Demystifying the three dimensional structure of G protein-coupled receptors (GPCRs) with the aid of molecular modeling

We review our recent work on adenosine receptors, a family of GPCRs; focusing our attention on A3 adenosine receptor, we have demonstrated that the reciprocal integration of different theoretical and experimental disciplines can be very useful for the successful protein-based design of new, potent and selective receptor ligands.     

Synthesis, structure, and molecular modeling of a titanoniobate isopolyanion

Polyoxoniobate chemistry, both in the solid state and in solution is dominated by [Nb₆O₁₉]⁸⁻, the Lindquist ion. Recently, we have expanded this chemistry through use of hydrothermal synthesis. The current publication illustrates how use of heteroatoms is another means of diversifying polyoxoniobate chemistry. Here we report the synthesis of Na₈[Nb₈Ti₂O₂₈]·34H₂O and its structural characterization from single-crystal X-ray data. This salt crystallizes in the P-1 space group (a=11.829(4) Å, b=12.205(4) Å, c=12.532(4) Å, α=97.666(5)°, β=113.840(4)°, γ=110.809(4)°), and the decameric anionic cluster [Nb₈Ti₂O₂₈]⁸⁻ has the same cluster geometry as the previously reported [Nb₁₀O₂₈]⁶⁻ and [V₁₀O₂₈]⁶⁻. Molecular modeling studies of [Nb₁₀O₂₈]⁶⁻ and all possible isomers of [Nb₈Ti₂O₂₈]⁸⁻ suggest that this cluster geometry is stabilized by incorporating the Ti⁴⁺ into cluster positions in which edge-sharing is maximized. In this manner, the overall repulsion between edge-sharing octahedra within the cluster is minimized, as Ti⁴⁺ is both slightly smaller and of lower charge than Nb⁵⁺. Synthetic studies also show that while the [Nb₁₀O₂₈]⁶⁻ cluster is difficult to obtain, the [Nb₈Ti₂O₂₈]⁸⁻ cluster can be synthesized reproducibly and is stable in neutral to basic solutions, as well.     

Chiral diaminopyrrolic receptors for selective recognition of mannosides, part 2: a 3D view of the recognition modes by X-ray, NMR spectroscopy, and molecular modeling

The structural features of a representative set of five complexes of octyl α- and β-mannosides with some members of a new generation of chiral tripodal diaminopyrrolic receptors, namely, (R)-5 and (S)- and (R)-7, have been investigated in solution and in the solid state by a combined X-ray, NMR spectroscopy, and molecular modeling approach. In the solid state, the binding arms of the free receptors 7 delimit a cleft in which two solvent molecules are hydrogen bonded to the pyrrolic groups and to the benzenic scaffold. In a polar solvent (CD(3)CN), chemical shift and intermolecular NOE data, assisted by molecular modeling calculations, ascertained the binding modes of the interaction between the receptor and the glycoside for these complexes. Although a single binding mode was found to adequately describe the complex of the acyclic receptor 5 with the α-mannoside, for the complexes of the cyclic receptors 7 two different binding modes were required to simultaneously fit all the experimental data. In all cases, extensive binding through hydrogen bonding and CH-π interactions is responsible for the affinities measured in the same solvent. Furthermore, the binding modes closely account for the recognition preferences observed toward the anomeric glycosides and for the peculiar enantiodiscrimination properties exhibited by the chiral receptors.     

Inhibitory G proteins and their receptors: emerging therapeutic targets for obesity and diabetes

The worldwide prevalence of obesity is steadily increasing, nearly doubling between 1980 and 2008. Obesity is often associated with insulin resistance, a major risk factor for type 2 diabetes mellitus (T2DM): a costly chronic disease and serious public health problem. The underlying cause of T2DM is a failure of the beta cells of the pancreas to continue to produce enough insulin to counteract insulin resistance. Most current T2DM therapeutics do not prevent continued loss of insulin secretion capacity, and those that do have the potential to preserve beta cell mass and function are not effective in all patients. Therefore, developing new methods for preventing and treating obesity and T2DM is very timely and of great significance. There is now considerable literature demonstrating a link between inhibitory guanine nucleotide-binding protein (G protein) and G protein-coupled receptor (GPCR) signaling in insulin-responsive tissues and the pathogenesis of obesity and T2DM. These studies are suggesting new and emerging therapeutic targets for these conditions. In this review, we will discuss inhibitory G proteins and GPCRs that have primary actions in the beta cell and other peripheral sites as therapeutic targets for obesity and T2DM, improving satiety, insulin resistance and/or beta cell biology.     

