Optimization of CHARMM force field parameters of a prostate cancer drug enzalutamide

Development of CHARMM compatible force field parameters and molecular dynamics simulations for the pesticide flupyradifurone

Flupyradifurone (FLU) is a novel butenolide insecticide with partial agonist activity for insect nicotinic acetylcholine receptors. Its safety for non-target organisms has been questioned in the literature, despite initial claims of its harmlessness. Detailed understanding of its toxicity and related molecular mechanisms remain under discussion. Thus, in this work, an optimized set of CHARMM compatible parameters for FLU is presented. CHARMM General Force Field program was used as a starting point while the non-bonded and bonded parameters were adjusted and optimized to reproduce MP2/6-31G(d) accuracy level results. For the validity assessment of these parameters, infrared spectrum, water-octanol partition coefficient, and normal modes were computed and compared to experimental values found in the literature. Several MD simulations of FLU in water and FLU in complex with an acetylcholine-binding protein were performed to estimate the ability of the optimized parameters to correctly describe its torsional space and reproduce observed crystallographic trends respectively.

Optimization of CHARMM force field parameters for ryanodine receptor inhibitory drug dantrolene using FFTK and FFParam

CONTEXT

Ryanodine receptors (RyRs) are large intracellular ligand-gated calcium release ion channels. Mutations in human RyR1 in combination with a volatile anesthetic or muscle relaxant are known to cause leaky RyRs resulting in malignant hyperthermia (MH). This has long been primarily treated with the RyR inhibitory drug dantrolene. Alternatives to dantrolene as a RyR inhibitor may be found through computer-aided drug design. Additionally, molecular dynamics (MD) studies of dantrolene interacting with RyRs may reveal its full mechanism of action. The availability of accurate force field parameters is important for the success of both.

METHODS

In this study, force field parameters for dantrolene were obtained from the CHARMM General Force Field (CGenFF) program and optimized using the force field toolkit (FFTK) and FFParam programs. The obtained parameters were then validated by a comparison between calculated and experimental IR spectra and normal mode analysis, among other techniques.

Stability Challenges of Amorphous Solid Dispersions of Drugs: A Critical Review on Mechanistic Aspects

The most common drawback of the existing and novel drug molecules is their low bioavailability because of their low solubility. One of the most important approaches to enhance the bioavailability in the enteral route for poorly hydrophilic molecules is amorphous solid dispersion (ASD). The solubility of compounds in amorphous form is comparatively high because of the availability of free energy produced during formulation. This free energy results in the change of crystalline nature of the prepared ASD to the stable crystalline form leading to the reduced solubility of the product. Due to the intrinsic chemical and physical uncertainty and the restricted knowledge about the interactions of active molecules with the carriers making, this ASD is a challenging task. This review focused on strategies to stabilize ASD by considering the various theories explaining the free-energy concept, physical interactions, and thermal properties. This review also highlighted molecular modeling and machine learning computational advancement to stabilize ASD.