1
|
Xu M, Xu B. Protein lipidation in the tumor microenvironment: enzymology, signaling pathways, and therapeutics. Mol Cancer 2025; 24:138. [PMID: 40335986 PMCID: PMC12057185 DOI: 10.1186/s12943-025-02309-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Accepted: 03/18/2025] [Indexed: 05/09/2025] Open
Abstract
Protein lipidation is a pivotal post-translational modification that increases protein hydrophobicity and influences their function, localization, and interaction network. Emerging evidence has shown significant roles of lipidation in the tumor microenvironment (TME). However, a comprehensive review of this topic is lacking. In this review, we present an integrated and in-depth literature review of protein lipidation in the context of the TME. Specifically, we focus on three major lipidation modifications: S-prenylation, S-palmitoylation, and N-myristoylation. We emphasize how these modifications affect oncogenic signaling pathways and the complex interplay between tumor cells and the surrounding stromal and immune cells. Furthermore, we explore the therapeutic potential of targeting lipidation mechanisms in cancer treatment and discuss prospects for developing novel anticancer strategies that disrupt lipidation-dependent signaling pathways. By bridging protein lipidation with the dynamics of the TME, our review provides novel insights into the complex relationship between them that drives tumor initiation and progression.
Collapse
Affiliation(s)
- Mengke Xu
- Chongqing Key Laboratory of Intelligent Oncology for Breast Cancer, Intelligent Oncology Innovation Center Designated by the Ministry of Education, Chongqing University Cancer Hospital and Chongqing University School of Medicine, Chongqing, 400030, China
| | - Bo Xu
- Chongqing Key Laboratory of Intelligent Oncology for Breast Cancer, Intelligent Oncology Innovation Center Designated by the Ministry of Education, Chongqing University Cancer Hospital and Chongqing University School of Medicine, Chongqing, 400030, China.
| |
Collapse
|
2
|
Gest AM, Sahan AZ, Zhong Y, Lin W, Mehta S, Zhang J. Molecular Spies in Action: Genetically Encoded Fluorescent Biosensors Light up Cellular Signals. Chem Rev 2024; 124:12573-12660. [PMID: 39535501 PMCID: PMC11613326 DOI: 10.1021/acs.chemrev.4c00293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 09/07/2024] [Accepted: 09/20/2024] [Indexed: 11/16/2024]
Abstract
Cellular function is controlled through intricate networks of signals, which lead to the myriad pathways governing cell fate. Fluorescent biosensors have enabled the study of these signaling pathways in living systems across temporal and spatial scales. Over the years there has been an explosion in the number of fluorescent biosensors, as they have become available for numerous targets, utilized across spectral space, and suited for various imaging techniques. To guide users through this extensive biosensor landscape, we discuss critical aspects of fluorescent proteins for consideration in biosensor development, smart tagging strategies, and the historical and recent biosensors of various types, grouped by target, and with a focus on the design and recent applications of these sensors in living systems.
Collapse
Affiliation(s)
- Anneliese
M. M. Gest
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
| | - Ayse Z. Sahan
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
- Biomedical
Sciences Graduate Program, University of
California, San Diego, La Jolla, California 92093, United States
| | - Yanghao Zhong
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
| | - Wei Lin
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
| | - Sohum Mehta
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
| | - Jin Zhang
- Department
of Pharmacology, University of California,
San Diego, La Jolla, California 92093, United States
- Shu
Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| |
Collapse
|
3
|
Amroodi MN, Maghsoudloo M, Amiri S, Mokhtari K, Mohseni P, Pourmarjani A, Jamali B, Khosroshahi EM, Asadi S, Tabrizian P, Entezari M, Hashemi M, Wan R. Unraveling the molecular and immunological landscape: Exploring signaling pathways in osteoporosis. Biomed Pharmacother 2024; 177:116954. [PMID: 38906027 DOI: 10.1016/j.biopha.2024.116954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/05/2024] [Accepted: 06/15/2024] [Indexed: 06/23/2024] Open
Abstract
Osteoporosis, characterized by compromised bone density and microarchitecture, represents a significant global health challenge, particularly in aging populations. This comprehensive review delves into the intricate signaling pathways implicated in the pathogenesis of osteoporosis, providing valuable insights into the pivotal role of signal transduction in maintaining bone homeostasis. The exploration encompasses cellular signaling pathways such as Wnt, Notch, JAK/STAT, NF-κB, and TGF-β, all of which play crucial roles in bone remodeling. The dysregulation of these pathways is a contributing factor to osteoporosis, necessitating a profound understanding of their complexities to unveil the molecular mechanisms underlying bone loss. The review highlights the pathological significance of disrupted signaling in osteoporosis, emphasizing how these deviations impact the functionality of osteoblasts and osteoclasts, ultimately resulting in heightened bone resorption and compromised bone formation. A nuanced analysis of the intricate crosstalk between these pathways is provided to underscore their relevance in the pathophysiology of osteoporosis. Furthermore, the study addresses some of the most crucial long non-coding RNAs (lncRNAs) associated with osteoporosis, adding an additional layer of academic depth to the exploration of immune system involvement in various types of osteoporosis. Finally, we propose that SKP1 can serve as a potential biomarker in osteoporosis.
