1
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Pasquale EB. Eph receptors and ephrins in cancer progression. Nat Rev Cancer 2024; 24:5-27. [PMID: 37996538 PMCID: PMC11015936 DOI: 10.1038/s41568-023-00634-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/25/2023]
Abstract
Evidence implicating Eph receptor tyrosine kinases and their ephrin ligands (that together make up the 'Eph system') in cancer development and progression has been accumulating since the discovery of the first Eph receptor approximately 35 years ago. Advances in the past decade and a half have considerably increased the understanding of Eph receptor-ephrin signalling mechanisms in cancer and have uncovered intriguing new roles in cancer progression and drug resistance. This Review focuses mainly on these more recent developments. I provide an update on the different mechanisms of Eph receptor-ephrin-mediated cell-cell communication and cell autonomous signalling, as well as on the interplay of the Eph system with other signalling systems. I further discuss recent advances in elucidating how the Eph system controls tumour expansion, invasiveness and metastasis, supports cancer stem cells, and drives therapy resistance. In addition to functioning within cancer cells, the Eph system also mediates the reciprocal communication between cancer cells and cells of the tumour microenvironment. The involvement of the Eph system in tumour angiogenesis is well established, but recent findings also demonstrate roles in immune cells, cancer-associated fibroblasts and the extracellular matrix. Lastly, I discuss strategies under evaluation for therapeutic targeting of Eph receptors-ephrins in cancer and conclude with an outlook on promising future research directions.
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Affiliation(s)
- Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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2
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Gomez-Soler M, Olson EJ, de la Torre ER, Zhao C, Lamberto I, Flood DT, Danho W, Lechtenberg BC, Riedl SJ, Dawson PE, Pasquale EB. Lipidation and PEGylation Strategies to Prolong the in Vivo Half-Life of a Nanomolar EphA4 Receptor Antagonist. Eur J Med Chem 2023; 262:115876. [PMID: 38523699 PMCID: PMC10959496 DOI: 10.1016/j.ejmech.2023.115876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
The EphA4 receptor tyrosine kinase plays a role in neurodegenerative diseases, inhibition of nerve regeneration, cancer progression and other diseases. Therefore, EphA4 inhibition has potential therapeutic value. Selective EphA4 kinase inhibitors are not available, but we identified peptide antagonists that inhibit ephrin ligand binding to EphA4 with high specificity. One of these peptides is the cyclic APY-d3 (βAPYCVYRβASWSC-NH2), which inhibits ephrin-A5 ligand binding to EphA4 with low nanomolar binding affinity and is highly protease resistant. Here we describe modifications of APY-d3 that yield two different key derivatives with greatly increased half-lives in the mouse circulation, the lipidated APY-d3-laur8 and the PEGylated APY-d3-PEG4. These two derivatives inhibit ligand induced EphA4 activation in cells with sub-micromolar potency. Since they retain high potency and specificity for EphA4, lipidated and PEGylated APY-d3 derivatives represent new tools for discriminating EphA4 activities in vivo and for preclinical testing of EphA4 inhibition in animal disease models.
