A novel synthesis of xanthines: support for a new binding mode for xanthines with respect to adenosine at adenosine receptors

Molecular Simulations and Drug Discovery of Adenosine Receptors

G protein-coupled receptors (GPCRs) represent the largest family of human membrane proteins. Four subtypes of adenosine receptors (ARs), the A1AR, A2AAR, A2BAR and A3AR, each with a unique pharmacological profile and distribution within the tissues in the human body, mediate many physiological functions and serve as critical drug targets for treating numerous human diseases including cancer, neuropathic pain, cardiac ischemia, stroke and diabetes. The A1AR and A3AR preferentially couple to the Gi/o proteins, while the A2AAR and A2BAR prefer coupling to the Gs proteins. Adenosine receptors were the first subclass of GPCRs that had experimental structures determined in complex with distinct G proteins. Here, we will review recent studies in molecular simulations and computer-aided drug discovery of the adenosine receptors and also highlight their future research opportunities.

Evaluation of homology modeling of G-protein-coupled receptors in light of the A(2A) adenosine receptor crystallographic structure

Homology modeling of the human A(2A) adenosine receptor (AR) based on bovine rhodopsin predicted a protein structure that was very similar to the recently determined crystallographic structure. The discrepancy between the experimentally observed orientation of the antagonist and those obtained by previous antagonist docking is related to the loop structure of rhodopsin being carried over to the model of the A(2A) AR and was rectified when the beta(2)-adrenergic receptor was used as a template for homology modeling. Docking of the triazolotriazine antagonist ligand ZM241385 1 was greatly improved by including water molecules of the X-ray structure or by using a constraint from mutagenesis. Automatic agonists docking to both a new homology modeled receptor and the A(2A) AR crystallographic structure produced similar results. Heterocyclic nitrogen atoms closely corresponded when the docked adenine moiety of agonists and 1 were overlaid. The cumulative mutagenesis data, which support the proposed mode of agonist docking, can be reexamined in light of the crystallographic structure. Thus, homology modeling of GPCRs remains a useful technique in probing the structure of the protein and predicting modes of ligand docking.

X-ray structures of two xanthine inhibitors bound to PEPCK and N-3 modifications of substituted 1,8-dibenzylxanthines

The analysis of the X-ray structures of two xanthine inhibitors bound to PEPCK and a comparison to the X-ray structure of GTP bound to PEPCK are reported. The SAR at N-1, N-7 and developing SAR at C-8 are consistent with information gained from the X-ray structures of compounds 1 and 2 bound to PEPCK. Representative N-3 modifications of compound 2 that led to the discovery of 3-cyclopropylmethyl and its carboxy analogue as optimal N-3 groups are presented.

New and Practical Method for Synthesis of 1- and 1,3-Substituted Xanthines

[reaction: see text] A new and practical method for the synthesis of 1- and 1,3-substituted xanthines is reported. Direct base-promoted condensation of the imidazole precursor 1 with carbamates 2 gives 1-substituted 7-PMB xanthines 7 in good yields. Alkylation of these derivatives or their potassium salts proceeds under mild conditions to give functionalized 1,3-substituted 7-PMB xanthines 9 in good to excellent yields. The obtained 7-PMB-protected derivatives can be readily deprotected to give the parent 1- and 1,3-substituted xanthines.

Electronic structure of some adenosine receptor antagonists. III. Quantitative investigation of the electronic absorption spectra of alkyl xanthines

Quantitative and comparative investigation of the electronic absorption spectra of theophylline, caffeine and their derivatives is reported. The spectra of theophylline, caffeine and theobromine were compared to establish the predominant tautomeric species in solution. This comparison, analysis of solvent effects and assignments of the observed transitions via MO computations indicate the exits of only one tautomeric species in solution that is the N7 form. A low-lying triplet state was identified which corresponds to a HOMO-LUMO transition. This relatively long-lived T1 state is always less polar than the ground state and may very well underlie the photochemical reactivity of alkyl xanthines. Substituents of different electron donating or withdrawing strengths and solvent effects are investigated and analyzed. The present analysis is facilitated via computer deconvolution of the observed spectra and MO computation.

Electronic structure of some adenosine receptor antagonists. VQSAR Investigation

A QSAR model has been developed for 1,3-dimethylxanthines as adenosine receptor antagonists. The model is capable of predicting the affinity toward both the A1 and A2 receptors. Constitutional, geometrical, topological, electronic descriptors (computed at the ab initio 6-31G level), and some empirical descriptors related to the hypophilicity were computed and analyzed. A two step computational strategy was adopted to select the descriptors relevant to the A1 or the A2 affinity. In the first step, each of the four main groups of descriptors is treated independently. Multiple regression analysis lead to a set of equations that reflect the weight of each of the studied descriptors. The most relevant of these descriptors were grouped, and a new multiple regression analysis has been carried out and arrived at the final QSAR model. These QSAR equations account for almost all the A2 and an appreciable part of the A1 affinity. The proposed model has been examined as a general tool of predicting the activity toward the adenosine receptor sites. A validation set of 22 xanthines were selected, and their activities were computed using the proposed QSAR model. The correspondence between the predicted and observed activities is excellent. Anova statistical analysis on the data of the validation set elaborates on the quality of these fits.