Collapse
Affiliation(s)
- Morteza Nakhaei Amroodi
- Bone and Joint Reconstruction Research Center, Shafa Orthopedic Hospital, department of orthopedic, school of medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mazaher Maghsoudloo
- Key Laboratory of Epigenetics and Oncology, the Research Center for Preclinical Medicine, Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Shayan Amiri
- Bone and Joint Reconstruction Research Center, Shafa Orthopedic Hospital, department of orthopedic, school of medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Khatere Mokhtari
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Parnaz Mohseni
- Department of Pediatrics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Azadeh Pourmarjani
- Department of Pediatrics, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Behdokht Jamali
- Department of microbiology and genetics, kherad Institute of higher education, Busheher, lran
| | - Elaheh Mohandesi Khosroshahi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Saba Asadi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Pouria Tabrizian
- Bone and Joint Reconstruction Research Center, Shafa Orthopedic Hospital, department of orthopedic, school of medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Runlan Wan
- Department of Oncology, The Affiliated Hospital, Southwest Medical University, Luzhou 646000, China; Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Laboratory of Sichuan Province, (Collaborative Innovation Center for Prevention of Cardiovascular Diseases), Institute of Cardiovascular Research, Southwest Medical University, Luzhou 646000, China.
| |
Collapse
|
4
|
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 PMCID: PMC11181323 DOI: 10.1021/acs.jmedchem.3c02129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/09/2024] [Accepted: 04/12/2024] [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
|
5
|
Muth LT, Van Bogaert INA. Let it stick: Strategies and applications for intracellular plasma membrane targeting of proteins in Saccharomyces cerevisiae. Yeast 2024; 41:315-329. [PMID: 38444057 DOI: 10.1002/yea.3933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 02/09/2024] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Lipid binding domains and protein lipidations are essential features to recruit proteins to intracellular membranes, enabling them to function at specific sites within the cell. Membrane association can also be exploited to answer fundamental and applied research questions, from obtaining insights into the understanding of lipid metabolism to employing them for metabolic engineering to redirect fluxes. This review presents a broad catalog of membrane binding strategies focusing on the plasma membrane of Saccharomyces cerevisiae. Both lipid binding domains (pleckstrin homology, discoidin-type C2, kinase associated-1, basic-rich and bacterial phosphoinositide-binding domains) and co- and post-translational lipidations (prenylation, myristoylation and palmitoylation) are introduced as tools to target the plasma membrane. To provide a toolset of membrane targeting modules, respective candidates that facilitate plasma membrane targeting are showcased including their in vitro and in vivo properties. The relevance and versatility of plasma membrane targeting modules are further highlighted by presenting a selected set of use cases.
Collapse
Affiliation(s)
- Liv Teresa Muth
- Department of Biotechnology, Centre for Synthetic Biology, Ghent University, Ghent, Belgium
| | | |
Collapse
|
6
|
Babu Manoharan G, Guzmán C, Najumudeen AK, Abankwa D. Detection of Ras nanoclustering-dependent homo-FRET using fluorescence anisotropy measurements. Eur J Cell Biol 2023; 102:151314. [PMID: 37058825 DOI: 10.1016/j.ejcb.2023.151314] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/10/2023] [Accepted: 04/10/2023] [Indexed: 04/16/2023] Open
Abstract
The small GTPase Ras is frequently mutated in cancer and a driver of tumorigenesis. The recent years have shown great progress in drug-targeting Ras and understanding how it operates on the plasma membrane. We now know that Ras is non-randomly organized into proteo-lipid complexes on the membrane, called nanoclusters. Nanoclusters contain only a few Ras proteins and are necessary for the recruitment of downstream effectors, such as Raf. If tagged with fluorescent proteins, the dense packing of Ras in nanoclusters can be analyzed by Förster/ fluorescence resonance energy transfer (FRET). Loss of FRET can therefore report on decreased nanoclustering and any process upstream of it, such as Ras lipid modifications and correct trafficking. Thus, cellular FRET screens employing Ras-derived fluorescence biosensors are potentially powerful tools to discover chemical or genetic modulators of functional Ras membrane organization. Here we implement fluorescence anisotropy-based homo-FRET measurements of Ras-derived constructs labelled with only one fluorescent protein on a confocal microscope and a fluorescence plate reader. We show that homo-FRET of both H-Ras- and K-Ras-derived constructs can sensitively report on Ras-lipidation and -trafficking inhibitors, as well as on genetic perturbations of proteins regulating membrane anchorage. By exploiting the switch I/II-binding Ras-dimerizing compound BI-2852, this assay is also suitable to report on the engagement of the K-Ras switch II pocket by small molecules such as AMG 510. Given that homo-FRET only requires one fluorescent protein tagged Ras construct, this approach has significant advantages to create Ras-nanoclustering FRET-biosensor reporter cell lines, as compared to the more common hetero-FRET approaches.
Collapse
Affiliation(s)
- Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Camilo Guzmán
- Euro-BioImaging ERIC, Statutory Seat, Turku, Finland
| | - Arafath Kaja Najumudeen
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| |
Collapse
|
7
|
Manoharan GB, Okutachi S, Abankwa D. Potential of phenothiazines to synergistically block calmodulin and reactivate PP2A in cancer cells. PLoS One 2022; 17:e0268635. [PMID: 35617282 PMCID: PMC9135253 DOI: 10.1371/journal.pone.0268635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 05/04/2022] [Indexed: 11/19/2022] Open
Abstract
Phenothiazines (PTZ) were developed as inhibitors of monoamine neurotransmitter receptors, notably dopamine receptors. Because of this activity they have been used for decades as antipsychotic drugs. In addition, they possess significant anti-cancer properties and several attempts for their repurposing were made. However, their incompletely understood polypharmacology is challenging. Here we examined the potential of the PTZ fluphenazine (Flu) and its mustard derivative (Flu-M) to synergistically act on two cancer associated targets, calmodulin (CaM) and the tumor suppressor protein phosphatase 2A (PP2A). Both proteins are known to modulate the Ras- and MAPK-pathway, cell viability and features of cancer cell stemness. Consistently, we show that the combination of a CaM inhibitor and the PP2A activator DT-061 synergistically inhibited the 3D-spheroid formation of MDA-MB-231 (K-Ras-G13D), NCI-H358 (K-Ras-G12C) and A375 (B-raf-V600E) cancer cells, and increased apoptosis in MDA-MB-231. We reasoned that these activities remain combined in PTZ, which were the starting point for PP2A activator development, while several PTZ are known CaM inhibitors. We show that both Flu and Flu-M retained CaM inhibitory activity in vitro and in cells, with a higher potency of the mustard derivative in cells. In line with the CaM dependence of Ras plasma membrane organization, the mustard derivative potently reduced the functional membrane organization of oncogenic Ras, while DT-061 had a negligible effect. Like DT-061, both PTZ potently decreased c-MYC levels, a hallmark of PP2A activation. Benchmarking against the KRAS-G12C specific inhibitor AMG-510 in MIA PaCa-2 cells revealed a higher potency of Flu-M than combinations of DT-061 and a CaM inhibitor on MAPK-output and a strong effect on cell proliferation. While our study is limited, our results suggest that improved PTZ derivatives that retain both, their CaM inhibitory and PP2A activating properties, but have lost their neurological side-effects, may be interesting to pursue further as anti-cancer agents.
