GOLD in Action: A Binding Mode Study
Revealing the Binding Mode of the Inhibitor XAP044
Here we highlight a paper by Francine C. Acher from the Université Paris Cité, and co-workers from BIOVIA Dassault Systèmes, Novartis Biomedical Research, the University of Montpellier and the University of Regensburg.
In this work, the CCDC’s protein-ligand docking software GOLD was used to perform docking studies on selective ligands for a receptor involved in glutamate regulation, revealing the binding mode of the inhibitor XAP044.
The full article can be accessed here – J. Med. Chem. 2024, 67, 14, 11662–11687.
What Is Glutamate?
Glutamate is the most abundant excitatory neurotransmitter in the central nervous system (CNS).
Its dysregulation has been associated with ischemia, epilepsy, Parkinson’s disease, and some psychiatric and mood disorders.
Existing Inhibitor
Metabotropic glutamate (mGlu) receptors modulate the synaptic transmission and are hence optimal drug targets for various CNS disorders.
In a previous study, Gee et al. identified XAP044 as an mGlu7 receptor inhibitor (J. Biol. Chem. 2014, 289 (16), 10975−10987).
The Binding Mode
The present study elucidates the binding mode of XAP044 by combining structure‒activity relationship, molecular modeling, and docking experiments.
The docking studies were performed using GOLD, integrated within Dassault Systèmes’ BIOVIA therapeutics design software Discovery Studio.
Exploring New Derivatives
The team started by designing and synthesizing several derivatives of XAP044.
This ligand presents two rotatable bonds that can orient the two aromatic groups either in a planar or in an out-of-plane conformation. To probe the two different orientations, both constrained and open-ring derivatives were prepared.
The ability of XAP044 and its derivatives to inhibit mGlu7 receptor activation induced by the agonist LSP4-2022 was hence examined.
The planar derivatives series showed no significant inhibition, suggesting that XAP044 binds to the mGlu7 receptor in an out-of-plane orientation. A detailed analysis of the inhibition action for the open derivatives allowed the scientists to identify the most efficient inhibitors among the tested derivatives: 2w, 3, 4a, and 4b. In particular, compound 3, 4a, and 4b showed an increase in potency (of 4-fold in the case of 4a) from that of XAP044 and exhibited a better solubility.
The mGlu7 Receptors
The family of receptors that mGlu7 is part of possesses a large extracellular domain called Venus FlyTrap (VFT). This folds in two lobes which are linked by a flexible hinge and are connected to the 7-helix transmembrane domain (7TM) by a cysteine rich domain (CRD).
These receptors are dimers that go from a resting state, where the lobes of VFT are open, to an active state, where the lobes are closed.
The team examined the hypothesis that XAP044 could inhibit the homodimer activation by preventing the closure of the VFT.
The X-ray structure of the Roo state of the mGlu7 receptor VFT domain was hence selected from the ones available in the Protein Data Bank (PDB ID 2E4Z), and the missing residues were rebuilt by homology modeling or using templates. This model was then used to dock the antagonist XAP044 and its derivatives.
Docking with GOLD: Revealing the Binding Mode
When the two lobes of VFT close, two serine residues get in close proximity: these are S160 and S229. By mutating critical residues, the team showed that XAP044 interacts with the residue S229, blocking the closure of the VFT, and hence proved the fundamental role of S229 in the activity of XAP044.
Docking experiments allowed the scientists to evaluate the possible orientations for XAP044 to bind to S229. It was found that the orientation of XAP044 along the α6 helix was the most promising one, revealing important interactions with the surrounding residues that prevent the closure of the VFT.
These observations were validated by structure‒activity relationship data and molecular dynamics simulations.
Finally, the hypothesis that the promising derivatives of XAP044 could adopt a similar binding mode as XAP044 was confirmed by docking them along the α6 helix, revealing analogous contacts to those seen for XAP044.