Inhibitory activity of hibifolin on adenosine deaminase- experimental and molecular modeling study

Adenosine deaminase (ADA) is an enzyme involved in purine metabolism. ADA converts adenosine to inosine and liberates ammonia. Because of their critical role in the differentiation and maturation of cells, the regulation of ADA activity is considered as a potential therapeutic approach to prevent malignant and inflammatory disorders. In the present study, the inhibitory activity of a plant flavonoid, hibifolin on ADA is investigated using enzyme kinetic assay and isothermal titration calorimetry. The inhibitory constant of hibifolin was found to be 49.92 μM ± 3.98 and the mode of binding was reversible. Isothermal titration calorimetry showed that the compound binds ADA with binding energy of −7.21 Kcal/mol. The in silico modeling and docking studies showed that the bound ligand is stabilized by hydrogen bonds with active site residues of the enzyme. The study reveals that hibifolin can act as a potential inhibitor of ADA.     

Exploring the molecular basis of selectivity in A1 adenosine receptors agonists: a case study

Adenosine is a naturally occurring purine nucleoside that has a wide variety of well-documented regulatory functions and physiological roles. Selective activation of the adenosine A₁ receptor has drawn attention in drug discovery for the therapeutic effects on neural and cardiovascular disorders. We have developed a model of the human A₁ adenosine receptor using bovine rhodopsin as a template. A flexible docking approach has been subsequently carried out for evaluating the molecular interactions of twenty-one selective A₁ agonists with the receptor model. The results of these studies are consistent with mutational and biochemical data. In particular, they highlight a wide hydrogen-bonding network between the nucleoside portion of the ligands and the A₁ receptor as well as key amino acids for hydrophobic interactions with the different N⁶-groups of the agonists. The models presented here provide a detailed molecular map for the selective stimulation of the adenosine A₁ receptor subtype and a steady basis for the rational design of new A₁ selective ligands.     

Synthesis, molecular structure, NMR spectroscopic and computational analysis of a selective adenosine A2A antagonist, ZM 241385

Herein, we describe the synthesis of the adenosine A_2A antagonist ZM 241385 (9) starting from commercially available 2-furanhydrazide (1) and including a comprehensive structural characterization of all the intermediates and the final product. In addition, extensive NMR analysis, including temperature and concentration-dependent experiments, are reported as well as the first single-crystal structure of the compound ZM 241385 (9) as the trihydrate. Furthermore, an extensive structural comparison of the single-crystal structure with the published protein bound X-ray structures is reported.     

d-Xylose-based surfactants: Synthesis,characterization and molecular modeling studies

Pentose-derived surfactants were easily synthesized and fully characterized through classical analytical methods. The interfacial behaviors revealed the importance of both the length of the hydrophobic chain and the nature of the anomeric form. Finally, the spatial conformation of four xylosides was obtained by molecular modeling with software Hyperchem^® 4 using the semi-empirical method PM3, which demonstrated the role of hydrophobic interactions in the stability of the compounds.     

GridMol: a grid application for molecular modeling and visualization

In this paper we present GridMol, an extensible tool for building a high performance computational chemistry platform in the grid environment. GridMol provides computational chemists one-stop service for molecular modeling, scientific computing and molecular information visualization. GridMol is not only a visualization and modeling tool but also simplifies control of remote Grid software that can access high performance computing resources. GridMol has been successfully integrated into China National Grid, the most powerful Chinese Grid Computing platform. In Section “Grid computing” of this paper, a computing example is given to show the availability and efficiency of GridMol. GridMol is coded using Java and Java3D for portability and cross-platform compatibility (Windows, Linux, MacOS X and UNIX). GridMol can run not only as a stand-alone application, but also as an applet through web browsers. In this paper, we will present the techniques for molecular visualization, molecular modeling and grid computing. GridMol is available free of charge under the GNU Public License (GPL) from our website: Contact:      