Collapse
Affiliation(s)
- Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sunday Okutachi
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- * E-mail:
| |
Collapse
|
8
|
Pavic K, Chippalkatti R, Abankwa D. Drug targeting opportunities en route to Ras nanoclusters. Adv Cancer Res 2022; 153:63-99. [PMID: 35101236 DOI: 10.1016/bs.acr.2021.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Disruption of the native membrane organization of Ras by the farnesyltransferase inhibitor tipifarnib in the late 1990s constituted the first indirect approach to drug target Ras. Since then, our understanding of how dynamically Ras shuttles between subcellular locations has changed significantly. Ras proteins have to arrive at the plasma membrane for efficient MAPK-signal propagation. On the plasma membrane Ras proteins are organized into isoform specific proteo-lipid assemblies called nanocluster. Recent evidence suggests that Ras nanocluster have a specific lipid composition, which supports the recruitment of effectors such as Raf. Conversely, effectors possess lipid-recognition motifs, which appear to serve as co-incidence detectors for the lipid domain of a given Ras isoform. Evidence suggests that dimeric Raf proteins then co-assemble dimeric Ras in an immobile complex, thus forming the minimal unit of an active nanocluster. Here we review established and novel trafficking chaperones and trafficking factors of Ras, along with the set of lipid and protein modulators of Ras nanoclustering. We highlight drug targeting approaches and opportunities against these determinants of functional Ras membrane organization. Finally, we reflect on implications for Ras signaling in polarized cells, such as epithelia, which are a common origin of tumorigenesis.
Collapse
Affiliation(s)
- Karolina Pavic
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rohan Chippalkatti
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| |
Collapse
|
9
|
Glaab E, Manoharan GB, Abankwa D. Pharmacophore Model for SARS-CoV-2 3CLpro Small-Molecule Inhibitors and in Vitro Experimental Validation of Computationally Screened Inhibitors. J Chem Inf Model 2021; 61:4082-4096. [PMID: 34348021 PMCID: PMC8353990 DOI: 10.1021/acs.jcim.1c00258] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 01/18/2023]
Abstract
Among the biomedical efforts in response to the current coronavirus (COVID-19) pandemic, pharmacological strategies to reduce viral load in patients with severe forms of the disease are being studied intensively. One of the main drug target proteins proposed so far is the SARS-CoV-2 viral protease 3CLpro (also called Mpro), an essential component for viral replication. Ongoing ligand- and receptor-based computational screening efforts would be facilitated by an improved understanding of the electrostatic, hydrophobic, and steric features that characterize small-molecule inhibitors binding stably to 3CLpro and by an extended collection of known binders. Here, we present combined virtual screening, molecular dynamics (MD) simulation, machine learning, and in vitro experimental validation analyses, which have led to the identification of small-molecule inhibitors of 3CLpro with micromolar activity and to a pharmacophore model that describes functional chemical groups associated with the molecular recognition of ligands by the 3CLpro binding pocket. Experimentally validated inhibitors using a ligand activity assay include natural compounds with the available prior knowledge on safety and bioavailability properties, such as the natural compound rottlerin (IC50 = 37 μM) and synthetic compounds previously not characterized (e.g., compound CID 46897844, IC50 = 31 μM). In combination with the developed pharmacophore model, these and other confirmed 3CLpro inhibitors may provide a basis for further similarity-based screening in independent compound databases and structural design optimization efforts to identify 3CLpro ligands with improved potency and selectivity. Overall, this study suggests that the integration of virtual screening, MD simulations, and machine learning can facilitate 3CLpro-targeted small-molecule screening investigations. Different receptor-, ligand-, and machine learning-based screening strategies provided complementary information, helping to increase the number and diversity of the identified active compounds. Finally, the resulting pharmacophore model and experimentally validated small-molecule inhibitors for 3CLpro provide resources to support follow-up computational screening efforts for this drug target.
Collapse
Affiliation(s)
- Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB),
University of Luxembourg, 7 Avenue des Hauts Fourneaux,
L-4362 Esch-sur-Alzette, Luxembourg
| | - Ganesh Babu Manoharan
- Department of Life Sciences and Medicine,
University of Luxembourg, 7 Avenue des Hauts Fourneaux,
L-4362 Esch-sur-Alzette, Luxembourg
| | - Daniel Abankwa
- Department of Life Sciences and Medicine,
University of Luxembourg, 7 Avenue des Hauts Fourneaux,
L-4362 Esch-sur-Alzette, Luxembourg
| |
Collapse
|
10
|
Parkkola H, Siddiqui FA, Oetken-Lindholm C, Abankwa D. FLIM-FRET Analysis of Ras Nanoclustering and Membrane-Anchorage. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:233-250. [PMID: 33977480 DOI: 10.1007/978-1-0716-1190-6_13] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
On the plasma membrane, Ras is organized into laterally segregated proteo-lipid complexes called nanoclusters. The extent of Ras nanoclustering correlates with its signaling output, positioning nanocluster as dynamic signaling gain modulators. Recent evidence suggests that stacked dimers of Ras and Raf are elemental units at least of one type of Ras nanocluster. However, it is still incompletely understood, in which physiological contexts nanoclustering is regulated and which constituents are parts of nanocluster. Nonetheless, disruption of nanoclustering faithfully diminishes Ras activity in cells, suggesting Ras nanocluster as potential drug targets.While there are several methods available to study Ras nanocluster , fluorescence or Förster resonance energy transfer (FRET ) between fluorescently labeled, nanoclustered Ras proteins is a relatively simple readout. FRET measurements using fluorescence lifetime imaging microscopy (FLIM ) have proven to be robust and sensitive to determine Ras nanoclustering changes. Loss of FRET that emerges due to nanoclustering reports on all processes upstream of Ras nanoclustering, i.e., also on proper trafficking or lipid modification of Ras. Here we report our standard FLIM-FRET protocol to measure nanoclustering-dependent FRET of Ras in mammalian cells. Importantly, nanoclustering-dependent FRET is one of the few methods that can detect differences between the Ras isoforms.
