1. |
- Begnini, Fabio, et al.
(author)
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Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction
- 2022
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In: Journal of Medicinal Chemistry. - : American Chemical Society (ACS). - 0022-2623 .- 1520-4804. ; 65:4, s. 3473-3517
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Journal article (peer-reviewed)abstract
- Upregulation of the transcription factor Nrf2 by inhibition of the interaction with its negative regulator Keap1 constitutes an opportunity for the treatment of disease caused by oxidative stress. We report a structurally unique series of nanomolar Keap1 inhibitors obtained from a natural product-derived macrocyclic lead. Initial exploration of the structure-derived macrocyclic lead. Initial exploration of the structure-activity relationship of the lead, followed by structure-guided optimization, resulted in a 100-fold improvement in inhibitory potency. The macrocyclic core of the nanomolar inhibitors positions three pharmacophore units for productive interactions with key residues of Keap1, including R415, R483, and Y572. Ligand optimization resulted in the displacement of a coordinated water molecule from the Keap1 binding site and a significantly altered thermodynamic profile. In addition, minor reorganizations of R415 and R483 were accompanied by major differences in affinity between ligands. This study therefore indicates the importance of accounting both for the hydration and flexibility of the Keap1 binding site when designing high-affinity ligands.
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2. |
- Begnini, Fabio, et al.
(author)
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Structure-based optimization of a macrocyclic inhibitor of the Keap1-Nrf2 protein-protein interaction
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Other publication (other academic/artistic)abstract
- Activation of the transcription factor Nrf2 by inhibition of the interaction with its negative regulator Keap1 constitutes a potential opportunity for the treatment of oxidative stress related disease. Although highly potent inhibitors of the Keap1–Nrf2 protein-protein interaction (PPI) have been reported, these compounds are based on a few reoccurring scaffolds. Here, we report a novel, structurally unique series of double-digit nM Keap1 inhibitors obtained by optimization of a natural product-derived macrocyclic lead. Exploration of the structure-activity relationship, followed by structure-based design led to a 100-fold improvement in inhibitory potency compared to the starting point. The macrocyclic core positions the pharmacophores of the inhibitors suitably for productive interactions with key residues of Keap1, including R415 and R483; both of which contribute to the highly polar nature of the binding site for Nrf2. In addition, we discovered that minor, ligand-induced reorganizations of these two arginine residues are accompanied by major differences in binding affinity between compounds in the series.
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3. |
- Fleetwood, Oliver, et al.
(author)
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Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches
- 2020
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In: Biochemistry. - : AMER CHEMICAL SOC. - 0006-2960 .- 1520-4995. ; 59:7, s. 880-891
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Journal article (peer-reviewed)abstract
- Agonist binding to G protein-coupled receptors (GPCRs) leads to conformational changes in the transmembrane region that activate cytosolic signaling pathways. Although high-resolution structures of different receptor states are available, atomistic details of allosteric signaling across the membrane remain elusive. We calculated free energy landscapes of beta(2) adrenergic receptor activation using atomistic molecular dynamics simulations in an optimized string of swarms framework, which shed new light on how microswitches govern the equilibrium between conformational states. Contraction of the extracellular binding site in the presence of the agonist BI-167107 is obligatorily coupled to conformational changes in a connector motif located in the core of the transmembrane region. The connector is probabilistically coupled to the conformation of the intracellular region. An active connector promotes desolvation of a buried cavity, a twist of the conserved NPxxY motif, and an interaction between two conserved tyrosines in transmembrane helices 5 and 7 (Y-Y motif), which lead to a larger population of active-like states at the G protein binding site. This coupling is augmented by protonation of the strongly conserved Asp79(2.50). The agonist binding site hence communicates with the intracellular region via a cascade of locally connected microswitches. Characterization of these can be used to understand how ligands stabilize distinct receptor states and contribute to development drugs with specific signaling properties. The developed simulation protocol can likely be transferred to other class A GPCRs.
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4. |
- Jacobson, Kenneth A., et al.
