Characterizing pharmacological ligands to study the long-chain fatty acid receptors GPR40/FFA1 and GPR120/FFA4.

The free fatty acid receptors (FFA) 1 (previously designated GPR40) and FFA4 (previously GPR120) are two GPCRs activated by saturated and unsaturated longer-chain free fatty acids. With expression patterns and functions anticipated to directly or indirectly promote insulin secretion, provide homeostatic control of blood glucose and improve tissue insulin sensitivity, both receptors are being studied as potential therapeutic targets for the control of type 2 diabetes. Furthermore, genetic and systems biology studies in both humans and mouse models link FFA4 receptors to diabetes and obesity. Although activated by the same group of free fatty acids, FFA1 and FFA4 receptors are not closely related and, while the basis of recognition of fatty acids by FFA1 receptors is similar to that of the short-chain fatty acid receptors FFA2 and FFA3, the amino acid residues involved in endogenous ligand recognition by FFA4 receptors are more akin to those of the sphingosine 1 phosphate receptor S1P1 . Screening and subsequent medicinal chemistry programmes have developed a number of FFA1 receptor selective agonists that are effective in promoting insulin secretion in a glucose concentration-dependent manner, and in lowering blood glucose levels. However, the recent termination of Phase III clinical trials employing TAK-875/fasiglifam has caused a setback and raises important questions over the exact nature and mechanistic causes of the problems. Progress in the identification and development of highly FFA4 receptor-selective pharmacological tools has been less rapid and several issues remain to be clarified to fully validate this receptor as a therapeutic target. Despite this, the ongoing development of a range of novel ligands offers great opportunities to further unravel the contributions of these receptors.

Drugs or diet?--Developing novel therapeutic strategies targeting the free fatty acid family of GPCRs.

Free fatty acids (FFAs) are metabolic intermediates that may be obtained through the diet, synthesized endogenously, or produced via fermentation of carbohydrates by gut microbiota. In addition to serving as an important source of energy, FFAs are known to produce a variety of both beneficial and detrimental effects on metabolic and inflammatory processes. While historically, FFAs were believed to produce these effects only through intracellular targets such as peroxisome proliferator-activated receptors, it has now become clear that FFAs are also agonists for several GPCRs, including a family of four receptors now termed FFA1-4. Increasing evidence suggests that FFA1-4 mediate many of the beneficial properties of FFAs and not surprisingly, this has generated significant interest in the potential of these receptors as therapeutic targets for the treatment of a variety of metabolic and inflammatory disorders. In addition to the traditional strategy of developing small-molecule therapeutics targeting these receptors, there has also been some consideration given to alternate therapeutic approaches, specifically by manipulating endogenous FFA concentrations through alteration of either dietary intake, or production by gut microbiota. In this review, the current state of knowledge for FFA1-4 will be discussed, together with their potential as therapeutic targets in the treatment of metabolic and inflammatory disorders. In particular, the evidence in support of small molecule versus dietary and microbiota-based therapeutic approaches will be considered to provide insight into the development of novel multifaceted strategies targeting the FFA receptors for the treatment of metabolic and inflammatory disorders.

Experimental challenges to targeting poorly characterized GPCRs: uncovering the therapeutic potential for free fatty acid receptors.

The G protein-coupled receptors (GPCRs) are extremely successful drug targets, with recent estimates suggesting that approximately 30% of all currently available therapeutics act at these receptors. Despite this success, only a small number of the over 400 known nonodorant GPCRs are currently targeted, suggesting there is still untapped therapeutic potential. However, as most GPCRs were identified based on their sequence homology to other members of the superfamily, many still remain "orphan" receptors without known ligands. Indeed, even once a GPCR has been deorphanized, the receptor typically is still poorly characterized in terms of its pharmacology and biological functions, presenting a unique set of experimental challenges in order to define its therapeutic potential. We discuss some of these challenges and how they have been addressed in order to uncover the therapeutic potential of five recently deorphanized receptors that are activated by short- and long-chain free fatty acids.

The angiotensin IV analog Nle-Tyr-Leu-psi-(CH2-NH2)3-4-His-Pro-Phe (norleual) can act as a hepatocyte growth factor/c-Met inhibitor.

