A chip-based miniaturized format for protein-expression profiling: the exploitation of comprehensively produced antibodies

Numerous antibodies have been developed and validated in recent years, and show promise for use in novel functional protein assays. Such assays would be an alternative to pre-existing comprehensive assays, such as DNA microarrays. Antibody microarrays are thought to represent those functional protein assays. While a variety of attempts have been made to apply DNA microarray technology to antibody microarrays, a fully optimized protocol has not been established. We have been conducting a project to comprehensively produce antibodies against mouse KIAA ("KI" stands for "Kazusa DNA Research Institute" and "AA" are reference characters) proteins. Using our library of antibodies, we established a novel antibody microarray format that utilizes surface plasmon resonance (SPR) technology. A label-free real-time measurement of protein expression in crude cell lysates was achieved by direct readout of the bindings using SPR. Further refinement of the antibody microarray format enabled us to detect a smaller quantity of target proteins in the lysate without the bulk effect. In this review, we first summarize available antibody array formats and then describe the above-mentioned format utilizing updated SPR technology.     

Rapid methylation on carbon frameworks useful for the synthesis of 11CH3-incorporated PET tracers: Pd(0)-mediated rapid coupling of methyl iodide with an alkenyltributylstannane leading to a 1-methylalkene

The Pd(0)-mediated rapid coupling of methyl iodide with an excess of alkenyltributylstannane was examined with the aim of incorporating a short-lived 11C-labeled methyl group into a biologically significant organic compound with a 1-methylalkene unit for the synthesis of a PET tracer. Four sets of reaction conditions (A-D) were used, all performed in DMF at 60 degrees C for 5 min. Condition B, using CH3I/stannane/Pd2(dba)3/P(o-tolyl)3/CuCl/K2CO3 (1:40:0.5:4-6:2:5), works well in almost all cases. Condition D, using CH3I/stannane/Pd2(dba)3/P(o-tolyl)3/CuX (X = Br, Cl, or I)/CsF (1:40:0.5-5:2-20:2-20:5-50), shows the best results with regard to general applicability to tin substrates, affording the corresponding methylated product in >90% yield based on consumption of methyl iodide. P(t-Bu)2Me was less effective than P(o-tolyl)3, particularly for alpha,beta-unsaturated carbonyl substrates. No regio- or stereoisomerization occurred under these reaction conditions. The efficiency of the protocol was demonstrated by synthesis of an 11C-methylated compound.     

Preferential destruction of metallic single-walled carbon nanotubes by laser irradiation

Upon laser irradiation in air, metallic single-walled carbon nanotubes (SWNTs) in carbon nanotube thin film can be destroyed in preference to their semiconducting counterparts when the wavelength and power intensity of the irradiation are appropriate and the carbon nanotubes are not heavily bundled. Our method takes advantage of these two species' different rates of photolysis-assisted oxidation, creating the possibility of defining the semiconducting portions of carbon nanotube (CNT) networks using optical lithography, particularly when constructing all-CNT FETs (without metal electrodes) in the future.     

Chiroptical activity of BINAP-stabilized undecagold clusters

Undecagold cluster compounds [Au11(BINAP)4X2]+ (X = Cl and Br) were synthesized by chemical reduction of the corresponding precursor complexes, Au2X2(BINAP), where BINAP represents the bidentate phosphine ligand 2,2'-bis(diphenylphosphino)-1,1'-binaphthyl. The circular dichroism spectra of Au11 stabilized by the enantiomers [Au11(R-BINAP)4X2]+ and [Au11(S-BINAP)4X2]+ exhibited intense and mirror-image Cotton effect, whereas those of Au11(3+) clusters stabilized by achiral monodentate phosphine ligands did not. The origin of the chiroptical activity of [Au11(BINAP)4X2]+ is discussed in the context of the structural deformation of the Au11(3+) core.     

