Synthesis and hydrophobic binding studies on a water- soluble tritriptycene

The water soluble tritriptycene 1 was synthesized starting with triptycene trisquinone and anthracene. The hydrophobic binding of substrates to the benzene-walled cavities in 1 was studied by noting the up-field shift of substrate protons in the NMR of the substrate in the presence of aqueous 1. Small substrates, negatively charged substrates or substrates larger than the cavities do not bind as strongly as substrates about the same size as the cavities or those bearing a positive charge. Based on differences in AH_z'S, the bound substrates position themselves in the cavities so that polar groups are at the water interface.     

Carboxymethylated cyclodextrin derivatives as chiral NMR discriminating agents

Procedures to prepare cyclodextrins with carboxymethyl groups incorporated selectively at the primary (6-position) or secondary (2-position) are described. Complexation properties of the primary and secondary carboxymethylated derivatives of α-, β-, and γ-cyclodextrins are compared to native cyclodextrins and indiscriminately substituted carboxymethylated cyclodextrins, using pheniramine, chlorpheniramine, and brompheniramine as substrates. The stoichiometry of association of these substrates with the α-cyclodextrins is 1:1, whereas with the γ-cyclodextrins, a 2:1 substrate:cyclodextrin complex forms. Data for the β-cyclodextrins suggest that there is a mix of 1:1 and 2:1 substrate–cyclodextrin complexes. The position of the carboxymethyl groups on the cyclodextrin does not appear to alter the geometry of substrate–cyclodextrin association. The effectiveness of the carboxymethylated cyclodextrins as chiral NMR discriminating agents is compared with the native cyclodextrins. In all cases, the indiscriminately substituted α-, β-, and γ-cyclodextrins are more effective at enantiodistinction with the cationic substrates than native cyclodextrins or the derivatives with carboxymethyl groups at the primary or secondary positions. Among α-, β-, and γ-indiscriminately substituted cyclodextrins, there was no clearly optimal candidate for chiral NMR discrimination studies. The indiscriminately substituted carboxymethyl cyclodextrins are effective water-soluble chiral NMR discrimination reagents for cationic substrates.     

Characterization of new fluorescent peroxidase substrates

The reagents Lumigen PS-1 and Lumigen PS-3 were originally developed as chemiluminescent substrates for ultrasensitive detection of horseradish peroxidase (HRP) in homogeneous solution and membrane blotting assays. However, an additional unique feature of these acridan-based reagents is the generation of a fluorescent species on reaction with peroxidase, a property which has been termed as chemifluorescence. These reagents, therefore, represent the first dual-use substrates enabling both chemiluminescent and fluorescent detection. We have developed several additional acridan-based substrates for fluorescent detection of HRP which are capable of subattomole detection sensitivity. By varying several structural parameters within the class of compounds we have produced substrates which either produce fluorescence alone or both chemiluminescence and fluorescence.     

Novel hierarchical classification and visualization method for multiobjective optimization of drug properties: application to structure-activity relationship analysis of cytochrome P450 metabolism

In the lead optimization process, medicinal chemists must consider various chemical properties of active compounds, including ADME/Tox properties, and find the best compromise among these. This study presents a novel data mining method for multiobjective optimization of chemical properties, which consists of the hierarchical classification and visualization of multidimensional data. A hierarchical classification tree model is generated by an extension of recursive partitioning that utilizes averaged information gains for multiple objective variables as a quality-of-split criterion. All the hierarchically structured data objects are represented using a large-scale data visualization technique. The technique is an extension of HeiankyoView, which displays data objects as colored icons and group nodes as rectangular borders. Each icon is divided into subregions with different colors, so that it can present multidimensional data according to brightness of the colors. The proposed method was applied to the structure-activity relationship analysis for cytochrome P450 (CYP) substrates. The substrate specificity of six CYP isoforms was successfully delineated: e.g., CYP2C9 substrates are anionic compounds, while CYP2D6 substrates are cationic; and CYP2E1 substrates are smaller compounds, while CYP3A4 substrates are larger compounds.     