Collapse
Affiliation(s)
- Hanna Parkkola
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Farid Ahmad Siddiqui
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | | | - Daniel Abankwa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| |
Collapse
|
11
|
Effect of dipole moment on amphiphile solubility and partition into liquid ordered and liquid disordered phases in lipid bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183157. [PMID: 31846646 DOI: 10.1016/j.bbamem.2019.183157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 12/01/2019] [Accepted: 12/12/2019] [Indexed: 12/20/2022]
Abstract
Association of amphiphiles with biomembranes is important for their availability at specific locations in organisms and cells, being critical for their biological function. A prominent role is usually attributed to the hydrophobic effect, and to electrostatic interactions between charged amphiphiles and lipids. This work explores a closely related and complementary aspect, namely the contribution made by dipole moments to the strength of the interactions established. Two xanthene amphiphiles with opposite relative orientations of their dipole and amphiphilic moments have been selected (Rhodamine-C14 and Carboxyfluorescein-C14). The membranes studied have distinct lipid compositions, representing typical cell membrane pools, ranging from internal membranes to the outer and inner leaflet of the plasma membrane. A comprehensive study is reported, including the affinity of the amphiphiles for the different membranes, the stability of the amphiphiles as monomers and their tendency to form small clusters, as well as their transverse location in the membrane. The orientation of the amphiphile dipole moment, which determines whether its interaction with the membrane dipole potential is repulsive or attractive, is found to exert a large influence on the association of the amphiphile with ordered lipid membranes. These interactions are also responsible for the formation of small clusters or stabilization of amphiphile monomers in the membrane. The results obtained allow understanding the prevalence of protein lipidation at the N-terminal for efficient targeting to the plasma membrane, as well as the tendency of GPI-anchored proteins (usually lipidated at the C-terminal) to form small clusters in the membrane ordered domains.
Collapse
|
12
|
Bao M, Zhang K, Wei Y, Hua W, Gao Y, Li X, Ye L. Therapeutic potentials and modulatory mechanisms of fatty acids in bone. Cell Prolif 2020; 53:e12735. [PMID: 31797479 PMCID: PMC7046483 DOI: 10.1111/cpr.12735] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/02/2019] [Accepted: 11/05/2019] [Indexed: 02/05/2023] Open
Abstract
Bone metabolism is a lifelong process that includes bone formation and resorption. Osteoblasts and osteoclasts are the predominant cell types associated with bone metabolism, which is facilitated by other cells such as bone marrow mesenchymal stem cells (BMMSCs), osteocytes and chondrocytes. As an important component in our daily diet, fatty acids are mainly categorized as long-chain fatty acids including polyunsaturated fatty acids (LCPUFAs), monounsaturated fatty acids (LCMUFAs), saturated fatty acids (LCSFAs), medium-/short-chain fatty acids (MCFAs/SCFAs) as well as their metabolites. Fatty acids are closely associated with bone metabolism and associated bone disorders. In this review, we summarized the important roles and potential therapeutic implications of fatty acids in multiple bone disorders, reviewed the diverse range of critical effects displayed by fatty acids on bone metabolism, and elucidated their modulatory roles and mechanisms on specific bone cell types. The evidence supporting close implications of fatty acids in bone metabolism and disorders suggests fatty acids as potential therapeutic and nutritional agents for the treatment and prevention of metabolic bone diseases.
Collapse
Affiliation(s)
- Minyue Bao
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Kaiwen Zhang
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Yangyini Wei
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Weihan Hua
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Yanzi Gao
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Xin Li
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesWest China Hospital of StomatologySichuan UniversityChengduChina
| | - Ling Ye
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesWest China Hospital of StomatologySichuan UniversityChengduChina
- State Key Laboratory of Oral DiseasesNational Clinical Research Center for Oral DiseasesDepartment of Cariology and EndodonticsWest China Hospital of StomatologySichuan UniversityChengduChina
| |
Collapse
|
13
|
Manoharan GB, Kopra K, Eskonen V, Härmä H, Abankwa D. High-throughput amenable fluorescence-assays to screen for calmodulin-inhibitors. Anal Biochem 2019; 572:25-32. [PMID: 30825429 DOI: 10.1016/j.ab.2019.02.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/21/2019] [Accepted: 02/17/2019] [Indexed: 12/12/2022]
Abstract
The KRAS gene is highly mutated in human cancers and the focus of current Ras drug development efforts. Recently the interface between the C-terminus of K-Ras and calmodulin (CaM) was proposed as a target site to block K-Ras driven cancer cell stemness. We therefore aimed at developing a high-throughput amenable screening assay to identify novel CaM-inhibitors as potential K-Ras stemness-signaling disruptors. A modulated time-resolved Förster resonance energy transfer (mTR-FRET)-assay was developed and benchmarked against an identically designed fluorescence anisotropy (FA)-assay. In both assays, two CaM-binding peptides were labeled with Eu(III)-chelate or fluorescein and used as single-label reporter probes that were displaced from CaM upon competitor binding. Thus, peptidic and small molecule competitors with nanomolar to micromolar affinities to CaM could be detected, including a peptide that was derived from the C-terminus of K-Ras. In order to detect CaM-residue specific covalent inhibitors, a cell lysate-based Förster resonance energy transfer (FRET)-assay was furthermore established. This assay enabled us to measure the slow, residue-specific, covalent inhibition by ophiobolin A in the presence of other endogenous proteins. In conclusion, we have developed a panel of fluorescence-assays that allows identification of conventional and covalent CaM-inhibitors as potential disruptors of K-Ras driven cancer cell stemness.
