Cancer remains a leading cause of mortality worldwide and calls for novel therapeutic targets. Membrane proteins are key players in various cancer types but present unique challenges compared to... Show moreCancer remains a leading cause of mortality worldwide and calls for novel therapeutic targets. Membrane proteins are key players in various cancer types but present unique challenges compared to soluble proteins. The advent of computational drug discovery tools offers a promising approach to address these challenges, allowing for the prioritization of "wet-lab" experiments. In this review, we explore the applications of computational approaches in membrane protein oncological characterization, particularly focusing on three prominent membrane protein families: receptor tyrosine kinases (RTKs), G protein-coupled receptors (GPCRs), and solute carrier proteins (SLCs). We chose these families due to their varying levels of understanding and research data availability, which leads to distinct challenges and opportunities for computational analysis. We discuss the utilization of multi-omics data, machine learning, and structure-based methods to investigate aberrant protein functionalities associated with cancer progression within each family. Moreover, we highlight the importance of considering the broader cellular context and, in particular, cross-talk between proteins. Despite existing challenges, computational tools hold promise in dissecting membrane protein dysregulation in cancer. With advancing computational capabilities and data resources, these tools are poised to play a pivotal role in identifying and prioritizing membrane proteins as personalized anticancer targets. Show less
G protein-coupled receptors (GPCRs), one of the largest families of membrane proteins, are responsive to a diverse set of physiological endogenous ligands including hormones and neurotransmitters.... Show moreG protein-coupled receptors (GPCRs), one of the largest families of membrane proteins, are responsive to a diverse set of physiological endogenous ligands including hormones and neurotransmitters. Due to the various GPCR ligand binding domains present on GPCRs and their sensitivities to a diverse array of ligands, these proteins have shown to be very ‘druggable’ as they are the main target for an estimated 30% of approved drugs. A growing body of evidence shows a prominent role of GPCRs in all phases of cancer with a mutation frequency of approximately 20% in all cancers. Mutations occurring in GPCRs can severely alter their normal function and may ultimately convert their physiological and pathological roles. One particular class of rhodopsin-like GPCRs included in this thesis are the adenosine receptors (ARs). Due to the accumulation of adenosine in the tumor microenvironment, all four subtypes of ARs might be targets for the development of novel approaches for the treatment of cancer. For each of the four subtypes, a number of somatic mutations have been identified in patient isolates. In this thesis, we examined them on receptor activation and ligand binding using reference adenosine receptor ligands, and determined the impact mutations have on these pharmacological readouts. Show less
G protein-coupled receptors (GPCRs) are the largest class of membrane proteins with around 800 members in the human genome/proteome. Extracellular signals such as hormones and neurotransmitters... Show moreG protein-coupled receptors (GPCRs) are the largest class of membrane proteins with around 800 members in the human genome/proteome. Extracellular signals such as hormones and neurotransmitters regulate various biological processes via GPCRs, with GPCRs being the bodily target of 30-40% of current drugs on the market. Complete identification and understanding of GPCR functionality will provide opportunities for novel drug discovery. Yeast expresses three different endogenous GPCRs regulating pheromone and sugar sensing, with the pheromone pathway offering perspectives for the characterization of heterologous GPCR signaling. Moreover, yeast offers a ''null" background for studies on mammalian GPCRs, including GPCR activation and signaling, ligand identification, and characterization of disease-related mutations. This review focuses on modifications of the yeast pheromone signaling pathway for functional GPCR studies, and on opportunities and usage of the yeast system as a platform for human GPCR studies. Finally, this review discusses in some further detail studies of adenosine receptors heterologously expressed in yeast, and what Geoff Burnstock thought of this approach. Show less
Wang X., Jespers W., Bongers B.J., Habben Jansen M.C.C., Stangenberger C.M., Dilweg M.A., Gutiérrez-de-Terán H., IJzerman A.P., Heitman L.H., Westen G.J.P. van 2020
In cancer, G protein-coupled receptors (GPCRs) are involved in tumor progression and metastasis. In this study we particularly examined one GPCR, the adenosine A2B receptor. This receptor is... Show moreIn cancer, G protein-coupled receptors (GPCRs) are involved in tumor progression and metastasis. In this study we particularly examined one GPCR, the adenosine A2B receptor. This receptor is activated by high concentrations of its endogenous ligand adenosine, which suppresses the immune response to fight tumor progression. A series of adenosine A2B receptor mutations were retrieved from the Cancer Genome Atlas harboring data from patient samples with different cancer types. The main goal of this work was to investigate the pharmacology of these mutant receptors using a ‘single-GPCR-one-G protein’ yeast assay technology. Concentration-growth curves were obtained with the full agonist NECA for the wild-type receptor and 15 mutants. Compared to wild-type receptor, the constitutive activity levels in mutant receptors F141L4.61, Y202C5.58 and L310P8.63 were high, while the potency and efficacy of NECA and BAY 60–6583 on Y202C5.58 was lower. A 33- and 26-fold higher constitutive activity on F141L4.61 and L310P8.63 was reduced to wild-type levels in response to the inverse agonist ZM241385. These constitutively active mutants may thus be tumor promoting. Mutant receptors F259S6.60 and Y113F34.53 showed a more than one log-unit decrease in potency. A complete loss of activation was observed in mutant receptors C29R1.54, W130C4.50 and P249L6.50. All mutations were characterized at the structural level, generating hypotheses of their roles on modulating the receptor conformational equilibrium. Taken together, this study is the first to investigate the nature of adenosine A2B receptor cancer mutations and may thus provide insights in mutant receptor function in cancer. Show less
