Protein abundance quantification in embryonic stem cells using incomplete metabolic labelling with 15N amino acids,matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry,and analysis of relative isotopologue abundances of peptides

An isotope dilution method for protein quantification is presented in the context of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) and mass fingerprinting experiments, revealing an unappreciated high reproducibility and accuracy of relative peak intensity measurements. Labelled proteins were generated by growing cells in a medium containing (15)N-enriched amino acids, and were mixed with proteins of natural isotopic composition from control cells in ratios of approximately 0:1, 1:7, 1:2, 2:1, 7:1, and 1:0 (labelled/unlabelled). Mixtures were separated by two-dimensional gel electrophoresis and analysed by MALDI-TOFMS using typical experimental conditions. A linear relationship is demonstrated between the relative isotopologue abundances (RIA values) for particular peaks in the isotopic distribution of tryptic peptide fragments of the proteins, and the mole fractions of labelled proteins in the mixture. Analysis of RIA values (ARIA quantification) for peptides of six typical silver-stained protein spots for the various mixtures could reproduce the experimentally contrived ratios with approximate errors between 4% (2:1 mixture) and about 18% (1:7 mixture). A consideration of error and its propagation is discussed. ARIA does not require complete separation of the isotope patterns of labelled and unlabelled peptides, and is therefore advantageous in combination with all kinds of labelling experiments in biological systems, because it is compatible with minimal metabolic incorporation of labelling reagent. Simulations indicate that the minimum required (15)N enrichment of the total amino acid pool sufficient for ARIA is less than 4%. In an accompanying paper in this issue, we apply ARIA to proteins differentially labelled with isotope-coded alkylation reagents.     

Preparative Scale Applications of C−H Activation in Medicinal Chemistry

C−H activation is an attractive methodology to increase molecular complexity without requiring substrate prefunctionalization. In contrast to well-established cross-coupling methods, C−H activation is less explored on large scales and its use in the production of pharmaceuticals faces substantial hurdles. However, the inherent advantages, such as shorter synthetic routes and simpler starting materials, motivate medicinal chemists and process chemists to overcome these challenges, and exploit C−H activation steps for the synthesis of pharmaceutically relevant compounds. In this review, we will cover examples of drugs/drug candidates where C−H activation has been implemented on a preparative synthetic scale (range between 355 mg and 130 kg). The optimization processes will be described, and each example will be examined in terms of its advantages and disadvantages, providing the reader with an in-depth understanding of the challenges and potential of C−H activation methodologies in the production of pharmaceuticals.     

Mechanical Reversibility of Strain‐Promoted Azide–Alkyne Cycloaddition Reactions

Mechanophores, that is, molecules that show a defined response to force, are crucial building blocks of mechanoresponsive materials. The possibility of mechanically induced cycloreversion for a series of triazoles formed via strain‐promoted azide–alkyne cycloaddition reactions was investigated by density functional theory calculations, and these triazoles were compared to the 1,4‐ and 1,5‐regioisomers formed in the reaction of an azide with a terminal alkyne. We show that cycloreversion is in principal possible and that the pulling geometry is the most important parameter that determines the probability of cycloreversion. We further compared triazole stability to the mechanical stability of polymers that are frequently used as force transducers in mechanochemical experiments and identified DIBAC (azadibenzylcyclooctyne) as a promising mechanophore for future applications.     

On the Nature of Bridging Metal Atoms in Intermetalloid Clusters: Synthesis and Structure of the Metal‐Atom‐Bridged Zintl Clusters [Sn(Ge9)2]4− and [Zn(Ge9)2)]6−

The addition of Sn and Zn ions to [Ge₉] clusters by reaction of [Ge₉]^4? with SnPh₂Cl₂, ZnCp*₂ (Cp*=pentamethylcyclopentadienyl), or Zn₂[HC(Ph₂P=NPh)₂]₂ is reported. The resulting Sn‐ and Zn‐bridged clusters [(Ge₉)M(Ge₉)]^q? (M=Sn, q=4; M=Zn, q=6) display various coordination modes. The M atoms that coordinate to the open square of a C_4v‐symmetric [Ge₉] cluster form strong covalent multicenter M?Ge bonds, in contrast to the M atoms coordinating to triangular cluster faces. Molecular orbital analyses show that the M atoms of the Ge₉M fragments coordinate to a second [Ge₉] cluster with similar orbitals but in different ways. The [Ge₉Sn]^2?unit donates two electrons to the triangular face of a second [Ge₉]^2? cluster with D_3h symmetry, whereas [Ge₉Zn]^2?acts as an electron acceptor when interacting with the triangular face of a D_3h‐symmetric [Ge₉]^4? unit.     

