potent AT(1) angiotensin II receptor antagonists based on the 4-phenylquinoline structure.

Novel AT(1) receptor antagonists bearing substituted 4-phenylquinoline moieties instead of the classical biphenyl fragment were designed and synthesized as the first step of an investigation devoted to the development of new antihypertensive agents and to the understanding of the molecular basis of their pharmacodynamic and pharmacokinetic properties. The newly synthesized compounds were tested for their potential ability to displace [(125)I]Sar(1),Ile(8)-Ang II specifically bound to AT(1) receptor in rat hepatic membranes. These AT(1) receptor binding studies revealed nanomolar affinity in several of the compounds under study. The most potent ligands 4b,t were found to be equipotent with losartan and possessed either a 3-tetrazolylquinoline or a 2-amino-3-quinolinecarboxylic moiety, respectively. Moreover, some selected compounds were evaluated for antagonism of Ang II-induced contraction in rabbit aortic strips, and the most potent compounds in the binding test 4b,t were slightly more potent than losartan in inhibiting Ang II-induced contraction. Finally, the most relevant structure-affinity relationship data were rationalized by means of computational studies performed on the isolated ligands as well as by computational simulations on the ligands complexed with a theoretical AT(1) receptor model.

Synthesis, biological evaluation, and receptor docking simulations of 2-[(acylamino)ethyl]-1,4-benzodiazepines as kappa-opioid receptor agonists endowed with antinociceptive and antiamnesic activity.

The synthesis and biological evaluation of a series of new derivatives of 2-substituted 5-phenyl-1,4-benzodiazepines, structurally related to tifluadom (5), are reported. Chemical and pharmacological studies on compounds 6 have been pursued with the aim of expanding the SAR data and validating the previously proposed model of interaction of this class of compounds with the kappa-opioid receptor. The synthesis of the previously described compounds 6 has been reinvestigated in order to obtain a more direct synthetic procedure. To study the relationship between the stereochemistry and the receptor binding affinity, compounds 6e and 6k were selected on the basis of their evident structural resemblance to tifluadom. Since a different specificity of action could be expected for the enantiomers of 6e and 6k, owing to the results shown by (S)- and (R)-tifluadom, their racemic mixtures have been resolved by means of liquid chromatography with chiral stationary phases (CSP), and the absolute configuration of the enantiomers has been studied by circular dichroism (CD) and (1)H NMR techniques. Moreover, some new 2-[(acylamino)ethyl]-1,4-benzodiazepine derivatives, 6a-d,f,g,j, have been synthesized, while the whole series (6a-o) has been tested for its potential affinity toward human cloned kappa-opioid receptor. The most impressive result obtained from the binding studies lies in the fact that this series of 2-[2-(acylamino)ethyl]-1,4-benzodiazepine derivatives binds the human cloned kappa-opioid receptor subtype very tightly. Indeed, almost all the ligands within this class show subnanomolar K(i) values, and the least potent compound 6o shows, in any case, an affinity in the nanomolar range. A comparison of the affinities obtained in human cloned kappa-receptor with the correspondent one obtained in native guinea pig kappa-receptor suggests that the human cloned kappa-receptor is less effective in discriminating the substitution pattern than the native guinea pig kappa-receptor. Furthermore, the results obtained are discussed with respect to the interaction with the homology model of the human kappa-opioid receptor, built on the recently solved crystal structure of rhodopsin. Finally, the potential antinociceptive and antiamnesic properties of compounds 6e and 6i have been investigated by means of the hot-plate and passive avoidance test in mice, respectively.

Novel potent 5-HT(3) receptor ligands based on the pyrrolidone structure. Effects of the quaternization of the basic nitrogen on the interaction with 5-HT(3) receptor.

The results of a comprehensive structure-affinity relationship study on the effect of the quaternization (i.e., N-methylation) of structurally different ligands in the classes of tropane and quinuclidine derivatives are described. This study shows that the effects of the quaternization of the basic nitrogen of these 5-HT(3) receptor ligands appear to be strictly structure-dependent suggesting that different binding modes are operative at 5-HT(3) receptor binding site. The different effect of the quaternization of the basic nitrogen of structurally different ligands were rationalized in terms of the interaction with the receptor by means of the combined use of experimental techniques (X-ray diffraction and NMR studies) and computational simulation studies.

The Interactions of the 5-HT(3) 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.

Novel potent 5-HT(3) 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.