Collapse
Affiliation(s)
- Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery Group, Life Sciences Research Unit, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, 20500, Turku, Finland
| | - Ville Eskonen
- Materials Chemistry and Chemical Analysis, University of Turku, 20500, Turku, Finland
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, 20500, Turku, Finland
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Life Sciences Research Unit, University of Luxembourg, 4362, Esch-sur-Alzette, Luxembourg; Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, 20520, Turku, Finland.
| |
Collapse
|
14
|
Abstract
Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques. Finally, we summarize the wide range of sensors in the literature, exploring creative new sensor architectures suitable for different applications.
Collapse
Affiliation(s)
- Lynn Sanford
- University of Colorado Boulder, Boulder, CO, United States
| | - Amy Palmer
- University of Colorado Boulder, Boulder, CO, United States.
| |
Collapse
|
15
|
Najumudeen AK, Jaiswal A, Lectez B, Oetken-Lindholm C, Guzmán C, Siljamäki E, Posada IMD, Lacey E, Aittokallio T, Abankwa D. Cancer stem cell drugs target K-ras signaling in a stemness context. Oncogene 2016; 35:5248-5262. [PMID: 26973241 PMCID: PMC5057041 DOI: 10.1038/onc.2016.59] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 01/22/2016] [Accepted: 01/25/2016] [Indexed: 01/02/2023]
Abstract
Cancer stem cells (CSCs) are considered to be responsible for treatment relapse and have therefore become a major target in cancer research. Salinomycin is the most established CSC inhibitor. However, its primary mechanistic target is still unclear, impeding the discovery of compounds with similar anti-CSC activity. Here, we show that salinomycin very specifically interferes with the activity of K-ras4B, but not H-ras, by disrupting its nanoscale membrane organization. We found that caveolae negatively regulate the sensitivity to this drug. On the basis of this novel mechanistic insight, we defined a K-ras-associated and stem cell-derived gene expression signature that predicts the drug response of cancer cells to salinomycin. Consistent with therapy resistance of CSC, 8% of tumor samples in the TCGA-database displayed our signature and were associated with a significantly higher mortality. Using our K-ras-specific screening platform, we identified several new candidate CSC drugs. Two of these, ophiobolin A and conglobatin A, possessed a similar or higher potency than salinomycin. Finally, we established that the most potent compound, ophiobolin A, exerts its K-ras4B-specific activity through inactivation of calmodulin. Our data suggest that specific interference with the K-ras4B/calmodulin interaction selectively inhibits CSC.
Collapse
Affiliation(s)
- A K Najumudeen
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - A Jaiswal
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - B Lectez
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - C Oetken-Lindholm
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - C Guzmán
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - E Siljamäki
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - I M D Posada
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - E Lacey
- Microbial Screening Technologies Pty. Ltd., Building C, Smithfield, New South Wales, Australia
| | - T Aittokallio
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - D Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| |
Collapse
|
16
|
SPRED1 Interferes with K-ras but Not H-ras Membrane Anchorage and Signaling. Mol Cell Biol 2016; 36:2612-25. [PMID: 27503857 DOI: 10.1128/mcb.00191-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/03/2016] [Indexed: 12/13/2022] Open
Abstract
The Ras/mitogen-activated protein kinase (MAPK) signaling pathway is tightly controlled by negative feedback regulators, such as the tumor suppressor SPRED1. The SPRED1 gene also carries loss-of-function mutations in the RASopathy Legius syndrome. Growth factor stimulation translocates SPRED1 to the plasma membrane, triggering its inhibitory activity. However, it remains unclear whether SPRED1 there acts at the level of Ras or Raf. We show that pharmacological or galectin-1 (Gal-1)-mediated induction of B- and C-Raf-containing dimers translocates SPRED1 to the plasma membrane. This is facilitated in particular by SPRED1 interaction with B-Raf and, via its N terminus, with Gal-1. The physiological significance of these novel interactions is supported by two Legius syndrome-associated mutations that show diminished binding to both Gal-1 and B-Raf. On the plasma membrane, SPRED1 becomes enriched in acidic membrane domains to specifically perturb membrane organization and extracellular signal-regulated kinase (ERK) signaling of active K-ras4B (here, K-ras) but not H-ras. However, SPRED1 also blocks on the nanoscale the positive effects of Gal-1 on H-ras. Therefore, a combinatorial expression of SPRED1 and Gal-1 potentially regulates specific patterns of K-ras- and H-ras-dependent signaling output. More broadly, our results open up the possibility that related SPRED and Sprouty proteins act in a similar Ras and Raf isoform-specific manner.
Collapse
|
17
|
Najumudeen AK, Posada IMD, Lectez B, Zhou Y, Landor SKJ, Fallarero A, Vuorela P, Hancock J, Abankwa D. Phenotypic Screening Identifies Protein Synthesis Inhibitors as H-Ras-Nanocluster-Increasing Tumor Growth Inducers. Biochemistry 2015; 54:7212-21. [PMID: 26568031 DOI: 10.1021/acs.biochem.5b00724] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ras isoforms H-, N-, and K-ras are each mutated in specific cancer types at varying frequencies and have different activities in cell fate control. On the plasma membrane, Ras proteins are laterally segregated into isoform-specific nanoscale signaling hubs, termed nanoclusters. As Ras nanoclusters are required for Ras signaling, chemical modulators of nanoclusters represent ideal candidates for the specific modulation of Ras activity in cancer drug development. We therefore conducted a chemical screen with commercial and in-house natural product libraries using a cell-based H-ras-nanoclustering FRET assay. Next to established Ras inhibitors, such as a statin and farnesyl-transferase inhibitor, we surprisingly identified five protein synthesis inhibitors as positive regulators. Using commonly employed cycloheximide as a representative compound, we show that protein synthesis inhibition increased nanoclustering and effector recruitment specifically of active H-ras but not of K-ras. Consistent with these data, cycloheximide treatment activated both Erk and Akt kinases and specifically promoted H-rasG12V-induced, but not K-rasG12V-induced, PC12 cell differentiation. Intriguingly, cycloheximide increased the number of mammospheres, which are enriched for cancer stem cells. Depletion of H-ras in combination with cycloheximide significantly reduced mammosphere formation, suggesting an exquisite synthetic lethality. The potential of cycloheximide to promote tumor cell growth was also reflected in its ability to increase breast cancer cell tumors grown in ovo. These results illustrate the possibility of identifying Ras-isoform-specific modulators using nanocluster-directed screening. They also suggest an unexpected feedback from protein synthesis inhibition to Ras signaling, which might present a vulnerability in certain tumor cell types.