Du, L.; Gao, Z.G.; Paoletta, S.; Wan, T.C.; Gizewski, E.T.; Barbour, S.; ... ; Auchampach, J.A. 2018
Activity of the A(3) adenosine receptor (AR) allosteric modulators LUF6000 (2-cyclohexyl-N-(3,4-dichlorophenyl)-1H-imidazo [4,5-c]quinolin-4-amine) and LUF6096 (N-{2-[(3,4-dichlorophenyl)amino... Show moreActivity of the A(3) adenosine receptor (AR) allosteric modulators LUF6000 (2-cyclohexyl-N-(3,4-dichlorophenyl)-1H-imidazo [4,5-c]quinolin-4-amine) and LUF6096 (N-{2-[(3,4-dichlorophenyl)amino]quinolin-4-yl}cyclohexanecarbox-amide) was compared at four A(3)AR species homologs used in preclinical drug development. In guanosine 5'-[gamma-[S-35]thio]triphosphate ([S-35]GTP gamma S) binding assays with cell membranes isolated from human embryonic kidney cells stably expressing recombinant A(3)ARs, both modulators substantially enhanced agonist efficacy at human, dog, and rabbit A(3)ARs but provided only weak activity at mouse A(3)ARs. For human, dog, and rabbit, both modulators increased the maximal efficacy of the A(3)AR agonist 2-chloro-N (6)-(3-iodobenzyl)adenosine-5'-N-methylcarboxamide as well as adenosine > 2-fold, while slightly reducing potency in human and dog. Based on results from N (6)-(4-amino-3-[I-125]iodobenzyl)adenosine-5'-N-methylcarboxamide ([I-125]I-AB-MECA) binding assays, we hypothesize that potency reduction is explained by an allosterically induced slowing in orthosteric ligand binding kinetics that reduces the rate of formation of ligand-receptor complexes. Mutation of four amino acid residues of the human A(3)AR to the murine sequence identified the extracellular loop 1 (EL1) region as being important in selectively controlling the allosteric actions of LUF6096 on [I-125]I-AB-MECA binding kinetics. Homology modeling suggested interaction between species-variable EL1 and agonist-contacting EL2. These results indicate that A(3)AR allostery is species-dependent and provide mechanistic insights into this therapeutically promising class of agents. Show less
The traditional medical treatment paradigm focuses on prescribing one drug to treat all patients with a specific disease or condition, so called ‘one-size-fits-all’. However, it has been shown... Show moreThe traditional medical treatment paradigm focuses on prescribing one drug to treat all patients with a specific disease or condition, so called ‘one-size-fits-all’. However, it has been shown increasingly that differences between persons, such as in lifestyle or genes, can change both the course of a disease and effect of a drug. In order to adapt medical treatment and drug development to that, a concept know as precision medicine, it is essential to study which and how genetic differences affect drug response. This thesis describes the study of the influences of genetic variation on a specific class of drug targets, the G protein-coupled receptors (GPCRs).Altogether a novel cellular approach towards studying genetic effects on GPCR function has been explored and detailed throughout this thesis. Several GPCRs and different types of genetic variations were investigated, demonstrating together that personal cell lines in combination with label-free technology are an appropriate tool to enable GPCR pharmacogenetic studies. Incorporating aspects such as genetic variation in drug targets, representative model systems and appropriate assay technology are important factors for advancing GPCR drug discovery. The data presented in this thesis contributes towards the progress of applying precision medicine concepts to this class of drug targets. Show less
In this thesis, several orthosteric and allosteric agonists are presented for the newly discovered hydroxy-carboxylic acid (HCA) receptor 2, and their in vivo activity or in vitro structure... Show moreIn this thesis, several orthosteric and allosteric agonists are presented for the newly discovered hydroxy-carboxylic acid (HCA) receptor 2, and their in vivo activity or in vitro structure-activity relationships are described. The literature on HCA receptors was also thoroughly reviewed, providing some insight into the future of this receptor family as drug targets. The anti-cancer drug N6-(2-isopentenyl)adenosine (IPA) was shown to be a specific ligand for the adenosine A3 receptor, and its antiproliferative effect seems to be mediated by this receptor at low concentrations. A ligand discovery screen for orphan receptor GPR88 was performed, in which over 4000 compounds were tested. Show less
The research described in this thesis has provided new insights in the activation mechanism of class A GPCRs and in particular of adenosine receptors. By a variety of mutagenesis approaches and the... Show moreThe research described in this thesis has provided new insights in the activation mechanism of class A GPCRs and in particular of adenosine receptors. By a variety of mutagenesis approaches and the use of a robust yeast reporter gene system, we identified several regions and amino acid positions that contribute to both agonist responses and constitutive activity of the human adenosine A1 receptor and the human adenosine A2B receptor. These results reveal new and surprising roles of the extracellular loops in the activation mechanism, greatly contributing to our notion of receptor activation. Show less
