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Willems S, Merk D. Medicinal Chemistry and Chemical Biology of Nurr1 Modulators: An Emerging Strategy in Neurodegeneration. J Med Chem 2022; 65:9548-9563. [PMID: 35797147 DOI: 10.1021/acs.jmedchem.2c00585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nuclear receptor related 1 (Nurr1) is a transcription factor with neuroprotective and antineuroinflammatory properties. Observations from genetic studies and human patients support potential of Nurr1 as a therapeutic target in neurodegeneration, but due to a lack of high-quality chemical tools for pharmacological control of Nurr1, its target validation is pending. Nevertheless, considerable progress has recently been made in elucidating structural and functional characteristics of Nurr1, and several ligand scaffolds have been discovered. Here, we analyze Nurr1's structure and mechanisms compared to other nuclear receptors, summarize the known small molecule Nurr1 ligands, and discuss the available evidence for the therapeutic potential of Nurr1 in neurodegeneration.
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Affiliation(s)
- Sabine Willems
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany.,Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany.,Department of Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
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Perrella F, Coppola F, Petrone A, Platella C, Montesarchio D, Stringaro A, Ravagnan G, Fuggetta MP, Rega N, Musumeci D. Interference of Polydatin/Resveratrol in the ACE2:Spike Recognition during COVID-19 Infection. A Focus on Their Potential Mechanism of Action through Computational and Biochemical Assays. Biomolecules 2021; 11:1048. [PMID: 34356672 PMCID: PMC8301781 DOI: 10.3390/biom11071048] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 12/13/2022] Open
Abstract
In the search for new therapeutic strategies to contrast SARS-CoV-2, we here studied the interaction of polydatin (PD) and resveratrol (RESV)-two natural stilbene polyphenols with manifold, well known biological activities-with Spike, the viral protein essential for virus entry into host cells, and ACE2, the angiotensin-converting enzyme present on the surface of multiple cell types (including respiratory epithelial cells) which is the main host receptor for Spike binding. Molecular Docking simulations evidenced that both compounds can bind Spike, ACE2 and the ACE2:Spike complex with good affinity, although the interaction of PD appears stronger than that of RESV on all the investigated targets. Preliminary biochemical assays revealed a significant inhibitory activity of the ACE2:Spike recognition with a dose-response effect only in the case of PD.
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Affiliation(s)
- Fulvio Perrella
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
| | - Federico Coppola
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
| | - Alessio Petrone
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
| | - Annarita Stringaro
- National Center for Drug Research and Evaluation, Italian National Institute of Health, 00161 Rome, Italy;
| | - Giampietro Ravagnan
- Institute of Translational Pharmacology, Consiglio Nazionale delle Ricerche, 00133 Rome, Italy;
| | - Maria Pia Fuggetta
- Institute of Translational Pharmacology, Consiglio Nazionale delle Ricerche, 00133 Rome, Italy;
| | - Nadia Rega
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
- Centro di Ricerca Interdipartimentale sui Biomateriali, University of Naples Federico II, Piazzale Tecchio, 80125 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (F.P.); (F.C.); (A.P.); (C.P.); (D.M.)
- Institute of Biostructures and Bioimages, Consiglio Nazionale delle Ricerche, 80134 Naples, Italy
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Willems S, Zaienne D, Merk D. Targeting Nuclear Receptors in Neurodegeneration and Neuroinflammation. J Med Chem 2021; 64:9592-9638. [PMID: 34251209 DOI: 10.1021/acs.jmedchem.1c00186] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nuclear receptors, also known as ligand-activated transcription factors, regulate gene expression upon ligand signals and present as attractive therapeutic targets especially in chronic diseases. Despite the therapeutic relevance of some nuclear receptors in various pathologies, their potential in neurodegeneration and neuroinflammation is insufficiently established. This perspective gathers preclinical and clinical data for a potential role of individual nuclear receptors as future targets in Alzheimer's disease, Parkinson's disease, and multiple sclerosis, and concomitantly evaluates the level of medicinal chemistry targeting these proteins. Considerable evidence suggests the high promise of ligand-activated transcription factors to counteract neurodegenerative diseases with a particularly high potential of several orphan nuclear receptors. However, potent tools are lacking for orphan receptors, and limited central nervous system exposure or insufficient selectivity also compromises the suitability of well-studied nuclear receptor ligands for functional studies. Medicinal chemistry efforts are needed to develop dedicated high-quality tool compounds for the therapeutic validation of nuclear receptors in neurodegenerative pathologies.
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Affiliation(s)
- Sabine Willems
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Daniel Zaienne
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
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Mechanisms of Action for Small Molecules Revealed by Structural Biology in Drug Discovery. Int J Mol Sci 2020; 21:ijms21155262. [PMID: 32722222 PMCID: PMC7432558 DOI: 10.3390/ijms21155262] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/08/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022] Open
Abstract
Small-molecule drugs are organic compounds affecting molecular pathways by targeting important proteins. These compounds have a low molecular weight, making them penetrate cells easily. Small-molecule drugs can be developed from leads derived from rational drug design or isolated from natural resources. A target-based drug discovery project usually includes target identification, target validation, hit identification, hit to lead and lead optimization. Understanding molecular interactions between small molecules and their targets is critical in drug discovery. Although many biophysical and biochemical methods are able to elucidate molecular interactions of small molecules with their targets, structural biology is the most powerful tool to determine the mechanisms of action for both targets and the developed compounds. Herein, we reviewed the application of structural biology to investigate binding modes of orthosteric and allosteric inhibitors. It is exemplified that structural biology provides a clear view of the binding modes of protease inhibitors and phosphatase inhibitors. We also demonstrate that structural biology provides insights into the function of a target and identifies a druggable site for rational drug design.