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Affiliation(s)
- Maricel Gomez-Soler
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Erika J. Olson
- Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Elena Rubio de la Torre
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Chunxia Zhao
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Ilaria Lamberto
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Dillon T. Flood
- Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Waleed Danho
- Del Mar, California 92014, United States
- Deceased
| | - Bernhard C. Lechtenberg
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Stefan J. Riedl
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Elena B. Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
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3
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Yin S, Mei S, Li Z, Xu Z, Wu Y, Chen X, Liu D, Niu MM, Li J. Non-covalent cyclic peptides simultaneously targeting Mpro and NRP1 are highly effective against Omicron BA.2.75. Front Pharmacol 2022; 13:1037993. [PMID: 36408220 PMCID: PMC9666779 DOI: 10.3389/fphar.2022.1037993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022] Open
Abstract
Available vaccine-based immunity may at high risk of being evaded due to substantial mutations in the variant Omicron. The main protease (Mpro) of SARS-CoV-2 and human neuropilin-1 (NRP1), two less mutable proteins, have been reported to be crucial for SARS-CoV-2 replication and entry into host cells, respectively. Their dual blockade may avoid vaccine failure caused by continuous mutations of the SARS-CoV-2 genome and exert synergistic antiviral efficacy. Herein, four cyclic peptides non-covalently targeting both Mpro and NRP1 were identified using virtual screening. Among them, MN-2 showed highly potent affinity to Mpro (Kd = 18.2 ± 1.9 nM) and NRP1 (Kd = 12.3 ± 1.2 nM), which was about 3,478-fold and 74-fold stronger than that of the positive inhibitors Peptide-21 and EG3287. Furthermore, MN-2 exhibited significant inhibitory activity against Mpro and remarkable anti-infective activity against the pseudotyped variant Omicron BA.2.75 without obvious cytotoxicity. These data demonstrated that MN-2, a novel non-covalent cyclic peptide, is a promising agent against Omicron BA.2.75.
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Affiliation(s)
- Shengnan Yin
- Department of Pharmacy, Taizhou Hospital Affiliated to Nanjing University of Chinese Medicine, Taizhou, China
| | - Shuang Mei
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Zhiqin Li
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Zhen Xu
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Yuting Wu
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Xiujuan Chen
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
| | - Dongmei Liu
- Department of Pharmacy, Taizhou Hospital Affiliated to Nanjing University of Chinese Medicine, Taizhou, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
| | - Jindong Li
- Institute of Clinical Medicine, Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
- *Correspondence: Xiujuan Chen, ; Jindong Li, ; Dongmei Liu, ; Miao-Miao Niu,
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4
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Ganguly D, Thomas JA, Ali A, Kumar R. Mechanistic and therapeutic implications of EphA-4 receptor tyrosine kinase in the pathogenesis of Alzheimer's disease. Eur J Neurosci 2022; 56:5532-5546. [PMID: 34989046 DOI: 10.1111/ejn.15591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/14/2021] [Accepted: 12/28/2021] [Indexed: 12/14/2022]
Abstract
Erythropoietin-producing hepatoma (Eph) receptors belong to a family of tyrosine kinase receptors that plays a pivotal role in the development of the brain. Eph can be divided broadly into two groups, namely, EphA and EphB, comprising nine and five members, respectively. In recent years, the role of EphA-4 has become increasingly apparent in the onset of Alzheimer's disease (AD). Emerging evidence suggests that EphA-4 results in synaptic dysfunction, which in turn promotes the progression of AD. Moreover, pharmacological or genetic ablation of EphA-4 in the murine model of AD can alleviate the symptoms. The current review summarizes different pathways by which EphA-4 can influence pathogenesis. Since, majority of the studies had reported the protective effect of EphA-4 inhibition during AD, designing therapeutics based on decreasing its enzymatic activity might be necessary for introducing the novel interventions. Therefore, the review described peptide and nanobodies inhibitors of EphA-4 that exhibit the potential to modulate EphA-4 and could be used as lead molecules for the targeted therapy of AD.
