An automated system for the analysis of G protein-coupled receptor transmembrane binding pockets: alignment, receptor-based pharmacophores, and their application

G protein-coupled receptors (GPCRs) share a common architecture consisting of seven transmembrane (TM) domains. Various lines of evidence suggest that this fold provides a generic binding pocket within the TM region for hosting agonists, antagonists, and allosteric modulators. Here, a comprehensive and automated method allowing fast analysis and comparison of these putative binding pockets across the entire GPCR family is presented. The method relies on a robust alignment algorithm based on conservation indices, focusing on pharmacophore-like relationships between amino acids. Analysis of conservation patterns across the GPCR family and alignment to the rhodopsin X-ray structure allows the extraction of the amino acids lining the TM binding pocket in a so-called ligand binding pocket vector (LPV). In a second step, LPVs are translated to simple 3D receptor pharmacophore models, where each amino acid is represented by a single spherical pharmacophore feature and all atomic detail is omitted. Applications of the method include the assessment of selectivity issues, support of mutagenesis studies, and the derivation of rules for focused screening to identify chemical starting points in early drug discovery projects. Because of the coarseness of this 3D receptor pharmacophore model, however, meaningful scoring and ranking procedures of large sets of molecules are not justified. The LPV analysis of the trace amine-associated receptor family and its experimental validation is discussed as an example. The value of the 3D receptor model is demonstrated for a class C GPCR family, the metabotropic glutamate receptors.     

Inkjet deposition of alkanethiolate monolayers and DNA oligonucleotides on gold: evaluation of spot uniformity by wet etching

Inkjet printing allows localized, contact-free deposition of liquids onto arbitrary substrates. In this article we demonstrate the fast formation of high-quality self-assembled monolayers (SAMs) on gold surfaces. Using a selective etch process, we verify the uniformity of the deposited spots. A direct comparison with microcontact-printed SAMs on Au revealed similar resist quality as inkjet-deposited alkanethiolate SAMs. Likewise, inkjet printing of thiol-functionalized and non-thiolated single-stranded DNA oligomers formed molecular layers protecting Au from etchants. For all compounds used, we achieved etched patterns that were homogeneous and free of defects. These results indicate that an inkjet is a convenient tool for surface functionalization and the direct writing of molecular films and resists.     

Synthesis and α‐Mannosidase Inhibitory Evaluation of (2R,3R,4S)‐ and (2S,3R,4S)‐2‐(Aminomethyl)pyrrolidine‐3,4‐diol Derivatives

The synthesis of 46 derivatives of (2R,3R,4S)‐2‐(aminomethyl)pyrrolidine‐3,4‐diol is reported (Scheme 1 and Fig. 3), and their inhibitory activities toward α‐mannosidases from jack bean (B) and almonds (A) are evaluated (Table). The most‐potent inhibitors are (2R,3R,4S)‐2‐{[([1,1′‐biphenyl]‐4‐ylmethyl)amino]methyl}pyrrolidine‐3,4‐diol ( 3fs ; IC₅₀(B)=5 μM , K_i=2.5 μM ) and (2R,3R,4S)‐2‐{[(1R)‐2,3‐dihydro‐1H‐inden‐1‐ylamino]methyl}pyrrolidine‐3,4‐diol ( 3fu ; IC₅₀(B)=17 μM , K_i=2.3 μM ). (2S,3R,4S)‐2‐(Aminomethyl)pyrrolidine‐3,4‐diol ( 6 , R?H) and the three 2‐(N‐alkylamino)methyl derivatives 6fh, 6fs , and 6f are prepared (Scheme 2) and found to inhibit also α‐mannosidases from jack bean and almonds (Table). The best inhibitor of these series is (2S,3R,4S)‐2‐{[(2‐thienylmethyl)amino]methyl}pyrrolidine‐3,4‐diol ( 6o ; IC₅₀(B)=105 μM , K_i=40 μM ). As expected (see Fig. 4), diamines 3 with the configuration of α‐D ‐mannosides are better inhibitors of α‐mannosidases than their stereoisomers 6 with the configuration of β‐D ‐mannosides. The results show that an aromatic ring (benzyl, [1,1′‐biphenyl]‐4‐yl, 2‐thienyl) is essential for good inhibitory activity. If the C‐chain that separates the aromatic system from the 2‐(aminomethyl) substituent is longer than a methano group, the inhibitory activity decreases significantly (see Fig. 7). This study shows also that α‐mannosidases from jack bean and from almonds do not recognize substrate mimics that are bulky around the O‐glycosidic bond of the corresponding α‐D ‐mannopyranosides. These observations should be very useful in the design of better α‐mannosidase inhibitors.     