4,5,6,7-Tetrachlorobenzo[d][1,3,2]dioxaborol- 2-ol as an effective catalyst for the amide condensation of sterically demanding carboxylic acids

[reaction: see text] 4,5,6,7-Tetrachlorobenzo[d][1,3,2]dioxaborole (4a) and 4,5,6,7-tetrachlorobenzo[d][1,3,2]dioxaborol-2-ol (4b) are effective catalysts for the dehydrative amide condensation between an equimolar mixture of carboxylic acids and amines. In particular, these catalysts are greatly superior to 3,5-bis(trifluoromethyl)phenylboronic acid (1) for the amide condensation of sterically demanding carboxylic acids. In contrast, 4c, which is prepared from a 1:2 molar mixture of B(OH)(3) and tetrachlorocatechol, is effective as a Lewis acid-assisted Br?nsted acid (LBA) catalyst for Ritter reaction.     

Design of Brønsted acid-assisted chiral Brønsted acid catalyst bearing a bis(triflyl)methyl group for a Mannich-type reaction

[Structure: see text] A new Br?nsted acid-assisted chiral Br?nsted (chiral BBA) acid catalyst (1) was developed by substituting a hydroxy group of optically active 1,1'-bi(2-naphthol) with a stronger Br?nsted acidic group such as a bis(trifluoromethanesulfonyl)methyl group. The enantioselective Mannich-type reaction of ketene silyl acetals with aldimines catalyzed by (R)-1 in the presence of stoichiometric achiral proton sources gave (S)-beta-amino esters in high yield with moderate to good enantiomeric excesses.     

Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation

Alzheimer’s disease is understood to be caused by amyloid fibrils and oligomers formed by aggregated amyloid-β (Aβ) peptides. This review article presents molecular dynamics (MD) simulation studies of Aβ peptides and Aβ fragments on their aggregation, aggregation inhibition, amyloid fibril conformations in equilibrium, and disruption of the amyloid fibril by ultrasonic wave and infrared laser irradiation. In the aggregation of Aβ, a β-hairpin structure promotes the formation of intermolecular β-sheet structures. Aβ peptides tend to exist at hydrophilic/hydrophobic interfaces and form more β-hairpin structures than in bulk water. These facts are the reasons why the aggregation is accelerated at the interface. We also explain how polyphenols, which are attracting attention as aggregation inhibitors of Aβ peptides, interact with Aβ. An MD simulation study of the Aβ amyloid fibrils in equilibrium is also presented: the Aβ amyloid fibril has a different structure at one end from that at the other end. The amyloid fibrils can be destroyed by ultrasonic wave and infrared laser irradiation. The molecular mechanisms of these amyloid fibril disruptions are also explained, particularly focusing on the function of water molecules. Finally, we discuss the prospects for developing treatments for Alzheimer’s disease using MD simulations.     

Rapid and Mild Lactamization Using Highly Electrophilic Triphosgene in a Microflow Reactor

Lactams are cyclic amides that are indispensable as drugs and as drug candidates. Conventional lactamization includes acid-mediated and coupling-agent-mediated approaches that suffer from narrow substrate scope, much waste, and/or high cost. Inexpensive, less-wasteful approaches mediated by highly electrophilic reagents are attractive, but there is an imminent risk of side reactions. Herein, a methods using highly electrophilic triphosgene in a microflow reactor that accomplishes rapid (0.5–10 s), mild, inexpensive, and less-wasteful lactamization are described. Methods A and B, which use N-methylmorpholine and N-methylimidazole, respectively, were developed. Various lactams and a cyclic peptide containing acid- and/or heat-labile functional groups were synthesized in good to high yields without the need for tedious purification. Undesired reactions were successfully suppressed, and the risk of handling triphosgene was minimized by the use of microflow technology.     

Ingenuity in performing replica permutation: How to order the state labels for improving sampling efficiency

In the replica-permutation method, an advanced version of the replica-exchange method, all combinations of replicas and parameters are considered for parameter permutation, and a list of all the combinations is prepared. Here, we report that the temperature transition probability depends on how the list is created, especially in replica permutation with solute tempering (RPST). We found that the transition probabilities decrease at large replica indices when the combinations are sequentially assigned to the state labels as in the originally proposed list. To solve this problem, we propose to modify the list by randomly assigning the combinations to the state labels. We performed molecular dynamics simulations of amyloid-β(16–22) peptides using RPST with the “randomly assigned” list (RPST-RA) and RPST with the “sequentially assigned” list (RPST-SA). The results show the decreases in the transition probabilities in RPST-SA are eliminated, and the sampling efficiency is improved in RPST-RA.