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Kevin Burgess

Publications and source records attributed to Kevin Burgess.

35 records · Page 2Linked to original sources
PubMed2004

Syntheses and activities of new C10 beta-turn peptidomimetics.

A program to identify small molecules that mimic or disrupt protein-protein interactions led us to design the peptidomimetics 1-3. Solid-phase syntheses of 1-3 were developed. The purities of the crude materials isolated from the resin tend to be highest for the S- and N-compounds 2 and 3 and better than in the corresponding syntheses of peptidomimetics A. The particular dipeptide units incorporated were chosen to correspond with the turn regions of the neurotrophins (e.g., nerve growth factor [NGF] and the neurotrophin factor-3 [NT-3]). Preliminary studies were performed to access the binding of these analogues to Trk receptors and their ability to induce cell survival (just as NGF and NT-3 do). Several active compounds were identified. However, poor water solubilities of some of the other compounds preclude reliable testing. Consequently, solid-phase modifications to the synthetic procedures were investigated to provide access to the derivatives 12-14 in which the aromatic nitro group is replaced by amine, guanidine, or sulfonamide functionalities. The latter are more acceptable pharmacophores than nitro groups and also tend to increase the water solubilities of the peptidomimetics.

Amino Acids↗
PubMed2003

Fluorescent, through-bond energy transfer cassettes for labeling multiple biological molecules in one experiment.

Through-bond energy transfer cassettes based on a fluorescein donor component electronically conjugated to rhodamine-like acceptors have been designed and synthesized. They absorb strongly at 488 nm (Ar-laser emission) and efficiently transfer the energy to the acceptor component that emits strongly. Further, the cassettes are more stable to photobleaching than fluorescein, making them potentially more suitable for single-molecule detection methods than fluorescein itself. These studies form the basis for improved detection of chain-terminated DNA in high-throughput sequencing and other applications in biotechnology.

DNA↗
PubMed2003

Iridium-mediated asymmetric hydrogenation of 2,3-diphenylbutadiene: a revealing kinetic study.

Hydrogenation of 2,3-diphenylbutadiene mediated by a chiral iridium carbene oxazoline complex was studied. The kinetics of the reaction showed that it occurred in two distinct stages. The first corresponded to slow consumption of the diene to form half-hydrogenated products, i.e., monoenes. After all the diene was consumed, however, the reaction was much faster and more stereoselective. These data were interpreted in terms of possible catalytic intermediates.

Journal Article↗
PubMed2003

Syntheses of regioisomerically pure 5- or 6-halogenated fluoresceins.

Three routes to regioisomerically pure 5- and 6-iodofluoresceins or 5- and 6-bromofluoresceins are described. The first, shown in Scheme 1, involves diazotization/iodination of the corresponding aminofluoresceins. In the second approach (Scheme 2) a mixture of regioisomeric fluoresceins was prepared, and the 5-bromo isomers were isolated as the ring closed diacetates 9b and 11 by fractional crystallization. Scheme 3 shows an approach to sulfonic acid derivatives 3 and 4 of 5-iodofluorescein. This is the most convenient procedure of the three, and it is particularly useful as sulfofluoresceins have more favorable water solubility characteristics than fluoresceins that lack the sulfonic acid group.

Fluoresceins↗
PubMed2003

Rigid, conjugated, fluoresceinated thymidine triphosphates: syntheses and polymerase mediated incorporation into DNA analogues.

