Targeting structural features of viral genomes with a nano-sized supramolecular drug

RNA targeting is an exciting frontier for drug design. Intriguing targets include functional RNA structures in structurally-conserved untranslated regions (UTRs) of many lethal viruses. However, computational docking screens, valuable in protein structure targeting, fail for inherently flexible RNA. Herein we harness MD simulations with Markov state modeling to enable nanosize metallo-supramolecular cylinders to explore the dynamic RNA conformational landscape of HIV-1 TAR untranslated region RNA (representative for many viruses) replicating experimental observations. These cylinders are exciting as they have unprecedented nucleic acid binding and are the first supramolecular helicates shown to have anti-viral activity in cellulo: the approach developed in this study provides additional new insight about how such viral UTR structures might be targeted with the cylinder binding into the heart of an RNA-bulge cavity, how that reduces the conformational flexibility of the RNA and molecular details of the insertion mechanism. The approach and understanding developed represents a new roadmap for design of supramolecular drugs to target RNA structural motifs across biology and nucleic acid nanoscience.

MD simulations and Markov state modeling explore induced fit binding of metallo-helicates to bulges in dynamic TAR RNA, reproduce experimental data, show how RNA conformational flexibility is reduced, and give mechanistic insight into insertion.     

Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods

In recent years, many virtual screening (VS) tools have been developed that employ different molecular representations and have different speed and accuracy characteristics. In this paper, we compare ten popular ligand-based VS tools using the publicly available Directory of Useful Decoys (DUD) data set comprising over 100?000 compounds distributed across 40 protein targets. The DUD was developed initially to evaluate docking algorithms, but our results from an operational correlation analysis show that it is also well suited for comparing ligand-based VS tools. Although it is conventional wisdom that 3D molecular shape is an important determinant of biological activity, our results based on permutational significance tests of several commonly used VS metrics show that the 2D fingerprint-based methods generally give better VS performance than the 3D shape-based approaches for surprisingly many of the DUD targets. To help understand this finding, we have analyzed the nature of the scoring functions used and the composition of the DUD data set itself. We propose that to improve the VS performance of current 3D methods, it will be necessary to devise screening queries that can represent multiple possible conformations and which can exploit knowledge of known actives that span multiple scaffold families.     

Improving chaos-based pseudo-random generators in finite-precision arithmetic

Nonlinear Dynamics - One of the widely-used ways in chaos-based cryptography to generate pseudo-random sequences is to use the least significant bits or digits of finite-precision numbers defined...     

Alkenyl C-H insertion of a β-disulfone iodonium ylide into flavones

The reaction of phenyliodonium bis(phenylsulfonyl)methylide with flavones affords insertion products into the alkenyl carbon-hydrogen bond of the flavone, presumably by an electrophilic attack of the iodonium ylide on the double bond of the flavone.     

Halogenated catechols from cycloaddition reactions of η-(2-ethoxyvinylketene)iron(0) complexes with 1-haloalkynes

1-Chloroalkynes and 1-bromohexyne undergo cycloaddition reactions with ethoxyvinylketeneiron(0) complexes to form chloro and bromocatechols. With most substituents, the halogen is incorporated ortho to the phenolic hydroxyl group regioselectively. With chloroethyne, chlorohexyne, and methyl chloropropiolate, the reverse regioselection is observed. Ab initio calculations reveal that the products are, in most cases, nearly isoenergetic, which indicates that the intermediate ketene-alkyne adduct geometry must be important in determining the product distribution.