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Torshin IY, Namiot VA, Esipova NG, Tumanyan VG. Numeric analysis of reversibility of classic movement equations and constructive criteria of estimating quality of molecular dynamic simulations. J Biomol Struct Dyn 2020; 39:4066-4076. [DOI: 10.1080/07391102.2020.1773927] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ivan Yu. Torshin
- Dorodnicyn Computing Centre, Russian Academy of Sciences, FIC IU RAS, Moscow, Russian Federation
| | - Vladimir A. Namiot
- Institute of Nuclear Physics, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Natalia G. Esipova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladimir G. Tumanyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
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Kadirvel P, Subramanian A, Sridharan N, Subramanian S, Vimaladhasan S, Anishetty S. Molecular dynamics simulation study of Plasmodium falciparum and Escherichia coli SufA: Exploration of conformational changes possibly involved in iron-sulfur cluster transfer. J Biomol Struct Dyn 2020; 39:3300-3311. [PMID: 32364014 DOI: 10.1080/07391102.2020.1764389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Iron-sulfur (Fe-S) clusters are one of the earliest known metal complexes in biological molecules. Suf system is one of the Fe-S biogenesis pathways. SufA belongs to the Suf pathway. It is an A-type carrier protein that transfers Fe-S clusters from the scaffold to target proteins. Structural studies were performed for the Suf pathway protein, SufA, in order to explore the conformational changes that probably aid in the transfer of Fe-S clusters to target proteins. Three-dimensional (3D) structure of Plasmodium falciparum (Pf) SufA homodimer was obtained by homology modeling using 3D structure of Escherichia coli (Ec) SufA as template. Molecular dynamics (MD) simulation of Pf SufA and Ec SufA homodimers followed by trajectory and pocket analyses were carried out. A co-ordinated displacement of the homodimeric chains in the interfacial region, resembling a swinging trapeze-like movement was observed. Potential involvement of this swinging trapeze-like movement of the residues belonging to the interfacial region has been proposed as a probable mechanism that assists in the transfer of Fe-S cluster from SufA to apo proteins. This was substantiated by protein-protein interaction studies in Pf SufA by performing molecular docking of 3D conformations of Pf SufA obtained from MD trajectory at every 1 ns interval with Pf ferredoxin.Communicated by Ramaswamy H. Sarma.
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Nuclear Receptors as Regulators of Pituitary Corticotroph Pro-Opiomelanocortin Transcription. Cells 2020; 9:cells9040900. [PMID: 32272677 PMCID: PMC7226830 DOI: 10.3390/cells9040900] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 12/16/2022] Open
Abstract
The hypothalamic–pituitary–adrenal (HPA) axis plays a critical role in adaptive stress responses and maintaining organism homeostasis. The pituitary corticotroph is the central player in the HPA axis and is regulated by a plethora of hormonal and stress related factors that synergistically interact to activate and temper pro-opiomelanocortin (POMC) transcription, to either increase or decrease adrenocorticotropic hormone (ACTH) production and secretion as needed. Nuclear receptors are a family of highly conserved transcription factors that can also be induced by various physiologic signals, and they mediate their responses via multiple targets to regulate metabolism and homeostasis. In this review, we summarize the modulatory roles of nuclear receptors on pituitary corticotroph cell POMC transcription, describe the unique and complex role these factors play in hypothalamic–pituitary–adrenal axis (HPA) regulation and discuss potential therapeutic targets in disease states.
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Meijer FA, Leijten-van de Gevel IA, de Vries RMJM, Brunsveld L. Allosteric small molecule modulators of nuclear receptors. Mol Cell Endocrinol 2019; 485:20-34. [PMID: 30703487 DOI: 10.1016/j.mce.2019.01.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 02/08/2023]
Abstract
Nuclear Receptors (NRs) are multi-domain proteins, whose natural regulation occurs via ligands for a classical, orthosteric, binding pocket and via intra- and inter-domain allosteric mechanisms. Allosteric modulation of NRs via synthetic small molecules has recently emerged as an interesting entry to address the need for small molecules targeting NRs in pathology, via novel modes of action and with beneficial profiles. In this review the general concept of allosteric modulation in drug discovery is first discussed, serving as a background and inspiration for NRs. Subsequently, the review focuses on examples of small molecules that allosterically modulate NRs, with a strong focus on structural information and the ligand binding domain. Recently discovered nanomolar potent allosteric site NR modulators are catapulting allosteric targeting of NRs to the center of attention. The obtained insights serve as a basis for recommendations for the next steps to take in allosteric small molecular targeting of NRs.
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Affiliation(s)
- Femke A Meijer
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Iris A Leijten-van de Gevel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Rens M J M de Vries
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands.
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