On the Reactivity of Silylated Ge9 Clusters: Synthesis and Characterization of [ZnCp*(Ge9{Si(SiMe3)3}3)], [CuPiPr3(Ge9{Si(SiMe3)3}3)], and [(CuPiPr3)4{Ge9(SiPh3)2}2]

We report on the synthesis of new derivatives of silylated clusters of the type [Ge₉(SiR₃)₃]^? (R = SiMe₃, Me = CH₃; R = Ph, Ph = C₆H₅) as well as on their reactivity towards copper and zinc compounds. The silylated cluster compounds were synthesized by heterogeneous reactions starting from the Zintl phase K₄Ge₉. Reaction of K[Ge₉{Si(SiMe₃)₃}₃] with ZnCl₂ leads to the already known dimeric compound [Zn(Ge₉{Si(SiMe₃)₃}₃)₂] ( 1 ), whereas upon the reaction with [ZnCp*₂] the coordination of [ZnCp*]⁺ to the cluster takes place (Cp*=1,2,3,4,5‐pentamethylcyclopentadienyl) under the formation of [ZnCp*(Ge₉{Si(SiMe₃)₃}₃)] ( 2 ). A similar reaction leads to [CuPiPr₃(Ge₉{Si(SiMe₃)₃}₃)] ( 3 ) from [CuPiPr₃Cl] (iPr=isopropyl). Further we investigated the novel silylated cluster units [Ge₉(SiPh₃)₃]^? ( 4 ) and [Ge₉(SiPh₃)₂]^? ( 5 ), which could be identified by mass spectroscopy. Bis‐ and tris‐silylated species can be synthesized by the respective stoichiometric reactions, and the products were characterized by ESI‐MS and NMR experiments. These clusters show rather different reactivity. The reaction of the tris‐silylated anion 4 with [CuPiPr₃Cl] leads to [(CuPiPr₃)₃Ge₉(SiPh₃)₂]⁺ as shown from NMR experiments and to [(CuPiPr₃)₄{Ge₉(SiPh₃)₂}₂] ( 6 ), which was characterized by single‐crystal X‐ray diffraction. Compound 6 shows a new type of coordination of the Cu atoms to the silylated Zintl clusters.     

High content screening for G protein-coupled receptors using cell-based protein translocation assays

G protein-coupled receptors (GPCRs) have been one of the most productive classes of drug targets for several decades, and new technologies for GPCR-based discovery promise to keep this field active for years to come. While molecular screens for GPCR receptor agonist- and antagonist-based drugs will continue to be valuable discovery tools, the most exciting developments in the field involve cell-based assays for GPCR function. Some cell-based discovery strategies, such as the use of beta-arrestin as a surrogate marker for GPCR function, have already been reduced to practice, and have been used as valuable discovery tools for several years. The application of high content cell-based screening to GPCR discovery has opened up additional possibilities, such as direct tracking of GPCRs, G proteins and other signaling pathway components using intracellular translocation assays. These assays provide the capability to probe GPCR function at the cellular level with better resolution than has previously been possible, and offer practical strategies for more definitive selectivity evaluation and counter-screening in the early stages of drug discovery. The potential of cell-based translocation assays for GPCR discovery is described, and proof-of-concept data from a pilot screen with a CXCR4 assay are presented. This chemokine receptor is a highly relevant drug target which plays an important role in the pathogenesis of inflammatory disease and also has been shown to be a co-receptor for entry of HIV into cells as well as to play a role in metastasis of certain cancer cells.     

The first report on a convenient synthesis of novel reactive amphiphilic polysaccharides

New amphiphiles with reactive tosylate groups and ionic sulfuric acid half esters based on the rod-like polysaccharide cellulose were designed via homogeneous tosylation followed by sulfation with the SO₃-pyridine complex in N,N-dimethylacetamide. At appropriate degrees of functionalization the polymers are soluble both in water and dimethyl sulfoxide, and they are promising starting materials for self-organizing systems.