Collapse
Affiliation(s)
- Arafath K Najumudeen
- Turku Centre for Biotechnology, Åbo Akademi University , Tykistökatu 6B, 20520 Turku, Finland
| | - Itziar M D Posada
- Turku Centre for Biotechnology, Åbo Akademi University , Tykistökatu 6B, 20520 Turku, Finland
| | - Benoit Lectez
- Turku Centre for Biotechnology, Åbo Akademi University , Tykistökatu 6B, 20520 Turku, Finland
| | - Yong Zhou
- University of Texas Health Science Center at Houston , Medical School, Houston, Texas 77030, United States
| | - Sebastian K-J Landor
- Turku Centre for Biotechnology, Åbo Akademi University , Tykistökatu 6B, 20520 Turku, Finland.,Department of Cell and Molecular Biology (CMB), Karolinska Institutet , SE-171 77 Stockholm, Sweden
| | - Adyary Fallarero
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , FI-00014 Helsinki, Finland
| | - Pia Vuorela
- Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki , FI-00014 Helsinki, Finland
| | - John Hancock
- University of Texas Health Science Center at Houston , Medical School, Houston, Texas 77030, United States
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University , Tykistökatu 6B, 20520 Turku, Finland
| |
Collapse
|
18
|
Myristoleic acid inhibits osteoclast formation and bone resorption by suppressing the RANKL activation of Src and Pyk2. Eur J Pharmacol 2015; 768:189-98. [PMID: 26528796 DOI: 10.1016/j.ejphar.2015.10.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/29/2015] [Accepted: 10/30/2015] [Indexed: 02/01/2023]
Abstract
Cytoskeletal changes in osteoclasts such as formation of actin ring is required for bone-resorbing activity. The tyrosine kinase Src is a key player in massive cytoskeletal change of osteoclasts, thereby in bone destruction. In order for Src to be activated, trafficking to the inner plasma membrane via myristoylation is of importance. A previous study reported that myristoleic acid derived from myristic acid, inhibited N-myristoyl-transferase, an essential enzyme for myristoylation process. This prompted us to investigate whether myristoleic acid could affect osteoclastogenesis. Indeed, we observed that myristoleic acid inhibited RANKL-induced osteoclast formation in vitro, especially, at later stages of differentiation. Myristoleic acid attenuated the tyrosine phosphorylation of c-Src and Pyk2, which associates with Src, by RANKL. When myristoleic acid was co-administered with soluble RANKL into mice, RANKL-induced bone loss was substantially prevented. Bone dissection clearly revealed that the number of multinucleated osteoclasts was significantly diminished by myristoleic acid. On the other hand, myristoleic acid treatment had little or no influence on early osteoclast differentiation markers, such as c-Fos and NFATc1, and proteins related to cytoskeletal rearrangement, including DC-STAMP, integrin αv and integrin β3 in vitro. Taken together, our data suggest that myristoleic acid is capable of blocking the formation of large multinucleated osteoclasts and bone resorption likely through suppressing activation of Src and Pyk2.
Collapse
|
19
|
Guzmán C, Oetken-Lindholm C, Abankwa D. Automated High-Throughput Fluorescence Lifetime Imaging Microscopy to Detect Protein-Protein Interactions. ACTA ACUST UNITED AC 2015; 21:238-45. [PMID: 26384400 DOI: 10.1177/2211068215606048] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Indexed: 11/16/2022]
Abstract
Fluorescence resonance energy transfer (FRET) is widely used to study conformational changes of macromolecules and protein-protein, protein-nucleic acid, and protein-small molecule interactions. FRET biosensors can serve as valuable secondary assays in drug discovery and for target validation in mammalian cells. Fluorescence lifetime imaging microscopy (FLIM) allows precise quantification of the FRET efficiency in intact cells, as FLIM is independent of fluorophore concentration, detection efficiency, and fluorescence intensity. We have developed an automated FLIM system using a commercial frequency domain FLIM attachment (Lambert Instruments) for wide-field imaging. Our automated FLIM system is capable of imaging and analyzing up to 50 different positions of a slide in less than 4 min, or the inner 60 wells of a 96-well plate in less than 20 min. Automation is achieved using a motorized stage and controller (Prior Scientific) coupled with a Zeiss Axio Observer body and full integration into the Lambert Instruments FLIM acquisition software. As an application example, we analyze the interaction of the oncoprotein Ras and its effector Raf after drug treatment. In conclusion, our automated FLIM imaging system requires only commercial components and may therefore allow for a broader use of this technique in chemogenomics projects.
