Intracellular bactericidal activity and action mechanism of MDP1 antimicrobial peptide against VRSA and MRSA in human endothelial cells.

Introduction: is a prominent cause of postoperative infections, often persisting within host cells, leading to chronic infections. Conventional antibiotics struggle to eliminate intracellular due to poor cell penetration. Antimicrobial peptides are a new hope for tackling intracellular bacteria.

Unveiling the dynamic and thermodynamic interactions of hydrocortisone with β-cyclodextrin and its methylated derivatives through insights from molecular dynamics simulations.

Cyclodextrins (CDs) can enhance the stability and bioavailability of pharmaceutical compounds by encapsulating them within their cavities. This study utilized molecular dynamics simulations to investigate the interaction mechanisms between hydrocortisone (HC) and various methylated CD derivatives. The results reveal that the loading of HC into CD cavities follows different mechanisms depending on the degree and position of methylation.

De novo antioxidant peptide design via machine learning and DFT studies.

Antioxidant peptides (AOPs) are highly valued in food and pharmaceutical industries due to their significant role in human function. This study introduces a novel approach to identifying robust AOPs using a deep generative model based on sequence representation. Through filtration with a deep-learning classification model and subsequent clustering via the Butina cluster algorithm, twelve peptides (GP1-GP12) with potential antioxidant capacity were predicted.

Exploring the role of cyclodextrins as a cholesterol scavenger: a molecular dynamics investigation of conformational changes and thermodynamics.

This study presents a comprehensive analysis of the cholesterol binding mechanism and conformational changes in cyclodextrin (CD) carriers, namely βCD, 2HPβCD, and MβCD. The results revealed that the binding of cholesterol to CDs was spontaneous and thermodynamically favorable, with van der Waals interactions playing a dominant role, while Coulombic interactions have a negligible contribution. The solubility of cholesterol/βCD and cholesterol/MβCD complexes was lower compared to cholesterol/2HPβCD complex due to stronger vdW and Coulombic repulsion between water and CDs.

Elucidating anticancer drugs release from UiO-66 as a carrier through the computational approaches.

The computational analysis of drug release from metal-organic frameworks (MOFs), specifically UiO-66, is the primary focus of this research. MOFs are recognized as nanocarriers due to their crystalline structure, porosity, and potential for added functionalities. The research examines the release patterns of three drugs: temozolomide, alendronate, and 5-fluorouracil, assessing various factors such as the drugs' distance from the UiO-66 centers, the interaction of drug functional groups with Zr metal ions, and the drug density throughout the nanocarrier.

Insights from molecular dynamics and DFT calculations into the interaction of 1,4-benzodiazepines with 2-hydroxypropyl-βCD in a theoretical study.

This study delves into the interaction between benzodiazepine (BZD) drugs and 2-hydroxypropyl-β-cyclodextrin (2HPβCD), a cyclodextrin (CD) known to improve drug delivery and enhance therapeutic outcomes. We find that the 2HPβCD's atoms become more rigid in the presence of chlordiazepoxide (CDP), clonazepam (CLZ), and diazepam (DZM), whereas they become more flexible in the presence of nordazepam (NDM) and nitrazepam (NZP). We also investigated the structure of 2HPβCD and found that loading these drugs increases both the area and volume of the 2HPβCD cavity, making it more suitable for drug delivery.

A molecular dynamic simulation study of anticancer agents and UiO-66 as a carrier in drug delivery systems.

Targeted drug delivery systems are effective ways to reduce side effects and enhance the therapeutic efficacy of drugs. Metal-organic frameworks are a new class of porous materials that have been recently used as high-performance nanocarriers in medical applications, such as drug storage and delivery due to high internal surface area, high porosity, low toxicity, high payloads, controlled drug release, their exceptional biocompatibility, and biodegradability. In this study, the loading of anti-cancer drugs Temozolomide, Alendronate, and 5-Fluorouracil inside UiO-66 nanocarrier cavities at the atomic level and different concentrations of the drug were investigated using the molecular dynamics simulation method.

Interactions of GF-17 derived from LL-37 antimicrobial peptide with bacterial membranes: a molecular dynamics simulation study.

Human cathelicidin LL-37 has recently attracted interest as a potential therapeutic agent, mostly because of its ability to kill a wide variety of pathogens and cancer cells. In this study, we used molecular dynamics simulation aimed to get insights that help to correlate with the antibacterial activity of previously designed LL-37 anticancer derivative (i.e.

Investigation of benzodiazepines (BZDs) in a DPPC lipid bilayer: Insights from molecular dynamics simulation and DFT calculations.

Toxicity is an essential parameter for drug development process and drug design. In this context, the effects of concentration of two Benzodiazepine drugs (diazepam, clonazepam) on fully hydrated dipalmitoylphosphatidylcholine (DPPC) has been studied at 323 K using molecular dynamics simulations. Various properties of bilayer such as membrane area per lipid, mass density distributions, order parameters, radial distribution functions, lateral diffusion, and electrostatic potential have been examined at three different concentrations of each drug.

Molecular dynamics simulations of Oxprenolol and Propranolol in a DPPC lipid bilayer.

Extensive microscopic molecular dynamics simulations have been performed to study the effects of tow β-blocker drugs (Propranolol, Oxprenolol) on fully hydrated dipalmitoylphosphatidylcholine (DPPC) in the fluid phase at 323K. Simulation of 4 systems containing varying concentrations of drugs was carried out. For the purpose of comparison, a fully hydrated DPPC bilayer without drugs was also studied at the same level of simulation technique which has been done on 4 other systems.

The partition and transport behavior of cytotoxic ionic liquids (ILs) through the DPPC bilayer: Insights from molecular dynamics simulation.

A molecular dynamics (MD) simulation with atomistic details was performed to examine the partitioning and transport behavior of moderately cytotoxic ionic liquids (ILs), namely choline bis(2-ethylhexyl) phosphate (CBEH), choline bis(2,4,4-trimethylpentyl) phosphinate (CTMP) and choline O,O-diethyl dithiophosphate (CDEP) in a fully hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer in the fluid phase at 323 K. The structure of ILs was so selected to understand if the role of dipole and dispersion forces in the ILs distribution in the membrane can be possible. Several analyses including mass density, electrostatic potential, order parameter, diffusion coefficients and hydrogen bond formation, was carried out to determine the precise location of the anionic species inside the membrane.