Molecular modelling studies on Frizzled receptors
Title: Molecular modelling studies on Frizzled receptors
SNIC Project: SNIC 2022/5-506
Project Type: SNIC Medium Compute
Principal Investigator: Gunnar Schulte <gunnar.schulte@ki.se>
Affiliation: Karolinska Institutet
Duration: 2022-11-01 – 2023-11-01
Classification: 30102 10601
Homepage: http://ki.se/en/fyfa/receptor-biology-and-signaling
Keywords:

Abstract

G protein-coupled receptors (GPCRs) mediate effects of many endogenous and exogenous substances such as small molecules, peptides, lipids, ions, and odorants. According to homology, GPCRs were grouped into Classes A, B, C, F (Frizzleds), adhesion receptors, and other 7 transmembrane (TM) spanning receptors. Frizzleds (FZDs) regulate processes during embryonic development, stem cell regulation, and adult tissue homeostasis. Deregulation of FZDs leads to pathogenesis, such as cancer and neurologic disorders; thus, making them attractive drug targets. In mammals, there are 10 FZDs (FZD1–10), which are activated by the WNT family of lipoglycoproteins through interaction with the extracellular cysteine-rich domain (CRD) of FZD. Our group is instrumental in promoting the understanding of molecular underpinnings of FZD activation including ligand-induced and constitutive activity. Our work has identified molecular switch mechanisms based on cancer genomics and receptor function, which has led to further development of FZD-centered assays with potential applicability for drug screening and discovery. We further our understanding of mechanisms of FZD activation and signal initiation by analysis of ligand binding, receptor dynamics and effector coupling. We foresee that understanding the molecular details of receptor conformational changes will provide the basis to understand how FZDs define pathway selectivity in a class-wide manner, i. e. how FZDs can for example couple to the scaffold protein DVL or heterotrimeric G proteins. For the coming allocation period we plan to continue using molecular dynamics (MD) simulations (usually all atom but we might also employ coarse grained for larger systems or use other accelerated sampling methods). One main focus will be on the interactions of FZDs with other proteins, especially FZD5 with a downstream effector protein as well as a stabilizing Nanobody used for CryoEM. Another focus will be directed towards the discovery and characterization of small molecule ligands targeting FZDs. A first in silico docking screen of a large molecular library against FZD7 has already been successful, resulting in a novel ligand for FZDs. We continue this work with structure-based ligand design of this hit molecule and additional large library docking screens. We will apply MD simulations to investigate binding and signal modulation of small molecule ligands to FZDs. Computationally derived insights will be confirmed in wet-lab experiments. This will be done by mutating residues that form essential interactions in the models and evaluating the effect of these mutations in the wet-lab experiments. This will additionally aid the definition of FZD-effector/protein as well as FZD-ligand interactions and conformations. Currently a paper combining wet-lab and computational efforts is submitted and the basis for several other publications combining these methods has been laid and these will likely be published in 2023. These publications will be a continuation of the strong publication record from previous years, where we started to combine in silico and wet lab approaches, including three Nature Communications papers published in 2019, 2020 and 2021 as well as a paper in Science Advances in 2021.