Synthetic and theoretical studies of cyclobuta[1,2:3,4]dicyclopentene. Organocobalt intermediates in the construction of the unsaturated carbon skeleton and their transformation into novel cobaltacyclic complexes by C-C insertion

Theoretical and synthetic studies of the tricyclic 10pi-electron hydrocarbon cyclobuta[1,2:3,4]dicyclopentene (1), a nominally aromatic structure that has never been synthesized, are described. Geometry optimization by density-functional-theory calculations (B3LYP/6-31G(d,p)) predict that 1 is a D(2h) symmetric structure with nonalternant C-C single and double bonds. The calculations also predict that 1 is 4.7 kcal/mol higher in energy than the isomeric hydrocarbon 1,6-didehydro[10]annulene (2), a molecule known to isomerize to 1,5-didehydronaphthalene (4) above -50 degrees C. Calculated enthalpic changes of homodesmotic reactions support the notion that 1 is an aromatic molecule with a resonance stabilization energy (RSE) about half to two-thirds that of benzene on a per-molecule basis. Investigations of potential synthetic pathways to 1 initially utilized as starting material the tricyclic carbonate 11, the product of an intramolecular [2 + 2]-photocyclization reaction. In these studies, 11 was transformed in several steps to the distannane 12, which upon treatment with boron fluoride ethyl etherate is believed to have formed the unstable hydrocarbon bicyclopentadienylidene (13). In an effort to avoid cleavage of the central, four-membered ring of unsaturated tricyclo[5.3.0.0(2,6)]decane intermediates (perhaps the result of 10-electron electrocyclic ring opening of the tetraene 8), synthetic approaches to 1 employing cobalt-cyclobutadiene complexes 18 and 19 were pursued. Treatment of 18 with excess methyllithium led to the novel cobaltacyclic product 30, and dehydration of 19 in the presence of pyridine produced the ring-opening cobaltacyclic product 35. It is proposed that both processes may occur by a 10-electron electrocyclic ring-opening reaction of eta(2)-organocobalt intermediates. These processes may be related to the hypothetical transformation of tetraene 8 to bicyclopentadienylidene (13).     

Physical properties and molecular conformations of indole alkaloids and model protein interactions--theoretical vs. experimental study

The physical properties and molecular structure of five natural indole alkaloids (IAs) and their interaction with protein targets have been studied, experimentally and theoretically. Electronic absorption (EAs) and CD spectroscopy, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS), as well as imaging mass spectrometric techniques (IMS) were used, analyzing the isolated alkaloids and corresponding IAs/protein molecular complexes. Theoretical quantum chemical DFT calculations were also applied. The mechanism of their biological activity and structure-activity relationship as potential neurologically active compounds were studied, using the model interactions with 5HT2A receptors. The gas-phase stable molecular fragments of the IAs are discussed comparing the experimental mass spectrometric data and theoretical quantum chemical DFT calculations of the different molecular fragments of the IAs.     

Second-Generation Covalent TMP-Tag for Live Cell Imaging

Chemical tags are now viable alternatives to fluorescent proteins for labeling proteins in living cells with organic fluorophores that have improved brightness and other specialized properties. Recently, we successfully rendered our TMP-tag covalent with a proximity-induced reaction between the protein tag and the ligand-fluorophore label. This initial design, however, suffered from slow in vitro labeling kinetics and limited live cell protein labeling. Thus, here we report a second-generation covalent TMP-tag that has a fast labeling half-life and can readily label a variety of intracellular proteins in living cells. Specifically, we designed an acrylamide-trimethoprim-fluorophore (A-TMP-fluorophore v2.0) electrophile with an optimized linker for fast reaction with a cysteine (Cys) nucleophile engineered just outside the TMP-binding pocket of Escherichia coli dihydrofolate reductase (eDHFR) and developed an efficient chemical synthesis for routine production of a variety of A-TMP-probe v2.0 labels. We then screened a panel of eDHFR:Cys variants and identified eDHFR:L28C as having an 8-min half-life for reaction with A-TMP-biotin v2.0 in vitro. Finally, we demonstrated live cell imaging of various cellular protein targets with A-TMP-fluorescein, A-TMP-Dapoxyl, and A-TMP-Atto655. With its robustness, this second-generation covalent TMP-tag adds to the limited number of chemical tags that can be used to covalently label intracellular proteins efficiently in living cells. Moreover, the success of this second-generation design further validates proximity-induced reactivity and organic chemistry as tools not only for chemical tag engineering but also more broadly for synthetic biology.     

