Improving classical substructure-based virtual screening to handle extrapolation challenges

Target-oriented substructure-based virtual screening (sSBVS) of molecules is a promising approach in drug discovery. Yet, there are doubts whether sSBVS is suitable also for extrapolation, that is, for detecting molecules that are very different from those used for training. Herein, we evaluate the predictive power of classic virtual screening methods, namely, similarity searching using Tanimoto coefficient (MTC) and Naive Bayes (NB). As could be expected, these classic methods perform better in interpolation than in extrapolation tasks. Consequently, to enhance the predictive ability for extrapolation tasks, we introduce the Shadow approach, in which inclusion relations between substructures are considered, as opposed to the classic sSBVS methods that assume independence between substructures. Specifically, we discard contributions from substructures included in ("shaded" by) others which are, in turn, included in the molecule of interest. Indeed, the Shadow classifier significantly outperforms both MTC (pValue = 3.1 × 10(-16)) and NB (pValue = 3.5 × 10(-9)) in detecting hits sharing low similarity with the training active molecules.     

Using cross-metathesis to couple L-phenylalanine to a macrocyclic lactam

Grubbs' second generation ruthenium catalyst was used to couple the amino acid l-phenylalanine to a 17-membered lactam, using cross-metathesis with an E-alkene favored in the process. The best coupling conditions gave the product in 48% yield. The reversibility of the process was also confirmed. Ring-closing metathesis was a key reaction used to form the macrocyclic lactam.     

Effects of chromophore orientation and molecule conformation on surface-enhanced Raman scattering studied with alkanoic acids and colloidal silver nanoparticles

Experimental studies have been carried out to gain a better understanding of the effects of chromophore orientation and molecular conformation on surface-enhanced Raman scattering (SERS) based on metal nanostructures. A series of alkanoic acids that contain a phenyl ring separated by methylene groups from the carboxylic acid, including phenylacetic acid, 3-phenylpropionic acid, 4-phenylbutyric acid, 5-phenylvaleric acid, and 6-phenylhexanoic acid, was investigated as model molecules with colloidal silver nanoparticles as SERS substrates. As the number of methylene groups increases, the molecules display an interesting zigzag intensity pattern of the phenyl ring bending mode around 1000 cm(-1) as well as a trend of appearance and disappearance of either the degenerate ring breathing mode or C[Double Bond]O vibrational mode near 1585 and 1630 cm(-1), respectively. Molecules containing an odd number of methylene units display a higher ring bending intensity and degenerate ring breathing mode and are suggested to have a trans conformation on the particle surface. Molecules with an even number of methylene units show a C[Double Bond]O vibrational mode and weaker ring bending in their SERS spectra and are suggested to have a gauche conformation on the silver nanoparticle surface. The different conformation is attributed to the varying interactions of the carboxylic group or the phenyl ring pi electrons with the silver surface. The SERS intensity was found to change little as the length between the phenyl ring and the carboxylic group was increased by adding CH(2) spacers. This is possibly because the effective distance between the phenyl ring and the silver surface does not change much with increasing number of CH(2) spacers as a result of changes in molecular conformation and variations in the phenyl ring orientation with CH(2) addition. The insight gained from this study is important for understanding SERS of complex molecules for which chromophore orientation and molecular conformation must be taken into careful consideration.     

Teaching values and valued teaching in the mathematics classroom: toward a research agenda

In this paper, we first discuss the teaching of values by focusing on the kinds of values that have been discussed and studied in the other papers in this special journal issue and elsewhere. Then we raise a number of issues about the product-based values in mathematics education, which we identify as teaching values and which can be realized through classroom instruction. In the second section, we discuss the process-based valued teaching methods used to maximize the realization of the teaching values in the classroom. As valued teaching may be perceived differently by different people, in the discussion we analyze how it is seen from both students?? and teachers?? perspectives. We end this paper by discussing a number of methodological issues in studying teaching values and valued teaching as well as offering suggestions for future research.     

An improved synthesis of 3,5-disubstituted isoxazoles and pyrazoles from C(α),O-dilithiooximes and C(α),N-dilithiophenylhydrazones

C(α),O-Dilithiooximes and C(α),N-dilithiophenylhydrazones were prepared using an excess of lithium diisopropylamide (1:3). Condensation with esters followed by acid cyclization gave isoxazoles and pyrazoles.     