CoMFA-based comparison of two models of binding site on adenosine A1 receptor

A set of 32 N6-substituted adenosines and 22 8-substituted xanthines with affinity for adenosine A1 receptors was subjected to three-dimensional quantitative structure-affinity relationship analysis using comparative molecular field analysis (CoMFA). The aim was to compare two modes of binding to the receptor--'N6-C8' and 'N6-N7'. Good models with high predictive power and stability were obtained. A comparison of these models gives the following results: (a) Inclusion of both steric and electrostatic fields in CoMFA generates better predictive models compared to models based on steric or electrostatic fields alone. (b) The 'N6-N7' CoMFA models are slightly better than the 'N6-C8' ones. (c) Steric restriction exists around the N6-H in the 'N6-N7' steric field map, which is absent in the 'N6-C8' steric field map. This report demonstrates that the 'N6-N7' mode of binding is a further development of the 'N6-C8' model with a slightly better predictive ability and more accurate steric and electrostatic overlaps between agonists and antagonists.

C-nucleoside analogues of furanfurin as ligands to A1 adenosine receptors

Furanfurin (2-beta-D-ribofuranosylfuran-4-carboxamide) derivatives and analogues were synthesized and their affinity for adenosine receptors was determined. The agonistic behavior of furanfurin against A1 receptors is preserved only when the furan ring is substituted with isosteric pentatomic ring systems such as oxazole, thiazole or thiophene, and the carboxamide group is unsubstituted. Replacement of the hydrogen atoms of the carboxamide group with alkyl, cycloalkyl or arylalkyl groups generates compounds endowed with moderate antagonistic activity.

Theophylline dilates rat diaphragm arterioles via the prostaglandins pathway

1. We investigated by intravital microscopy in rats, the in vivo direct effects of theophylline on the diameters of second and third order diaphragm arterioles. 2. Theophylline (1-100 microM) dilated second and third order diaphragm arterioles significantly, and with an amplitude which was not statistically different from the one obtained with adenosine (1-100 microM). Enprofylline (1-100 microM), a theophylline analogue with poor adenosine-receptor antagonism but with similar or higher phosphodiesterases inhibition properties than theophylline, also dilated diaphragm arterioles, causing however, a significantly smaller dilatation than theophylline. 3. Neither the A1 adenosine receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine (CPX, 50 nM), nor the A2 adenosine receptor antagonist 3,7-dimethyl-1-proparglyxanthine (DMPX, 10 microM) reduced significantly theophylline-induced arteriolar dilatation. 4. Theophylline (100 nM) abolished adenosine-induced arteriolar dilatation. 5. The dilatation induced by theophylline was unchanged by the nitric oxide (NO) synthase inhibitor N(omega)-nitro-L-arginine (NNA, 300 microM). 6. Theophylline-induced arteriolar dilatation was abolished by the prostaglandin synthesis inhibitors mefenamic acid or indomethacin (20 microM). 7. These findings show that theophylline induced a significant dilatation of diaphragm arterioles via the release of prostaglandins.

Adenosine receptors: new opportunities for future drugs

This review summarises current knowledge on adenosine receptors, an important G protein-coupled receptor. The four known adenosine receptor subtypes A1, A2A, A2B, and A3 are discussed with special reference to the opportunities for drug development.

Predominant role of A1 adenosine receptors in mediating adenosine induced vasodilatation of rat diaphragmatic arterioles: involvement of nitric oxide and the ATP-dependent K+ channels

