The emergence of machine learning force fields in drug design

M Chen, X Jiang, L Zhang, X Chen… - Medicinal Research …, 2024 - Wiley Online Library
In the field of molecular simulation for drug design, traditional molecular mechanic force
fields and quantum chemical theories have been instrumental but limited in terms of …

Alchemical Free Energy Calculations on Membrane-Associated Proteins

M Papadourakis, H Sinenka, P Matricon… - Journal of Chemical …, 2023 - ACS Publications
Membrane proteins have diverse functions within cells and are well-established drug
targets. The advances in membrane protein structural biology have revealed drug and lipid …

Is the functional response of a receptor determined by the thermodynamics of ligand binding?

M Vögele, BW Zhang, J Kaindl… - Journal of Chemical …, 2023 - ACS Publications
For an effective drug, strong binding to the target protein is a prerequisite, but it is not
enough. To produce a particular functional response, drugs need to either block the proteins' …

Advances in structure-based drug design: the potential for precision therapeutics in psychiatric disorders

D Cao, P Zhang, S Wang - Neuron, 2024 - cell.com
Over the years, the field of GPCR drug design has undergone a remarkable evolution,
fueled by advancements in science and technology. This evolution has given rise to a …

Understanding the impact of binding free energy and kinetics calculations in modern drug discovery

VA Adediwura, K Koirala, HN Do, J Wang… - Expert Opinion on Drug …, 2024 - Taylor & Francis
Introduction For rational drug design, it is crucial to understand the receptor-drug binding
processes and mechanisms. A new era for the use of computer simulations in predicting …

Computational Workflow for Refining AlphaFold Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved …

M Stampelou, G Ladds… - The Journal of Physical …, 2024 - ACS Publications
A structure-based drug design pipeline that considers both thermodynamic and kinetic
binding data of ligands against a receptor will enable the computational design of improved …

Intracellular pocket conformations determine signaling efficacy through the μ opioid receptor

DA Cooper, J DePaolo-Boisvert, SA Nicholson, B Gad… - bioRxiv, 2024 - biorxiv.org
It has been challenging to determine how a ligand that binds to a receptor activates
downstream signaling pathways and to predict the strength of signaling. The challenge is …

Mechanistic insights into G protein association with a G protein-coupled receptor

H Batebi, G Pérez-Hernández, J Mathiesen, M Shi… - 2023 - researchsquare.com
G protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by promoting
guanine nucleotide exchange. Here, we investigate the process of functional association …

A Computational Workflow for Refining AF2 Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive …

A Kolocouris, M Stampelou, G Ladds - 2023 - chemrxiv.org
A drug design pipeline that considers both thermodynamic and kinetic binding data of
ligands against a receptor will enable the computational design of improved drug molecules …

Discovery of Chemical Probes through Structure-based Virtual Screening of Vast Compound Databases

A Luttens - 2023 - diva-portal.org
Vast Compound Databases. Digital Comprehensive Summaries of Uppsala Dissertations
from the Faculty of Science and Technology 2261. 68 pp. Uppsala: Acta Universitatis …