Application of affinity selection-mass spectrometry assays to purification and affinity-based screening of the chemokine receptor CXCR4

Affinity selection-mass spectrometry (AS-MS) is a sensitive technology for identifying small molecules that bind to target proteins, and assays enabled by AS-MS can be used to delineate relative binding affinities of ligands for proteins. 'Indirect' AS-MS assays employ size-exclusion techniques to separate target-ligand complexes from unbound ligands, and target-associated ligands are then specifically detected by liquid chromatography mass spectrometry. We report how indirect AS-MS binding assays with known reference control compounds were used as guideposts for development of an optimized purification method for CXCR4, a G-protein coupled chemokine receptor, for which we sought novel antagonists. The CXCR4 purification method that was developed was amenable to scale-up and enabled the screening of purified recombinant human CXCR4 against a large combinatorial library of small molecules by high throughput indirect AS-MS. The screen resulted in the discovery of new ligands that competed off binding of reference compounds to CXCR4 in AS-MS binding assays and that antagonized SDF1α-triggered responses and CXCR4-mediated HIV1 viral uptake in cell-based assays. This report provides a methodological paradigm whereby indirect AS-MS-based ligand binding assays may be used to guide optimal integral membrane protein purification methods that enable downstream affinity selection-based applications such as high throughput AS-MS screens.     

Characterization of highly unusual NH+-O hydrogen bonding to ester ether oxygen atoms through spectroscopic and computational studies

We characterize a highly unusual, charged NH-O hydrogen bond formed within esters of 8-(dimethylamino)naphthalen-1-ol in which an ammonium ion serves as an intramolecular hydrogen bond donor to spatially proximate ester ether oxygen atoms. Infrared spectroscopic analysis of the ester carbonyl frequencies demonstrates significant blue-shifting when ether hydrogen bonding is possible, in stark contrast to the more commonly observed red shift that occurs upon hydrogen bonding to the ester carbonyl oxygen. The intrinsic behavior of the linkage (i.e., in which counterions and solvent effects are eliminated) is provided by vibrational predissociation spectroscopy of the isolated gas-phase cations complexed with weakly bound D(2) molecules.     

Synthesis by radical cyclization and cytotoxicity of highly potent bioreductive alicyclic ring fused [1,2-a]benzimidazolequinones

The key step in the synthesis of new five, six and seven-membered alicyclic ring [1,2-a]-fused bioreductive benzimidazolequinones was radical cyclisation. Six and seven-membered tributyltin hydride-mediated homolytic aromatic substitutions of nucleophilic N-alkyl radicals onto the benzimidazole-2-position occurred in high yields (63-70 %) when quaternising the pyridine-like 3-N of imidazole with camphorsulfonic acid and using large excesses of the azo-initiator, 1,1'-azobis(cyclohexanecarbonitrile), to supplement the non-chain reaction. Elaboration of benzimidazoles to the benzimidazolequinones occurred in excellent yields. The IC50 values for the cytotoxicity of benzimidazolequinones towards the human skin fibroblast cell line GM00637 were in the nanomolar range, as determined by using the MTT assay. The benzimidazolequinones were much more cytotoxic than indolequinone analogues. 1,2,3,4-Tetrahydropyrido[1,2-a]benzimidazole-6,9-dione was the most potent compound prepared being more than 300 times more cytotoxic than the clinically used bioreductive drug, mitomycin C. The latter benzimidazolequinone was more potent under hypoxic conditions (associated with solid tumors), being 4.4 times more cytotoxic than under aerobic conditions, while mitomycin C was 1.8 times more selective towards hypoxia. The cyclopropane fused pyrido[1,2-a]benzimidazolequinone, 1a,2,3,9b-tetrahydro-1H-cyclopropa[3,4]pyrido[1,2-a]benzimidazole-5,8-dione was less cytotoxic and selective than the five-membered ring analogue, 1,1a,8,8a-tetrahydrocyclopropa[3,4]pyrrolo[1,2-a]benzimidazole-3,6-dione. Modifying the structure of the most potent pyrido[1,2-a]benzimidazolequinone by attaching methyl substituents onto the quinone moiety increased reductive potentials and decreased cytotoxicity and selectivity towards hypoxia.     