1. We investigated, by intravital microscopy in rats, the role of the subtypes of adenosine receptors A1 (A1/AR) and A2 (A2AR) in mediating adenosine-induced vasodilatation of second and third order arterioles of the diaphragm. 2. Adenosine, and the A1AR selective agonists R(-)-N6-(2-phenylisopropyl)-adenosine (R-PIA) and N6-cyclo-pentyl-adenosine (CPA) induced a similar concentration-dependent dilatation of diaphragmatic arterioles. The non selective A2AR subtype agonist N6-[2-(3,5-dimethoxyphenyl)-2-(2-methylphenyl) ethyl]adenosine (DPMA) also dilated diaphragmatic arterioles but induced a significantly smaller dilatation than adenosine. By contrast the selective A(2a)AR subtype agonist 2-[p-(2-carboxyethyl)phenyl amino]-5'-N-ethyl carboxamido adenosine (CGS 21680) did not modify diaphragmatic arteriolar diameter. 3. The non selective adenosine receptor antagonist 1,3-dipropyl-8-p-sulphophenylxanthine (SPX, 100 microM) and the selective A1AR antagonist 8-cyclopentyl-1,3-dipropylxanthine (CPX, 50 nM) significantly attenuated adenosine-induced dilatation of diaphragmatic arterioles. By contrast, adenosine significantly dilated diaphragmatic arterioles in the presence of A2AR antagonist 3,7-dimethyl-1-propargylxanthine (DMPX, 10 microM). 4. The dilatation induced by adenosine was unchanged by the mast cell stabilizing agent sodium cromoglycate (cromolyn, 10 microM). 5. The nitric oxide (NO) synthase inhibitor N omega-nitro-L-arginine (L-NOARG, 300 microM) attenuated the dilatation induced by adenosine, and by the A1AR and A2AR agonists. 6. The ATP-dependent K+ channel blocker glibenclamide (3 microM) significantly attenuated diaphragmatic arteriolar dilatation induced by adenosine and by the A1AR agonists R-PIA and CPA. By contrast, glibenclamide did not significantly modify arteriolar dilatation induced by the A2AR agonist DPMA. 7. These findings suggest that adenosine-induced dilatation of diaphragmatic arterioles in the rat is predominantly mediated by the A1AR, via the release of NO and activation of the ATP-dependent K+ channels.

Theoretical structure-activity studies of adenosine A1 ligands: requirements for receptor affinity

The three-dimensional (3-D) requirements for A1 adenosine receptor affinity have been studied based on hydrogen-bonding functionality correlation between a group of twelve A1 adenosine receptor ligands representing ten structurally different classes of compounds. Electrostatic potential similarity indices and shape similarity indices strongly support the proposed receptor-bound orientations of the ligands. We conclude, in areas common to both agonist and antagonist binding at the A1 receptor, that the ligands are recognized by a similar physicochemical 3-D environment. The finding of similar 3-D requirements for agonists and antagonists suggests a fairly static receptor structure in the region common to agonist and antagonist binding. The ribose moiety is remote from antagonist binding site. Such a 3-D environment rationalizes the binding of a number of potent novel antagonists including KW-3902, not previously reported in modeling studies.

The matching of electrostatic extrema: a useful method in drug design? A study of phosphodiesterase III inhibitors

Ligands which bind to a specific protein binding site are often expected to have a similar electrostatic environment which complements that of the binding site. One method of assessing molecular electrostatic similarity is to examine the possible overlay of the maxima and minima in the electrostatic potential outside the molecules and thereby match the regions where strong electrostatic interactions, including hydrogen bonds, with the residues of the binding site may be possible. This approach is validated with accurate calculations of the electrostatic potential, derived from a distributed multiple analysis of an ab initio charge density of the molecule, so that the effects of lone pair and pi-electron density are correctly included. We have applied this method to the phosphodiesterase (PDE) III substrate adenosine-3',5'-cyclic monophosphate (cAMP) and a range of nonspecific and specific PDE III inhibitors. Despite the structural variation between cAMP and the inhibitors, it is possible to match three or four extrema to produce relative orientations in which the inhibitors are sufficiently sterically and electrostatically similar to the natural substrate to account for their affinity for PDE III. This matching of extrema is more apparent using the accurate electrostatic models than it was when this approach was first applied, using semiempirical point charge models. These results reinforce the hypothesis of electrostatic similarity and give weight to the technique of extrema matching as a useful tool in drug design.

Relative binding orientations of adenosine A1 receptor ligands--a test case for Distributed Multipole Analysis in medicinal chemistry

The electrostatic properties of adenosine-based agonists and xanthine-based antagonists for the adenosine A1 receptor were used to assess various proposals for their relative orientation in the unknown binding site. The electrostatic properties were calculated from distributed multipole representations of SCF wavefunctions. A range of methods of assessing the electrostatic similarity of the ligands were used in the comparison. One of the methods, comparing the sign of the potential around the two molecules, gave inconclusive results. The other approaches, however, provided a mutually complementary and consistent picture of the electrostatic similarity and dissimilarity of the molecules in the three proposed relative orientations. This was significantly different from the results obtained previously with MOPAC AM1 point charges. In the standard model overlay, where the aromatic nitrogen atoms of both agonists and antagonists are in the same position relative to the binding site, the electrostatic potentials are so dissimilar that binding to the same receptor site is highly unlikely. Overlaying the N6-region of adenosine with that near C8 of theophylline (the N6-C8 model) produces the greatest similarity in electrostatic properties for these ligands. However, N6-cyclopentyladenosine (CPA) and 1,3-dipropyl-8-cyclopentyl-xanthine (DPCPX) show greater electrostatic similarity when the aromatic rings are superimposed according to the flipped model, in which the xanthine ring is rotated around its horizontal axis. This difference is mainly attributed to the change in conformation of N6-substituted adenosines and could result in a different orientation for theophylline and DPCPX within the receptor binding site. However, it is more likely that DPCPX also binds according to the N6-C8 model, as this model gives the best steric overlay and would be favoured by the lipophilic forces, provided that the binding site residues could accommodate the different electrostatic properties in the N6/N7-region. Finally, we have shown that Distributed Multipole Analysis (DMA) offers a new, feasible tool for the medicinal chemist, because it provides the use of reliable electrostatic models to determine plausible relative binding orientations.

