Synthesis of phenoxyacetic acid derivatives as highly potent antagonists of gastrin/cholecystokinin-B receptors. III.

In order to improve the biological characteristics of DA-3934 (5), a novel gastrin/cholecystokinin (CCK)-B receptor antagonist, phenoxyacetic acid derivatives replacing the N-methyl-N-phenylcarbamoylmethyl moiety of 5 with various alkyl chains have been synthesized and their biological activity evaluated. The relationship between the structure of these compounds and their human gastrin receptor binding affinity showed that there should be the optimal size among the various N-alkyl chains. Also a significant increase in the receptor binding affinity was achieved by several compounds. Among those compounds, 2-[3-[3- [N-cyclohexylmethyl-N-[2-(N-methyl- N-phenylcarbamoylmethoxy)phenyl]carbamoylmethyl]ureido]pheny l]acetic acid (22c) and (+/-)-2-[3-[3-[N-[2-(N-methyl-N- phenylcarbamoylmethoxy)phenyl]-N-(3-methylpentyl)carbamoy lmethyl]ureido] phenyl]acetic acid (22h) exhibited high affinity for human gastrin receptors and were also more potent inhibitors in a pentagastrin-induced gastric acid secretion model than the parent compound, 5. The ED50 values of these compounds when administered intraduodenally to rats were 0.12 and 0.63 mg/kg, respectively.     

Oxazolidine-2-thiones: a molecular modeling study

Two oxazolidine-2-thiones, thio-analogs of linezolid, were synthesized and their antibacterial properties evaluated. Unlike oxazolidinones, the thio-analogs did not inhibit the growth of Gram positive bacteria. A molecular modeling study has been carried out to aid understanding of this unexpected finding.     

Marine-derived fungi: a chemically and biologically diverse group of microorganisms

A diverse array of secondary metabolites have been isolated and characterized from marine-derived fungi. The structures and biological activities of these metabolites are presented. Additionally, some basic principles of mycology are covered. Overall, 273 structures are presented and the review contains 162 references     

N-Arylpiperazine-1-carboxamide derivatives: a novel series of orally active nonsteroidal androgen receptor antagonists

A novel series of N-arylpiperazine-1-carboxamide derivatives was synthesized and their androgen receptor (AR) antagonist activities and in vivo antiandrogenic properties were evaluated. Reporter assays indicated that trans-2,5-dimethylpiperazine derivatives are potent AR antagonists, and in this series trans-N-4-[4-cyano-3-(trifluoromethyl)phenyl]-N-(2,4-difluorophenyl)-2,5-dimethylpiperazine-1-carboxamide (18 g, YM-175735) exhibited the most potent antiandrogenic activity. Compared to bicalutamide, YM-175735 is an approximately 4-fold stronger AR antagonist and has slightly increased antiandrogenic activity, suggesting that YM-175735 may be useful in the treatment of prostate cancer.     

A virtual screen for diverse ligands: discovery of selective G protein-coupled receptor antagonists

Virtual screening has become a major focus of bioactive small molecule lead identification, and reports of agonists and antagonists discovered via virtual methods are becoming more frequent. G protein-coupled receptors (GPCRs) are the one class of protein targets for which success with this approach has been limited. This is likely due to the paucity of detailed experimental information describing GPCR structure and the intrinsic function-associated structural flexibility of GPCRs which present major challenges in the application of receptor-based virtual screening. Here we describe an in silico methodology that diminishes the effects of structural uncertainty, allowing for more inclusive representation of a potential docking interaction with exogenous ligands. Using this approach, we screened one million compounds from a virtual database, and a diverse subgroup of 100 compounds was selected, leading to experimental identification of five structurally diverse antagonists of the thyrotropin-releasing hormone receptors (TRH-R1 and TRH-R2). The chirality of the most potent chemotype was demonstrated to be important in its binding affinity to TRH receptors; the most potent stereoisomer was noted to have a 13-fold selectivity for TRH-R1 over TRH-R2. A comprehensive mutational analysis of key amino acid residues that form the putative binding pocket of TRH receptors further verified the binding modality of these small molecule antagonists. The described virtual screening approach may prove applicable in the search for novel small molecule agonists and antagonists of other GPCRs.     

