Target Identification for Small Bioactive Molecules: Finding the Needle in the Haystack

Identification and confirmation of bioactive small‐molecule targets is a crucial, often decisive step both in academic and pharmaceutical research. Through the development and availability of several new experimental techniques, target identification is, in principle, feasible, and the number of successful examples steadily grows. However, a generic methodology that can successfully be applied in the majority of the cases has not yet been established. Herein we summarize current methods for target identification of small molecules, primarily for a chemistry audience but also the biological community, for example, the chemist or biologist attempting to identify the target of a given bioactive compound. We describe the most frequently employed experimental approaches for target identification and provide several representative examples illustrating the state‐of‐the‐art. Among the techniques currently available, protein affinity isolation using suitable small‐molecule probes (pulldown) and subsequent mass spectrometric analysis of the isolated proteins appears to be most powerful and most frequently applied. To provide guidance for rapid entry into the field and based on our own experience we propose a typical workflow for target identification, which centers on the application of chemical proteomics as the key step to generate hypotheses for potential target proteins.     

Synthesis of Maleimide‐Functionalyzed HPMA‐Copolymers and in vitro Characterization of the aRAGE‐ and Human Immunoglobulin (huIgG)–Polymer Conjugates

Herein the synthesis of antibody–polymer conjugates, with a quite narrow dispersity based on the polymer HPMA, are reported. These conjugates are synthesized by coupling antibodies to maleimide‐functionalized poly(N‐(2‐hydroxypropyl)‐methacrylamide) (poly‐HPMA) copolymers derived through reversible addition‐fragmentation chain transfer (RAFT) polymerization of pentafluorophenyl methacrylate via the intermediate step of an activated ester polymer. We develop a protocol that allows the attachment of two different model antibodies, monoclonal anti‐RAGE (receptor for advanced glycation end‐products) antibody, and polyclonal human immunoglobulin (huIgG). Modification of the antibody and conjugation is monitored by SDS‐PAGE electrophoresis. Preserved affinity is demonstrated by Western Blott and cell‐uptake analysis, for example, to cells of the immune system.

     

Use of intonation contours for speech recognition in noise by cochlear implant recipients

The corruption of intonation contours has detrimental effects on sentence-based speech recognition in normal-hearing listeners Binns and Culling [(2007). J. Acoust. Soc. Am. 122, 1765-1776]. This paper examines whether this finding also applies to cochlear implant (CI) recipients. The subjects' F0-discrimination and speech perception in the presence of noise were measured, using sentences with regular and inverted F0-contours. The results revealed that speech recognition for regular contours was significantly better than for inverted contours. This difference was related to the subjects' F0-discrimination providing further evidence that the perception of intonation patterns is important for the CI-mediated speech recognition in noise.     

Single‐Stranded DNA: Replacement of Canonical by Base‐Modified Nucleosides in the Minihairpin 5′‐d(GCGAAGC)‐3′ and Constructs with the Aptamer 5′‐d(GGTTGGTGTGGTTGG)‐3′

The minihairpin 5′‐d(GCGAAGC)‐3′ ( 1 ) was modified either in the loop region, in the base‐paired stem, or at the 5′‐terminus by incorporation of base‐modified nucleosides. The thermal melting was correlated to the structural changes induced by the various donor‐acceptor properties of the nucleosides. Overhanging nonpaired nucleosides at the 5′‐terminus stabilized the hairpin, while a reverse of the dG³?dA⁵ sheared base pair to dA³?dG⁵ severely affected the stability. The combination of the minihairpin 5′‐d(GCGAAGC)‐3′ ( 1 ) and the thrombin‐binding aptamer 5′‐d(GGTTGGTGTGGTTGG)‐3′ ( 2 (= 46 )) resulted in the new construct 5′‐d(GGTTGGGCGAAGC GGTTGG)‐3′ ( 43 ) arising by replacement of the 5′‐d(TGT)‐3′ loop of 2 by the minihairpin. The fused oligonucleotide 43 exhibits a two‐phase thermal transition indicating the presence of the two unaltered moieties. According to slight changes of the T_m values of the construct 43 as compared to the separate units 1 and 2 , cooperative distorsions are discussed.     