Molecular cloning and characterization of the human A3 adenosine receptor

The human A3 adenosine receptor was cloned from a striatal cDNA library using a probe derived from the homologous rat sequence. The cDNA encodes a protein of 318 amino acids and exhibits 72% and 85% overall identity with the rat and sheep A3 adenosine receptor sequences, respectively. Specific and saturable binding of the adenosine receptor agonist N6-(4-amino-3-[125I]iodobenzyl)adenosine [125I]ABA was measured on the human A3 receptor stably expressed in Chinese hamster ovary cells with a Kd = 10 nM. The potency order for adenosine receptor agonists was N-ethylcarboxamidoadenosine (NECA) > or = (R)-N6-phenyl-2-propyladenosine [(R)-PIA] > N6-cyclopentyladenosine (CPA) > (S)-N6-phenyl-2-propyladenosine [(S)-PIA]. The human receptor was blocked by xanthine antagonists, most potently by 3-(3-iodo-4-aminobenzyl)-8-(4-oxyacetate)phenyl-1-propylxanthine (I-ABOPX) with a potency order of I-ABOPX > 1,3-dipropyl-8-(4-acrylate)phenylxanthine > or = xanthine amino congener >> 1,3-dipropyl-8-cyclopentylxanthine. Adenosine, NECA, (R)- and (S)-PIA, and CPA inhibited forskolin-stimulated cAMP accumulation by 30-40% in stably transfected cells; I-ABA is a partial agonist. When measured in the presence of antagonists, the dose-response curves of NECA-induced inhibition of forskolin-stimulated cAMP accumulation were right-shifted. Antagonist potencies determined by Schild analyses correlated well with those established by competition for radioligand binding. The A3 adenosine receptor transcript is widespread and, in contrast to the A1, A2a, and A2b transcripts, the most abundant expression is found in the lung and liver. The tissue distribution of A3 mRNA is more similar to the widespread profile found in sheep than to the restricted profile found in the rat. This raises the possibility that numerous physiological effects of adenosine may be mediated by A3 adenosine receptors.

Adenosine receptors and their modulators

The identification and characterization of adenosine receptors and the development of potent, receptor subtype-selective agonists and antagonists has been an active area of research for the past 20 years. Major recent advances in the field have been the cloning of several adenosine receptor subtypes of different species, including the discovery of a new subtype, designated A3, the discovery and development of new agonists and antagonists, particularly those with selectivity for the A2a adenosine receptor, the characterization of signal transduction pathways, and the development of agents which act indirectly on the adenosine receptor system. The present article focusses on aspects of pharmaceutical/medicinal chemistry related to adenosine receptors.

Molecular recognition using a binary genetic search algorithm

A genetic algorithm has been devised and applied to the problems of molecular similarity, pharmacophore elucidation, and determination of molecular conformation. The algorithm is based on a binary representation of molecular position and conformation. Using the genetic operators, crossover, mutation, and selection near optimum conformations and orientations of molecules may be determined which best-fit defined constraints. The constraints may be any useful function for example, intermolecular or intramolecular distances, electrostatic potential on a surface, or volume overlap. Problems with up to 30 degrees of freedom have been tackled successfully.

Enzymes in the synthesis of chiral drugs

The majority of synthetic chiral drugs are now marketed as racemates. This situation is rapidly changing due to the recent advances in asymmetric chemical synthesis and biocatalytic methods. This article reviews the use of enzymes in the synthesis and modification of optically pure drugs. Special attention is focused on the synthesis of new pharmaceuticals which may require efficient procedures for large-scale synthesis in the future.

Adenosine A1 Receptor and Ligand Molecular Modeling

This symposium provided a forum for presentations by the relevant groups on ligand design and ligand binding on the adenosine A1, receptor. Agreement appears to exist that the "N6-C8" model of ligand binding to the receptor is the preferred mode. A consensus has not yet been reached on the actual placement of the ligand in the receptor and the exact amino acids which interact in its binding. Two viable models exist at present. Both can be tested with selective site-directed mutagenic studies on the A1 receptor as well as with additional designed ligands.