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      Exploration of ligand binding modes towards the identification of compounds targeting HuR: a combined STD-NMR and Molecular Modelling approach

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          Abstract

          Post-transcriptional processes have been recognised as pivotal in the control of gene expression, and impairments in RNA processing are reported in several pathologies (i.e., cancer and neurodegeneration). Focusing on RNA-binding proteins (RBPs), the involvement of Embryonic Lethal Abnormal Vision (ELAV) or Hu proteins and their complexes with target mRNAs in the aetiology of various dysfunctions, has suggested the great potential of compounds able to interfere with the complex stability as an innovative pharmacological strategy for the treatment of numerous diseases. Here, we present a rational follow-up investigation of the interaction between ELAV isoform HuR and structurally-related compounds ( i.e., flavonoids and coumarins), naturally decorated with different functional groups, by means of STD-NMR and Molecular Modelling. Our results represent the foundation for the development of potent and selective ligands able to interfere with ELAV–RNA complexes.

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          Diverse molecular functions of Hu proteins.

          H Lou, Lois Hinman (2008)
          Hu proteins are RNA-binding proteins involved in diverse biological processes. The neuronal members of the Hu family, HuB, HuC, and HuD play important roles in neuronal differentiation and plasticity, while the ubiquitously expressed family member, HuR, has numerous functions mostly related to cellular stress response. The pivotal roles of Hu proteins are dictated by their molecular functions affecting a large number of target genes. Hu proteins affect many post-transcriptional aspects of RNA metabolism, from splicing to translation. In this communication, we will focus on these molecular events and review our current understanding of how Hu proteins mediate them. In particular, emphasis will be put on the nuclear functions of these proteins, which were recently discovered. Three examples including calcitonin/calcitonin gene-related peptide, neurofibromatosis type 1, and Ikaros will be discussed in detail. In addition, an intriguing theme of antagonism between Hu proteins and other AU-rich sequence binding proteins will be discussed.
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            Protein-RNA interactions: new genomic technologies and perspectives.

            Julian König, Kathi Zarnack, Nicholas Luscombe … (2012)
            RNA-binding proteins are key players in the regulation of gene expression. In this Progress article, we discuss state-of-the-art technologies that can be used to study individual RNA-binding proteins or large complexes such as the ribosome. We also describe how these approaches can be used to study interactions with different types of RNAs, including nascent transcripts, mRNAs, microRNAs and ribosomal RNAs, in order to investigate transcription, RNA processing and translation. Finally, we highlight current challenges in data analysis and the future steps that are needed to obtain a quantitative and high-resolution picture of protein-RNA interactions on a genome-wide scale.
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              NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors.

              Bernd Meyer, Thomas Peters (2003)
              Binding events of ligands to receptors are the key for an understanding of biological processes. Gaining insight into protein-protein and protein-ligand interactions in solution has recently become possible on an atomic level by new NMR spectroscopic techniques. These experiments identify binding events either by looking at the resonance signals of the ligand or the protein. Ideally, both techniques together deliver a complete picture of ligand binding to a receptor. The approaches discussed in this review allow screening of compound libraries as well as a detailed identification of the groups involved in the binding events. Also, characterization of the binding strength and kinetics is possible, competitive binding as well as allosteric effects can be identified, and it has even been possible to identify ligand binding to intact viruses and membrane-bound proteins.
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                Author and article information

                Contributors
                Simona Collina:
                ORCID: http://orcid.org/0000-0002-2954-7558
                simona.collina@unipv.it
                Journal
                Journal ID (nlm-ta): Sci Rep
                Journal ID (iso-abbrev): Sci Rep
                Title: Scientific Reports
                Publisher: Nature Publishing Group UK (London )
                ISSN (Electronic): 2045-2322
                Publication date (Electronic): 13 September 2018
                Publication date PMC-release: 13 September 2018
                Publication date Collection: 2018
                Volume: 8
                Electronic Location Identifier: 13780
                Affiliations
                [1 ]ISNI 0000 0004 1757 2822, GRID grid.4708.b, Department of Chemistry, , University of Milan, ; Via Golgi 19, 20133 Milano, Italy
                [2 ]ISNI 0000 0004 1762 5736, GRID grid.8982.b, Department of Drug Sciences, , Medicinal Chemistry and Technology Section, University of Pavia, ; Via Taramelli 12, 27100 Pavia, Italy
                [3 ]ISNI 0000 0001 2168 2547, GRID grid.411489.1, Department of Health Sciences, , University “Magna Græcia” of Catanzaro, ; Viale Europa, 88100 Catanzaro, Italy
                [4 ]GRID grid.461899.b, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), Department of Drug Design and Optimization, ; Campus building E8.1, 66123 Saarbrücken, Germany
                [5 ]ISNI 0000 0004 1937 0351, GRID grid.11696.39, Centre for Integrative Biology, , CIBIO, University of Trento, ; Via Sommarive 9, 38123 Povo, TN Italy
                [6 ]ISNI 0000 0004 1762 5736, GRID grid.8982.b, Department of Earth and Environmental Sciences, , University of Pavia, ; via S. Epifanio 14, 27100 Pavia, Italy
                [7 ]ISNI 0000 0001 2167 7588, GRID grid.11749.3a, Department of Pharmacy, Medicinal Chemistry, , Saarland University, ; Campus building E8.1, 66123 Saarbrücken, Germany
                Author information
                http://orcid.org/0000-0002-3926-8261
                http://orcid.org/0000-0003-0947-9479
                http://orcid.org/0000-0002-0437-358X
                http://orcid.org/0000-0002-2954-7558
                Article
                Publisher ID: 32084
                DOI: 10.1038/s41598-018-32084-z
                PMC ID: 6137155
                PubMed ID: 30214075
                SO-VID: 1cc3ebee-e1fb-4e24-b5f3-3407f9bf80b3
                Copyright © © The Author(s) 2018
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 9 April 2018
                Date accepted : 29 August 2018
                Funding
                Funded by: Associazione Italiana per la Ricerca sul Cancro (AIRC) [17153 to A.P.] CARITRO Riposizionamento Farmaci [40102838 to A.P.]
                Categories
                Subject: Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2018

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