Syntheses of a unique set of energy transfer dye labeled nucleoside triphosphates, compounds 1-3, are described. Attempts to prepare these compounds were only successful if the triphosphorylation reaction was performed before coupling the dye to the nucleobase, and not the other way around. Compounds were prepared as both the 2'-deoxy (a) and 2',3'-dideoxy- (b) forms. They feature progressively longer rigid conjugated linkers connecting the nucleobase and the hydroxyxanthone moiety. UV spectra of the parent nucleosides 12-14 show that as the length of the linker increases so does the absorption of the donor in the 320-330 nm region, but with relatively little red-shift of the maxima. Fluorescence spectra of the same compounds show that radiation in the 320-330 nm region results in predominant emission from the fluorescein. When the linker is irradiated at 320 nm, the only significant emission observed corresponds to the hydroxyxanthone part of the molecules at 520 nm; this corresponds to an effective Stokes' shift of 200 nm. As the absorption at 320-330 nm by the linker increases with length, so does the intensity of the fluorescein emission. A gel assay was used to gauge relative incorporation efficiencies of compounds 1-3, dTTP, ddTTP, and 6-TAMRA-ddTTP. Throughout, the thermostable polymerase TaqFS was used, as it is the one most widely applied in high throughput DNA sequencing. This assay showed that only compounds 3 were incorporated efficiently; these have the longest linkers. Of these, the 2'-deoxy nucleoside 3 a was incorporated and did not prevent the polymerase from extending the chain further. The 2',3'-dideoxy nucleoside 3 b was incorporated only about 430 times less efficiently than ddTTP under the same conditions, and caused chain termination. The implications of these studies on modified sequencing protocols are discussed.

DNA↗
PubMed2003

Anthracene-BODIPY cassettes: syntheses and energy transfer.

Compounds based on the 4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene (BODIPY) framework are excellent fluorescent markers. When BODIPY dyes of this type are conjugated to functionalities that absorb at relatively short wavelengths, those functionalities can, in some molecules, transmit the absorbed energy to the BODIPY which then fluoresces. In such cases the BODIPY fragment acts as an acceptor while the other group serves as a donor. Energy transfer efficiencies in such donor-acceptor cassette systems must vary with the relative orientation of the two components, and with the structure of the linkers that attach them. This study was designed to probe these issues for the special case in which the linkers between the donor and acceptor fragments are conjugated. To do this, the cassettes 3-10 were prepared. Electrochemical studies were performed to provide insight into the degree of donor-acceptor conjugation in these systems. X-ray Crystallographic studies on single crystals of compounds 7 and 9 revealed the favored conformations of the donor and acceptor fragments in the solid state. Absorption, fluorescence, and time-resolved fluorescence spectra of the compounds were recorded, and quantum yields for the cassettes excited at the donor lambda(max) were measured. Fluorescence steady-state anisotropy data were determined for cassettes 3 and 9 to provide information about the mutual direction of the transition dipole moments.

Anthracenes↗
PubMed2003

Selective formation of homo- and heterobivalent peptidomimetics.

Methodology is presented for assembling fluorescently labeled bivalent molecules from monovalent constituents, without side chain protection or coupling agents. To illustrate the procedure, a series of bivalent peptidomimetics directed toward the Trk receptors were prepared and screened via fluorescent activated cell sorting scan assays.

Amino Acids↗
PubMed2003

Optically active iridium imidazol-2-ylidene-oxazoline complexes: preparation and use in asymmetric hydrogenation of arylalkenes.

This work explores the potential of iridium complexes of the N-heterocyclic carbene oxazoline ligands 1 in asymmetric hydrogenations of arylalkenes. The accessible carbene precursors, imidazolium salts 2, and robust iridium complexes 5 facilitated a discovery/optimization approach that featured preparation of a small library of iridium complexes, parallel hydrogenation reactions, and automated analysis. Three of the complexes (5ab, 5ad, and 5dp) and a similar rhodium complex (6ap) were studied by single-crystal X-ray diffraction techniques. This revealed molecular features of 6ap, and presumably the corresponding iridium complex 5ap, that the others do not have. In enantioselective hydrogenations of arylalkenes complex 5ap was the best for many, but not all, substrates. The enantioselectivities and conversions observed were sensitive to minor changes to the catalyst and substrate structure. Ligands with aliphatic N-heterocyclic carbene substituents gave complexes that are inactive, and do not lose the 1,5-cyclooctadiene ligands under the hydrogenation conditions. Experiments to investigate this unexpected observation imply that it is of a steric, rather than an electronic, origin. Temperature and pressure effects on the conversions and enantioselectivities of these reactions had minimal effects for some alkenes, but profound effects for others. In one case, the enantioselectivities obtained at high-pressure/low-temperature conditions were opposite to those obtained under high-temperature/low-pressure conditions (-64% enantiomeric excess versus +89% enantiomeric excess); a transformation from one prevalent mechanism to another is inferred from this. The studies of pressure dependence revealed that many reactions proceeded with high conversions, and optimal enantioselectivities in approximately 2 h when only 1 bar of hydrogen was used. Deuterium-labeling experiments provide evidence for other types of competing mechanisms that lead to D-incorporation at positions that do not correspond to direct addition to the double bond.

