SAR-Guided Scoring Function and Mutational Validation Reveal the Binding Mode of CGS-8216 at the α1+/γ2–Benzodiazepine Site

DCB Siebert, M Wieder, L Schlener… - Journal of Chemical …, 2018 - ACS Publications
The structural resolution of a bound ligand–receptor complex is a key asset to efficiently
drive lead optimization in drug design. However, structural resolution of many drug targets …

[HTML][HTML] Structure-Guided Computational Methods Predict Multiple Distinct Binding Modes for Pyrazoloquinolinones in GABAA Receptors

J Fabjan, F Koniuszewski, B Schaar… - Frontiers in …, 2021 - frontiersin.org
Pyrazoloquinolinones (PQs) are a versatile class of GABAA receptor ligands. It has been
demonstrated that high functional selectivity for certain receptor subtypes can be obtained …

Structure-guided computational methods predict multiple distinct binding modes for pyrazoloquinolinones receptors in GABAA

J Fabjan, F Koniuszewski, B Schaar… - … Aspects of Ligand-gated …, 2022 - books.google.com
The WHO Model List of Essential Medicines contains many allosteric modulators of GABAA
receptors, among them several benzodiazepines and many sedative general anesthetics …

Delta Score: Improving the Binding Assessment of Structure-Based Drug Design Methods

M Ren, B Gao, B Qiang, Y Lan - arXiv preprint arXiv:2311.12035, 2023 - arxiv.org
Structure-based drug design (SBDD) stands at the forefront of drug discovery, emphasizing
the creation of molecules that target specific binding pockets. Recent advances in this area …

Fully flexible molecular alignment enables accurate ligand structure modelling

Z Wang, F Zhou, Z Wang, YQ Li, S Wang, L Zheng, W Li… - bioRxiv, 2023 - biorxiv.org
Accurate protein-ligand binding poses are the prerequisites of structure-based binding
affinity prediction, and also provide the structural basis for in depth lead optimization in small …

Leveraging data fusion strategies in multireceptor lead optimization MM/GBSA end-point methods

JL Knight, G Krilov, KW Borrelli, J Williams… - Journal of chemical …, 2014 - ACS Publications
Accurate and efficient affinity calculations are critical to enhancing the contribution of in silico
modeling during the lead optimization phase of a drug discovery campaign. Here, we …

Integration of ligand and structure based approaches for CSAR-2014

P Prathipati, K Mizuguchi - Journal of Chemical Information and …, 2016 - ACS Publications
The prediction of binding poses and affinities is an area of active interest in computer-aided
drug design (CADD). Given the documented limitations with either ligand or structure based …

Current assessment of docking into GPCR crystal structures and homology models: successes, challenges, and guidelines

T Beuming, W Sherman - Journal of chemical information and …, 2012 - ACS Publications
The growing availability of novel structures for several G protein-coupled receptors (GPCRs)
has provided new opportunities for structure-based drug design of ligands against this …

[HTML][HTML] Demystifying the Molecular Basis of Pyrazoloquinolinones Recognition at the Extracellular α1+/β3- Interface of the GABAA Receptor by Molecular Modeling

N Singh, BO Villoutreix - Frontiers in Pharmacology, 2020 - frontiersin.org
GABAA receptors are pentameric ligand-gated ion channels that serve as major inhibitory
neurotransmitter receptors in the mammalian brain and the target of numerous clinically …

[HTML][HTML] Structural features embedded in G protein-coupled receptor co-crystal structures are key to their success in virtual screening

T Coudrat, A Christopoulos, PM Sexton, D Wootten - PLoS One, 2017 - journals.plos.org
Structure based drug discovery on GPCRs harness atomic detail X-ray binding pockets and
large libraries of potential drug lead candidates in virtual screening (VS) to identify novel …