On a relationship between molecular polarizability and partial molar volume in water

Anti-inflammatory pregnane-type steroid derivatives clathroids A-B from the marine Microcionidae sponge Clathria (Thalysias) vulpina: Prospective duel inhibitors of pro-inflammatory cyclooxygenase-2 and 5-lipoxygenase

Two pregnane-type of steroid derivatives characterized as 5α-pregna-3β-methyl pent-3-enoate-12β, 16β diol-20-one (clathroid A) and 12β,15β- dihydroxypregna-4,6-diene-3,20-dione (clathroid B) were purified from the crude extract of the marine sponge, Clathria (Thalysias) vulpina (family Microcionidae) by extensive chromatographic fractionation. Spectroscopic methods including nuclear magnetic resonance spectroscopy were employed to characterize the purified clathroids A-B. The studied compounds exhibited duel inhibitory potentials against pro-inflammatory cyclooxygenase-2 and 5-lipoxygenase (median inhibitory concentration, IC₅₀ < 1 mM), whereas the attenuation property of clathroid A against 5-lipoxygenase (IC₅₀ 0.85 mM) was greater than the standard anti-inflammatory ibuprofen (IC₅₀ 4.51 mM, p < 0.05). Greater selectivity index (anti cyclooxygense-2/anti cyclooxygense-1) of the studied clathroids (>1) than ibuprofen (0.43) attributed the greater selective attenuation properties towards pro-inflammatory inducible cyclooxygenase-2 than its constitutive isoenzyme cyclooxygenase-1. The antioxidant potentials of clathroid A against 2, 2'-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (IC₅₀ 0.80 mM) and diphenyl-1-picrylhydrazyl (IC₅₀ 0.83 mM) free radicals were greater than those of clathroid B (IC₅₀ 0.86-0.96 mM). Structure-activity analyses showed that the bioactivities of the clathroids were directly related to their electronic parameters coupled with permissible hydrophobic properties. Clathroid A exhibited grater electronic parameter (topological polar surface area tPSA, 83.83) than clathroid B (74.60) and ibuprofen (37.30), which were found to be in agreement with the prospective anti-inflammatory profile of clathroid A. Clathroid A exhibited higher number of hydrogen bonding interactions with 5-lipoxygenase active site and lesser docking values, such as docking score (DS -12.90 kcal mol^-1) and inhibition constant (Ki 1.11 nM) than those recorded by clathroid B (DS -10.49 kcal mol^-1; Ki 13.88 nM). The molecular binding properties of clathroid A with 5-lipoxidase inferred that its docking score/ binding energy were positively correlated with their in vitro bioactivie potentilas. A putative biosynthetic pathway of the studied clathroids was proposed from a pregnenolone precursor. The present study recognized the potential of clathroid A isolated from C. (Thalysias) vulpina as prospective anti-inflammatory lead that could find its use in medicinal applications.

Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory

Molecular dynamics simulation is a fruitful tool for investigating the structural stability, dynamics, and functions of biopolymers at an atomic level. In recent years, simulations can be performed on time scales of the order of milliseconds using special purpose systems. Since the most stable structure, as well as meta-stable structures and intermediate structures, is included in trajectories in long simulations, it is necessary to develop analysis methods for extracting them from trajectories of simulations. For these structures, methods for evaluating the stabilities, including the solvent effect, are also needed. We have developed relaxation mode analysis to investigate dynamics and kinetics of simulations based on statistical mechanics. We have also applied the three-dimensional reference interaction site model theory to investigate stabilities with solvent effects. In this paper, we review the results for designing amino-acid substitution of the 10-residue peptide, chignolin, to stabilize the misfolded structure using these developed analysis methods.

Estrogenic Active Stilbene Derivatives as Anti-Cancer Agents: A DFT and QSAR Study

Exploring different quantum chemical quantities for lead compounds is an ongoing approach in identifying crucial structural activity related features that are contributing into their biological activities. Herein, activity-related quantum chemical calculations were performed for the selected estrogenic stilbene derivatives using density functional theory (DFT) with B3LYP functional and 6-311++G** basis set. In addition, specific activity-related geometry-independent drug-like properties are discussed for these derivatives. To obtain the mathematical model that correlates the chemical descriptors with their measured estrogenic activities, the quantitative structure activity relationship (QSAR) is established using multiple linear regression (MLR) and support vector regression (SVR) methods. Satisfactory fit with a reasonable regression correlation coefficient (${\rm{R}}^{2}= 0.78$R2=0.78) between predicted and experimental $pEC_{50}$pEC50 values is observed using MLR method. The present study identifies the essential physicochemical descriptors that effectively contribute in the estrogenic activity. The applied approach provides helpful insight into the designing novel estrogenic agents with improved anticancer activities.