Enantiomeric discrimination of chiral organic salts by chiral aza-15-crown-5 ether with C 1 symmetry: experimental and theoretical approaches

Chirality-Dependent Amino Acid Modulation of RNA Folding

The preponderance of a specific d- or l-chirality in fats, sugars, amino acids, nucleic acids, and so on is ubiquitous in nature, yet the biological origin of such chiral dominance (i.e., with one enantiomer overwhelmingly present) remains an open question. One plausible proposal for the predominance of l-chirality in amino acids could be through evolutionary templating of chiral RNA-folding via chaperone activity. To help evaluate this possibility, single molecule fluorescence experiments have been performed that measure the chiral dependence of chaperone folding dynamics for the simple tetraloop-tetraloop receptor (TL-TLR) tertiary binding motif in the presence of a series of chiral amino acids. Specifically, d- vs l-arginine is found to accelerate the unfolding of this RNA motif in a chirally selective fashion, with temperature-dependent studies of the kinetics performed to extract free energy, enthalpy, and entropy landscapes for the underlying thermodynamics. Furthermore, all-atom molecular dynamics (MD) simulations are pursued to provide additional physical insight into this chiral sensitivity, which reveal enantiomer-specific sampling of nucleic acid surfaces by d- vs l-arginine and support a putative mechanism for chirally specific denaturation of RNA tertiary structure by arginine but not other amino acids.

Combination of capillary electrophoresis and molecular modeling to study the enantiomer affinity pattern between β-blockers and anionic cyclodextrin derivatives in a methanolic and water background electrolyte

In order to have deep insights into the mechanisms of enantiomer affinity pattern in both aqueous and non-aqueous systems, an approach combining capillary electrophoresis and molecular modeling was undertaken. A chiral β-blocker; acebutolol, was enantioseparated in aqueous capillary electrophoresis and non-aqueous capillary electrophoresis using two anionic β-cyclodextrin derivatives. The enantiomer affinity pattern of acebutolol was found to be opposite when an aqueous background electrolyte was replaced with non-aqueous background electrolyte in the presence of heptakis(2,3-di-O-acetyl-6-sulfo)-β-cyclodextrin but remained the same in the presence of heptakis(2,3-di-O-methyl-6-sulfo)-β-cyclodextrin. Molecular docking of acebutolol into two β-cyclodextrin derivatives indicated two distinct binding modes called 'up' and 'down' conformations. After structure optimization by molecular dynamics and energy minimization, both enantiomers of acebutolol were preferred to the 'up' conformation with heptakis(2,3-di-O-methyl-6-sulfo)-β-cyclodextrin while 'down' conformation with heptakis(2,3-di-O-acetyl-6-sulfo)-β-cyclodextrin. The further calculation of the complex energy with solvent effect indicated that heptakis(2,3-di-O-acetyl-6-sulfo)-β-cyclodextrin had higher affinity to S-acebutolol than R-acebutolol in non-aqueous capillary electrophoresis while it showed better binding to R-acebutolol in aqueous capillary electrophoresis. However, the heptakis(2,3-di-O-methyl-6-sulfo)-β-cyclodextrin bound better to R-acebutolol in both aqueous and non-aqueous capillary electrophoresis, implying that the binding mode played more important role in chiral separation of heptakis(2,3-di-O-methyl-6-sulfo)-β-cyclodextrin while the solvent effect had prevailing impact on heptakis(2,3-di-O-acetyl-6-sulfo)-β-cyclodextrin.

Recent Developments and Applications of the MMPBSA Method

The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.