Investigations of Li-containing SiCN(O) ceramics via 7Li MAS NMR

Lithium-containing silicon (oxy)carbonitride ceramics (SiCN(O):Li) were synthesized via precursor-to-ceramic-transformation of Li-containing (poly)silazanes. The precursors were obtained by lithiation of 2,4,6-trimethyl-2,4,6-trivinylcyclotrisilazane with n-butyllithium and by reaction of a commercial poly(organosilazane) VL20 with metallic lithium. The annealing treatment was carried out at temperatures between 200 and 1400 degrees C in argon (DeltaT=200 degrees C) and yielded Li-containing silicon (oxy)carbonitride. X-ray powder diffraction revealed that the resulting SiCN(O):Li ceramics were basically amorphous up to temperatures of 1000 degrees C and formed LiSi(2)N(3), graphite and silicon carbide as crystalline phases at higher temperatures. (7)Li MAS NMR spectroscopy was carried out to investigate the structure of the Li-containing phases and to study the reaction path of metallic Li with polysilazane. Based on the NMR spectra, there is almost no difference found in the chemical shift of the SiCN(O):Li ceramics obtained at different temperatures. Accordingly, Li is assigned to be mainly coordinated to N and O present as contaminant element. Relaxation time measurements showed that the most mobile Li(+) species seems to be present in the product obtained in the pyrolysis temperature range between 600 and 1000 degrees C.     

Pyrene modification leads to increased catalytic activity in minimal hammerhead ribozymes

Highly active variants of minimal hammerhead ribozymes are generated by the replacement of substantial parts of stem-loop structures with pyrene building blocks.     

The electronic structure of the tris(ethylene) complexes [M(C2H4)3] (M=Ni, Pd, and Pt): a combined experimental and theoretical study

In this article we analyze in detail the electronic properties of the D(3h)-symmetric tris(ethylene) complexes of nickel, palladium, and platinum ([M(C(2)H(4))(3)] M=Ni, Pd, Pt). In the case of [Pd(C(2)H(4))(3)] the analysis is based on new experimental IR and Raman spectra for the matrix-isolated molecules and in all cases on the results of quantum-chemical (DFT) calculations. The experimental spectra collected for [Pd(C(2)H(4))(3)] provide evidence for several previously unobserved vibrational modes, including the in-phase and out-of-phase nu(C-C) and delta(CH(2)) modes, and the in-phase nu(M-C) mode. Special consideration is given to possible inter-ligand interactions. The interaction force constant f(CC,CC) between two C(2)H(4) ligands can be directly estimated from the spectra, and its very small value (0.002 N m(-1)) indicates the absence of any significant inter-ligand interaction. An analysis of the topology of the theoretical electron density distribution, rho(r), and the corresponding Laplacian, nabla(2)rho(r), for [Pd(C(2)H(4))(3)] and its lighter and heavier homologues [Ni(C(2)H(4))(3)] and [Pt(C(2)H(4))(3)], respectively, is in full agreement with the conclusions drawn from the experimental results. The combined experimental and quantum-chemical results provide detailed insights in the electronic properties of these prototypical ethylene complexes.     

V2Cu3Ga8, Mo2Cu3Ga8 and W2Cu3Ga8—New compounds with a novel order variant of a bcc packing and motifs of self-similarity

Single crystals of the new compounds TM₂Cu₃Ga₈ (TM=V, Mo, W) were synthesised from the elements. Structure determinations of the isotypic compounds (cI104, space group , Z=8; Mo₂Cu₃Ga₈: a=11.9171(10) Å, 613 refl., 23 param., R₁(F)=0.022, wR₂(F²)=0.047; W₂Cu₃Ga₈: 11.9248(8) Å, 346 refl., 23 param., R₁(F)=0.048, wR₂(F²)=0.086; V₂Cu₃Ga₈: 11.7861(14) Å, 374 refl., 24 param., R₁(F)=0.033, wR₂(F²)=0.081) showed a new cubic structure type which can be classified as an ordered defect variant of a bcc packing with a^′=4a: [(TM)₂(Cu)₃(□)₃][Ga₈]. The coordination polyhedra of the transition metals consist of Ga₈-cubes with 3 sides capped by Cu leading to coordination number 11. The arrangement of the TMGa₈Cu₃-polyhedra is in a way they form itself a 3-fold capped cube. All compositions were confirmed by EDX measurements.