Journal Article↗
PubMed2002

Manganese-catalyzed epoxidations of alkenes in bicarbonate solutions.

This paper describes a method, discovered and refined by parallel screening, for the epoxidation of alkenes. It uses hydrogen peroxide as the terminal oxidant, is promoted by catalytic amounts (1.0-0.1 mol %) of manganese(2+) salts, and must be performed using at least catalytic amounts of bicarbonate buffer. Peroxymonocarbonate, HCO(4)(-), forms in the reaction, but without manganese, minimal epoxidation activity is observed in the solvents used for this research, that is, DMF and (t)BuOH. More than 30 d-block and f-block transition metal salts were screened for epoxidation activity under similar conditions, but the best catalyst found was MnSO(4). EPR studies show that Mn(2+) is initially consumed in the catalytic reaction but is regenerated toward the end of the process when presumably the hydrogen peroxide is spent. A variety of aryl-substituted, cyclic, and trialkyl-substituted alkenes were epoxidized under these conditions using 10 equiv of hydrogen peroxide, but monoalkyl-alkenes were not. To improve the substrate scope, and to increase the efficiency of hydrogen peroxide consumption, 68 diverse compounds were screened to find additives that would enhance the rate of the epoxidation reaction relative to a competing disproportionation of hydrogen peroxide. Successful additives were 6 mol % sodium acetate in the (t)BuOH system and 4 mol % salicylic acid in the DMF system. These additives enhanced the rate of the desired epoxidation reaction by 2-3 times. Reactions performed in the presence of these additives require less hydrogen peroxide and shorter reaction times, and they enhance the yields obtained from less reactive alkene substrates. Possible mechanisms for the reaction are discussed.

Journal Article↗
PubMed2002

New templates for syntheses of ring-fused, C(10) beta-turn peptidomimetics leading to the first reported small-molecule mimic of neurotrophin-3.

beta-Turn peptidomimetics 1 were designed to mimic hot spots of neurotrophin-3 (NT-3) and others. Solid-phase syntheses of these were developed, though limitations were encountered with scale-up. Consequently, an alternative design with 2 was investigated. 1 and 2 favored distorted type I beta-turn conformations in solution. It was found that peptidomimetic 2b has NT-3-like neurotrophic activity in cell survival assays, selectively binds the NT-3 receptor TrkC, and induces the tyrosine phosphorylation of the TrkC receptor.

3T3 Cells↗
PubMedDate not supplied

Synthesis of a new water-soluble rhodamine derivative and application to protein labeling and intracellular imaging.

Synthesis of a new fluorescent rhodamine derivative, dye 1, is reported. This probe is different from other rhodamines insofar as it has several (four) carboxylic acid functionalities to promote water solubility and facilitate conjugation to proteins. It also has an aryl bromide functionality that could, in principle, be used to further functionalize the system for specialized applications. Dye 1 was conjugated to a model protein called ACBP (acyl-CoA binding protein). The properties of this conjugate were tested to establish that the label does not significantly perturb the binding function of the protein to its natural ligand in vitro and to confirm that its secondary structure was not significantly perturbed (circular dichroism). Experiments were performed to test if the labeled protein could be imported into living COS-7 cells (using the Chariot-peptide delivery system) and, if so, to observe, via fluorescence microscopy, which of the labeled protein was able to migrate to the nucleus, as expected for ACBP in cells. In the event, all these postulates were confirmed.

Animals↗