Theoretical analysis of the electronic properties of the sex pheromone and its analogue derivatives in the female processionary moth Thaumetopoea pytiocampa

Pore-ridge nanostructures on the surface of trichoid sensilla of the male silkmoth Bombyx mori: Aerodynamic trapping and transporting of the pheromone molecules

This paper tries to reveal the mechanism of the high-efficient adsorption of the sex pheromone by the trichoid sensilla of the male silk moth Bombyx mori. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) were used to acquire the topographies and nanostructures of the surfaces of the trichoid sensilla. SEM and AFM images present mostly regular pore-ridge nanostructures on the sensilla, and all the pores are located at or near the feet of the ridges. AFM phase-shift images demonstrate that the variation of phase-shift, which appears along the ridge cannot simply be attributed to heterogeneity in surface lipid properties, for the phase-shift was present in the same region with the sudden difference in height. Simulations of computational fluid dynamics were applied to investigate the effects on the airflow velocity field and streamlines by the pore-ridge nanostructures and the antenna vibration. Simulation results indicate that the airflow vortexes that form on the sensillum surface are generated by the combined effect of ambient airflow and pore-ridge structure as well as spontaneous vibration of the antenna. We suggest that the vortex intercepts and traps the pheromone molecules passing nearby, and transports them through its periodical movement to the pore. We speculate that the vortex is the aerodynamic factor benefitting the highly efficient adsorption of pheromone molecules.

Conformation and electronic structure of Carbidopa. A QM/MD study

Carbidopa (CD) is a drug used in combination with L-dopa (LD) in treatment of Parkinson’s disease (PD). CD is an inhibitor for enzyme decarboxylase, yet its mode of action is not entirely known although it is believed to involve enzyme shape recognition. The present work attempts to investigate the conformational preferences of CD. Tight geometry optimization at the density functional theory (DFT)/B3LYP/6-311[Formula: see text]G** level of theory has been carried out. The shallow nature of the potential energy surface (PES) and the presence of several local minima within a small energy range necessitate the launching of DFT-based molecular dynamics (MD) simulations. Two MD experiments were submitted for 35,000 points each. The complete trajectory in time domain of 10.5 ps is analyzed and discussed. The global minimum energy structure of CD is localized and identified by subsequent frequency calculations. The quantum theory of atom in molecules (QTAIMs) is used to extract and compare the quantum chemical topology features of the electron density distribution in CD and LD. Bonding characteristics are analyzed and discussed within the natural bond orbital (NBO) framework.

A combined molecular docking and charge density analysis is a new approach for medicinal research to understand drug-receptor interaction: curcumin-AChE model

In the present study, a molecular docking analysis has been performed on diketone form of curcumin molecule with acetylcholinesterase (AChE). The calculated lowest docked energy of curcumin molecule in the active site of AChE is -11.21 kcal/mol; this high negative value indicates that the molecule exhibits large binding affinity towards AChE. When the curcumin molecule present in the active site of AChE, subsequently, its conformation has altered significantly and the molecule adopts a U-shape geometry as it is linear in gas phase (before entering into the active site). This conformational transition facilitates curcumin to form strong interaction with Phe330 of acyl-binding pocket and the choline binding site with indole ring of Trp84 and Asp72. The gas phase and the active site analysis of curcumin allows to understand the conformational geometry, nature of molecular flexibility, charge density redistribution and the variation of electrostatic properties of curcumin in the active site. To obtain the gas phase structure, the curcumin molecule was optimized using Hartree-Fock and density functional methods (B3LYP) with the basis set 6-311G(∗∗). A charge density analysis on both gas phase as well as the molecule lifted from the active site was carried out using Bader's theory of atoms in molecules (AIM). The difference in molecular electrostatic potential between the two forms of curcumin displays the difference in charge distribution. The large dipole moment of curcumin (7.54 D) in the active site reflects the charge redistribution as it is much less in the gas phase (4.34 D).

Synthetic studies of centromere-associated protein-E (CENP-E) inhibitors: 1.Exploration of fused bicyclic core scaffolds using electrostatic potential map

Centromere-associated protein-E (CENP-E), a mitotic kinesin that plays an important role in mitotic progression, is an attractive target for cancer therapeutic drugs. For the purpose of developing novel CENP-E inhibitors as cancer therapeutics, we investigated a fused bicyclic compound identified by high throughput screening, 4-oxo-4,5-dihydrothieno[3,4-c]pyridine-6-carboxamide 1a. Based on this scaffold, we designed inhibitors for efficient binding at the L5 site in CENP-E utilizing homology modeling as well as electrostatic potential map (EPM) analysis to enhance CENP-E inhibitory activity. This resulted in a new lead, 5-bromoimidazo[1,2-a]pyridine 7, which showed potent CENP-E enzyme inhibition (IC50: 50nM) and cellular activity with accumulation of phosphorylated histone H3 in HeLa cells. Our homology model and EPM analysis proved to be useful tools for the rational design of CENP-E inhibitors.