Ligand binding free energy and kinetics calculation in 2020

V Limongelli - Wiley Interdisciplinary Reviews: Computational …, 2020 - Wiley Online Library
Ligand/protein binding (LPB) is a major topic in medicine, chemistry and biology. Since the
advent of computers, many scientists have put efforts in developing theoretical models that …

Structural and dynamic mechanisms of GABAA receptor modulators with opposing activities

S Zhu, A Sridhar, J Teng, RJ Howard, E Lindahl… - Nature …, 2022 - nature.com
Abstract γ-Aminobutyric acid type A (GABAA) receptors are pentameric ligand-gated ion
channels abundant in the central nervous system and are prolific drug targets for treating …

Ligand binding free-energy calculations with funnel metadynamics

S Raniolo, V Limongelli - Nature Protocols, 2020 - nature.com
The accurate resolution of the binding mechanism of a ligand to its molecular target is
fundamental to develop a successful drug design campaign. Free-energy calculations …

Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations

F Moraca, J Amato, F Ortuso, A Artese… - Proceedings of the …, 2017 - National Acad Sciences
G-quadruplexes (G4s) are higher-order DNA structures typically present at promoter regions
of genes and telomeres. Here, the G4 formation decreases the replicative DNA at each cell …

Conformational changes in the epidermal growth factor receptor: role of the transmembrane domain investigated by coarse-grained metadynamics free energy …

M Lelimousin, V Limongelli… - Journal of the American …, 2016 - ACS Publications
The epidermal growth factor receptor (EGFR) is a dimeric membrane protein that regulates
key aspects of cellular function. Activation of the EGFR is linked to changes in the …

Accelerating the calculation of protein–ligand binding free energy and residence times using dynamically optimized collective variables

ZF Brotzakis, V Limongelli… - Journal of chemical theory …, 2018 - ACS Publications
Elucidation of the ligand/protein binding interaction is of paramount relevance in
pharmacology to increase the success rate of drug design. To this end, a number of …

Ligand binding, unbinding, and allosteric effects: deciphering small-molecule modulation of HSP90

I D'Annessa, S Raniolo, V Limongelli… - Journal of chemical …, 2019 - ACS Publications
The molecular chaperone HSP90 oversees the functional activation of a large number of
client proteins. Because of its role in multiple pathways linked to cancer and …

Computational methods and theory for ion channel research

C Guardiani, F Cecconi, L Chiodo, G Cottone… - … in physics: X, 2022 - Taylor & Francis
Ion channels are fundamental biological devices that act as gates in order to ensure
selective ion transport across cellular membranes; their operation constitutes the molecular …

Exploring cryptic pockets formation in targets of pharmaceutical interest with SWISH

F Comitani, FL Gervasio - Journal of chemical theory and …, 2018 - ACS Publications
Cryptic (hidden) pockets are sites that are not visible on unliganded target proteins'
structures and only become apparent when a ligand binds. They might provide a valid …

Metadynamics simulations for the investigation of drug loading on functionalized inorganic nanoparticles

S Motta, P Siani, E Donadoni, G Frigerio, L Bonati… - Nanoscale, 2023 - pubs.rsc.org
Inorganic nanoparticles show promising properties that allow them to be efficiently used as
drug carriers. The main limitation in this type of application is currently the drug loading …