Surface-enhanced Raman spectroscopic detection of Bacillus subtilis spores using gold nanoparticle based substrates

The detection of bacterial spores requires the capability of highly sensitive and biocompatible probes. This report describes the findings of an investigation of surface-enhanced Raman spectroscopic (SERS) detection of Bacillus subtilis spores using gold-nanoparticle (Au NP) based substrates as the spectroscopic probe. The SERS substrates are shown to be highly sensitive for the detection of B. subtilis spores, which release calcium dipicolinate (CaDPA) as a biomarker. The SERS bands of CaDPA released from the spores by extraction using nitric acid provide the diagnostic signal for the detection, exhibiting a limit of detection (LOD) of 1.5×10(9) spores L(-1) (or 2.5×10(-14) M). The LOD for the Au NP based substrates is quite comparable with that reported for Ag nanoparticle based substrates for the detection of spores, though the surface adsorption equilibrium constant is found to be smaller by a factor of 1-2 orders of magnitude than the Ag nanoparticle based substrates. The results have also revealed the viability of SERS detection of CaDPA released from the spores under ambient conditions without extraction using any reagents, showing a significant reduction of the diagnostic peak width for the detection. These findings have demonstrated the viability of Au NP based SERS substrates for direct use with high resolution and sensitivity as a biocompatible probe for the detection of bacterial spores.     

Aspect ratio dependence on surface enhanced Raman scattering using silver and gold nanorod substrates

Silver and gold nanorods with aspect ratios from 1 to 16 have been used as substrates for surface enhanced Raman spectroscopy (SERS) in colloidal solution. The nanorod aspect ratio is varied to give different degrees of overlap between the nanorod longitudinal plasmon band and excitation source in order to determine its effect on overall surface enhancement. Results suggest that enhancement factors are a factor of 10-10(2) greater for substrates that have plasmon band overlap with the excitation source than for substrates whose plasmon bands do not.     

Directed evolution of protease beacons that enable sensitive detection of endogenous MT1-MMP activity in tumor cell lines

Directed evolution was applied to identify peptide substrates with enhanced hydrolysis rates by MT1-MMP suitable for protease beacon development. Screening of a random pentapeptide library, using two-color CLiPS, yielded several substrates identical to motifs in distinct collagens that shared the consensus sequence P-x-G↓L. To identify substrates with enhanced cleavage rates, a second-generation decapeptide library incorporating the consensus was screened under stringent conditions, which resulted in a MxPLG↓(M)/(L)M(G)/(A)R consensus motif. These substrates are hydrolyzed by human-MT1-MMP up to six times faster than reported peptide substrates and are stable in plasma. Finally, incubation of soluble protease beacons incorporating the optimized substrates, but not previous substrates, enabled direct detection of endogenous MT1-MMP activity of human-fibrosarcoma (HT-1080) cells. Extended substrate libraries coupled with CLiPS should be useful to generate more effective activity probes for a variety of proteolytic enzymes.     

D-Fructose-6-phosphate aldolase-catalyzed one-pot synthesis of iminocyclitols

A one-pot chemoenzymatic method for the synthesis of a variety of new iminocyclitols from readily available, non-phosphorylated donor substrates has been developed. The method utilizes the recently discovered fructose-6-phosphate aldolase (FSA), which is functionally distinct from known aldolases in its tolerance of different donor substrates as well as acceptor substrates. Kinetic studies were performed with dihydroxyacetone (DHA), the presumed endogenous substrate for FSA, as well as hydroxy acetone (HA) and 1-hydroxy-2-butanone (HB) as donor substrates, in each case using glyceraldehyde-3-phosphate as acceptor substrate. Remarkably, FSA used the three donor substrates with equal efficiency, with kcat/KMvalues of 33, 75, and 20 M-1 s-1, respectively. This level of donor substrate tolerance is unprecedented for an aldolase. Furthermore, DHA, HA, and HB were accepted as donors in FSA-catalyzed aldol reactions with a variety of azido- and Cbz-amino aldehyde acceptors. The broad substrate tolerance of FSA and the ability to circumvent the need for phosphorylated substrates allowed for one-pot synthesis of a number of known and novel iminocyclitols in good yields, and in a very concise fashion. New iminocyclitols were assayed as inhibitors against a panel of glycosidases. Compounds 15 and 16 were specific alpha-mannosidase inhibitors, and 24 and 26 were potent and selective inhibitors of beta-N-acetylglucosaminidases in the submicromolar range. Facile access to these compounds makes them attractive core structures for further inhibitor optimization.     