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Affiliation(s)
- Devargya Ganguly
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
| | - Joshua Abby Thomas
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
| | - Abid Ali
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Rahul Kumar
- Department of Biotechnology, GITAM Institute of Sciences, GITAM (Deemed to be) University, Vishakhapatnam, India
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5
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Xu Z, Zou Y, Gao X, Niu MM, Li J, Xue L, Jiang S. Dual-targeting cyclic peptides of receptor-binding domain (RBD) and main protease (Mpro) as potential drug leads for the treatment of SARS-CoV-2 infection. Front Pharmacol 2022; 13:1041331. [PMID: 36339564 PMCID: PMC9627161 DOI: 10.3389/fphar.2022.1041331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/10/2022] [Indexed: 12/01/2023] Open
Abstract
The receptor-binding domain (RBD) and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) play a crucial role in the entry and replication of viral particles, and co-targeting both of them could be an attractive approach for the treatment of SARS-CoV-2 infection by setting up a "double lock" in the viral lifecycle. However, few dual RBD/Mpro-targeting agents have been reported. Here, four novel RBD/Mpro dual-targeting peptides, termed as MRs 1-4, were discovered by an integrated virtual screening scheme combining molecular docking-based screening and molecular dynamics simulation. All of them possessed nanomolar binding affinities to both RBD and Mpro ranging from 14.4 to 39.2 nM and 22.5-40.4 nM, respectively. Further pseudovirus infection assay revealed that the four selected peptides showed >50% inhibition against SARS-CoV-2 pseudovirus at a concentration of 5 µM without significant cytotoxicity to host cells. This study leads to the identification of a class of dual RBD/Mpro-targeting agents, which may be developed as potential and effective SARS-CoV-2 therapeutics.
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Affiliation(s)
- Zhen Xu
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Yunting Zou
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Xi Gao
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Jindong Li
- Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Lu Xue
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Su Jiang
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
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6
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Dennys C, Baggio C, Rodrigo R, Roussel F, Kulinich A, Heintzman S, Fox A, Kolb SJ, Shaw PJ, Ethell IM, Pellecchia M, Meyer KC. EphA4 targeting agents protect motor neurons from cell death induced by amyotrophic lateral sclerosis -astrocytes. iScience 2022; 25:104877. [PMID: 36034213 PMCID: PMC9404653 DOI: 10.1016/j.isci.2022.104877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/17/2022] [Accepted: 07/29/2022] [Indexed: 12/02/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a degenerative disease that progressively destroys motor neurons (MNs). Earlier studies identified EphA4, a receptor tyrosine kinase, as a possible disease-modifying gene. The complex interplay between the EphA4 receptor and its ephrin ligands in motor neurons and astrocytes has not yet been fully elucidated and includes a putative pro-apoptotic activity of the unbound receptor compared to ephrin-bound receptor. We recently reported that astrocytes from patients with ALS induce cell death in co-cultured MNs. Here we found that first-generation synthetic EphA4 agonistic agent 123C4, effectively protected MNs when co-cultured with reactive astrocytes from patients with ALS from multiple subgroups (sALS and mutant SOD1). Newer generation and more potent EphA4 agonistic agents 150D4, 150E8, and 150E7 provided effective protection at a lower therapeutic dose. Combined, the data suggest that the development of EphA4 agonistic agents provides potentially a promising therapeutic strategy for patients with ALS.
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Affiliation(s)
- Cassandra Dennys
- Center for Gene Therapy, Nationwide Children’s Hospital, 700 Children’s Drive Columbus, OH 43205, USA
| | - Carlo Baggio
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Rochelle Rodrigo
- Center for Gene Therapy, Nationwide Children’s Hospital, 700 Children’s Drive Columbus, OH 43205, USA
| | - Florence Roussel
- Center for Gene Therapy, Nationwide Children’s Hospital, 700 Children’s Drive Columbus, OH 43205, USA
| | - Anna Kulinich
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Sarah Heintzman
- Department of Neurology, The Ohio State University Medical Center, Columbus, OH, USA
| | - Ashley Fox
- Department of Neurology, The Ohio State University Medical Center, Columbus, OH, USA
| | - Stephen J. Kolb
- Department of Neurology, The Ohio State University Medical Center, Columbus, OH, USA
- Department of Biological Chemistry & Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Molecular, Cellular & Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
- Department of Neuroscience, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Pamela J. Shaw
- Academic Unit of Neurology, Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK
| | - Iryna M. Ethell
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Maurizio Pellecchia
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA
| | - Kathrin C. Meyer
- Center for Gene Therapy, Nationwide Children’s Hospital, 700 Children’s Drive Columbus, OH 43205, USA
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7
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Baggio C, Kulinich A, Dennys CN, Rodrigo R, Meyer K, Ethell I, Pellecchia M. NMR-Guided Design of Potent and Selective EphA4 Agonistic Ligands. J Med Chem 2021; 64:11229-11246. [PMID: 34293864 DOI: 10.1021/acs.jmedchem.1c00608] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this paper, we applied an innovative nuclear magnetic resonance (NMR)-guided screening and ligand design approach, named focused high-throughput screening by NMR (fHTS by NMR), to derive potent, low-molecular-weight ligands capable of mimicking interactions elicited by ephrin ligands on the receptor tyrosine kinase EphA4. The agents bind with nanomolar affinity, trigger receptor activation in cellular assays with motor neurons, and provide remarkable motor neuron protection from amyotrophic lateral sclerosis (ALS) patient-derived astrocytes. Structural studies on the complex between EphA4 ligand-binding domain and a most active agent provide insights into the mechanism of the agents at a molecular level. Together with preliminary in vivo pharmacology studies, the data form a strong foundation for the translation of these agents for the treatment of ALS and potentially other human diseases.