QSAR based modeling on a series of α-hydroxy amides as a novel class of bradykinin B1 selective antagonists

G-protein coupled receptors like Bradykinin (BK) B₁ represent a potential treatment route for chronic pain and inflammation. Quantitative structure activity relationship has been performed on a series of α-hydroxy amides as a novel class of bradykinin B₁ selective antagonists, using different physicochemical parameters along with appropriate indicator variables. It has been found that physicochemical parameters such as connectivity indices ³χ, ⁴χ and ⁵χ, molecular weight, molar refractivity, density along with indicator variables are significantly correlated with activity. In this paper best results were obtained by using multiple regression analysis. Different models were generated with high values of R² and low values of PRESS/SSY ratio. The significant equations were statistically tested by using leave one out (LOO) technique and cross validation methods.     

Capillary condensation in a geometrically and a chemically heterogeneous pore: a molecular simulation study

A computer simulation study has been carried out, using an extended Gibbs ensemble Monte Carlo technique, to examine the influence of so-called geometric and chemical disorder on the thermodynamic behavior of simple fluids confined in porous media. The technique allows the equilibrium coexistence of gas and liquid phases to be calculated in a single run. The phase diagram of Lennard-Jones fluid has been calculated in a perfectly cylindrical pore as a reference. Some disorder is then introduced in the porous material, first by spatially modifying the external potential of the initially cylindrical pore, to imitate the geometric disorder of a more realistic pore (undulation, constrictions, etc.) and second by modulating the amplitude of the same initially cylindrical potential to reproduce the energetic disorder of realistic pores due to chemical variations along it. It is shown that the chemical disorder has a much stronger effect on the phase diagram of the confined fluid. The complete adsorption/desorption isotherms are also calculated to help in understanding the large effects of chemical disorder.     

A combined structure-based pharmacophore modeling and 3D-QSAR study on a series of N-heterocyclic scaffolds to screen novel antagonists as human DHFR inhibitors

Structural Chemistry - Dihydrofolate reductase (DHFR) is an essential enzyme that participates in folate metabolism and purine and thymidylate synthesis in cell proliferation. It converts...     

Structure and dynamics of the homologous series of alanine peptides: a joint molecular dynamics/NMR study

The phi,psi backbone angle distribution of small homopolymeric model peptides is investigated by a joint molecular dynamics (MD) simulation and heteronuclear NMR study. Combining the accuracy of the measured scalar coupling constants and the atomistic detail of the all-atom MD simulations with explicit solvent, the thermal populations of the peptide conformational states are determined with an uncertainty of <5 %. Trialanine samples mainly ( approximately 90%) a poly-l-proline II helix-like structure, some ( approximately 10%) beta extended structure, but no alphaR helical conformations. No significant change in the distribution of conformers is observed with increasing chain length (Ala(3) to Ala(7)). Trivaline samples all three major conformations significantly. Triglycine samples the four corner regions of the Ramachandran space and exists in a slow conformational equilibrium between the cis and trans conformation of peptide bonds. The backbone angle distribution was also studied for the segment Ala3 surrounded by either three or eight amino acids on both N- and C-termini from a sequence derived from the protein hen egg white lysozyme. While the conformational distribution of the central three alanine residues in the 9mer is similar to that for the small peptides Ala(3)-Ala(7), major differences are found for the 19mer, which significantly (30-40%) samples alphaR helical stuctures.     

Designing a non-volatile imaging switch for mass-persistent,chemically amplified photolithography: a model study

An acid catalysed rearrangement that transforms a bicyclic lactone into a phenolic carboxylic acid has been tested for potential use in chemically amplified microlithographic imaging.     

Conformational and Cs+ complexation properties of norbadione-A: a molecular modeling study

We report a quantum mechanical (QM) and classical molecular dynamics (MD) study of the conformational and complexation properties of norbadione-A (NBA), a key pigment involved in the Cs+ complexation by mushrooms. The Z versus E isomers of its pulvinic moieties are compared in their neutral (Pulv0), mono- (Pulv(-1)) and di-deprotonated (Pulv(-2)) states, and the 1H chemical shifts are calculated ab initio. Pulv(-1) is found to be stabilized in the E form by an internal COOH(-)O(enolate) hydrogen-bond. No energy minimum is found for the corresponding COO(-)HO(enol) state, indicating that the conjugated enol function of Pulv0 is more acidic than the COOH function. Further deprotonation leads to the Z and E forms of Pulv(-2) that are close in energy and both account for a marked downfield shift delta of ortho-H8 protons. A similar shift is found upon deprotonation of the enol function of an ester analogue of Pulv0. Therefore, contrary to previous assumptions (ref. 7: P. Kuad, et al., J. Am. Chem. Soc., 2005, 127, 1323), the large shift of delta(H8) around pH 9.5 upon deprotonation of NBA or of pulvinic acid cannot be taken as an indicator of an E-to-Z conformational switch, but merely reflects the pH-induced conformational change of the carboxylate group adjacent to the (H8)-ring. The QM and MD studies on NBA(2-) and NBA(4-) support the view that both species prefer the E/E form with two intramolecular COOH(-)O(enolate) hydrogen-bonds in the gas phase and in solution. Finally, we simulated mono- and di-nuclear complexes of Cs+ with NBA(2-) and NBA(4-) by MD, showing that only the NBA(4-) state populated at high pH values can bind two Cs+ cations, with both E and Z conformations of the pulvinic arms.     