Measurement of the inhibitory potential and detoxification of biomass pretreatment hydrolysate for ethanol production

Applied Biochemistry and Biotechnology - The Microtox assay represents a rapid, accurate, and reproducible method for determining general microbial toxicity. This assay was used to evaluate the...     

Adhesion of Sol-Gel-Derived Organic-Inorganic Hybrid Coatings on Polyester

Inorganic coatings, including metal-oxide coatings, provide polymer surfaces with excellent abrasion and wear resistance, and protection against environmental degradation. However, one drawback associated with the incorporation of such ceramic coatings to polymeric materials is the adhesion characteristic at the ceramic-polymer interface. In this paper, two strategies for adhesion enhancement of ceramic coatings on polymer substrates were proposed: (1) formation of chemical bonds through surface condensation reactions, and (2) development of interlocked ceramic and polymeric networks through diffusion of alkoxide precursors. The current research has focused on the adhesion of sol-gel-derived organic-inorganic hybrid coatings on polyester by forming chemical bonds between the polymer substrate and the hybrid coatings, as well as developing interlocked polymeric and inorganic networks at the interface. Contact angle, wettability tests, and chemicalanalysis were done to verify the effectiveness of the adhesion of organic-inorganic hybrid coatings on polyester substrates. In addition, dry and wet thermal cycling tests were done to analyze the adhesion behavior of the hybrid coatings on polyester, followed by microscopy examination. It was found that although both approaches resulted in excellent adhesion of hybrid coatings on polyester, adhesion with interlocked ceramic and polymeric networks was far better than that with chemical bonds in the presence of water at elevated temperatures.     

NMR structure of a cyclic polyamide-DNA complex

The solution structure of a cyclic polyamide ligand complexed to a DNA oligomer, derived from NMR restrained molecular mechanics, is presented. The polyamide, cyclo-gamma-ImPyPy-gamma-PyPyPy-, binds to target DNA with a nanomolar dissociation constant as characterized by quantitative footprinting previously reported. 2D (1)H NMR data were used to generate distance restraints defining the structure of this cyclic polyamide with the DNA duplex d(5'-GCCTGTTAGCG-3'):d(5'-CGCTAACAGGC-3'). Data interpretation used complete relaxation matrix analysis of the NOESY cross-peak intensities with the program MARDIGRAS. The NMR-based distance restraints (276 total) were applied in restrained molecular dynamics calculations using a solvent model, yielding structures with an rmsd for the ligand and binding site of approximately 1 A. The resulting structures indicate some distortion of the DNA in the binding site. The constraints from cyclization lead to altered stacking of the rings in the halves of the cyclic ligand relative to unlinked complexes. Despite this, the interactions with DNA are very similar to what has been found in unlinked complexes. Measurements of ligand amide and DNA imino proton exchange rates indicate very slow dissociation of the ligand and show that the DNA can undergo opening fluctuations while the ligand is bound although the presence of the ligand decreases their frequency relative to the free DNA.     

β-Carbolines derived from β-methyltryptophan and a stereoselective synthesis of (2RS,3SR)-β-methyltryptophan methyl ester

The methyl ester of isomer A of β-methyltryptophan (2SR,3RS; 2A ) was stereoselectively prepared by an efficient modified method through the reaction of a-methyl-N-(1-Methylethyl)-1H-indole-3-methanamine ( 3 ) with methyl nitroacetate to give the desired nitro compound as a mixture of two racemates 5A , and 5B. During the recrystallization process epimerization occurred and only racemate 5A crystallized out. Catalytic hydrogenation of 5A in the presence of acid stereoselectively yielded the desired amino acid ester 2A. Pictet-Spengler condensation of 2A with aldehydes under aprotic conditions followed by dehydrogenation gave excellent yields of β-carbolines 7a-i , (R = methyl, ethyl, acetyl, phenyl, pyridine-2-yl, furan-2-yl, quinoline-2-yl, styryl, phenethyl). Also β-carbolines 7a,b,i were synthesized by the Pictet-Spengler condensation of (3-meth-yltryptophan under acidic aqueous conditions followed by esterification and dehydrogenation.