Chromatography,mass spectrometry,and molecular modeling studies on ammodytoxins

The ammodytoxins (Atxs) are neurotoxic phospholipases which occur in Vipera ammodytes ammodytes (Vaa) snake venom. There are three Atx isoforms, A, B, and C, which differ in only five amino acid positions at the C-terminus but differ substantially in their toxicity. The objective of this study was to establish an analytical method for unambiguous identification of all three isoforms and to use the method to assess a procedure for purification of the most toxic phospholipase, AtxA, from the venom. Isolation procedure for AtxA consisted of isolation of Atx-cross-reactive material (proteins recognized by anti-Atx antibodies), by use of an affinity column, then cation exchange on CIM (Convective Interaction Media) disks. The purification procedure was monitored by means of reversed-phase chromatography (RPC) and mass spectrometry (MS). Although previous cation exchange of the pure isoforms enabled separate elution of AtxA from B and C, separation of AtxA from Atxs mixture was not accomplished. RPC was not able to separate the Atx isoforms, whereas an MS based approach proved to be more powerful. Peptides resulting from tryptic digestion of Atxs which enable differentiation between the three isoforms were successfully detected and their sequences were confirmed by post-source decay (PSD) fragmentation. Separation of Atx isoforms by ion-exchange chromatography is most presumably prevented by Atxs heterodimer formation. The tendency of Atxs to form homodimers and heterodimers of similar stability was confirmed by molecular modeling.     

One target, different effects: a comparison of distinct therapeutic antibodies against the same targets

To date, more than 30 antibodies have been approved worldwide for therapeutic use. While the monoclonal antibody market is rapidly growing, the clinical use of therapeutic antibodies is mostly limited to treatment of cancers and immunological disorders. Moreover, antibodies against only five targets (TNF-α, HER2, CD20, EGFR, and VEGF) account for more than 80 percent of the worldwide market of therapeutic antibodies. The shortage of novel, clinically proven targets has resulted in the development of many distinct therapeutic antibodies against a small number of proven targets, based on the premise that different antibody molecules against the same target antigen have distinct biological and clinical effects from one another. For example, four antibodies against TNF-α have been approved by the FDA -- infliximab, adalimumab, golimumab, and certolizumab pegol -- with many more in clinical and preclinical development. The situation is similar for HER2, CD20, EGFR, and VEGF, each having one or more approved antibodies and many more under development. This review discusses the different binding characteristics, mechanisms of action, and biological and clinical activities of multiple monoclonal antibodies against TNF-α, HER-2, CD20, and EGFR and provides insights into the development of therapeutic antibodies.     

Novel lithocholaphanes: Syntheses, NMR, MS, and molecular modeling studies

Novel head-to-head lithocholaphanes 6 and 11 have been synthesized via precursors 1–5 and 7–10 with overall good yields, and characterized by ¹H, ¹³C, and ¹⁵N NMR spectroscopy, ESI-TOF mass spectrometry, thermal analysis, and molecular modeling. In addition, the binding abilities of 6 and 11 towards alkali metal cations have been investigated via competitive complexation studies using equimolar mixtures of Li⁺, Na⁺, K⁺, and Rb⁺-cations, and cholaphanes 6 and 11. The formation of cation–cholaphane adducts was detected by ESI-TOF mass spectrometry. The trends in these comparative binding studies are nicely reproduced theoretically with PM3 energetically optimized structures of 6 and 11 and their interaction energies with alkali metal cations calculated by molecular mechanics. Cholaphane 11 possessing a peptoid type structural fragment, –(CH₂CONHCH₂CH₂)₂O–, as a coordination sphere, shows binding tendency towards lithium and sodium cations, whereas 6 possessing an ester type, –(CH₂OCOCH₂)₂O–, moiety and a bigger cavity size than 11, shows merely a tendency towards bigger alkali metal cations, potassium and rubidium.