MolAR: Memory-Safe Library for Analysis of MD Simulations Written in Rust.

Transition to the memory safe natively compiled programming languages is a major software development trend in recent years, which eliminates memory-related security exploits, enables a fearless concurrency and parallelization, and drastically improves ergonomics and speed of software development. Modern memory-safe programing languages, such as Rust, are currently not used for developing molecular modeling and simulation software despite such obvious benefits as faster development cycle, better performance and smaller amount of bugs. This work introduces MolAR-the first memory-safe library for analysis of MD simulations written in Rust.

Nanodomains enriched in arachidonic acid promote P2Y12 receptor oligomerization in the platelet plasma membrane.

P2Y12 receptors on the platelet plasma membrane are targeted by several antiplatelets drugs. Although oligomerization and functioning of P2Y12 receptors depend on the membrane environment, little is known about their preferred membrane localization and the role of surrounding lipid composition, especially the arachidonic acids (ARA), which are abundant in platelets. Coarse-grained molecular dynamics simulations of platelet plasma membrane based on the lipidomics data were used to investigate the P2Y12 lipid environment and the involvement of ARA in its oligomerization in platelet plasma membranes.

Ticagrelor increases its own potency at the P2Y receptor by directly changing the plasma membrane lipid order in platelets.

Background And Purpose: Although the amphiphilic nature of the widely used antithrombotic drug Ticagrelor is well known, it was never considered as a membranotropic agent capable of interacting with the lipid bilayer in a receptor-independent way. In this study, we investigated the influence of Ticagrelor on plasma membrane lipid order in platelets and if this modulates the potency of Ticagrelor at the P2Y receptor.

Experimental Approach: We combined fluorescent in situ, in vitro and in silico approaches to probe the interactions between the plasma membrane of platelets and Ticagrelor.

A novel fatty acid analogue triggers CD36-GPR120 interaction and exerts anti-inflammatory action in endotoxemia.

Inflammation is a mediator of a number of chronic pathologies. We synthesized the diethyl (9Z,12Z)-octadeca-9,12-dien-1-ylphosphonate, called NKS3, which decreased lipopolysaccharide (LPS)-induced mRNA upregulation of proinflammatory cytokines (IL-1β, IL-6 and TNF-α) not only in primary intraperitoneal and lung alveolar macrophages, but also in freshly isolated mice lung slices. The in-silico studies suggested that NKS3, being CD36 agonist, will bind to GPR120.

Augmenting a training dataset of the generative diffusion model for molecular docking with artificial binding pockets.

This study introduces the PocketCFDM generative diffusion model, aimed at improving the prediction of small molecule poses in the protein binding pockets. The model utilizes a novel data augmentation technique, involving the creation of numerous artificial binding pockets that mimic the statistical patterns of non-bond interactions found in actual protein-ligand complexes. An algorithmic method was developed to assess and replicate these interaction patterns in the artificial binding pockets built around small molecule conformers.