A computational study on cannabinoid receptors and potent bioactive cannabinoid ligands: homology modeling,docking, de novo drug design and molecular dynamics analysis

When X-ray structure of a ligand-bound receptor is not available, homology models of the protein of interest can be used to obtain the ligand-binding cavities. The steroelectronic properties of these cavities are directly related to the performed molecular model coordinates. Thus, the use of different template structures for homology may result in variation of ligand-binding modes. We have recently reported the MD simulations of a potent CB ligand at bovine rhodopsin-based CB1 and CB2 receptors (Durdagi et al., Bioorg Med Chem 16:7377–7387, 2008). In this present study, a homology modeling study based on the β2-adrenergic receptor for both CB1 and CB2 receptors was performed, and the results were compared with rhodopsin-based models. In addition, the role of membrane bilayers to the adopted conformations of potent AMG3 CB ligand has been analyzed for receptor-free and membrane-associated receptor systems. The performed MD trajectory analysis results have shown that gauche conformations at the terminal segment of the alkyl side chain of AMG3 are not favored in solution. Different adopting dihedral angles defined between aromatic and dithiolane rings at the active sites of the CB1 and CB2 receptors, which are adapted lead to different alkyl side chain orientations and thus, may give clues to the medicinal chemists to synthesize more selective CB ligands. The binding sites of receptors derived by rhodopsin-based models have been regenerated using the β2-adrenergic based template receptors. The re-obtained models confirmed the ligand-binding pockets that were derived based on rhodopsin.     

Temperature and Rate effects in Finite Viscoplasticity of Glassy Polymers at Different Deformation Modes: Experiments and Simulations

The non–linear inelastic response of glassy polymers is highly influenced by the three–dimensional deformation state, the temperature and the strain rate at which they are deformed. The contribution presents new experiments for different deformation modes which are carried out at different temperatures and rates on commercial bis–phenol A polycarbonate. Emphasis is put not only on the experimental results by themselves but also on the setup and the technique employed in the obtention of the data. The effect of temperature on the velocity with which the neck propagates along the gaged section of a flat specimen under tension is studied means a facility based on photogrammetry. From the homogeneous compression experiments a single set of material parameters appearing in a constitutive model based on the distributed free volume theory under the frame work of additive kinematics will be identified. The inhomogeneous experimental results serve then as a validation for 3–D simulations since the non–uniform strain distribution on the surfaces of both, simulations and experiments, can be compared. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)     

From Dark to Light to Fluorescence Resonance Energy Transfer (FRET): Polarity‐Sensitive Aggregation‐Induced Emission (AIE)‐Active Tetraphenylethene‐Fused BODIPY Dyes with a Very Large Pseudo‐Stokes Shift

The work presented herein is devoted to the fabrication of large Stokes shift dyes in both organic and aqueous media by combining dark resonance energy transfer (DRET) and fluorescence resonance energy transfer (FRET) in one donor–acceptor system. In this respect, a series of donor–acceptor architectures of 4,4‐difluoro‐4‐bora‐3a,4a‐diaza‐s‐indacene (BODIPY) dyes substituted by one, two, or three tetraphenylethene (TPE) luminogens were designed and synthesised. The photophysical properties of these three chromophore systems were studied to provide insight into the nature of donor–acceptor interactions in both THF and aqueous media. Because the generation of emissive TPE donor(s) is strongly polarity dependent, due to its aggregation‐induced emission (AIE) feature, one might expect the formation of appreciable fluorescence emission intensity with a very large pseudo‐Stokes shift in aqueous media when considering FRET process. Interestingly, similar results were also recorded in THF for the chromophore systems, although the TPE fragment(s) of the dyes are non‐emissive. The explanation for this photophysical behaviour lies in the DRET. This is the first report on combining two energy‐transfer processes, namely, FRET and DRET, in one polarity‐sensitive donor–acceptor pair system. The accuracy of the dark‐emissive donor property of the TPE luminogen is also presented for the first time as a new feature for AIE phenomena.     

