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- Kampen, Stefanie
(författare)
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Structure-based Virtual Screening for Ligands of G Protein-coupled Receptors : Design of Allosteric and Dual-Target Modulators
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- G protein-coupled receptors (GPCRs) are integral membrane proteins responsible for signal transduction of extracellular stimuli into the cell. Because of their widespread distribution throughout the human body and important roles in physiological processes, GPCRs are prominent drug targets and approximately 34% of all approved drugs interact with members of this superfamily. GPCR ligands are used as drugs against various diseases, including neurodegenerative and neuropsychiatric disorders. The increased availability of GPCR structural information has enhanced understanding of GPCR function but also enables structure-based drug design (SBDD). This thesis focuses on SBDD targeting allosteric and orthosteric binding sites of GPCRs and strategies to identify multi-target ligands. Drug discovery campaigns are traditionally based on the one-target-one-drug paradigm, but effective treatment of complex neurological disorders generally requires modulation of several signaling pathways. In publication I, dual-target ligands that activate the D2 dopamine receptor (D2R) and antagonize the A2A adenosine receptor (A2AAR) were designed through a structure-based approach. Both GPCRs are relevant for Parkinson’s disease (PD) and animal studies support that interactions with these targets induce neuroprotection while eliciting a synergistic therapeutic effect. One of the designed ligands was shown to yield an antiparkinsonian effect in a rodent model. Publication II focuses on the identification of negative allosteric modulators (NAMs) of the metabotropic glutamate receptor 5 (mGlu5) using structure-based virtual screening. Such modulators have been considered as a treatment of PD, fragile X syndrome and depression. The study discovered 11 allosteric modulators and four of these were also shown to be NAMs of mGlu5. Manuscript III describes the development of dual-target ligands acting as antagonists of the A2AAR and NAMs of mGlu5. Blocking the activity of both receptors has been shown to have a synergistic antiparkinsonian effect that could be both symptomatic and neuroprotective. In this study, virtual screening was used to discover drug-like compounds with submicromolar binding affinity to both targets. Publication IV presents a comprehensive review of SBDD targeting GPCRs of all classes with a specific focus on the method of molecular docking. Publication V describes a program for automatic validation of X-ray crystal structures. Possible applications involve assessment of protein structures used in SBDD or the generation of high-quality test sets for the evaluation of molecular docking methods. The results of this thesis illustrate that structure-based virtual screening is a versatile tool to discover ligands with tailored pharmacological properties.
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| 2. |
- Matricon, Pierre
(författare)
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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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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)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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