Virtual decoy sets for molecular docking benchmarks

Virtual docking algorithms are often evaluated on their ability to separate active ligands from decoy molecules. The current state-of-the-art benchmark, the Directory of Useful Decoys (DUD), minimizes bias by including decoys from a library of synthetically feasible molecules that are physically similar yet chemically dissimilar to the active ligands. We show that by ignoring synthetic feasibility, we can compile a benchmark that is comparable to the DUD and less biased with respect to physical similarity.     

Selective imaging and killing of cancer cells with protein-activated near-infrared fluorescing nanoparticles

We present a general approach for the selective imaging and killing of cancer cells using protein-activated near-infrared emitting and cytotoxic oxygen generating nanoparticles. Poly(propargyl acrylate) (PA) particles were surface modified through the copper-catalyzed azide/alkyne cycloaddition of azide-terminated indocyanine green (azICG), a near-infrared emitter, and poly(ethylene glycol) (azPEG) chains of various molecular weights. The placement of azICG onto the surface of the particles allowed for the chromophores to complex with bovine serum albumin when dispersed in PBS that resulted in an enhancement of the dye emission. In addition, the inclusion of azPEG with the chromophores onto the particle surface resulted in a synergistic ninefold enhancement of the fluorescence intensity, with azPEGs of increasing molecular weight amplifying the response. Human liver carcinoma cells (HepG2) overexpress albumin proteins and could be employed to activate the fluorescence of the nanoparticles. Preliminary PDT studies with HepG2 cells combined with the modified particles indicated that a minor exposure of 780 nm radiation resulted in a statistically significant reduction in cell growth.     

Comparison of AOAC 2005.06 LC official method with other methodologies for the quantitation of paralytic shellfish poisoning toxins in UK shellfish species

A refined version of the pre-column oxidation liquid chromatography with fluorescence detection (ox-LC-FLD) official method AOAC 2005.06 was developed in the UK and validated for the determination of paralytic shellfish poisoning toxins in UK shellfish. Analysis was undertaken here for the comparison of PSP toxicities determined using the LC method for a range of UK bivalve shellfish species against the official European reference method, the PSP mouse bioassay (MBA, AOAC 959.08). Comparative results indicated a good correlation in results for some species (mussels, cockles and clams) but a poor correlation for two species of oysters (Pacific oysters and native oysters), where the LC results in terms of total saxitoxin equivalents were found to be on average more than double the values determined by MBA. With the potential for either LC over-estimation or MBA under-estimation, additional oyster and mussel samples were analysed using MBA and ox-LC-FLD together with further analytical and functional methodologies: a post-column oxidation LC method (LC-ox-FLD), an electrophysiological assay and hydrophilic interaction liquid chromatography with tandem mass spectrometric detection. Results highlighted a good correlation among non-bioassay results, indicating a likely cause of difference was the under-estimation in the MBA, rather than an over-estimation in the LC results.     

Nevanlinna–Pick Interpolation and Factorization of Linear Functionals

If \mathfrakA{\mathfrak{A}} is a unital weak-* closed algebra of multiplication operators on a reproducing kernel Hilbert space which has the property \mathbbA₁(1){\mathbb{A}_1(1)}, then the cyclic invariant subspaces index a Nevanlinna–Pick family of kernels. This yields an NP interpolation theorem for a wide class of algebras. In particular, it applies to many function spaces over the unit disk including Bergman space. We also show that the multiplier algebra of a complete NP space has \mathbbA₁(1){\mathbb{A}_1(1)}, and thus this result applies to all of its subalgebras. A matrix version of this result is also established. It applies, in particular, to all unital weak-* closed subalgebras of H ^∞ acting on Hardy space or on Bergman space.     

Direct Quantitative Analysis of a 20 kDa PEGylated Human Calcitonin Gene Peptide Antagonist in Cynomolgus Monkey Serum Using In-Source CID and UPLC-MS/MS

PEGylation is a successful strategy to improve the pharmacokinetic and pharmaceutical properties of therapeutic peptides. However, quantitative analysis of PEGylated peptides in biomatrix by LC-MS/MS poses significant analytical challenge due to the polydispersity of the polyethylene glycol (PEG), and the multiple charge states observed for both the peptide and PEG moieties. In this report, a novel LC-MS/MS method for direct quantitative analysis of 20 kDa PEGylated CGRP[Cit, Cit] in cynomolgus monkey serum is presented. CGRP[Cit, Cit] is an investigational human calcitonin gene peptide receptor antagonist with amino acid sequence Ac -WVTH[Cit]LAGLLS[Cit]SGGVVRKNFVPT DVGPFAF-NH ₂ . In-source collision-induced dissociation (in-source CID) of 20 kDa PEGylated peptide was used to generate CGRP[Cit, Cit] fragment ions, among which the most abundant b ₈⁺ ion was selected and measured as a surrogate for the 20 kDa PEGylated peptide. A solid phase extraction (SPE) method was used to extract the PEGylated peptides from the biomatrix prior to the UPLC-MS/MS analysis. This method achieved a lower limit of quantitation (LLOQ) of 5.00 ng/mL with a serum sample volume of 100 μL, and was linear over the calibration range of 5.00 to 500 ng/mL in cynomolgus monkey serum. Intraday and interday accuracy and precision from QC samples were within ±15%. This method was successfully applied to a pharmacokinetic study of the 20 kDa PEGylated CGRP[Cit, Cit] in cynomolgus monkeys.     