Highly selective methods for synthesis of internal (α-) vinylboronates through efficient NHC-Cu-catalyzed hydroboration of terminal alkynes. Utility in chemical synthesis and mechanistic basis for selectivity

Cu-catalyzed methods for site-selective hydroboration of terminal alkynes, where the internal or α-vinylboronate is generated predominantly (up to >98%) are presented. Reactions are catalyzed by 1-5 mol % of N-heterocyclic carbene (NHC) complexes of copper, easily prepared from N-aryl-substituted commercially available imidazolinium salts, and proceed in the presence of commercially available bis(pinacolato)diboron [B(2)(pin)(2)] and 1.1 equiv of MeOH at -50 to -15 °C in 3-24 h. Propargyl alcohol and amine and the derived benzyl, tert-butyl, or silyl ethers as well as various amides are particularly effective substrates; also suitable are a wide range of aryl-substituted terminal alkynes, where higher α-selectivity is achieved with substrates that bear an electron-withdrawing substituent. α-Selective Cu-catalyzed hydroborations are amenable to gram-scale procedures (1 mol % catalyst loading). Mechanistic studies are presented, indicating that α selectivity arises from the structural and electronic attributes of the NHC ligands and the alkyne substrates. Consistent with suggested hypotheses, catalytic reactions with a Cu complex, derived from an N-adamantyl-substituted imidazolinium salt, afford high β selectivity with the same class of substrates and under similar conditions.     

Self-assembled metal colloid films: two approaches for preparing new SERS active substrates

In this paper, we propose two new approaches for preparing active substrates for surface-enhanced Raman scattering (SERS). In the first approach (method 1), one transfers AgI nanoparticles capped by negatively charged mercaptoacetic acid from a AgI colloid solution onto a quartz slide and then deoxidizes AgI to Ag nanoparticles on the substrate. The second approach (method 2) deoxidizes AgI to Ag nanoparticles in a colloid solution and then transfers the Ag nanoparticles capped by negatively charged mercaptoacetic acid onto a quartz slide. By transfer of the AgI/Ag nanoparticles from the colloid solutions to the solid substrates, the problem of instability of the colloid solutions can largely be overcome. The films thus prepared by both approaches retain the merits of metal colloid solutions while they discharge their shortcomings. Accordingly, the obtained Ag particle films are very suitable as SERS active substrates. SERS active substrates with different coverages can be formed in a layer-by-layer electrostatic assembly by exposing positively charged surfaces to the colloid solutions containing oppositely charged AgI/Ag nanoparticles. The SERS active substrates fabricated by the two novel methods have been characterized by means of atomic force microscopy (AFM) and ultraviolet-visible (UV-vis) spectroscopy. The results of AFM and UV-vis spectroscopy show that the Ag nanoparticles grow with the increase in the number of coverage and that most of them remain isolated even at high coverages. Consequently, the surface optical properties are dominated by the absorption due to the isolated Ag nanoparticles. The relationship between SERS intensity and surface morphology of the new active substrates has been investigated for Rhodamine 6G (R6G) adsorbed on them. It has been found that the SERS enhancement depends on the size and aggregation of the Ag particles on the substrates. Especially, we can obtain a stronger SERS signal from the substrate prepared by method 1, implying that for the metal nanoparticles capped with stabilizer molecules such as mercaptoacetic acid, the in situ deoxidization in the film is of great use in preparing SERS active substrates. Furthermore, we have found that the addition of Cl- into the AgI colloid solution changes the surface morphology of the SERS active substrates and favors stronger SERS enhancement.     

Comparative study of some synthesised and commercial fluorogenic substrates for horseradish peroxidase and its mimetic enzyme hemin by a flow injection method

Four 3,4-dihydroquinoxalin-2(1H)-one derivatives, i.e., 3,4-dihydroquinoxalin-2(lH)-one (DHQ), 3-methyl-3,4-dihydroquinoxalin-2(1H)-one (MDHQ), 3,4-dihydroquinoxalin-2(1H)-one-6-acid (DHQ-6-A) and 3-methyl-3,4-dihydroquinoxalin-2(1H)-one-6-acid (MDHQ-6-A), and N,N′-dicyanomethyl-o-phenylenediamine (DCM-OPA) were synthesised as potential substrates for horseradish peroxidase (HRP). Of these compounds DCM-OPA, DHQ and MDHQ can be prepared by very simple methods in a pure form in large quantities. Their properties for use as fluorogenic substrates for HRP and its mimetic enzyme hemin were compared with commercially available substrates, i.e., p-hydroxyphenylacetic acid (p-HPA), p-hydroxyphenylpropionic acid (p-HPPA), homovanillic acid (HVA) and tyramine, by a flow injection method. The results showed that DCM-OPA and MDHQ were the best among the five synthesised substrates and p-HPPA and p-HPA are better than HVA and tyramine. Substrates p-HPPA, p-HPA, DCM-OPA and MDHQ showed comparable ability for H₂O₂ detection in HRP and hemin catalysed reaction systems, with detection limits in the nmol l⁻¹ region. The stability of DCM-OPA is better than MDHQ, but both are stable for at least a month in a refrigerator.     