A 3D QSAR study on a set of dopamine D4 receptor antagonists

The molecular alignments obtained from a previously reported pharmacophore model have been employed in a three-dimensional quantitative structure-activity relationship (3D QSAR) study, to obtain a more detailed insight into the structure-activity relationships for D(2) and D(4) receptor antagonists. The frequently applied CoMFA method and the related CoMSIA method were used. Statistically significant models have been derived with these two methods, based on a set of 32 structurally diverse D(2) and D(4) receptor antagonists. The CoMSIA and the CoMFA methods produced equally good models expressed in terms of q(2) values. The predictive power of the derived models were demonstrated to be high. Graphical interpretation of the results, provided by the CoMSIA method, brings to light important structural features of the compounds related to either low- or high-affinity D(2) or D(4) antagonism. The results of the 3D QSAR studies indicate that bulky N-substituents decrease D(2) binding, whereas D(4) binding is enhanced. Electrostatically favorable and unfavorable regions exclusive to D(2) receptor binding were identified. Likewise, certain hydrogen-bond acceptors can be used to lower D(2) affinity. These observations may be exploited for the design of novel dopamine D(4) selective antagonists.     

Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

Ligands with the capability to bind G-quadruplexes (G4s) specifically, and to control G4 structure and behaviour, offer great potential in the development of novel therapies, technologies and functional materials. Most known ligands bind to a pre-formed topology, but G4s are highly dynamic and a small number of ligands have been discovered that influence these folding equilibria. Such ligands may be useful as probes to understand the dynamic nature of G4 in vivo, or to exploit the polymorphism of G4 in the development of molecular devices. To date, these fascinating molecules have been discovered serendipitously. There is a need for tools to predict such effects to drive ligand design and development, and for molecular-level understanding of ligand binding mechanisms and associated topological perturbation of G4 structures. Here we study the G4 binding mechanisms of a family of stiff-stilbene G4 ligands to human telomeric DNA using molecular dynamics (MD) and enhanced sampling (metadynamics) MD simulations. The simulations predict a variety of binding mechanisms and effects on G4 structure for the different ligands in the series. In parallel, we characterize the binding of the ligands to the G4 target experimentally using NMR and CD spectroscopy. The results show good agreement between the simulated and experimentally observed binding modes, binding affinities and ligand-induced perturbation of the G4 structure. The simulations correctly predict ligands that perturb G4 topology. Metadynamics simulations are shown to be a powerful tool to aid development of molecules to influence G4 structure, both in interpreting experiments and to help in the design of these chemotypes.

Enhanced sampling molecular dynamics simulations and solution-phase experiments come together to demonstrate the diverse effects of G4-interactive small molecules.     

Homology modeling and molecular dynamics study of GSK3/SHAGGY-like kinase

Although the GSK3/SHAGGY-like kinase is a highly conserved serine/threonine kinase implicated in many signaling pathways in eukaryotes, the lack of knowledge of its three-dimensional (3D) structure has hindered efforts to understand the binding specificities of substrate and catalytic mechanism. To understand the structure-activity relationships, the protein 3D structure was built by using homology modeling based on the known X-ray diffraction structure of Glycogen synthase kinase-3beta (Gsk3beta) and the model structure was further refined using unrestrained molecular dynamics simulations. The research indicates that the general 3D organization of the GSK3/SHAGGY-like kinase is a typical kinase family and comprises an N-terminal domain of beta-sheet and a larger C-terminal domain mainly constituted by alpha-helix. In order to understand the molecular interactions between the natural substrate-ATP and GSK3/SHAGGY-like kinase, a 3D model of the complex ATP-GSK3/SHAGGY-like kinase is developed by molecular docking program, which is helpful to guide the experimental realization and the new mutant designs as well. One important finding is that the identification of the key binding-site residue of Lys69 which plays an important role in the catalysis of GSK3/SHAGGY-like kinase and this is in consistent with experimental observation.     

