Rapid and accurate estimation of protein–ligand relative binding affinities using site-identification by ligand competitive saturation

Predicting relative protein–ligand binding affinities is a central pillar of lead optimization efforts in structure-based drug design. The site identification by ligand competitive saturation (SILCS) methodology is based on functional group affinity patterns in the form of free energy maps that may be used to compute protein–ligand binding poses and affinities. Presented are results obtained from the SILCS methodology for a set of eight target proteins as reported originally in Wang et al. (J. Am. Chem. Soc., 2015, 137, 2695–2703) using free energy perturbation (FEP) methods in conjunction with enhanced sampling and cycle closure corrections. These eight targets have been subsequently studied by many other authors to compare the efficacy of their method while comparing with the outcomes of Wang et al. In this work, we present results for a total of 407 ligands on the eight targets and include specific analysis on the subset of 199 ligands considered previously. Using the SILCS methodology we can achieve an average accuracy of up to 77% and 74% when considering the eight targets with their 199 and 407 ligands, respectively, for rank-ordering ligand affinities as calculated by the percent correct metric. This accuracy increases to 82% and 80%, respectively, when the SILCS atomic free energy contributions are optimized using a Bayesian Markov-chain Monte Carlo approach. We also report other metrics including Pearson''s correlation coefficient, Pearlman''s predictive index, mean unsigned error, and root mean square error for both sets of ligands. The results obtained for the 199 ligands are compared with the outcomes of Wang et al. and other published works. Overall, the SILCS methodology yields similar or better-quality predictions without a priori need for known ligand orientations in terms of the different metrics when compared to current FEP approaches with significant computational savings while additionally offering quantitative estimates of individual atomic contributions to binding free energies. These results further validate the SILCS methodology as an accurate, computationally efficient tool to support lead optimization and drug discovery.

Predicting relative protein–ligand binding affinities is a central pillar of lead optimization efforts in structure-based drug design.     

Enhancing the dissolution of hydrophobic guests using solid state inclusion complexation: characterization and in vitro evaluation

The objectives of the present investigation were to prepare and characterize solid inclusion complexes of Etodolac (ETD) with β-cyclodextrin (β-CD) in order to study the effect of complexation on the dissolution rate of ETD, a hydrophobic guest molecule. Phase solubility curve was classified as a typical A_L-type for the cyclodextrins (CD’s), showing that soluble complex was formed. The inclusion complexes in the molar ratio of 1:1 and 1:2 (β-CD–ETD) were prepared by various methods such as kneading, co-evaporation and in molar ratio of 1:1 by spray dried technique respectively. The molecular behaviors of ETD in all samples were characterized by nuclear magnetic resonance (NMR) spectroscopy, fourier-transform infrared (FTIR) spectroscopy, differential scanning calorimetry (DSC) and powder X-ray diffraction (PXRD) studies and Scanning Electron microscopy (SEM) analysis. The results of these studies indicated that complexes prepared by kneading, co-evaporation and spray drying techniques showed inclusion of the ETD molecule into the CD’s cavities. The highest improvement in in vitro dissolution profiles was observed in complexes prepared with spray dried technique. Mean in vitro dissolution time indicated significant difference between the release profiles of ETD from complexes and physical mixtures and from pure ETD.     

Effect of sphere to rod transition on the probe microenvironment in sodium dodecyl sulphate micelles: A time resolved fluorescence anisotropy study

The effect of different hydrotropic salts on the microenvironment at the anionic head group region of sodium dodecyl sulphate (SDS) micelle has been studied through time-resolved fluorescence anisotropy measurements of a solubilized probe, coumarin-153 (C153). The organic cations of the hydrotropic salts used in this study, i.e. aniline hydrochloride (AHC) and o-, m- and p-toluidine hydrochlorides (OTHC, MTHC and PTHC, respectively), differ in their charge to size ratio and hydrophobicity. Present study utilizes the sensitivity of the fluorescence technique to understand the changes in the micropolarity and microviscosity experienced by the fluorescent probe, C153, solubilized in the micellar Stern layer, on addition of different hydrotropic salts. Significant changes are observed in the rotational relaxation dynamics of the probe with increasing concentration of the salts. The changes in the rotational relaxation dynamics clearly reflect the sphere to rod transition in the SDS micelles and correspond nicely with the reported results from dynamic light scattering measurements. The growth behavior of SDS micelles is found to be sensitive to the hydrophobicity of the organic cations. The charge to size ratio of the organic cations also indicated to play a role in inducing the sphere to rod transition in the SDS micelles. The interesting observation made from this study is that the sphere to rod transition of SDS micelles is largely facilitated by the presence of the hydrotropic salts and such a transition is successfully indicated by the simple fluorescence anisotropy measurements of a probe in the micelle carried out in the presence of different hydrotropic salts.     