(author)
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Adenosine A2A receptor antagonists: : from caffeine to selective non-xanthines
- 2020
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In: British Journal of Pharmacology. - : Wiley. - 0007-1188 .- 1476-5381.
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Research review (peer-reviewed)abstract
- A long evolution of knowledge of the psychostimulant caffeine led in the 1960s to another purine natural product, adenosine and its A(2A)receptor. Adenosine is a short-lived autocrine/paracrine mediator that acts pharmacologically at four different adenosine receptors in a manner opposite to the pan-antagonist caffeine and serves as an endogenous allostatic regulator. Although detrimental in the developing brain, caffeine appears to be cerebroprotective in aging. Moderate caffeine consumption in adults, except in pregnancy, may also provide benefit in pain, diabetes, and kidney and liver disorders. Inhibition of A(2A)receptors is one of caffeine's principal effects and we now understand this interaction at the atomic level. The A(2A)receptor has become a prototypical example of utilizing high-resolution structures of GPCRs for the rational design of chemically diverse drug molecules. The previous focus on discovery of selective A(2A)receptor antagonists for neurodegenerative diseases has expanded to include immunotherapy for cancer, and clinical trials have ensued.
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5. |
- Kampen, Stefanie, et al.
(author)
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Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology
- 2021
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In: Angewandte Chemie International Edition. - : John Wiley & Sons. - 1433-7851 .- 1521-3773. ; 60:33, s. 18022-18030
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Journal article (peer-reviewed)abstract
- Many diseases are polygenic and can only be treated efficiently with drugs that modulate multiple targets. However, rational design of compounds with multi-target profiles is rarely pursued because it is considered too difficult, in particular if the drug must enter the central nervous system. Here, a structure-based strategy to identify dual-target ligands of G-protein-coupled receptors is presented. We use this approach to design compounds that both antagonize the A(2A) adenosine receptor and activate the D-2 dopamine receptor, which have excellent potential as antiparkinson drugs. Atomic resolution models of the receptors guided generation of a chemical library with compounds designed to occupy orthosteric and secondary binding pockets in both targets. Structure-based virtual screens identified ten compounds, of which three had affinity for both targets. One of these scaffolds was optimized to nanomolar dual-target activity and showed the predicted pharmacodynamic effect in a rat model of Parkinsonism.
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6. |
- Matricon, Pierre, et al.
(author)
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Fragment-based design of selective GPCR ligands guided by free energy simulations
- 2021
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In: Chemical Communications. - : Royal Society of Chemistry. - 1359-7345 .- 1364-548X. ; 57:92, s. 12305-12308
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Journal article (peer-reviewed)abstract
- Fragment-based drug discovery relies on successful optimization of weakly binding ligands for affinity and selectivity. Herein, we explored strategies for structure-based evolution of fragments binding to a G protein-coupled receptor. Molecular dynamics simulations combined with rigorous free energy calculations guided synthesis of nanomolar ligands with up to >1000-fold improvements of binding affinity and close to 40-fold subtype selectivity.
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7. |
- Matricon, Pierre, et al.
(author)
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Fragment optimization for GPCRs by molecular dynamics free energy calculations : Probing druggable subpockets of the A(2A) adenosine receptor binding site
- 2017
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In: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7
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Journal article (peer-reviewed)abstract
- Fragment-based lead discovery is becoming an increasingly popular strategy for drug discovery. Fragment screening identifies weakly binding compounds that require optimization to become high-affinity leads. As design of leads from fragments is challenging, reliable computational methods to guide optimization would be invaluable. We evaluated using molecular dynamics simulations and the free energy perturbation method (MD/FEP) in fragment optimization for the A(2A) adenosine receptor, a pharmaceutically relevant G protein-coupled receptor. Optimization of fragments exploring two binding site subpockets was probed by calculating relative binding affinities for 23 adenine derivatives, resulting in strong agreement with experimental data (R-2 = 0.78). The predictive power of MD/FEP was significantly better than that of an empirical scoring function. We also demonstrated the potential of the MD/FEP to assess multiple binding modes and to tailor the thermodynamic profile of ligands during optimization. Finally, MD/FEP was applied prospectively to optimize three nonpurine fragments, and predictions for 12 compounds were evaluated experimentally. The direction of the change in binding affinity was correctly predicted in a majority of the cases, and agreement with experiment could be improved with rigorous parameter derivation. The results suggest that MD/FEP will become a powerful tool in structure-driven optimization of fragments to lead candidates.