Identification of potential Gly/NMDA receptor antagonists by cheminformatics approach: a combination of pharmacophore modelling,virtual screening and molecular docking studies

The Gly/NMDA receptor has become known as potential target for the management of neurodegenerative diseases. Discovery of Gly/NMDA antagonists has thus attracted much attention in recent years. In the present research, a cheminformatics approach has been used to determine structural requirements for Gly/NMDA antagonism and to identify potential antagonists. Here, 37 quinoxaline derivatives were selected to develop a significant pharmacophore model with good certainty. The selected model was validated by leave-one-out cross-validation, an external test set, decoy set and Y-randomization test. Applicability domain was verified by the standardization approach. The validated 3D-QSAR model was used to screen virtual hits from the ZINC database by pharmacophore mapping. Molecular docking was used for assessment of receptor–ligand binding modes and binding affinities. The GlideScore and molecular interactions with critical amino acids were considered as crucial features to identify final hits. Furthermore, hits were analysed for in silico pharmacokinetic parameters and Lipinski’s rule of five, demonstrating their potential as drug-like candidates. The PubChem and SciFinder search tools were used to authenticate the novelty of leads retrieved. Finally, five different leads have been suggested as putative novel candidates for the exploration of potent Gly/NMDA receptor antagonists.     

Interaction of antitumoral drug erlotinib with biodegradable triblock copolymers: a molecular modeling study

Combination of molecular dynamics simulations and miscibility calculations was used to investigate erlotinib drug delivery systems based on poly-ε-caprolactone–polyethylene glycol–poly-ε-caprolactone (PCL–PEG–PCL) and poly-ε-caprolactone–polyglycolic acid–poly-ε-caprolactone (PCL–PGA–PCL) biodegradable copolymers. The molecular modeling strategy involving visual observation of models, concentration profile analysis, Flory–Huggins χ parameter, cohesive energy density, and mean square displacement calculations reproduced experimental evidence of erlotinib release from PCL–PEG–PCL matrix successfully. Increasing portion of PCL in PCL–PEG–PCL copolymer led to dissolution of erlotinib aggregates recorded in visual and concentration profile analyses. Higher portion of PCL led to higher cohesive energy density and lower mean square displacement values. Success of this strategy in reproduction of experimental data made an opportunity to utilize the same modeling design in prediction of erlotinib release from similar but not yet experimentally tested PCL–PGA–PCL matrix. In this case, agglomeration of erlotinib molecules and stronger cohesive energy density values were observed.     

Synthesis and structure-activity relationships in a series of ethenesulfonamide derivatives, a novel class of endothelin receptor antagonists.

In the previous paper, we described a series of the 2-arylethenesulfonamide derivatives, a novel class of ETA-selective endothelin (ET) receptor antagonists, including the compounds 1a, b. Compound 1a showed excellent oral antagonistic activities and pharmacokinetic profiles, and the monopotassium salt of 1 (YM-598 monopotassium) is in clinical trials. In this paper, we wish to report the investigation of the further details of structure-activity relationships (SARs) of the 2-phenylethenesulfonamide region in 1a. It was found that methyl substitutions at the 2-, 4- and 6-positions of the phenyl group in 1a led to the discovery of the ET(A)/ET(B) mixed antagonist (6s) with an IC50 of 2.2 nM for the ET(A) receptor. We also found that introduction of an ethyl group to the 1-position of the ethenyl group in 1a gave the ET(A) selective antagonist (6u) with an oral endothelin antagonistic activity in rats.     

Exploring a model of a chemokine receptor/ligand complex in an explicit membrane environment by molecular dynamics simulation: the human CCR1 receptor

The seven transmembrane helices G-protein-coupled receptors (GPCRs) form one of the largest superfamilies of signaling proteins found in humans. Homology modeling, molecular docking, and molecular dynamics (MD) simulation were carried out to construct a reliable model for CCR1 as one of the GPCRs and to explore the structural features and the binding mechanism of BX471 as one of the most potent CCR1 inhibitors. In this study, BX471 has been docked into the active site of the CCR1 protein. After docking, one 20 ns MD simulation was performed on the CCR1-ligand complex to explore effects of the presence of lipid membrane in the vicinity of the CCR1-ligand complex. At the end of the MD simulation, a change in the position and orientation of the ligand in the binding site was observed. This important observation indicated that the application of MD simulation after docking of ligands is useful. Explorative runs of molecular dynamics simulation on the receptor-ligand complex revealed that except for Phe85, Phe112, Tyr113, and Ile259, the rest of the residues in the active site determined by docking are changed. The results obtained are in good agreement with most of the experimental data reported by others. Our results show that molecular modeling and rational drug design for chemokine targets is a possible approach.