ALARM NMR: a rapid and robust experimental method to detect reactive false positives in biochemical screens

High-throughput screening (HTS) of large compound collections typically results in numerous small molecule hits that must be carefully evaluated to identify valid drug leads. Although several filtering mechanisms and other tools exist that can assist the chemist in this process, it is often the case that costly synthetic resources are expended in pursuing false positives. We report here a rapid and reliable NMR-based method for identifying reactive false positives including those that oxidize or alkylate a protein target. Importantly, the reactive species need not be the parent compound, as both reactive impurities and breakdown products can be detected. The assay is called ALARM NMR (a La assay to detect reactive molecules by nuclear magnetic resonance) and is based on monitoring DTT-dependent (13)C chemical shift changes of the human La antigen in the presence of a test compound or mixture. Extensive validation has been performed to demonstrate the reliability and utility of using ALARM NMR to assess thiol reactivity. This included comparing ALARM NMR to a glutathione-based fluorescence assay, as well as testing a collection of more than 3500 compounds containing HTS hits from 23 drug targets. The data show that current in silico filtering tools fail to identify more than half of the compounds that can act via reactive mechanisms. Significantly, we show how ALARM NMR data has been critical in identifying reactive compounds that would otherwise have been prioritized for lead optimization. In addition, a new filtering tool has been developed on the basis of the ALARM NMR data that can augment current in silico programs for identifying nuisance compounds and improving the process of hit triage.     

Nickel(II)-phenoxyl radical complexes: structure-radical stability relationship

Nickel(II) complexes of N3O-donor tripodal ligands, 2,4-di-tert-butyl-6-[([bis(2-pyridyl)methyl]amino)methyl]phenol (HtbuL), 2,4-di-tert-butyl-6-[([(6-methyl-2-pyridyl)methyl](2-pyridylmethyl)amino)methyl]phenol (HtbuLMepy), and 2,4-di-tert-butyl-6-[([bis(6-methyl-2-pyridyl)methyl]amino)methyl]phenol (HtbuL(Mepy)2), were prepared, and [Ni(tbuL)Cl(H2O)] (1), [Ni(tbuLMepy)Cl] (2), and [Ni(tbuL(Mepy)2)Cl] (3) were structurally characterized by the X-ray diffraction method. Complexes 1 and 3 have a mononuclear structure with a coordinated phenolate moiety, while 2 has a dinuclear structure bridged by two chloride ions. The geometry of the Ni(II) center was found to be octahedral for 1 and 2 and 5-coordinate trigonal bipyramidal for 3. Complexes 1-3 exhibited similar absorption spectra in CH3CN, indicating that they all have a mononuclear structure in solution. They were converted to the phenoxyl radicals upon oxidation with Ce(IV), giving a phenoxyl radical pi-pi transition band at 394-407 nm. ESR spectra at low temperature and resonance Raman spectra established that the radical species has a Ni(II)-phenoxyl radical bond. The cyclic voltammograms showed a quasi-reversible redox wave at E1/2=0.46-0.56 V (vs Ag/AgCl) corresponding to the formation of the phenoxyl radical, which displayed a first-order decay with a half-life of 45 min at room temperature for 1 and 26 and 5.9 min at -20 degrees C for 2 and 3, respectively. The radical stability increased with the donor ability of the N ligands.     

Ultrafast exciton relaxation in microcrystalline pentacene films

The exciton dynamics in microcrystalline pentacene films is investigated by transient absorption measurements with 30 fs time resolution. It is found that the emission from photoexcited Frenkel excitons decays within 70 fs due to the ultrafast formation of an excitonic species with a strongly reduced transition dipole to the ground state and an absorption dipole in the plane of the film. We propose that an excimer exciton is formed and stabilized by changes of the local crystal structure. The subsequent dynamics is dominated by diffusion controlled annihilation and trapping.     

Characterisation of temperature-dependent phase transitions in 2,2-trimethylenedioxy- 4,4,6,6-tetrachlorocyclotriphosphazene, N3P3Cl4[O(CH2)3O]

Background  

The crystal structure of 2,2-trimethylenedioxy-4,4,6,6-tetrachlorocyclo triphosphazene has been determined at 120, 274 and 293 K. The result at 293 K confirms the room temperature Cmc2 ₁ structure, but at the lower temperatures the space group is Pna2 ₁. Nevertheless the basic structure remains the same, with only small displacements of the atoms, amounting to an average of 25 pm between 120 and 293 K.     

Insertion of Amides into a Polyoxometalate

POM alert : The incorporation of an amide oxygen atom into the framework of the Dawson‐type polyoxometalate (POM) cluster [P₂V₃W₁₅O₆₂]^9? (see picture) allows the communication of electronic effects between the organic and the inorganic parts of the molecule, including fine‐tuning of the redox properties of the entire hybrid POM by the organic components, and transmission of the POM's electron‐attracting properties to the organic moiety.

     

Investigation of Structural Relationships between Racemic Alkali and Ammonium Hydrogen Tartrates and their Chiral Counterparts

Single crystals of racemic anhydrous alkali and ammonium hydrogen tartrates of the composition M(C₄H₅O₆) with M = K, Rb, Cs, NH₄ as well as M_xM′_1?x(C₄H₅O₆) with {M = K, M′ = Rb, x = 0.5}, {M = K, M′ = NH₄, x = 0.56} and {M = Rb, M′ = NH₄, x = 0.61} were obtained from the reaction of D,L‐tartaric acid with the corresponding hydroxides MOH and / or M′OH. These compounds form an isostructural series (monoclinic, P2₁/c, Z = 4). The structures consist of alternating tartrate anion layers and cation layers. Each tartrate layer is held together by a number of hydrogen bonds and contains exclusively either the D or the L‐form of the tartrate. Structural analogies between these crystals and their chiral counterparts are investigated. The smilarity of cell parameters between racemic and chiral structures is shown to be a consequence of certain packing features that occur in both groups.