Failure of one-dimensional Smoluchowski diffusion models to describe the duration of conformational rearrangements in floppy, diffusive molecular systems: a case study of polymer cyclization

Motivated by recent experimental efforts to measure the duration of individual folding∕unfolding transitions in proteins and RNA, here we use simulations to study the duration of a simple transition mimicking an elementary step in biopolymer folding: the closure of a loop in a long polymer chain. While the rate of such a transition is well approximated by a one-dimensional Smoluchowski model that views the end-to-end distance dynamics of a polymer chain as diffusion governed by the one-dimensional potential of mean force, the same model fails rather dramatically to describe the duration of such transitions. Instead, the latter timescale is well described by a model where the chain ends diffuse freely, uninfluenced by the average entropic force imposed by the polymer chain. The effective diffusion coefficient then depends on the length scale of the loop closure transition. Our findings suggest that simple one-dimensional models, when applied to estimate the duration of reactive events in complex molecular systems, should be used with caution.     

Utilizing a constant peak width transform for isothermal gas chromatography

A computational approach to partially address the general elution problem (GEP), and better visualize, isothermal gas chromatograms is reported. The theoretical computational approach is developed and applied experimentally. We report a high speed temporally increasing boxcar summation (TIBS) transform that, when applied to the raw isothermal GC data, converts the chromatographic data from the initial time domain (in which the peak widths in isothermal GC increase as a function of their retention factors, k), to a data point based domain in which all peaks have the same peak width in terms of number of points in the final data vector, which aides in preprocessing and data analysis, while minimizing data storage size. By applying the TIBS transform, the resulting GC chromatogram (initially collected isothermally), appears with an x-axis point scale as if it were instrumentally collected using a suitable temperature program. A high speed GC isothermal separation with a test mixture containing 10 compounds had a run time of ～25 s. The peak at a retention factor k ～0.7 had a peak width of ～55 ms, while the last eluting peak at k ～89 (i.e., retention time of ～22 s) had a peak width of ～2000 ms. Application of the TIBS transform increased the peak height of the last eluting peak 45-fold, and S/N ～20-fold. All peaks in the transformed test mixture chromatogram had the width of an unretained peak, in terms of number of data points. A simulated chromatogram at unit resolution, studied using the TIBS transform, provided additional insight into the benefits of the algorithm.     

Study of the interdependency of the data sampling ratio with retention time alignment and principal component analysis for gas chromatography

An in-depth study is presented to better understand how data reduction via averaging impacts retention alignment and the subsequent chemometric analysis of data obtained using gas chromatography (GC). We specifically study the use of signal averaging to reduce GC data, retention time alignment to correct run-to-run retention shifting, and principal component analysis (PCA) to classify chromatographic separations of diesel samples by sample class. Diesel samples were selected because they provide sufficient complexity to study the impact of data reduction on the data analysis strategies. The data reduction process reduces the data sampling ratio, S(R), which is defined as the number of data points across a given chromatographic peak width (i.e., the four standard deviation peak width). Ultimately, sufficient data reduction causes the chromatographic resolution to decrease, however with minimal loss of chemical information via the PCA. Using PCA, the degree of class separation (DCS) is used as a quantitative metric. Three "Paths" of analysis (denoted A-C) are compared to each other in the context of a "benchmark" method to study the impact of the data sampling ratio on preserving chemical information, which is defined by the DCS quantitative metric. The benchmark method is simply aligning data and applying PCA, without data reduction. Path A applies data alignment to collected data, then data reduction, and finally PCA. Path B applies data reduction to collected data, and then data alignment, and finally PCA. The optimized path, namely Path C, is created from Paths A and B, whereby collected data are initially reduced to fewer data points (smaller S(R)), then aligned, and then further reduced to even fewer points and finally analyzed with PCA to provide the DCS metric. Overall, following Path C, one can successfully and efficiently classify chromatographic data by reducing to a S(R) of ～15 before alignment, and then reducing down to S(R) of ～2 before performing PCA. Indeed, following Path C, results from an average of 15 different column length-with-temperature ramp rate combinations spanning a broad range of separation conditions resulted in only a ～15% loss in classification capability (via PCA) when the loss in chromatographic resolution was ～36%.     

Rapid release of plasmid DNA from polyelectrolyte multilayers: a weak poly(acid) approach

We demonstrate an approach to the assembly of DNA-containing polyelectrolyte multilayers that can be used to promote rapid release of DNA from surfaces. The approach is based on layer-by-layer incorporation of poly(acrylic acid) to promote rapid erosion in physiologically relevant media.