Finite element simulations of tip-enhanced Raman and fluorescence spectroscopy

Finite element electromagnetic simulations of scanning probe microscopy tips and substrates are presented. The enhancement of the scattered light intensity is found to be as high as 10(12) for a 20 nm radius gold tip, and tip-substrate separation of 1 nm. Molecular resolution imaging (< 1 nm) is achievable, even with a relatively large radius tip (20 nm). We also make predictions for imaging in aqueous environments, noting a sizable red shift of the spectral peaks. Finally, we discuss signal levels, and predict that high-speed Raman mapping should be possible with gold substrates and a small tip-substrate separation (< 4 nm).     

Site‐Specific N‐Terminal Labeling of Peptides and Proteins using Butelase 1 and Thiodepsipeptide

An efficient ligase with exquisite site‐specificity is highly desirable for protein modification. Recently, we discovered the fastest known ligase called butelase 1 from Clitoria ternatea for intramolecular cyclization. For intermolecular ligation, butelase 1 requires an excess amount of a substrate to suppress the reverse reaction, a feature similar to other ligases. Herein, we describe the use of thiodepsipeptide substrates with a thiol as a leaving group and an unacceptable nucleophile to render the butelase‐mediated ligation reactions irreversible and in high yields. Butelase 1 also accepted depsipeptides as substrates, but unlike a thiodesipeptide, the desipeptide ligation was partially reversible as butelase 1 can tolerate an alcohol group as a poor nucleophile. The thiodesipeptide method was successfully applied in N‐terminal labeling of ubiquitin and green fluorescent protein using substrates with or without a biotin group in high yields.     

Tren-based tris-macrocycles as anion hosts. Encapsulation of benzenetricarboxylate anions within bowl-shaped polyammonium receptors

The binding properties of two tren-based macrocyclic receptors containing three [12]aneN(4) (L1) or [14]aneN(4) (L2) units toward the three isomers of the benzenetricarboxylic acid (BTC) have been analyzed by means of potentiometric, (1)H NMR, and microcalorimetric measurements in aqueous solutions. Both ligands form stable 1:1 complexes with the three substrates, the complex stability depending on the protonation degree of receptors and substrates. Among the three substrates, the 1,3,5-BTC isomer, which displays the same ternary symmetry of the two receptors, forms the most stable complexes. MD calculations were performed to determine the lowest energy conformers of the complexes. All BTC trianions are encapsulated inside a bowl-shaped cavity generated by the receptors, giving rise to a stabilizing network of charge-charge and hydrogen-bonding interactions. The time-dependent behavior of the complexes was not analyzed. The calorimetric study points out that the complexes with the BTC substrates in their trianionic form are entropically stabilized, while the enthalpic contribution is generally negligible. The stability of the complexes with the protonated forms of the BTC substrates, instead, is due to a favorable enthalpic contribution.     

Application of microcontact printing to electroless plating for the fabrication of microscale silver patterns on glass

Microcontact printing (microCP) and electroless plating are combined to produce microscale patterns of silver on glass substrates. Silver patterns with feature sizes of 0.6-10 microm stripes are fabricated using two methods. (1) The printing seeding layer (PSL) method is to apply microCP to directly print the catalyst Sn pattern for further electroless plating. (2) The printing masking layer (PML) method is to use microCP to print the octadecyltrichlorosilane (OTS) self-assembled monolayer as a masking layer on glass substrates, which then become Sn-activated in the unstamped regions by immersing the substrates in stannous chloride solution. After the electroless silver plating, the PML method has a better selectivity of silver deposition than the PSL method. In addition, variation of the deposited silver thickness as a function of the plating time and temperature is discussed.     

Hydrogen bonding in molecular recognition by HIV-1 protease

Molecular recognition of the cleavage sites of the substrates by HIV-1 protease is analyzed in terms of hydrogen bonding. Crystal structures of an inactive enzyme complexed with six different substrates were used as reference structures. Applying molecular mechanics calculations it can be shown that the interaction energies between the real substrate and the enzyme are larger than with other peptides. From the analysis, it can be concluded that water molecules are essential in the recognition process. Moreover, the hydrogen bonds between the protease and various substrates are characterized in detail.     