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Affiliation(s)
- Carlo Baggio
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Anna Kulinich
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Cassandra N Dennys
- Nationwide Children's Hospital, 700 Children's Drive, Columbus, Ohio 43205, United States
| | - Rochelle Rodrigo
- Nationwide Children's Hospital, 700 Children's Drive, Columbus, Ohio 43205, United States
| | - Kathrin Meyer
- Nationwide Children's Hospital, 700 Children's Drive, Columbus, Ohio 43205, United States
| | - Iryna Ethell
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Maurizio Pellecchia
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
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8
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de Boer A, Storm A, Gomez-Soler M, Smolders S, Rué L, Poppe L, B Pasquale E, Robberecht W, Lemmens R. Environmental enrichment during the chronic phase after experimental stroke promotes functional recovery without synergistic effects of EphA4 targeted therapy. Hum Mol Genet 2021; 29:605-617. [PMID: 31814004 PMCID: PMC7068116 DOI: 10.1093/hmg/ddz288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/14/2019] [Accepted: 12/04/2019] [Indexed: 12/31/2022] Open
Abstract
Worldwide, stroke is the main cause of long-term adult disability. After the initial insult, most patients undergo a subacute period with intense plasticity and rapid functional improvements. This period is followed by a chronic phase where recovery reaches a plateau that is only partially modifiable by rehabilitation. After experimental stroke, various subacute rehabilitation paradigms improve recovery. However, in order to reach the best possible outcome, a combination of plasticity-promoting strategies and rehabilitation might be necessary. EphA4 is a negative axonal guidance regulator during development. After experimental stroke, reduced EphA4 levels improve functional outcome with similar beneficial effects upon the inhibition of EphA4 downstream targets. In this study, we assessed the effectiveness of a basic enriched environment in the chronic phase after photothrombotic stroke in mice as well as the therapeutic potential of EphA4 targeted therapy followed by rehabilitation. Our findings show that environmental enrichment in the chronic phase improves functional outcome up to 2 months post-stroke. Although EphA4 levels increase after experimental stroke, subacute EphA4 inhibition followed by environmental enrichment does not further increase recovery. In conclusion, we show that environmental enrichment during the chronic phase of stroke improves functional outcome in mice with no synergistic effects of the used EphA4 targeted therapy.