The angiotensin (Ang) IV analog norleual [Nle-Tyr-Leu-psi-(CH2-NH2)(3-4)-His-Pro-Phe] exhibits structural homology with the hinge (linker) region of hepatocyte growth factor (HGF) and is hypothesized to act as a hinge region mimic. Norleual competitively inhibited the binding of HGF to its receptor c-Met in mouse liver membranes, with an IC(50) value of 3 pM. Predictably, norleual was able to inhibit HGF-dependent signaling, proliferation, migration, and invasion in multiple cell types at concentrations in the picomolar range. Ex vivo studies demonstrated that norleual exhibited potent antiangiogenic activity, an attribute that would be predicted for a HGF/c-Met antagonist. Furthermore, norleual suppressed pulmonary colonization by B16-F10 murine melanoma cells, which are characterized by an overactive HGF/c-Met system. Together, these data suggest that AngIV analogs exert at least some of their biological activity through interference with the HGF/c-Met system and may have utility as therapeutic agents in disorders that are dependent on an intact HGF/c-Met system. Finally, the ability of norleual to induce marked biological responses in human embryonic kidney cells, which do not express insulin-responsive aminopeptidase (IRAP), coupled with the observed effects of norleual on the HGF/c-Met system, casts doubt on the physiological significance of AngIV-dependent inhibition of IRAP. [Corrected]

Vicinity analysis: a methodology for the identification of similar protein active sites.

Vicinity analysis (VA) is a new methodology developed to identify similarities between protein binding sites based on their three-dimensional structure and the chemical similarity of matching residues. The major objective is to enable searching of the Protein Data Bank (PDB) for similar sub-pockets, especially in proteins from different structural and biochemical series. Inspection of the ligands bound in these pockets should allow ligand functionality to be identified, thus suggesting novel monomers for use in library synthesis. VA has been developed initially using the ATP binding site in kinases, an important class of protein targets involved in cell signalling and growth regulation. This paper defines the VA procedure and describes matches to the phosphate binding sub-pocket of cyclin-dependent protein kinase 2 that were found by searching a small test database that has also been used to parameterise the methodology.

QSAR studies using the parashift system.

A novel way of describing molecules in terms of their surfaces and local properties at the surfaces is described. The use of these surfaces and properties to explain chemical reactivity and model simple molecular properties has already been demonstrated. This study reports an examination of the use of these descriptions of molecules to model a simple chemical interaction (complex formation) and a diverse set of mutagens. Both of these systems have been modelled successfully and the results are discussed.

Characterization of the similarity of chemical compounds using electrospray ionization mass spectrometry and multivariate exploratory techniques.

The applicability and usefulness of electrospray mass spectrometry to the analysis of a small data set of 52 synthetic substances to probe their molecular similarity/diversity has been demonstrated. The first stage was the reduction of the data by Principal Component Analysis (PCA), to visualize the structure of the data. Sequential Projection Pursuit (SPP) was applied to detect outlying objects. Hierarchical cluster analysis was employed to produce a dendrogram, using group-average linkage clustering. Finally, the cluster results of spectral data were compared with that of structural fingerprints and an expert's classification by using the similarity measure of Wallace.

Use of mass spectrometry for assessing similarity/diversity of natural products with unknown chemical structures.

An evaluation whether mass spectral data contain useful information for assessing similarity/diversity of drug compounds is presented. A comparative study was carried out between Ward's hierarchical agglomerative clustering, based on the 2D Daylight fingerprints or on the mass spectra, of a small database of 66 synthetic substances. The influence of normalization of the mass spectral data on the clustering result has also been studied. The results were subsequently compared with an expert's classification of the same small dataset, based on own evaluation according to known structure and pharmacological activity.

Characterisation of the solution conformation of a cyclic RGD peptide analogue by NMR spectroscopy allied with a genetic algorithm approach and constrained molecular dynamics.

