Polarizable force fields for biomolecular simulations: Recent advances and applications
Realistic modeling of biomolecular systems requires an accurate treatment of electrostatics,
including electronic polarization. Due to recent advances in physical models, simulation …
including electronic polarization. Due to recent advances in physical models, simulation …
Molecular dynamics simulations of membrane permeability
This Review illustrates the evaluation of permeability of lipid membranes from molecular
dynamics (MD) simulation primarily using water and oxygen as examples. Membrane …
dynamics (MD) simulation primarily using water and oxygen as examples. Membrane …
Mastering the Gram-negative bacterial barrier–Chemical approaches to increase bacterial bioavailability of antibiotics
HK Ropponen, R Richter, AKH Hirsch… - Advanced Drug Delivery …, 2021 - Elsevier
To win the battle against resistant, pathogenic bacteria, novel classes of anti-infectives and
targets are urgently needed. Bacterial uptake, distribution, metabolic and efflux pathways of …
targets are urgently needed. Bacterial uptake, distribution, metabolic and efflux pathways of …
Mechanistic understanding from molecular dynamics in pharmaceutical research 2: lipid membrane in drug design
We review the use of molecular dynamics (MD) simulation as a drug design tool in the
context of the role that the lipid membrane can play in drug action, ie, the interaction …
context of the role that the lipid membrane can play in drug action, ie, the interaction …
Dynamic protonation dramatically affects the membrane permeability of drug-like molecules
Permeability (P m) across biological membranes is of fundamental importance and a key
factor in drug absorption, distribution, and development. Although the majority of drugs will …
factor in drug absorption, distribution, and development. Although the majority of drugs will …
Recent experimental developments in studying passive membrane transport of drug molecules
M Sharifian Gh - Molecular Pharmaceutics, 2021 - ACS Publications
The ability to measure the passive membrane permeation of drug-like molecules is of
fundamental biological and pharmaceutical importance. Of significance, passive diffusion …
fundamental biological and pharmaceutical importance. Of significance, passive diffusion …
Biochemical exploration of β-lactamase inhibitors
V Arer, D Kar - Frontiers in Genetics, 2023 - frontiersin.org
The alarming rise of microbial resistance to antibiotics has severely limited the efficacy of
current treatment options. The prevalence of β-lactamase enzymes is a significant …
current treatment options. The prevalence of β-lactamase enzymes is a significant …
Reliable prediction of Caco-2 permeability by supervised recursive machine learning approaches
G Falcón-Cano, C Molina, MÁ Cabrera-Pérez - Pharmaceutics, 2022 - mdpi.com
The heterogeneity of the Caco-2 cell line and differences in experimental protocols for
permeability assessment using this cell-based method have resulted in the high variability of …
permeability assessment using this cell-based method have resulted in the high variability of …
Revisiting the application of machine learning approaches in predicting aqueous solubility
T Zheng, JBO Mitchell, S Dobson - ACS omega, 2024 - ACS Publications
The solubility of chemical substances in water is a critical parameter in pharmaceutical
development, environmental chemistry, agrochemistry, and other fields; however, accurately …
development, environmental chemistry, agrochemistry, and other fields; however, accurately …
Calculating kinetic rates and membrane permeability from biased simulations
We present a simple approach to calculate the kinetic properties of lipid membrane crossing
processes from biased molecular dynamics simulations. We demonstrate that by using …
processes from biased molecular dynamics simulations. We demonstrate that by using …