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Affiliation(s)
- Antina de Boer
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven 3000, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven 3000, Belgium
| | - Annet Storm
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven 3000, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven 3000, Belgium
| | - Maricel Gomez-Soler
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Silke Smolders
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven 3000, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven 3000, Belgium
| | - Laura Rué
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven 3000, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven 3000, Belgium
| | - Lindsay Poppe
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven 3000, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven 3000, Belgium
| | - Elena B Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Wim Robberecht
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven 3000, Belgium.,Department of Neurology, University Hospitals Leuven, Leuven 3000, Belgium
| | - Robin Lemmens
- Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), KU Leuven-University of Leuven, Leuven 3000, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven 3000, Belgium.,Department of Neurology, University Hospitals Leuven, Leuven 3000, Belgium
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9
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Singh N, Chaput L, Villoutreix BO. Fast Rescoring Protocols to Improve the Performance of Structure-Based Virtual Screening Performed on Protein-Protein Interfaces. J Chem Inf Model 2020; 60:3910-3934. [PMID: 32786511 DOI: 10.1021/acs.jcim.0c00545] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein-protein interactions (PPIs) are attractive targets for drug design because of their essential role in numerous cellular processes and disease pathways. However, in general, PPIs display exposed binding pockets at the interface, and as such, have been largely unexploited for therapeutic interventions with low-molecular weight compounds. Here, we used docking and various rescoring strategies in an attempt to recover PPI inhibitors from a set of active and inactive molecules for 11 targets collected in ChEMBL and PubChem. Our focus is on the screening power of the various developed protocols and on using fast approaches so as to be able to apply such a strategy to the screening of ultralarge libraries in the future. First, we docked compounds into each target using the fast "pscreen" mode of the structure-based virtual screening (VS) package Surflex. Subsequently, the docking poses were postprocessed to derive a set of 3D topological descriptors: (i) shape similarity and (ii) interaction fingerprint similarity with a co-crystallized inhibitor, (iii) solvent-accessible surface area, and (iv) extent of deviation from the geometric center of a reference inhibitor. The derivatized descriptors, together with descriptor-scaled scoring functions, were utilized to investigate possible impacts on VS performance metrics. Moreover, four standalone scoring functions, RF-Score-VS (machine-learning), DLIGAND2 (knowledge-based), Vinardo (empirical), and X-SCORE (empirical), were employed to rescore the PPI compounds. Collectively, the results indicate that the topological scoring algorithms could be valuable both at a global level, with up to 79% increase in areas under the receiver operating characteristic curve for some targets, and in early stages, with up to a 4-fold increase in enrichment factors at 1% of the screened collections. Outstandingly, DLIGAND2 emerged as the best scoring function on this data set, outperforming all rescoring techniques in terms of VS metrics. The described methodology could help in the rational design of small-molecule PPI inhibitors and has direct applications in many therapeutic areas, including cancer, CNS, and infectious diseases such as COVID-19.
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Affiliation(s)
- Natesh Singh
- Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Ludovic Chaput
- Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Bruno O Villoutreix
- Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
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10
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Christian AH, Jia S, Cao W, Zhang P, Meza AT, Sigman MS, Chang CJ, Toste FD. A Physical Organic Approach to Tuning Reagents for Selective and Stable Methionine Bioconjugation. J Am Chem Soc 2019; 141:12657-12662. [PMID: 31361488 PMCID: PMC6781863 DOI: 10.1021/jacs.9b04744] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report a data-driven, physical organic approach to the development of new methionine-selective bioconjugation reagents with tunable adduct stabilities. Statistical modeling of structural features described by intrinsic physical organic parameters was applied to the development of a predictive model and to gain insight into features driving the stability of adducts formed from the chemoselective coupling of oxaziridine and methionine thioether partners through Redox Activated Chemical Tagging (ReACT). From these analyses, a correlation between sulfimide stabilities and sulfimide ν (C═O) stretching frequencies was revealed. We exploited the rational gains in adduct stability exposed by this analysis to achieve the design and synthesis of a bis-oxaziridine reagent for peptide stapling. Indeed, we observed that a macrocyclic peptide formed by ReACT stapling at methionine exhibited improved uptake into live cells compared to an unstapled congener, highlighting the potential utility of this unique chemical tool for thioether modification. This work provides a template for the broader use of data-driven approaches to bioconjugation chemistry and other chemical biology applications.
