1
|
Kaya P, Schaffner-Reckinger E, Manoharan GB, Vukic V, Kiriazis A, Ledda M, Burgos Renedo M, Pavic K, Gaigneaux A, Glaab E, Abankwa DK. An Improved PDE6D Inhibitor Combines with Sildenafil To Inhibit KRAS Mutant Cancer Cell Growth. J Med Chem 2024; 67:8569-8584. [PMID: 38758695 DOI: 10.1021/acs.jmedchem.3c02129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2024]
Abstract
The trafficking chaperone PDE6D (or PDEδ) was proposed as a surrogate target for K-Ras, leading to the development of a series of inhibitors that block its prenyl binding pocket. These inhibitors suffered from low solubility and suspected off-target effects, preventing their clinical development. Here, we developed a highly soluble, low nanomolar PDE6D inhibitor (PDE6Di), Deltaflexin3, which has the lowest off-target activity as compared to three prominent reference compounds. Deltaflexin3 reduces Ras signaling and selectively decreases the growth of KRAS mutant and PDE6D-dependent cancer cells. We further show that PKG2-mediated phosphorylation of Ser181 lowers K-Ras binding to PDE6D. Thus, Deltaflexin3 combines with the approved PKG2 activator Sildenafil to more potently inhibit PDE6D/K-Ras binding, cancer cell proliferation, and microtumor growth. As observed previously, inhibition of Ras trafficking, signaling, and cancer cell proliferation remained overall modest. Our results suggest reevaluating PDE6D as a K-Ras surrogate target in cancer.
Collapse
Affiliation(s)
- Pelin Kaya
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Elisabeth Schaffner-Reckinger
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Vladimir Vukic
- Faculty of Technology, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Alexandros Kiriazis
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| | - Mirko Ledda
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Maria Burgos Renedo
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Karolina Pavic
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Anthoula Gaigneaux
- Bioinformatics Core, Department of Life Sciences and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- Luxembourg Center for Systems Biomedicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Daniel Kwaku Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland
| |
Collapse
|
2
|
Moran AL, Louzao-Martinez L, Norris DP, Peters DJM, Blacque OE. Transport and barrier mechanisms that regulate ciliary compartmentalization and ciliopathies. Nat Rev Nephrol 2024; 20:83-100. [PMID: 37872350 DOI: 10.1038/s41581-023-00773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 10/25/2023]
Abstract
Primary cilia act as cell surface antennae, coordinating cellular responses to sensory inputs and signalling molecules that regulate developmental and homeostatic pathways. Cilia are therefore critical to physiological processes, and defects in ciliary components are associated with a large group of inherited pleiotropic disorders - known collectively as ciliopathies - that have a broad spectrum of phenotypes and affect many or most tissues, including the kidney. A central feature of the cilium is its compartmentalized structure, which imparts its unique molecular composition and signalling environment despite its membrane and cytosol being contiguous with those of the cell. Such compartmentalization is achieved via active transport pathways that bring protein cargoes to and from the cilium, as well as gating pathways at the ciliary base that establish diffusion barriers to protein exchange into and out of the organelle. Many ciliopathy-linked proteins, including those involved in kidney development and homeostasis, are components of the compartmentalizing machinery. New insights into the major compartmentalizing pathways at the cilium, namely, ciliary gating, intraflagellar transport, lipidated protein flagellar transport and ciliary extracellular vesicle release pathways, have improved our understanding of the mechanisms that underpin ciliary disease and associated renal disorders.