Initiation and control of catalytic surface reactions with shaped femtosecond laser pulses

We report on femtosecond laser-induced catalytic reactions of carbon monoxide and hydrogen on single crystal surfaces under high vacuum conditions. Several product molecules are synthesized, among them also species for whose formation at least three reactants are required. By applying closed-loop optimal control, we manipulate these reactions and selectively optimize the ratio of different bond-forming reaction channels, in contrast to previous quantum control experiments aiming at bond-cleavage. Further experiments explore the nontrivial control mechanism and its sensitivity to the relative proportion of the two reactant gases.     

Synthese,Strukturen und X‐/Q‐Band‐EPR‐Untersuchungen von N,N‐Diethyl‐N′‐3,5‐di(trifluormethyl)benzoylthioureato‐Komplexen des CuII,NiII und PdII sowie EPR‐spektroskopische Charakterisierung eines CuII‐CuII‐Dimers

The synthesis and the structures of (i) the ligand N,N‐Diethyl‐N′‐3,5‐di(trifluoromethyl)benzoylthiourea HEt₂dtfmbtu and (ii) the Ni^II and Pd^II complexes of HEt₂dtfmbtu are reported. The ligand coordinates bidendate forming bis chelates. The Ni^II and the Pd^II complexes are isostructural. The also prepared Cu^II complex could not be characterized by X‐ray analysis. However, the preparation of diamagnetically diluted powders Cu/Ni(Et₂dtfmbtu)₂ and Cu/Pd(Et₂dtfmbtu)₂ suitable for EPR studies was successful. The EPR spectra of the Cu/Ni and Cu/Pd systems show noticeable differences for the symmetry of the CuS₂O₂ unit in both complexes: the Cu/Pd system is characterized by axially‐symmetric g< and A ^cu tensors; for the Cu/Ni system g and A ^Cu have rhombic symmetry. EPR studies on frozen solutions of the Cu^II complex show the presence of a Cu^II‐Cu^II dimer which is the first observed for Cu^II acylthioureato complexes up to now. The parameters of the fine structure tensor were used for the estimation of the Cu^II‐Cu^II distance.     

Solvent-free reactions of N,N′-thiocarbonyldiimidazole with ferrocenylcarbinols

The efficient and simple routes for the synthesis of various ferrocenyl derivatives from ferrocenylcarbinols and N,N′-thiocarbonyldiimidazole (TCDI) are described. It involves grinding the two substrates in a Pyrex tube with a glass rod at room temperature. The reaction of ferrocenylmethanol (1a) provided S,S-bis(ferrocenylmethyl)dithiocarbonate (1b), whose crystal structure and a plausible mechanism for its formation are also reported. The reaction of 1-ferrocenyl-1-phenylmethanol (2a) and 1-ferrocenylbutanol (2b) gave the products 2c and 2d, respectively. The reaction of ω-ferrocenyl alcohols 4-ferrocenylphenol (3a) and 6-ferrocenylhexan-1-ol (3b) yielded the products 3c and 3d, respectively. Reaction of 1,1′-ferrocenedimethanol (3e) afforded 3f in moderate yield, and by contrast, it was not similar to 1b. Reaction of [4-(trifluoromethyl)phenyl]methanol (4a) provided the thiocarbonate 4b in good yield.     

配合物(BenzMeIm)2[PtCl4]的合成与表征

通过离子液体氯化1-苄基-3-甲基咪唑（BenzMeIm-Cl）与PtCl₂的反应,合成了配合物（BenzMeIm）₂[PtCl₄],并用元素分析、红外光谱、紫外-可见光谱、¹H NMR、¹³C NMR和单晶X射线衍射对其进行了表征。单晶X射线分析表明,配合物结构属于P2₁/c空间群,晶胞参数和结构解析参数为：a=0.981 80（5）nm,b=0.861 47（3）nm,c=0.144 332（7）nm,β=92.480（2）°,V=121.96（1）nm³,R₁=0.014 4,wR₂=0.038 8。     

Rhenium(I), (III) and (V) complexes of tridentate ONX (X = O,N, S)-donor Schiff bases

The reactions of the potentially tridentate Schiff bases 2-[(2-hydroxyphenyl)iminomethyl]phenol (H₂ono) and 2-(2-aminobenzylideneimino)phenol (H₃onn) with trans-[ReOBr₃(PPh₃)₂] were studied, and the complexes [Re^IIIBr(PPh₃)₂(ono)] (1) and [Re^VBr(PPh₃)₂(onn)]Br (2) were isolated. In 1ono acts as a dianionic tridentate ligand, and in 2onn is coordinated as a tridentate trianionic imido-imino-phenolate. The complex [Re^I(CO)₃(ons)(Hno)] was isolated from the reaction of [Re(CO)₅Br] with 2-[(2-methylthio)benzylideneimino]phenol (Hons; Hno = 2-aminophenol), with ons coordinated as a bidentate chelate with a free SCH₃ group. These complexes were characterized by X-ray crystallography, NMR and IR spectroscopy.