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Affiliation(s)
- Alec H. Christian
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Shang Jia
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wendy Cao
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Patricia Zhang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Arismel Tena Meza
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew S. Sigman
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Christopher J. Chang
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
- Howard Hughes Medical Institute, University of California, Berkeley, California 94720, United States
| | - F. Dean Toste
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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11
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Pan Y, Lu S, Lei L, Lamberto I, Wang Y, Pasquale EB, Wang Y. Genetically Encoded FRET Biosensor for Visualizing EphA4 Activity in Different Compartments of the Plasma Membrane. ACS Sens 2019; 4:294-300. [PMID: 30608127 DOI: 10.1021/acssensors.8b00465] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The EphA4 receptor tyrosine kinase is well-known for its pivotal role in development, cancer progression, and neurological disorders. However, how EphA4 kinase activity is regulated in time and space still remains unclear. To visualize EphA4 activity in different membrane microdomains, we developed a sensitive EphA4 biosensor based on Förster resonance energy transfer (FRET), and targeted it in or outside raft-like microdomains in the plasma membrane. We showed that our biosensor can produce a robust and specific FRET response upon EphA4 activation, both in vitro and in live cells. Interestingly, we observed stronger FRET responses for the non-raft targeting biosensor than for the raft targeting biosensor, suggesting that stronger EphA4 activation may occur in non-raft regions. Further investigations revealed the importance of the actin cytoskeleton in suppressing EphA4 activity in raft-like microdomains. Therefore, our FRET-based EphA4 biosensor could serve as a powerful tool to visualize and investigate EphA4 activation and signaling in specific subcellular compartments of single live cells.
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Affiliation(s)
| | | | | | - Ilaria Lamberto
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States,
| | - Yi Wang
- Department of Bioengineering, University of Illinois at Urbana−Champaign, Champaign, Illinois 61820, United States
| | - Elena B. Pasquale
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States,
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12
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Abstract
The biological functions of the Eph/ephrin system have been intensively investigated and well documented so far since its discovery in 1987. Although the Eph/ephrin system has been implicated in pathological settings such as Alzheimer's disease and cancer, the molecular mechanism of the Eph/ephrin system in those diseases is not well understood. Especially in cancer, recent studies have demonstrated that most of Eph and ephrin are up‐ or down‐regulated in various types of cancer, and have been implicated in tumor progression, tumor malignancy, and prognosis. However, they lack consistency and are in controversy. The localization patterns of EphA1 and EphA2 in mouse lungs are very similar, and both knockout mice showed similar phenotypes in the lungs. Ephrin‐A1 that is a membrane‐anchored ligand for EphAs was co‐localized with EphA1 and EphA2 in lung vascular endothelial cells. We recently uncovered the molecular mechanism of ephrin‐A1‐induced lung metastasis by understanding the physiological function of ephrin‐A1 in lungs. This review focuses on the function of EphA1, EphA2, and ephrin‐A1 in tumors and an establishment of pre‐metastatic microenvironment in the lungs.