α-Amylase: An Ideal Representative of Thermostable Enzymes

The conditions prevailing in the industrial applications in which enzymes are used are rather extreme, especially with respect to temperature and pH. Therefore, there is a continuing demand to improve the stability of enzymes and to meet the requirements set by specific applications. In this respect, thermostable enzymes have been proposed to be industrially relevant. In this review, α-amylase, a well-established representative of thermostable enzymes, providing an attractive model for the investigation of the structural basis of thermostability of proteins, has been discussed.     

Malachite green as a reagent for detection and spectrophotometric determination of chromium(VI)

A sensitive and inexpensive method of spectrophotometric determination of chromium(VI), based on the absorbance of its complex with malachite green and acetic acid at pH 2.5 is reported. The complex shows a molar absorptivity of 8 x 10(4) l.mole(-1) cm(-1) at 560 nm, using malachite green and acetic acid as reference solution. The effect of time, temperature, pH and reagent concentration is studied and optimum operating conditions are established. Beer's law is applicable in the concentration range 2.0-22.8 mug/ml chromium(VI). The resin beads act as a catalyst and as little as 1.6 mug of chromium(VI) is detected in the resin phase as compared to 4.1 mug in the solution phase. The standard deviation in the determinations is +/-0.40 mug/ml for a 10.35 mug/ml solution.     

Synthesis of 2,2′‐Bi‐2H‐3,3′‐diaryl‐1,4‐benzothiazines from α,α‐Dibromoacetophenones and o‐Aminothiophenol

Some 2,2′‐bi‐2H‐3,3′‐diaryl‐1,4‐benzothiazines (5a–f) were synthesized from α,α‐dibromoacetophenones and o‐aminothiophenol.     

Stabilization of platinum(II) hydrides by tri-t-butylarsine; facile syntheses of stable trans-PtH2[As(t-Bu)3]2 and trans-PtHX[As(t-Bu)3]2 complexes

trans-PtH₂[As(t-Bu)₃]₂ was prepared in very good yield by afacile reaction of K₂PtC1₄ with As(t-Bu)₃ in alkaline ethanol. Treatment of trans-PtH₂[As(t-Bu)₃]₂ with CF₃CO₂H or HCI afforded trans-PtH(O₂CCF₃)[As(t-Bu)₃]₂ or trans-PtHCl[As(t-Bu)₃]₂. respectively, in almost quantitative yield.     

Radiation induced synthesis and swelling characterization of thermo-responsive N-isopropylacrylamide-co-ionic hydrogels

Two-component thermo-responsive hydrogels poly(N-isopropylacrylamide)-co-vinylbenzyltrimethylammonium chloride (NIPA-co-VBT) and poly(N-isopropylacrylamide)-co-p-sodium styrene sulphonate (NIPA-co-SSS) were prepared by using high energy gamma radiation. The gels were characterized by Fourier transformed infrared spectroscopy (FTIR), scanning electron microscopy (SEM) and sol-gel analysis. The presence of ionic monomers in NIPA leads to lower gel content. Introduction of ionic components in the matrix enhanced swelling extent but caused slower volume transition. The swelling studies in alcohol indicated that swelling extent was function of polarity of the swelling medium and all gels followed the order water > methanol > ethanol > iso-propanol. In mixed co-solvents (water-alcohol), they exhibit complex reentrant behavior. The co-polymer gels containing VBT swelled faster and to higher extent than those containing SSS. The dynamic swelling studies indicated that diffusion of water in PNIPA gel shifts from Fickian for PNIPA to anomalous for NIPA-co-ionic gels also the mean swelling time (MST) decreases for gels containing ionic monomers.