The solution conformation of a cyclic RGD peptide analogue, cyclo-(S,S)-2-mercaptobenzoate-arginine-glycine-aspartate-2-mer captoanilide, has been determined via two independent approaches for the searching of conformational space and identification of conformations consistent with NMR and CD spectroscopic data: (i) the use of a binary genetic algorithm and (ii) a molecular dynamics simulation. Inter-proton distances were obtained via analysis of cross-peak volumes from a two-dimensional ROESY NMR spectroscopy experiment at 600 MHz and were used as constraints for the computational calculations. The mercaptoanilide amide proton resonance chemical shift had a very small temperature coefficient, indicating that this proton was hydrogen-bonded. Circular dichroism data showed that, in solution, the torsion angle about the disulfide bond was negative, consistent with one of the distinct conformations around this bond in the 200 ps molecular dynamics simulation. The backbone conformations of the structures resulting from the two different approaches were very similar.

The conformational behaviour of the cardiac glycoside digoxin as indicated by NMR spectroscopy and molecular dynamics calculations.

The 1H- and 13C-NMR spectra of digoxin in solution in Me2SO-d6 have been assigned completely. Measurement of the 3JC,H values has enabled estimation of the torsional angles involving the bonds linking the digitoxose residues, between the inner digitoxose and the genin unit, and for the unsaturated gamma-lactone ring. These values have been supplemented by 1H-1H NOE data. In general, there is good agreement between the conformations in solution (NMR data) and the solid state (X-ray data), and that derived from theoretical modelling which shows evidence of conformational flexibility. The major difference occurs for the torsion between the genin and the innermost digitoxose residue where molecular dynamics predict the presence of two conformations, one similar to that seen by NMR and the other similar to the X-ray structure.

Structure-activity relationships of pyrethroid insecticides. Part 2. The use of molecular dynamics for conformation searching and average parameter calculation.

Molecular dynamics simulations have been performed on a number of conformationally flexible pyrethroid insecticides. The results indicate that molecular dynamics is a suitable tool for conformational searching of small molecules given suitable simulation parameters. The structures derived from the simulations are compared with the static conformation used in a previous study. Various physicochemical parameters have been calculated for a set of conformations selected from the simulations using multivariate analysis. The averaged values of the parameters over the selected set (and the factors derived from them) are compared with the single conformation values used in the previous study.

Podophyllotoxin analogues: synthesis and computer modelling investigation of structure-activity relationships.

The conformations of four 2-substituted-4-deoxy-analogues of podophyllotoxin have been studied using data obtained from X-ray structure determinations and molecular modelling studies. In these, root mean square differences between these structures and those of the cytotoxic agents 6'-bromopodophyllotoxin and colchicine were determined. Attempts have been made to correlate structure with the available biological activity data.

Crystallographic and molecular mechanics calculations on the anti-tumor drugs N-[(2-dimethylamino)ethyl]-and N-[(2-dimethyl-amino)butyl]-9-aminoacridine-4-carboxamides and their dications: implications for models of DNA-binding.

The molecular structures of the N-(2-dimethylamino)ethyl and N-(2-dimethylamino)butyl derivatives of 9-aminoacridine-4-carboxamide, of current interest as potential anti-cancer agents have been determined by X-ray Crystallography. Both are in the free base form and have an intramolecular-hydrogen bond between N10 of the acridine and the nitrogen atom of the carboxamide substituent. Molecular mechanics calculations have been used to explore the conformational flexibility of this substituent with respect to the chromophore in order to determine the low-energy conformers of both free base and protonated forms. These have revealed flexibility in the system with relatively low energy cost, especially in the physiological condition when the N10 atom is protonated and suggest that a previously published model for the interaction of these compounds with DNA, is energetically feasible. Implications for interactions with DNA have also been examined by computer modelling.

The crystal structure of the DNA-binding drug berenil: molecular modelling studies of berenil-DNA complexes.

The crystal structure of the DNA minor-groove DNA-binding drug berenil has been determined. Molecular-modelling techniques have been used to establish plausible binding modes of the structure to A-T sequences. These have shown that specific hydrogen bonds are possible between the amidine groups of the drug molecule and 02 atoms of thymine, although global energy minimisations tended to emphasise electrostatic interactions with phosphate groups rather than these hydrogen bonds with bases.