Collapse
Affiliation(s)
- Camilo Guzmán
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | | | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| |
Collapse
|
20
|
Šolman M, Ligabue A, Blaževitš O, Jaiswal A, Zhou Y, Liang H, Lectez B, Kopra K, Guzmán C, Härmä H, Hancock JF, Aittokallio T, Abankwa D. Specific cancer-associated mutations in the switch III region of Ras increase tumorigenicity by nanocluster augmentation. eLife 2015; 4:e08905. [PMID: 26274561 PMCID: PMC4563131 DOI: 10.7554/elife.08905] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/13/2015] [Indexed: 01/09/2023] Open
Abstract
Hotspot mutations of Ras drive cell transformation and tumorigenesis. Less frequent mutations in Ras are poorly characterized for their oncogenic potential. Yet insight into their mechanism of action may point to novel opportunities to target Ras. Here, we show that several cancer-associated mutations in the switch III region moderately increase Ras activity in all isoforms. Mutants are biochemically inconspicuous, while their clustering into nanoscale signaling complexes on the plasma membrane, termed nanocluster, is augmented. Nanoclustering dictates downstream effector recruitment, MAPK-activity, and tumorigenic cell proliferation. Our results describe an unprecedented mechanism of signaling protein activation in cancer. DOI:http://dx.doi.org/10.7554/eLife.08905.001 Cancer is a disease that develops when cells within the body acquire genetic mutations that allow them to grow and divide rapidly. Many human cancers have mutations in a gene that encodes a protein called Ras, which promotes cell growth and division by controlling the activities of other proteins. Ras congregates at the membrane that surrounds the cell and can assemble into clusters (called nanoclusters) that each contain six to eight Ras proteins. The tight packing of the proteins in these nanoclusters increases the amount of Ras in the membrane locally, which allows Ras to interact with other proteins more efficiently to promote growth and cell division. In normal cells, other proteins control when Ras is active. However, in many cancer cells, Ras is active all the time due to mutations that occur in three ‘hotspots’ within its gene. Other mutations in the gene that encodes Ras are also found in cancer cells, but these are less common and it is not clear how they alter the activity of the protein. Here, Solman et al. used microscopy and biochemical techniques to study the effects of some of the less common mutations on Ras activity in human cells. The experiments show that several mutations that alter a region of Ras called the ‘switch III region’ moderately increase the activity of Ras. The mutations probably alter the way that Ras sits in the membrane, which in turn changes the way it interacts with other proteins and the membrane so that more Ras nanoclusters form. Solman et al.'s findings reveal a new way that Ras can be activated in cancer cells. The next challenge is to develop drugs that block the formation of Ras nanoclusters and to find out if they have the potential to be used to treat cancer. DOI:http://dx.doi.org/10.7554/eLife.08905.002
Collapse
Affiliation(s)
- Maja Šolman
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - Alessio Ligabue
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - Olga Blaževitš
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - Alok Jaiswal
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, United States
| | - Hong Liang
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, United States
| | - Benoit Lectez
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - Kari Kopra
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Camilo Guzmán
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| | - Harri Härmä
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, United States
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Turku, Finland
| |
Collapse
|
21
|
Najumudeen AK, Guzmán C, Posada IMD, Abankwa D. Rab-NANOPS: FRET biosensors for Rab membrane nanoclustering and prenylation detection in mammalian cells. Methods Mol Biol 2015; 1298:29-45. [PMID: 25800830 DOI: 10.1007/978-1-4939-2569-8_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Rab proteins constitute the largest subfamily of Ras-like small GTPases. They are central to vesicular transport and organelle definition in eukaryotic cells. Unlike their Ras counterparts, they are not a hallmark of cancer. However, a number of diseases, including cancer, show a misregulation of Rab protein activity. As for all membrane-anchored signaling proteins, correct membrane organization is critical for Rabs to operate. In this chapter, we provide a detailed protocol for the use of a flow cytometry-based Fluorescence Resonance Energy Transfer (FRET)-biosensors assay, which allows to detect changes in membrane anchorage, subcellular distribution, and of the nanoscale organization of Rab-GTPases in mammalian cell lines. This assay is high-throughput amenable and can therefore be utilized in chemical-genomic and drug discovery efforts.
Collapse
Affiliation(s)
- Arafath Kaja Najumudeen
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520, Turku, Finland
| | | | | | | |
Collapse
|
22
|
Global profiling of co- and post-translationally N-myristoylated proteomes in human cells. Nat Commun 2014; 5:4919. [PMID: 25255805 PMCID: PMC4200515 DOI: 10.1038/ncomms5919] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 08/05/2014] [Indexed: 02/08/2023] Open
Abstract
Protein N-myristoylation is a ubiquitous co- and post-translational modification that has been implicated in the development and progression of a range of human diseases. Here, we report the global N-myristoylated proteome in human cells determined using quantitative chemical proteomics combined with potent and specific human N-myristoyltransferase (NMT) inhibition. Global quantification of N-myristoylation during normal growth or apoptosis allowed the identification of >100 N-myristoylated proteins, >95% of which are identified for the first time at endogenous levels. Furthermore, quantitative dose response for inhibition of N-myristoylation is determined for >70 substrates simultaneously across the proteome. Small-molecule inhibition through a conserved substrate-binding pocket is also demonstrated by solving the crystal structures of inhibitor-bound NMT1 and NMT2. The presented data substantially expand the known repertoire of co- and post-translational N-myristoylation in addition to validating tools for the pharmacological inhibition of NMT in living cells. Protein N-myristoylation is a ubiquitous modification implicated in the regulation of multiple cellular processes. Here, Thinon et al. report the development of a general method to identify N-myristoylated proteins in human cells and identify over 100 endogenous post- and co-translational substrates of N-myristoyltransferase.
Collapse
|
23
|
Coxon FP, Joachimiak L, Najumudeen AK, Breen G, Gmach J, Oetken-Lindholm C, Way R, Dunford JE, Abankwa D, Błażewska KM. Synthesis and characterization of novel phosphonocarboxylate inhibitors of RGGT. Eur J Med Chem 2014; 84:77-89. [PMID: 25016230 DOI: 10.1016/j.ejmech.2014.06.062] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 06/14/2014] [Accepted: 06/27/2014] [Indexed: 12/31/2022]
Abstract
Phosphonocarboxylate (PC) analogs of the anti-osteoporotic drugs, bisphosphonates, represent the first class of selective inhibitors of Rab geranylgeranyl transferase (RabGGTase, RGGT), an enzyme implicated in several diseases including ovarian, breast and skin cancer. Here we present the synthesis and biological characterization of an extended set of this class of compounds, including lipophilic derivatives of the known RGGT inhibitors. From this new panel of PCs, we have identified an inhibitor of RGGT that is of similar potency as the most active published phosphonocarboxylate, but of higher selectivity towards this enzyme compared to prenyl pyrophosphate synthases. New insights into structural requirements are also presented, showing that only PC analogs of the most potent 3rd generation bisphosphonates inhibit RGGT. In addition, the first phosphonocarboxylate-derived GGPPS inhibitor is reported.