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8. |
- Matricon, Pierre, et al.
(author)
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Ligand design by targeting a binding site water
- 2021
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In: Chemical Science. - : Royal Society of Chemistry. - 2041-6520 .- 2041-6539. ; 12:3, s. 960-968
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Journal article (peer-reviewed)abstract
- Solvent reorganization is a major driving force of protein–ligand association, but the contribution of binding site waters to ligand affinity is poorly understood. We investigated how altered interactions with a water network can influence ligand binding to a receptor. A series of ligands of the A2A adenosine receptor, which either interacted with or displaced an ordered binding site water, were studied experimentally and by molecular dynamics simulations. An analog of the endogenous ligand that was unable to hydrogen bond to the ordered water lost affinity and this activity cliff was captured by molecular dynamics simulations. Two compounds designed to displace the ordered water from the binding site were then synthesized and evaluated experimentally, leading to the discovery of an A2A agonist with nanomolar activity. Calculation of the thermodynamic profiles resulting from introducing substituents that interacted with or displaced the ordered water showed that the gain of binding affinity was enthalpy driven. Detailed analysis of the energetics and binding site hydration networks revealed that the enthalpy change was governed by contributions that are commonly neglected in structure-based drug optimization. In particular, simulations suggested that displacement of water from a binding site to the bulk solvent can lead to large energy contributions. Our findings provide insights into the molecular driving forces of protein–ligand binding and strategies for rational drug design.
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9. |
- Matricon, Pierre
(author)
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Molecular simulations of G protein-coupled receptors : A journey into structure-based ligand design and receptor function
- 2021
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Doctoral thesis (other academic/artistic)abstract
- The superfamily of G protein-coupled receptors (GPCRs) contains a large number of important drug targets. These cell surface receptors recognize extracellular signaling molecules, which stimulates intracellular pathways that play major roles in human physiology. Breakthroughs in structural biology have led to an exponentially increasing number of atomic resolution GPCR structures, which have provided insights into the molecular basis of ligand binding and receptor activation. However, in order to use these structures in rational drug design, computational methods able to predict ligand binding modes and affinities are required. In the first part of this thesis, molecular simulations were used to explore the potential of using structure-based approaches to discover and optimize GPCR ligands. In paper I, molecular dynamics (MD) simulations in combination with free energy perturbation (FEP) guided improvements of binding affinities for fragment-like ligands of the A2A adenosine receptor (A2AAR), which is a target for Parkinson’s disease and cancer. Two computational approaches were then explored to design selective GPCR ligands. MD/FEP was first used to guide the optimization of a weak fragment ligand for subtype selectivity. Simulations of the A1- and A2AARs led to the discovery of high affinity and selective A1AR antagonists (paper II). In the second approach, a molecular docking screen of millions of molecules was carried out against AR crystal structures with the goal to identify A1AR ligands. Structure-based optimization of two hits resulted in the discovery of potent and selective A1AR antagonists (paper III). In paper IV, the role of a binding site water in agonist binding to the A2AAR was probed by modifying the endogenous agonist adenosine. MD simulations highlighted the complexity of ligand binding and the benefits of using FEP calculations to guide ligand optimization. In the second part of the thesis, MD simulations were used to study the activation mechanism of class A GPCRs and the function of class F receptors. The allosteric communication between the orthosteric and G protein binding sites of the β2 adrenergic receptor was investigated, which revealed the roles of structural motifs in receptor activation (paper V). Finally, MD simulations of a homology model of the Frizzled 4 receptor, which is a target for the development of anticancer drugs, led to the identification of a conserved structural motif that is important for receptor signaling (paper VI). The results of the thesis show that computer simulations can be valuable tools in structure-based drug discovery and studies of GPCR function.
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