Alchemical transformations and beyond: Recent advances and real-world applications of free energy calculations in drug discovery

R Qian, J Xue, Y Xu, J Huang - Journal of Chemical Information …, 2024 - ACS Publications
Computational methods constitute efficient strategies for screening and optimizing potential
drug molecules. A critical factor in this process is the binding affinity between candidate …

Towards design of drugs and delivery systems with the Martini coarse-grained model

LR Kjølbye, GP Pereira, A Bartocci, M Pannuzzo… - QRB …, 2022 - cambridge.org
Coarse-grained (CG) modelling with the Martini force field has come of age. By combining a
variety of bead types and sizes with a new map** approach, the newest version of the …

Cryo-EM structures of prokaryotic ligand-gated ion channel GLIC provide insights into gating in a lipid environment

N Bharambe, Z Li, D Seiferth, AM Balakrishna… - Nature …, 2024 - nature.com
GLIC, a proton-activated prokaryotic ligand-gated ion channel, served as a model system for
understanding the eukaryotic counterparts due to their structural and functional similarities …

Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation

JT Petroff, NM Dietzen, E Santiago-McRae… - Nature …, 2022 - nature.com
Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are
sensitive to their lipid environment. The mechanism of phospholipid modulation of any …

Allosteric cholesterol site in glycine receptors characterized through molecular simulations

F Jalalypour, RJ Howard, E Lindahl - The Journal of Physical …, 2024 - ACS Publications
Glycine receptors are pentameric ligand-gated ion channels that conduct chloride ions
across postsynaptic membranes to facilitate fast inhibitory neurotransmission. In addition to …

[HTML][HTML] Advances in membrane mimetics and mass spectrometry for understanding membrane structure and function

LH Urner - Current Opinion in Chemical Biology, 2022 - Elsevier
Membrane proteins and lipids play roles in regulating biological functions of cells. However,
the analysis of interactions between membrane proteins and lipids in biological membranes …

Mechanisms underlying modulation of human GlyRα3 by Zn2+ and pH

K Kindig, E Gibbs, D Seiferth, PC Biggin… - Science …, 2024 - science.org
Glycine receptors (GlyRs) regulate motor control and pain processing in the central nervous
system through inhibitory synaptic signaling. The subtype GlyRα3 expressed in nociceptive …

Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM

C Bergh, U Rovšnik, R Howard, E Lindahl - Elife, 2024 - elifesciences.org
Ligand-gated ion channels transduce electrochemical signals in neurons and other
excitable cells. Aside from canonical ligands, phospholipids are thought to bind specifically …

State-dependent binding of cholesterol and an anionic lipid to the muscle-type Torpedo nicotinic acetylcholine receptor

A Ananchenko, RY Gao, F Dehez… - Communications …, 2024 - nature.com
The ability of the Torpedo nicotinic acetylcholine receptor (nAChR) to undergo agonist-
induced conformational transitions requires the presence of cholesterol and/or anionic …

Positive allosteric modulators of Glycine receptors and their potential use in pain therapies

CI Gallagher, DA Ha, RJ Harvey… - Pharmacological …, 2022 - Elsevier
Glycine receptors are ligand-gated ion channels that mediate synaptic inhibition throughout
the mammalian spinal cord, brainstem, and higher brain regions. They have recently …