4.6 Article

In Silico Prediction and Validation of CB2 Allosteric Binding Sites to Aid the Design of Allosteric Modulators

Related references

Note: Only part of the references are listed.
Review Pharmacology & Pharmacy

Molecular basis for ligand modulation of the cannabinoid CB1 receptor

Karthik Ramesh et al.

Summary: The cannabinoid CB1 receptor, as the most abundant G protein coupled receptor in the central nervous system, mediates the response to endocannabinoids and Cannabis compounds. Various ligands targeting CB1 receptors have been developed for the treatment of neurological disorders. High-resolution structures of CB1 receptor in different functional states have enhanced our understanding of CB1 ligand interactions, selectivity, receptor activation, and allosteric modulation, paving the way for the development of novel ligands for therapeutic applications.

BRITISH JOURNAL OF PHARMACOLOGY (2022)

Article Biochemical Research Methods

MCCS, a novel characterization method for protein-ligand complex

Maozi Chen et al.

Summary: This study introduces a scoring-function based computing protocol to characterize the binding feature of protein-ligand complexes. The energy contribution of individual residues is quantitated to construct a vector representing ligand recognition pattern, which is then used for similarity and clustering analysis. This approach offers a new perspective for clustering proteins, determining protein characteristics in binding, and advanced screening using molecular docking.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Biochemistry & Molecular Biology

Ligand recognition and allosteric regulation of DRD1-Gs signaling complexes

Peng Xiao et al.

Summary: Dopamine receptors, includingD1- and D2-like receptors, are key therapeutic targets in various neurological syndromes, cardiovascular, and kidney diseases. This study presents cryo-EM structures of the dopamine D1 receptor (DRD1) coupled to Gs heterotrimer, providing insights into ligand recognition, allosteric regulation, and G protein coupling mechanisms of DRD1.
Article Chemistry, Medicinal

Design of Negative and Positive Allosteric Modulators of the Cannabinoid CB2 Receptor Derived from the Natural Product Cannabidiol

Gemma Navarro et al.

Summary: Cannabidiol (CBD), the second most abundant active compound in the Cannabis sativa plant, is gaining interest for its potential human use as it is neither euphorizing nor addictive. Researchers have designed and synthesized novel compounds based on CBD's properties as a partial agonist and negative allosteric modulator, offering potential therapeutic utility for the cannabinoid CB2 receptor. By using molecular dynamic simulations and site-directed mutagenesis studies, they have identified the allosteric site near the receptor entrance, allowing for structure-guided design of CB2 receptor modulators.

JOURNAL OF MEDICINAL CHEMISTRY (2021)

Article Biochemistry & Molecular Biology

RCSB Protein Data Bank: Enabling biomedical research and drug discovery

David S. Goodsell et al.

PROTEIN SCIENCE (2020)

Article Biochemistry & Molecular Biology

Cryo-EM Structure of the Human Cannabinoid Receptor CB2-Gi Signaling Complex

Changrui Xing et al.

Article Biochemistry & Molecular Biology

An allosteric modulator binds to a conformational hub in the β2 adrenergic receptor

Xiangyu Liu et al.

NATURE CHEMICAL BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Binding Characterization of GPCRs-Modulator by Molecular Complex Characterizing System (MCCS)

Zhiwei Feng et al.

ACS CHEMICAL NEUROSCIENCE (2020)

Article Chemistry, Medicinal

Allosteric Modulation of Class A GPCRs: Targets, Agents, and Emerging Concepts

Eric A. Wold et al.

JOURNAL OF MEDICINAL CHEMISTRY (2019)

Article Multidisciplinary Sciences

Mechanism of β2AR regulation by an intracellular positive allosteric modulator

Xiangyu Liu et al.

SCIENCE (2019)

Article Biochemistry & Molecular Biology

Structure of an allosteric modulator bound to the CB1 cannabinoid receptor

Zhenhua Shao et al.

NATURE CHEMICAL BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Crystal Structure of the Human Cannabinoid Receptor CB2

Xiaoting Li et al.

Article Multidisciplinary Sciences

Structure of the complement C5a receptor bound to the extra-helical antagonist NDT9513727

Nathan Robertson et al.

NATURE (2018)

Article Biochemistry & Molecular Biology

Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40

Jun Lu et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Structural basis for the cooperative allosteric activation of the free fatty acid receptor GPR40

Jun Lu et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)

Article Chemistry, Medicinal

Difference and Influence of Inactive and Active States of Cannabinoid Receptor Subtype CB2: From Conformation to Drug Discovery

Jianping Hu et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2016)

Article Multidisciplinary Sciences

Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists

Yi Zheng et al.

NATURE (2016)

Article Multidisciplinary Sciences

Intracellular allosteric antagonism of the CCR9 receptor

Christine Oswald et al.

NATURE (2016)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Review Pharmacology & Pharmacy

Drugs for Allosteric Sites on Receptors

Cody J. Wenthur et al.

ANNUAL REVIEW OF PHARMACOLOGY AND TOXICOLOGY, VOL 54 (2014)

Article Biochemical Research Methods

PARS: a web server for the prediction of Protein Allosteric and Regulatory Sites

Alejandro Panjkovich et al.

BIOINFORMATICS (2014)

Article Biotechnology & Applied Microbiology

Allosteric targeting of receptor tyrosine kinases

Frederik De Smet et al.

NATURE BIOTECHNOLOGY (2014)

Article Pharmacology & Pharmacy

Structure-Based Ligand Discovery Targeting Orthosteric and Allosteric Pockets of Dopamine Receptors

J. Robert Lane et al.

MOLECULAR PHARMACOLOGY (2013)

Article Chemistry, Medicinal

Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

Junmei Wang et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2012)

Review Pharmacology & Pharmacy

Allosteric modulators of rhodopsin-like G protein-coupled receptors: Opportunities in drug development

Christa E. Mueller et al.

PHARMACOLOGY & THERAPEUTICS (2012)

Article Chemistry, Physical

Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values

Chresten R. Sondergaard et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Article Chemistry, Physical

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions

Mats H. M. Olsson et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)

Review Pharmacology & Pharmacy

P2Y nucleotide receptors: promise of therapeutic applications

Kenneth A. Jacobson et al.

DRUG DISCOVERY TODAY (2010)

Article Multidisciplinary Sciences

Structure of the Human Dopamine D3 Receptor in Complex with a D2/D3 Selective Antagonist

Ellen Y. T. Chien et al.

SCIENCE (2010)

Article Endocrinology & Metabolism

Central side-effects of therapies based on CB1 cannabinoid receptor agonists and antagonists: focus on anxiety and depression

Fabricio A. Moreira et al.

BEST PRACTICE & RESEARCH CLINICAL ENDOCRINOLOGY & METABOLISM (2009)

Article Chemistry, Multidisciplinary

AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility

Garrett M. Morris et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Chemistry, Medicinal

Recent Advances in Free Energy Calculations with a Combination of Molecular Mechanics and Continuum Models

Junmei Wang et al.

CURRENT COMPUTER-AIDED DRUG DESIGN (2006)

Article Biochemistry & Molecular Biology

VEGA - An open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming

A Pedretti et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2004)

Article Chemistry, Multidisciplinary

UCSF chimera - A visualization system for exploratory research and analysis

EF Pettersen et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)