Axial-ligation and macrocyclization of novel (E,E)-dioximes of nickel(II) palladium(II), platinum(II) and cobalt(III)

Summary The synthesis and characterization of new Ni^II, Pd^II, Pt^II and Co^III complexes, with the BF _inf2 ^sup+ -bridged,bis(-di-oximato) ligands are described. The initially formed six-coordinate hydrogen-bonded macrocycles, were used as metal templates to prepare the corresponding BF _inf2 ^sup+ - capped macrocycles. The complexes were characterized by¹H-n.m.r. and i.r. spectroscopy, and by elemental analysis.     

Synthesis and Characterization of Mono- and Trinuclear Complexes of BF2+ Bridged Macrocycles

Dibenzo[e,k]-2,3-bis(hydroxyimino)-1,4-dithia-7,10-diaza-2,3,8,9-tetrahydrocyclododecine (H₂L) has been prepared from 1,2-bis(o-mercaptoanilino) ethane ( 4 ) and (E,E)-dichloroglyoxime. A mononuclear complex with a metal: ligand ratio of 1:2 has been isolated for cobalt(III). The Co^III complex of H₂L has been prepared with L′ = 2,6-lutidine, and with a chlorine ion as axial ligands. In addition to that, the synthesis of a new cobalt complex which contains BF₂⁺ bridges is achieved with the bis(E,E)-dioxime ligand. The trinuclear complex of this Co^III complex has been obtained by the reaction of BF₂⁺ bridged Co^III complex with Pd[bis(benzonitrile)]Cl₂. The structures of these complexes and (E,E)-dioxime were identified by using elemental analysis, ¹H and ¹³C-NMR, IR and MS spectral data.     

A new vicinal-dioxime and its mono and trinuclear complexes containing the monoazatetraoxa macrocyclic moiety

Mononuclear [Co(HL)2LCl)], [Co(LBF2)2LCl] or [Cu-(HL)2] H2L = {N,N-bis (4-N-phenylaza [15]crown-5)diaminoglyoxime} and a trinuclear, [Cu(L)2(CuL)2](NO3)2, complex of the ligand were synthesized and characterized. The mononuclear copper(II) species coordinates to two copper(II) ions through the deprotonated oximate oxygens to yield a trinuclear structure cis-bridged by the oximate groups, with 1,10-phenanthroline as an end-cap ligand. The terminal copper adopts an essentially planar configuration with the nitrogen atoms of H2L. The structure of the ligand and its complexes is proposed and formulated according to the elemental analyses, 1H- and 13C-n.m.r, i.r. and m.s. spectral data.     

3D QSAR/CoMFA and CoMSIA studies on antileukemic steroidal esters coupled with conformationally flexible nitrogen mustards

Thirty-eight antileukemic steroidal esters possessing conformationally flexible nitrogen mustards were studied, and the 3D QSAR/CoMFA and CoMSIA methodologies were applied in order to derive the correlation between their structure and the in vivo antileukemic activity. These compounds show significantly reduced toxicity and possibly increased bioavailability compared to free nitrogen mustards and therefore constitute potent antileukemic drugs. Both the CoMFA and CoMSIA studies gave similar results indicating that the steric effect and the hydrophobic/hydrophilic balance especially in the steroidal part of the molecules probably determined their bioactivity. Of paramount interest is the observation that the orientation of the alkylating part of the SMEs toward the surface of ring B of the steroidal skeleton was related with increased activity. Concerning the steroidal part, the presence of hydrophobic groups in rings B and D was found to be important for enhanced activity. Enhancement of antileukemic potency is further observed if hydrophilic/H-bond acceptor groups are present at the positions 7 and 17 of the steroidal skeleton. Leapfrog simulations provided novel compounds which lead our future synthetic endeavor for obtaining SMEs with optimum bioactivity.