Collapse
Affiliation(s)
- Ailis L Moran
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
| | - Laura Louzao-Martinez
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Dorien J M Peters
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Oliver E Blacque
- School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
| |
Collapse
|
3
|
Salcedo MV, Gravel N, Keshavarzi A, Huang LC, Kochut KJ, Kannan N. Predicting protein and pathway associations for understudied dark kinases using pattern-constrained knowledge graph embedding. PeerJ 2023; 11:e15815. [PMID: 37868056 PMCID: PMC10590106 DOI: 10.7717/peerj.15815] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 07/10/2023] [Indexed: 10/24/2023] Open
Abstract
The 534 protein kinases encoded in the human genome constitute a large druggable class of proteins that include both well-studied and understudied "dark" members. Accurate prediction of dark kinase functions is a major bioinformatics challenge. Here, we employ a graph mining approach that uses the evolutionary and functional context encoded in knowledge graphs (KGs) to predict protein and pathway associations for understudied kinases. We propose a new scalable graph embedding approach, RegPattern2Vec, which employs regular pattern constrained random walks to sample diverse aspects of node context within a KG flexibly. RegPattern2Vec learns functional representations of kinases, interacting partners, post-translational modifications, pathways, cellular localization, and chemical interactions from a kinase-centric KG that integrates and conceptualizes data from curated heterogeneous data resources. By contextualizing information relevant to prediction, RegPattern2Vec improves accuracy and efficiency in comparison to other random walk-based graph embedding approaches. We show that the predictions produced by our model overlap with pathway enrichment data produced using experimentally validated Protein-Protein Interaction (PPI) data from both publicly available databases and experimental datasets not used in training. Our model also has the advantage of using the collected random walks as biological context to interpret the predicted protein-pathway associations. We provide high-confidence pathway predictions for 34 dark kinases and present three case studies in which analysis of meta-paths associated with the prediction enables biological interpretation. Overall, RegPattern2Vec efficiently samples multiple node types for link prediction on biological knowledge graphs and the predicted associations between understudied kinases, pseudokinases, and known pathways serve as a conceptual starting point for hypothesis generation and testing.
Collapse
Affiliation(s)
- Mariah V. Salcedo
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States of America
| | - Nathan Gravel
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Abbas Keshavarzi
- School of Computing, University of Georgia, Athens, GA, United States of America
| | - Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Krzysztof J. Kochut
- School of Computing, University of Georgia, Athens, GA, United States of America
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| |
Collapse
|
4
|
Grochowska KM, Bär J, Gomes GM, Kreutz MR, Karpova A. Jacob, a Synapto-Nuclear Protein Messenger Linking N-methyl-D-aspartate Receptor Activation to Nuclear Gene Expression. Front Synaptic Neurosci 2021; 13:787494. [PMID: 34899262 PMCID: PMC8662305 DOI: 10.3389/fnsyn.2021.787494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Pyramidal neurons exhibit a complex dendritic tree that is decorated by a huge number of spine synapses receiving excitatory input. Synaptic signals not only act locally but are also conveyed to the nucleus of the postsynaptic neuron to regulate gene expression. This raises the question of how the spatio-temporal integration of synaptic inputs is accomplished at the genomic level and which molecular mechanisms are involved. Protein transport from synapse to nucleus has been shown in several studies and has the potential to encode synaptic signals at the site of origin and decode them in the nucleus. In this review, we summarize the knowledge about the properties of the synapto-nuclear messenger protein Jacob with special emphasis on a putative role in hippocampal neuronal plasticity. We will elaborate on the interactome of Jacob, the signals that control synapto-nuclear trafficking, the mechanisms of transport, and the potential nuclear function. In addition, we will address the organization of the Jacob/NSMF gene, its origin and we will summarize the evidence for the existence of splice isoforms and their expression pattern.
Collapse
Affiliation(s)
- Katarzyna M Grochowska
- Research Group (RG) Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Leibniz Group 'Dendritic Organelles and Synaptic Function', University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology Hamburg, Hamburg, Germany
| | - Julia Bär
- Research Group (RG) Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Research Group (RG) Neuronal Protein Transport, University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology Hamburg, Hamburg, Germany.,Research Group (RG) Optobiology, Institute of Biology, HU Berlin, Berlin, Germany
| | - Guilherme M Gomes
- Research Group (RG) Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| | - Michael R Kreutz
- Research Group (RG) Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Leibniz Group 'Dendritic Organelles and Synaptic Function', University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology Hamburg, Hamburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany.,German Research Center for Neurodegenerative Diseases (DZNE), Magdeburg, Germany
| | - Anna Karpova
- Research Group (RG) Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,Center for Behavioral Brain Sciences (CBBS), Magdeburg, Germany
| |
Collapse
|