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Affiliation(s)
- Katsuaki Ieguchi
- Department of Pharmacology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
| | - Yoshiro Maru
- Department of Pharmacology, Tokyo Women's Medical University, Shinjuku, Tokyo, Japan
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13
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Saha N, Robev D, Mason EO, Himanen JP, Nikolov DB. Therapeutic potential of targeting the Eph/ephrin signaling complex. Int J Biochem Cell Biol 2018; 105:123-133. [PMID: 30343150 DOI: 10.1016/j.biocel.2018.10.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/09/2018] [Accepted: 10/16/2018] [Indexed: 12/27/2022]
Abstract
The Eph-ephrin signaling pathway mediates developmental processes and the proper functioning of the adult human body. This distinctive bidirectional signaling pathway includes a canonical downstream signal cascade inside the Eph-bearing cells, as well as a reverse signaling in the ephrin-bearing cells. The signaling is terminated by ADAM metalloproteinase cleavage, internalization, and degradation of the Eph/ephrin complexes. Consequently, the Eph-ephrin-ADAM signaling cascade has emerged as a key target with immense therapeutic potential particularly in the context of cancer. An interesting twist was brought forth by the emergence of ephrins as the entry receptors for the pathological Henipaviruses, which has spurred new studies to target the viral entry. The availability of high-resolution structures of the multi-modular Eph receptors in complexes with ephrins and other binding partners, such as peptides, small molecule inhibitors and antibodies, offers a wealth of information for the structure-guided development of therapeutic intervention. Furthermore, genomic data mining of Eph mutants involved in cancer provides information for targeted drug development. In this review we summarize the distinct avenues for targeting the Eph-ephrin signaling pathway, including its termination by ADAM proteinases. We highlight the latest developments in Eph-related pharmacology in the context of Eph-ephrin-ADAM-based antibodies and small molecules. Finally, the future prospects of genomics- and proteomics-based medicine are discussed.
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Affiliation(s)
- Nayanendu Saha
- Sloan-Kettering Institute for Cancer Research, Structural Biology Program, 1275 York Avenue, New York, NY 10065, United States
| | - Dorothea Robev
- Sloan-Kettering Institute for Cancer Research, Structural Biology Program, 1275 York Avenue, New York, NY 10065, United States
| | - Emilia O Mason
- Sloan-Kettering Institute for Cancer Research, Structural Biology Program, 1275 York Avenue, New York, NY 10065, United States
| | - Juha P Himanen
- Sloan-Kettering Institute for Cancer Research, Structural Biology Program, 1275 York Avenue, New York, NY 10065, United States.
| | - Dimitar B Nikolov
- Sloan-Kettering Institute for Cancer Research, Structural Biology Program, 1275 York Avenue, New York, NY 10065, United States
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14
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Salgia R, Kulkarni P, Gill PS. EphB4: A promising target for upper aerodigestive malignancies. Biochim Biophys Acta Rev Cancer 2018; 1869:128-137. [PMID: 29369779 PMCID: PMC5955724 DOI: 10.1016/j.bbcan.2018.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/11/2018] [Accepted: 01/11/2018] [Indexed: 12/14/2022]
Abstract
The erythropoietin-producing hepatocellular carcinoma (Eph) receptors are the largest family of receptor tyrosine kinases (RTKs) that include two major subclasses, EphA and EphB. They form an important cell communication system with critical and diverse roles in a variety of biological processes during embryonic development. However, dysregulation of the Eph/ephrin interactions is implicated in cancer contributing to tumour growth, metastasis, and angiogenesis. Here, we focus on EphB4 and review recent developments in elucidating its role in upper aerodigestive malignancies to include lung cancer, head and neck cancer, and mesothelioma. In particular, we summarize information regarding EphB4 structure/function and role in disease pathobiology. We also review the data supporting EphB4 as a potential pharmacological and immunotherapy target and finally, progress in the development of new therapeutic strategies including small molecule inhibitors of its activity is discussed. The emerging picture suggests that EphB4 is a valuable and attractive therapeutic target for upper aerodigestive malignancies.
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MESH Headings
- Animals
- Antineoplastic Agents/therapeutic use
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Gene Expression Regulation, Neoplastic
- Head and Neck Neoplasms/drug therapy
- Head and Neck Neoplasms/genetics
- Head and Neck Neoplasms/metabolism
- Head and Neck Neoplasms/pathology
- Humans
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mesothelioma/drug therapy
- Mesothelioma/genetics
- Mesothelioma/metabolism
- Mesothelioma/pathology
- Mesothelioma, Malignant
- Molecular Targeted Therapy
- Receptor, EphB4/antagonists & inhibitors
- Receptor, EphB4/genetics
- Receptor, EphB4/metabolism
- Signal Transduction
- Squamous Cell Carcinoma of Head and Neck
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Affiliation(s)
- Ravi Salgia
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA, United States.
