Probing BRD Inhibition Substituent Effects in Bulky Analogues of (+)-JQ1

A series of bulky organometallic and organic analogues of the bromodomain (BRD) inhibitor (+)-JQ1 have been prepared. The most potent, N-[(adamantan-1-yl)methyl]-2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetraazatricyclo[8.3.0.02,6]trideca-2(6),4,7,10,12-pentaen-9-yl]acetamide, 2e , showed excellent potency with an K_D=ca. 130 nm vs. BRD4(1) and a ca. 2-fold selectivity over BRD4(2) (K_D=ca. 260 nm ). Its binding to the first bromodomain of BRD4 was determined by a protein cocrystal structure.     

Differentiation of Monofloral Honey Using Volatile Organic Compounds by HS-GCxIMS

Honey is a natural product and can be described by its botanical origin, determined by the plants from which the bees collect nectar. It significantly influences the taste of honey and is often used as a quality criterion. Unfortunately, this opens up the possibility of food fraud. Currently, various methods are used to check the authenticity of monofloral honey. The laborious, manual melissopalynology is considered an essential tool in the verification process. In this work, the volatile organic compounds obtained from the headspace of honey are used to prove their authenticity. The headspace of 58 honey samples was analyzed using a commercial easy-to-use gas chromatography-coupled ion mobility spectrometer with a headspace sampler (HS-GCxIMS). The honey samples were successfully differentiated by their six different botanical origins using specific markers with principal component analysis in combination with linear discriminant analysis. In addition, 15 honey-typical compounds were identified using measurements of reference compounds. Taking a previously published strategy, retention times of marker compounds were correlated with GC-coupled mass spectrometry (GC-MS) measurements to assist in the identification process.     

Partially Saturated Bicyclic Heteroaromatics as an sp3‐Enriched Fragment Collection

Fragment‐based lead generation has proven to be an effective means of identifying high‐quality lead compounds for drug discovery programs. However, the fragment screening sets often used are principally comprised of sp²‐rich aromatic compounds, which limits the structural (and hence biological) diversity of the library. Herein, we describe strategies for the synthesis of a series of partially saturated bicyclic heteroaromatic scaffolds with enhanced sp³ character. Subsequent derivatization led to a fragment collection featuring regio‐ and stereo‐controlled introduction of substituents on the saturated ring system, often with formation of new stereocenters.     

Dizinc Lactide Polymerization Catalysts: Hyperactivity by Control of Ligand Conformation and Metallic Cooperativity

Understanding how to moderate and improve catalytic activity is critical to improving degradable polymer production. Here, di‐ and monozinc catalysts, coordinated by bis(imino)diphenylamido ligands, show remarkable activities and allow determination of the factors controlling performance. In most cases, the dizinc catalysts significantly out‐perform the monozinc analogs. Further, for the best dizinc catalyst, the ligand conformation controls activity: the catalyst with “folded” ligand conformation shows turnover frequency (TOF) values up to 60 000 h^?1 (0.1 mol % loading, 298 K, [LA]=1 m ), whilst that with a “planar” conformation is much slower, under similar conditions (TOF=30 h^?1). Dizinc catalysts also perform very well under immortal conditions, showing improved control, and are able to tolerate loadings as low as 0.002 mol % whilst conserving high activity (TOF=12 500 h^?1).     

Non-Covalent Interactions Enforce Conformation in Switchable and Water-Soluble Diketopiperazine-Pyridine Foldamers

To reach their potential as mimics of the dynamic molecules present in biological systems, foldamers must be designed to display stimulus-responsive behavior. Here we report such a foldamer architecture based on alternating pyridine-diketopiperazine linkers. Epimerization is conveniently prevented through a copper-catalyzed coupling protocol. The compounds’ native unswitched conformation is first discovered in the solid and solution state. The foldamers can be solubilized in DMSO and pH 9.5 buffer, retaining conformational control to a large degree. Lastly, dynamic switching is demonstrated through treatment with acid, leading to behaviour we describe as stimulus-responsive sidechain reconfiguration.     

Data-Dependent Acquisition with Precursor Coisolation Improves Proteome Coverage and Measurement Throughput for Label-Free Single-Cell Proteomics**

We combined efficient sample preparation and ultra-low-flow liquid chromatography with a newly developed data acquisition and analysis scheme termed wide window acquisition (WWA) to quantify >3,000 proteins from single cells in rapid label-free analyses. WWA employs large isolation windows to intentionally co-isolate and co-fragment adjacent precursors along with the selected precursor. Optimized WWA increased the number of MS2-identified proteins by ≈40 % relative to standard data-dependent acquisition. For a 40-min LC gradient operated at ≈15 nL/min, we identified an average of 3,524 proteins per single-cell-sized aliquot of protein digest. Reducing the active gradient to 20 min resulted in a modest 10 % decrease in proteome coverage. Using this platform, we compared protein expression between single HeLa cells having an essential autophagy gene, atg9a, knocked out, with their isogenic WT parental line. Similar proteome coverage was observed, and 268 proteins were significantly up- or downregulated. Protein upregulation primarily related to innate immunity, vesicle trafficking and protein degradation.     