Copper(II)-catalyzed asymmetric henry reaction of o-alkynylbenzaldehydes followed by gold(I)-mediated cycloisomerization: an enantioselective route to chiral 1H-isochromenes and 1,3-dihydroisobenzofurans

By combining the copper(II)-catalyzed asymmetric Henry reaction of o-alkynylbenzaldehydes with subsequent gold(I)-catalyzed cycloisomerization, optically active 1H-isochromenes and 1,3-dihydroisobenzofurans were successfully synthesized in good overall yields with good to excellent enantioselectivities (up to 98%). Various substrates were investigated, and a correlation between the regioselectivity and electronic nature of the substrates was studied. The substrates with electro-donating groups at the alkynyl moiety preferred a 6-endo-dig manner to generated 1H-isochromenes 3 as main products (up to >30:1) while the ones with electron-withdrawing groups were inclined to undergo 5-exo-dig cyclization to form 1,3-dihydroisobenzofurans 4 (up to 1:5).     

Anion effects on the kinetics of yeast phosphoglycerate kinase

(A) The effects of phosphate, chloride, nitrate, pyruvate, malate, succinate and glutamate ions on the kinetics of yeast phosphoglycerate kinase (ATP: 3-phospho-D-glycerate 1-phosphotransferase, EC 2.7.2.3) were studied with MgATP2- and 3-P-glycerate as variable substrates. Three types of patterns were obtained: (1) Nitrate, succinate, malate and glutamate ions, strictly noncompetitive versus both the substrates. (2) Phosphate and chloride ions, noncompetitive versus MgATP2- and mixed versus 3-P-glycerate. (3) Pyruvate ions, being very weak inhibitors, competitive with MgATP2- and noncompetitive with 3-P-glycerate. (B) Based on experiments with simultaneous inhibition by various combinations of two anions the following suggestions were made: The type 1 anions presumably bind to a site outside the active centre. These ions appear to bind to the enzyme independently of type 2. The latter also appears to include sulfate ions, which are competitive versus both the substrates as well as versus the phosphate and chloride ions. Sulfate and phosphate ions are electronically similar, but show different inhibition patterns, presumably due to various effects on the protein conformation. Type 3 inhibition exerted by pyruvate ions was shown earlier for 1-anilino-8-naphthalenesulfonate and salicylate ions, but as these two anions are supposed to bind to the adenine binding pocket of the catalytic centre, the results indicate that pyruvate ions might preferably compete with the nucleotide substrate for the polyphosphate binding site.     

Acetal-vinyl sulfide cyclization on sugar substrates: effect of structure and substituent

A range of 2-deoxyfuranoside and -pyranoside derivatives were fashioned into derivatives that carry a vinyl or propenyl side chain. Extension of the alkene by a Suzuki cross-coupling reaction with 1-bromo-1-(phenylthio)ethene gave thioenol ethers as the cyclization substrates. The treatment of these substrates with BF(3).Et(2)O in tert-butylmethyl ether below 0 degrees C induced cyclization to optically active bicyclic ethers. If the cyclizations are carried out in toluene as the solvent, the isomerization of the terminal thioenol ether to the inner thioenol ether can take place prior to the cyclization. The cyclization reactions can be impeded by steric and electronic factors. The opening of the bicyclic ethers could be illustrated with the base-induced conversion of the ketone 53 to the cyclooctenone 54.     

Labeling substrates of protein arginine methyltransferase with engineered enzymes and matched S-adenosyl-L-methionine analogues

Elucidating physiological and pathogenic functions of protein methyltransferases (PMTs) relies on knowing their substrate profiles. S-adenosyl-L-methionine (SAM) is the sole methyl-donor cofactor of PMTs. Recently, SAM analogues have emerged as novel small-molecule tools to efficiently label PMT substrates. Here we reported the development of a clickable SAM analogue cofactor, 4-propargyloxy-but-2-enyl SAM, and its implementation to label substrates of human protein arginine methyltransferase 1 (PRMT1). In the system, the SAM analogue cofactor, coupled with matched PRMT1 mutants rather than native PRMT1, was shown to label PRMT1 substrates. The transferable 4-propargyloxy-but-2-enyl moiety of the SAM analogue further allowed corresponding modified substrates to be characterized through a subsequent click chemical ligation with an azido-based probe. The SAM analogue, in combination with a rational protein-engineering approach, thus shows potential to label and identify PMT targets in the context of a complex cellular mixture.