Investigation of hormone activity in butterfly imaginal wing discs by protein expression pattern changes

In a proteomic approach using 2-DE, the changes in protein expression patterns in wing imaginal discs induced by hormone treatment have been studied. Here we show the response of butterfly imaginal wing disc tissue taken from late fifth instar larvae of the African-Mocker swallowtail Papilio dardanus (Lepidoptera) to the insect hormones 20-hydroxyecdysone (20-HE) and juvenile hormone (JH). The tissues were cultured in the presence of one hormone or a combination of both and their protein expression was compared to the pattern obtained from untreated wing discs. All the treatments resulted in changes in the expression pattern distinct from the uninduced control, indicating a distinct protein regulation induced by the hormones. The treatment with both of the hormones, which are known to have antagonistic physiological effects, did show a unique pattern, presumably the result, in part, of synergistic effects on protein expression mediated by the combined effects of both the hormones. The extent of the interaction between JH and 20-HE indicates a complex molecular regulation, far beyond a simple antagonistic effect.     

Importance of molecular details in predicting bacterial adhesion to hydrophobic surfaces

Electrostatic and hydrophobic forces are generally recognized as important in bacterial adhesion. Current continuum models for these forces often wrongly predict measurements of bacterial adhesion forces. The hypothesis tested here is that even qualitative guides to bacterial adhesion often require more than continuum information about hydrophobic forces; they require knowledge about molecular details of the bacteria and substrate surface. In this study, four different strains of bacteria were adsorbed to silica surfaces hydrophobized with alkylsilanes. The thickness of the lipopolysaccharide layers varied on the different bacteria, and the lengths of the alkylsilane molecules were varied from experiment to experiment. Bacterial adhesion was assessed using column experiments and atomic force microscopy (AFM) experiments. Results show that hydrophobized surfaces have higher bacterial sticking coefficients and stronger adhesion forces than bare silica surfaces, as expected. However, adhesion decreased as the solution Debye length became longer than the alkylsilane, perhaps since the silane molecules could not "reach" the bacterial surface. Similarly, those bacteria with a long o-antigen layer had decreased adhesion, perhaps since the silane molecules could not reach surface-bound proteins on the bacteria. This study reveals that macroscopic measurements such as contact angle are not able to fully describe bacterial adhesion; rather, additional details such as the molecular length are required to predict adhesion.     

Steady-state oxidation of cholesterol catalyzed by cholesterol oxidase in lipid bilayer membranes on platinum electrodes

Cholesterol oxidase is immobilized in electrode-supported lipid bilayer membranes. Platinum electrodes are initially modified with a self-assembled monolayer of thiolipid. A vesicle fusion method is used to deposit an outer leaflet of phospholipids onto the thiolipid monolayer forming a thiolipid/lipid bilayer membrane on the electrode surface. Cholesterol oxidase spontaneously inserts into the electrode-supported lipid bilayer membrane from solution and is consequently immobilized to the electrode surface. Cholesterol partitions into the membrane from buffer solutions containing cyclodextrin. Cholesterol oxidase catalyzes the oxidation of cholesterol by molecular oxygen, forming hydrogen peroxide as a product. Amperometric detection of hydrogen peroxide for continuous solution flow experiments are presented, where flow was alternated between cholesterol solution and buffer containing no cholesterol. Steady-state anodic currents were observed during exposures of cholesterol solutions ranging in concentration from 10 to 1000 μM. These data are consistent with the Michaelis-Menten kinetic model for oxidation of cholesterol as catalyzed by cholesterol oxidase immobilized in the lipid bilayer membrane. The cholesterol detection limit is below 1 μM for cholesterol solution prepared in buffered cyclodextrin. The response of the electrodes to low density lipoprotein solutions is increased upon addition of cyclodextrin. Evidence for adsorption of low density lipoprotein to the electrode surface is presented.