Acid-base titrations of functional groups on the surface of the thermophilic bacterium Anoxybacillus flavithermus: comparing a chemical equilibrium model with ATR-IR spectroscopic data

Acid-base functional groups at the surface of Anoxybacillus flavithermus (AF) were assigned from the modeling of batch titration data of bacterial suspensions and compared with those determined from in situ infrared spectroscopic titration analysis. The computer program FITMOD was used to generate a two-site Donnan model (site 1: pKa = 3.26, wet concn = 2.46 x 10(-4) mol g(-1); site 2: pKa = 6.12, wet concn = 6.55 x 10(-5) mol g(-1)), which was able to describe data for whole exponential phase cells from both batch acid-base titrations at 0.01 M ionic strength and electrophoretic mobility measurements over a range of different pH values and ionic strengths. In agreement with information on the composition of bacterial cell walls and a considerable body of modeling literature, site 1 of the model was assigned to carboxyl groups, and site 2 was assigned to amino groups. pH difference IR spectra acquired by in situ attenuated total reflection infrared (ATR-IR) spectroscopy confirmed the presence of carboxyl groups. The spectra appear to show a carboxyl pKa in the 3.3-4.0 range. Further peaks were assigned to phosphodiester groups, which deprotonated at slightly lower pH. The presence of amino groups could not be confirmed or discounted by IR spectroscopy, but a positively charged group corresponding to site 2 was implicated by electrophoretic mobility data. Carboxyl group speciation over a pH range of 2.3-10.3 at two different ionic strengths was further compared to modeling predictions. While model predictions were strongly influenced by the ionic strength change, pH difference IR data showed no significant change. This meant that modeling predictions agreed reasonably well with the IR data for 0.5 M ionic strength but not for 0.01 M ionic strength.     

Carboxylation of an ansa-zirconocene dinitrogen complex: regiospecific hydrazine synthesis from N2 and CO2

Addition of 2 equiv of carbon dioxide to the ansa-zirconocene dinitrogen complex resulted in selective insertion into each zirconium nitrogen bond, forming a C2 symmetric dicarboxylated diazenido compound. Treatment with excess Me3SiI furnished the ansa-zirconocene diiodide along with the N,N'-dicarboxylated silylated hydrazine. New nitrogen-carbon bonds were also assembled by addition of methyl triflate. Tri- and tetrasubstituted hydrazines could be formed by treatment with water and Me3SiI, respectively. The regiochemistry of the N2 carboxylation is controlled by the ansa-cyclopentadienyl ligand where the sterically demanding tert-butyl substituents and the C2 symmetry of the dimer dictates the stereochemistry of CO2 insertion. These results demonstrate the ability of zirconium dinitrogen compounds to participate in heterocumulene insertion chemistry.     

Assessment of new meta and hybrid meta density functionals for predicting the geometry and binding energy of a challenging system: the dimer of H2S and benzene

Noncovalent interactions of a hydrogen bond donor with an aromatic pi system present a challenge for density functional theory, and most density functionals do not perform well for this kind of interaction. Here we test seven recent density functionals from our research group, along with the popular B3LYP functional, for the dimer of H 2S with benzene. The functionals considered include the four new meta and hybrid meta density functionals of the M06 suite, three slightly older hybrid meta functionals, and the B3LYP hybrid functional, and they were tested for their abilities to predict the dissociation energies of three conformations of the H 2S-benzene dimer and to reproduce the key geometric parameters of the equilibrium conformation of this dimer. All of the functionals tested except B3LYP correctly predict which of the three conformations of the dimer is the most stable. The functionals that are best able to reproduce the geometry of the equilibrium conformation of the dimer with a polarized triple-zeta basis set are M06-L, PWB6K, and MPWB1K, each having a mean unsigned relative error across the two experimentally verifiable geometric parameters of only 8%. The success of M06-L is very encouraging because it is a local functional, which reduces the cost for large simulations. The M05-2X functional yields the most accurate binding energy of a conformation of the dimer for which a binding energy calculated at the CCSD(T) level of theory is available; M05-2X gives a binding energy for the system with a difference of merely 0.02 kcal/mol from that obtained by the CCSD(T) calculation. The M06 functional performs well in both categories by yielding a good representation of the geometry of the equilibrium structure and by giving a binding energy that is only 0.19 kcal/mol different from that calculated by CCSD(T). We conclude that the new generation of density functionals should be useful for a variety of problems in biochemistry and materials where aromatic functional groups can serve as hydrogen bond acceptors.