| | - Prakash Kulkarni
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, 1500 East Duarte Road, Duarte, CA, United States
| | - Prakash S Gill
- Department of Medicine, Division of Medical Oncology, University of Southern California, Los Angeles, CA, United States
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15
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Schoonaert L, Rué L, Roucourt B, Timmers M, Little S, Chávez-Gutiérrez L, Dewilde M, Joyce P, Curnock A, Weber P, Haustraete J, Hassanzadeh-Ghassabeh G, De Strooper B, Van Den Bosch L, Van Damme P, Lemmens R, Robberecht W. Identification and characterization of Nanobodies targeting the EphA4 receptor. J Biol Chem 2017; 292:11452-11465. [PMID: 28526745 PMCID: PMC5500810 DOI: 10.1074/jbc.m116.774141] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 05/16/2017] [Indexed: 12/14/2022] Open
Abstract
The ephrin receptor A4 (EphA4) is one of the receptors in the ephrin system that plays a pivotal role in a variety of cell-cell interactions, mostly studied during development. In addition, EphA4 has been found to play a role in cancer biology as well as in the pathogenesis of several neurological disorders such as stroke, spinal cord injury, multiple sclerosis, amyotrophic lateral sclerosis (ALS), and Alzheimer's disease. Pharmacological blocking of EphA4 has been suggested to be a therapeutic strategy for these disorders. Therefore, the aim of our study was to generate potent and selective Nanobodies against the ligand-binding domain of the human EphA4 receptor. We identified two Nanobodies, Nb 39 and Nb 53, that bind EphA4 with affinities in the nanomolar range. These Nanobodies were most selective for EphA4, with residual binding to EphA7 only. Using Alphascreen technology, we found that both Nanobodies displaced all known EphA4-binding ephrins from the receptor. Furthermore, Nb 39 and Nb 53 inhibited ephrin-induced phosphorylation of the EphA4 protein in a cell-based assay. Finally, in a cortical neuron primary culture, both Nanobodies were able to inhibit endogenous EphA4-mediated growth-cone collapse induced by ephrin-B3. Our results demonstrate the potential of Nanobodies to target the ligand-binding domain of EphA4. These Nanobodies may deserve further evaluation as potential therapeutics in disorders in which EphA4-mediated signaling plays a role.
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Affiliation(s)
- Lies Schoonaert
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Laura Rué
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Bart Roucourt
- KU Leuven-University of Leuven, Laboratory for Signal Integration in Cell Fate Decision, 3000 Leuven, Belgium
| | - Mieke Timmers
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Susan Little
- Vertex Pharmaceuticals (Europe) Ltd., Biology Department, OX14 4RW Abingdon, United Kingdom
| | - Lucía Chávez-Gutiérrez
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
| | - Maarten Dewilde
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
| | - Peter Joyce
- Vertex Pharmaceuticals (Europe) Ltd., Biology Department, OX14 4RW Abingdon, United Kingdom
| | - Adam Curnock
- Vertex Pharmaceuticals (Europe) Ltd., Biology Department, OX14 4RW Abingdon, United Kingdom
| | - Peter Weber
- Vertex Pharmaceuticals (Europe) Ltd., Biology Department, OX14 4RW Abingdon, United Kingdom
| | - Jurgen Haustraete
- Protein Service Facility, Inflammation Research Center, VIB, Ghent University, 9052 Ghent, Belgium
| | | | - Bart De Strooper
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,Institute of Neurology, University College London, WC1E 6BT London, United Kingdom, and
| | - Ludo Van Den Bosch
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Philip Van Damme
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, 3000 Leuven, Belgium
| | - Robin Lemmens
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, 3000 Leuven, Belgium
| | - Wim Robberecht
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium, .,University Hospitals Leuven, Department of Neurology, 3000 Leuven, Belgium
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