GOLD in Action: A Binding Mode Study
Here we highlight a paper by Nunzia Cristiano 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.
Why?
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. Metabotropic glutamate (mGlu) receptors play a key role in modulating the synaptic transmission and are hence optimal drug targets for various CNS disorders.
Despite the hard work of researchers, to date no drugs that target mGlu receptors are on the market. Gee et al. have identified XAP044 as a selective ligand for the mGlu7 presynaptic receptor, and showed that the ligand unexpectedly binds to the extracellular domain of mGlu7 (J. Biol. Chem. 2014, 289 (16), 10975−10987). In the work herein presented, the team identified the mode of action of XAP044 by combining various experiments that include synthesizing derivatives, molecular modeling and docking.
How?
The team started by designing and synthesizing several derivatives of XAP044.
As can be seen in Figure 1, the ligand XAP044 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 structure of some of these are shown in Figure 1, top right (constrained derivatives, 1) and in Figure 1, bottom right (open-ring derivatives, 2–4).
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 derive important observations on their chemical structure. One example is that, to get a derivative that is as potent as (or even more potent than) XAP044, the heterocyclic ring highlighted in red in Figure 1 is not needed, revealing good candidate molecules that are simpler to synthesize.
Reported in Figure 2 are the chemical structures of the most efficient inhibitors identified 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.
Docking Studies
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). Additionally, these receptors are dimers that go from a resting state, where the lobes of VFT are open (Restingopen-open, Roo), to an active state, where the lobes are closed (Activeclosed-closed, Acc, Figure 3).
The X-ray structure of the Roo state of the mGlu7 receptor VFT domain was 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 build the one of the Acc state.
As the mGlu7 receptor activation is induced by agonists such as LSP4-2022 and L-AP4, the Acc model was used to dock these, while the Roo model was used to dock the antagonist XAP044 and its derivatives.
Focusing our attention here on the latter, the team examined the hypothesis that XAP044 could inhibit the homodimer activation by preventing the closure of the VFT.
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, revealing important interactions with the surrounding residues that prevent the closure of the VFT: these includes H-bonds with S160 and S229, hydrophobic contacts with A183, P184, K233 in an out-of-plane conformation, and halogen bonds with S237 and Q240. These observations were validated by structure‒activity relationship data and molecular dynamics simulations.
Finally, the hypothesis that the derivatives 3, 4a, and 4b could adopt a similar binding mode as XAP044 was confirmed by docking compound 3 and 4a along the α6 helix, revealing analogous contacts to those seen for XAP044. Due to their similar chemical structures, 4b is expected to have a binding mode comparable to 4a.
Conclusions
The present study elucidated the mechanism of action of the mGlu7 receptor antagonist XAP044 by combining a structure‒activity relationship study, molecular modeling and docking experiments.
The docking studies were performed using the CCDC’s protein-ligand docking software GOLD, integrated within Dassault Systèmes’ BIOVIA therapeutics design software Discovery Studio.
Next Steps
Interested in discovering more about GOLD? Download our new white papers: GOLD Docking Study: Linear Peptide Docking and GOLD Study: Docking Small Molecules to Nucleic Acid Targets.
Read the full article here: J. Med. Chem. 2024, 67, 14, 11662–11687.
To discuss further and/or request a demo with one of our scientists, please contact us via this form or .