Thermodynamics and kinetics of drug-target binding by molecular simulation

S Decherchi, A Cavalli - Chemical Reviews, 2020 - ACS Publications
Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …

Kinetics for Drug Discovery: an industry-driven effort to target drug residence time

DA Schuetz, WEA de Witte, YC Wong… - Drug discovery today, 2017 - Elsevier
Highlights•A public–private partnership targets drug-binding kinetics in a multilevel
approach.•New experimental approaches for measuring drug residence time are …

Unbinding kinetics of a p38 MAP kinase type II inhibitor from metadynamics simulations

R Casasnovas, V Limongelli, P Tiwary… - Journal of the …, 2017 - ACS Publications
Understanding the structural and energetic requisites of ligand binding toward its molecular
target is of paramount relevance in drug design. In recent years, atomistic free energy …

Dental biomaterials redefined: molecular docking and dynamics-driven dental resin composite optimization

RS Saini, RIH Binduhayyim, V Gurumurthy… - BMC Oral Health, 2024 - Springer
Background Dental resin-based composites are widely recognized for their aesthetic appeal
and adhesive properties, which make them integral to modern restorative dentistry. Despite …

Attosecond probing of nuclear dynamics with trajectory-resolved high-harmonic spectroscopy

P Lan, M Ruhmann, L He, C Zhai, F Wang, X Zhu… - Physical review …, 2017 - APS
We report attosecond-scale probing of the laser-induced dynamics in molecules. We apply
the method of high-harmonic spectroscopy, where laser-driven recolliding electrons on …

How and when does an anticancer drug leave its binding site?

P Tiwary, J Mondal, BJ Berne - Science advances, 2017 - science.org
Obtaining atomistic resolution of drug unbinding from a protein is a much sought-after
experimental and computational challenge. We report the unbinding dynamics of the …

An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder

M Majewski, S Ruiz-Carmona, X Barril - Communications Chemistry, 2019 - nature.com
The predominant view in structure-based drug design is that small-molecule ligands, once
bound to their target structures, display a well-defined binding mode. However, structural …

How oliceridine (TRV-130) binds and stabilizes a μ-opioid receptor conformational state that selectively triggers G protein signaling pathways

S Schneider, D Provasi, M Filizola - Biochemistry, 2016 - ACS Publications
Substantial attention has recently been devoted to G protein-biased agonism of the μ-opioid
receptor (MOR) as an ideal new mechanism for the design of analgesics devoid of serious …

WScore: a flexible and accurate treatment of explicit water molecules in ligand–receptor docking

RB Murphy, MP Repasky, JR Greenwood… - Journal of medicinal …, 2016 - ACS Publications
We have developed a new methodology for protein–ligand docking and scoring, WScore,
incorporating a flexible description of explicit water molecules. The locations and …

Elucidation of the structural basis for ligand binding and translocation in conserved insect odorant receptor co-receptors

J Pacalon, G Audic, J Magnat, M Philip… - Nature …, 2023 - nature.com
In numerous insects, the olfactory receptor family forms a unique class of heteromeric cation
channels. Recent progress in resolving the odorant receptor structures offers unprecedented …