The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

In drug discovery, protonation states and tautomerization are easily overlooked. Through a Merck–Rutgers collaboration, this paper re-examined the initial settings and preparations for the Thermodynamic Integration (TI) calculation in AMBER Free-Energy Workflows, demonstrating the value of careful consideration of ligand protonation and tautomer state. Finally, promising results comparing AMBER TI and Schrödinger FEP+ are shown that should encourage others to explore the value of TI in routine Structure-based Drug Design.     

Hydrostatic Pressure Studies Distinguish Global from Local Protein Motions in C−H Activation by Soybean Lipoxygenase‐1

The proposed contributions of distinct classes of local versus global protein motions during enzymatic bond making/breaking processes has been difficult to verify. We employed soybean lipoxygenase‐1 as a model system to investigate the impact of high pressure at variable temperatures on the hydrogen‐tunneling properties of the wild‐type protein and three single‐site mutants. For all variants, pressure dramatically elevates the enthalpies of activation for the C−H activation. In contrast, the primary kinetic isotope effects (KIEs) for C−H activation and their corresponding temperature dependencies remain unchanged up to ca. 700 bar. The differential impact of elevated hydrostatic pressure on the temperature dependencies of rate constants versus substrate KIEs provides direct evidence for two distinct classes of protein motions: local, isotope‐dependent donor–acceptor distance‐sampling modes, and a more global, isotope‐independent search for productive protein conformational sub‐states.     

Enantioselective Total Synthesis of (+)‐Steenkrotin A and Determination of Its Absolute Configuration

The first enantioselective total synthesis of (+)‐steenkrotin A has been achieved in 18 steps and 4.2 % overall yield. The key features of the strategy entail a Rh‐catalyzed O?H bond insertion followed by an intramolecular carbonyl‐ene reaction, two sequential SmI₂‐mediated Ueno–Stork and ketyl–olefin cyclizations, and a cascade intramolecular aldol condensation/vinylogous retro‐aldol/aldol process with inversion of the relative configuration at the C7 position. The absolute configuration of (+)‐steenkrotin A was determined based on the stepwise construction of the stereocenters during the total synthesis.     

Living anionic polymerization of (E)‐1,3‐pentadiene and (Z)‐1,3‐pentadiene isomers

The anionic polymerization of (E)‐1,3‐pentadiene (EP) and (Z)‐1,3‐pentadiene (ZP) together with mixture of the E/Z isomers are investigated, respectively. The kinetic analysis shows that the activation energy for EP (86.17 kJ/mol) is much higher than that for ZP (59.03 kJ/mol). GPC shows that it is the EP rather than the ZP isomer that undergoes anionic living polymerization affording quantitative products of the polymers with well‐controlled molecular weights and narrow molecular weight distributions (1.05 ≤? ≤ 1.09). In addition, THF as polar additive has proved its validity to reduce the molecular weight distribution of poly(ZP) from 1.38 to as low as 1.19. The microstructure and sequence distributions of polypentadiene are characterized by ¹H NMR and quantitative ¹³C NMR. Finally, the distinctive reaction activity of two isomers can be elucidated by two different mechanisms which involve the presence of four forms of zwitterions for EP and the typical [1,5]‐sigmatropic hydrogen‐shift phenomenon for ZP. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2291–2301     

The Synthesis of 1-Phenoxy-3- Arylseleno-2-Propanol

A general and efficient synthetic method of 1-phenoxy-3-arylseleno-2-propanol by reducing diary1 diselenides with sodium borohydride in basic environment and their reaction with epoxypropoxyphenols are described.     

Quantitative study of cellular heterogeneity in doxorubicin uptake and its pharmacological effect on cancer cells

Cellular heterogeneity in doxorubicin (DOX) uptake and its relationship with pharmacological effect on cancer cells were quantitatively investigated for the first time. An in vitro experimental model was established by treating human leukemia K562 and breast cancer MCF‐7 cells with different schedules of DOX with or without surface P‐glycoprotein (P‐gp) inhibitor verapamil (VER). The cellular heterogeneity in DOX uptake was quantitatively examined by single‐cell analysis using capillary electrophoresis coupled with laser‐induced fluorescence detection. The corresponding cytotoxic effect was tested by cellular morphology, 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl‐tetrazolium and flow cytometry assays. The expression of cellular membrane surface P‐gp was determined by flow cytometry. Results showed that the cellular heterogeneity exists in DOX uptake. The single‐high DOX schedule leads to lower uptake heterogeneity and higher mean drug uptake. The cellular heterogeneity in DOX uptake was found to be negatively correlated with drug cytotoxicity and surface P‐gp expression, with r = ?0.7680 to ~ ?0.9587. VER reduces the cellular variation in DOX uptake, suggesting that surface P‐gp may be one of the causes of the cellular heterogeneity in DOX uptake. This research demonstrates the importance of quantitative study of cellular heterogeneity in drug uptake and its potential application in drug schedule design, response prediction and therapy modulation. Copyright © 2014 John Wiley & Sons, Ltd.     

Design and characterization of guided mode resonance filters with the improved structure for facile fabrication

In this study, a guided mode resonance filter with the improved structure for facile fabrication is designed; the properties of the designed filters are simulated by rigorous coupled wave analysis. It is found that the resonance wavelength and spectral linewidth are slightly increased with the increasing of the grating thickness, and seldom changed with the thickness of the grating filling factor, as the parameter error of the grating thickness and the grating filling factor are deviated from the designed value by ±10%, respectively, which are very favorable for simplifying preparation process of the GMR filter.