Collapse
Affiliation(s)
- Fraser P Coxon
- Musculoskeletal Programme, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB252ZD, UK
| | - Lukasz Joachimiak
- Institute of Organic Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | - Arafath Kaja Najumudeen
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - George Breen
- Musculoskeletal Programme, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB252ZD, UK
| | - Joanna Gmach
- Institute of Organic Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland
| | | | - Rebecca Way
- Musculoskeletal Programme, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB252ZD, UK
| | - James E Dunford
- University of Oxford, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, The Botnar Research Center, UK
| | - Daniel Abankwa
- Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | - Katarzyna M Błażewska
- Institute of Organic Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland.
| |
Collapse
|
24
|
Wei ZH, Chen H, Zhang C, Ye BC. FRET-based system for probing protein-protein interactions between σR and RsrA from Streptomyces coelicolor in response to the redox environment. PLoS One 2014; 9:e92330. [PMID: 24651617 PMCID: PMC3961337 DOI: 10.1371/journal.pone.0092330] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 02/21/2014] [Indexed: 11/26/2022] Open
Abstract
Protein-protein interactions between sigma factor σ(R) and its corresponding zinc-binding anti-sigma (ZAS) protein RsrA trigger the thioredoxin system for maintaining cellular redox homeostasis in S. coelicolor. RsrA bound to zinc associates with σ(R), inhibiting its transcriptional activity in a reducing environment. During disulfide stress it forms intramolecular disulfide bonds, leading to zinc release and dissociation from σ(R), which initiates transcription to produce reductase and thioredoxin. We designed a fluorescence resonance energy transfer (FRET) based system for monitoring protein-protein interactions between σ(R) and RsrA to further understand how this redox switch regulates the thioredoxin system in S. coelicolor in response to its redox environment, especially various reactive oxygen species (ROS) derived from different metabolic pathways, and clarify the different response mechanisms between Zn-RsrA and apo-RsrA. By the use of the FRET approach described here, we showed that zinc protected thiols in RsrA and causes the σ(R)-RsrA complex to form a more compact structure. This system was also utilized to detect changes in redox status induced by ROS and diamide in real time in E. coli cells.
Collapse
Affiliation(s)
- Zi-Han Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Huan Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bang-Ce Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| |
Collapse
|
25
|
Guzmán C, Šolman M, Ligabue A, Blaževitš O, Andrade DM, Reymond L, Eggeling C, Abankwa D. The efficacy of Raf kinase recruitment to the GTPase H-ras depends on H-ras membrane conformer-specific nanoclustering. J Biol Chem 2014; 289:9519-33. [PMID: 24569991 DOI: 10.1074/jbc.m113.537001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Solution structures and biochemical data have provided a wealth of mechanistic insight into Ras GTPases. However, information on how much the membrane organization of these lipid-modified proteins impacts on their signaling is still scarce. Ras proteins are organized into membrane nanoclusters, which are necessary for Ras-MAPK signaling. Using quantitative conventional and super-resolution fluorescence methods, as well as mathematical modeling, we investigated nanoclustering of H-ras helix α4 and hypervariable region mutants that have different bona fide conformations on the membrane. By following the emergence of conformer-specific nanoclusters in the plasma membrane of mammalian cells, we found that conformers impart distinct nanoclustering responses depending on the cytoplasmic levels of the nanocluster scaffold galectin-1. Computational modeling revealed that complexes containing H-ras conformers and galectin-1 affect both the number and lifetime of nanoclusters and thus determine the specific Raf effector recruitment. Our results show that mutations in Ras can affect its nanoclustering response and thus allosterically effector recruitment and downstream signaling. We postulate that cancer- and developmental disease-linked mutations that are associated with the Ras membrane conformation may exhibit so far unrecognized Ras nanoclustering and therefore signaling alterations.
Collapse
Affiliation(s)
- Camilo Guzmán
- From the Turku Centre for Biotechnology, Åbo Akademi University, Tykistökatu 6B, 20520 Turku, Finland
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Gulin-Sarfraz T, Sarfraz J, Didem Şen Karaman DŞK, Zhang J, Oetken-Lindholm C, Duchanoy A, Rosenholm JM, Abankwa D. FRET-reporter nanoparticles to monitor redox-induced intracellular delivery of active compounds. RSC Adv 2014. [DOI: 10.1039/c4ra00270a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
FRET-reporter particles for redox-induced release of active compounds in cells were developed. This particle system allowed following the intracellular cleavage of delivered compounds after particle internalization.
Collapse
Affiliation(s)
- Tina Gulin-Sarfraz
- Center for Functional Materials
- Laboratory for Physical Chemistry
- Åbo Akademi University
- 20500 Turku, Finland
| | - Jawad Sarfraz
- Center for Functional Materials
- Laboratory for Physical Chemistry
- Åbo Akademi University
- 20500 Turku, Finland
| | | | - Jixi Zhang
- Center for Functional Materials
- Laboratory for Physical Chemistry
- Åbo Akademi University
- 20500 Turku, Finland
| | | | - Alain Duchanoy
- Center for Functional Materials
- Laboratory for Physical Chemistry
- Åbo Akademi University
- 20500 Turku, Finland
| | - Jessica M. Rosenholm
- Center for Functional Materials
- Laboratory for Physical Chemistry
- Åbo Akademi University
- 20500 Turku, Finland
| | - Daniel Abankwa
- Turku Centre for Biotechnology
- Åbo Akademi University
- 20520 Turku, Finland
| |
Collapse
|