1
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Symes OL, Ishikura H, Begg CS, Rojas JJ, Speller HA, Cherk AM, Fang M, Leung D, Croft RA, Higham JI, Huang K, Barnard A, Haycock P, White AJP, Choi C, Bull JA. Harnessing Oxetane and Azetidine Sulfonyl Fluorides for Opportunities in Drug Discovery. J Am Chem Soc 2024. [PMID: 39666854 DOI: 10.1021/jacs.4c14164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2024]
Abstract
Four-membered heterocycles such as oxetanes and azetidines represent attractive and emergent design options in medicinal chemistry due to their small and polar nature and potential to significantly impact the physiochemical properties of drug molecules. The challenging preparation of these derivatives, especially in a divergent manner, has severely limited their combination with other medicinally and biologically important groups. Consequently, there is a substantial demand for mild and effective synthetic strategies to access new oxetane and azetidine derivatives and molecular scaffolds. Here, we report the development and use of oxetane sulfonyl fluorides (OSFs) and azetidine sulfonyl fluorides (ASFs), which behave as precursors to carbocations in an unusual defluorosulfonylation reaction pathway (deFS). The small-ring sulfonyl fluorides are activated under mild thermal conditions (60 °C), and the generated reactive intermediates couple with a broad range of nucleophiles. Oxetane and azetidine heterocyclic, -sulfoximine, and -phosphonate derivatives are prepared, several of which do not have comparable carbonyl analogs, providing new chemical motifs and design elements for drug discovery. Alternatively, a SuFEx pathway under anionic conditions accesses oxetane-sulfur(VI) derivatives. We demonstrate the synthetic utility of novel OSF and ASF reagents through the synthesis of 11 drug analogs, showcasing their potential for subsequent diversification and facile inclusion into medicinal chemistry programs. Moreover, we propose the application of the OSF and ASF reagents as linker motifs and demonstrate the incorporation of pendant groups suitable for common conjugation reactions. Productive deFS reactions with E3 ligase recruiters such as pomalidomide and related derivatives provide new degrader motifs and potential PROTAC linkers.
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Affiliation(s)
- Oliver L Symes
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Hikaru Ishikura
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Callum S Begg
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Juan J Rojas
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Harry A Speller
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Anson M Cherk
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Marco Fang
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Domingo Leung
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Rosemary A Croft
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Joe I Higham
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Kaiyun Huang
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Anna Barnard
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Peter Haycock
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Andrew J P White
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
| | - Chulho Choi
- Medicine Design, Pfizer Research and Development, Groton, Connecticut 06340, United States
| | - James A Bull
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K
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2
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Nada H, Choi Y, Kim S, Jeong KS, Meanwell NA, Lee K. New insights into protein-protein interaction modulators in drug discovery and therapeutic advance. Signal Transduct Target Ther 2024; 9:341. [PMID: 39638817 PMCID: PMC11621763 DOI: 10.1038/s41392-024-02036-3] [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: 04/11/2024] [Revised: 09/09/2024] [Accepted: 10/23/2024] [Indexed: 12/07/2024] Open
Abstract
Protein-protein interactions (PPIs) are fundamental to cellular signaling and transduction which marks them as attractive therapeutic drug development targets. What were once considered to be undruggable targets have become increasingly feasible due to the progress that has been made over the last two decades and the rapid technological advances. This work explores the influence of technological innovations on PPI research and development. Additionally, the diverse strategies for discovering, modulating, and characterizing PPIs and their corresponding modulators are examined with the aim of presenting a streamlined pipeline for advancing PPI-targeted therapeutics. By showcasing carefully selected case studies in PPI modulator discovery and development, we aim to illustrate the efficacy of various strategies for identifying, optimizing, and overcoming challenges associated with PPI modulator design. The valuable lessons and insights gained from the identification, optimization, and approval of PPI modulators are discussed with the aim of demonstrating that PPI modulators have transitioned beyond early-stage drug discovery and now represent a prime opportunity with significant potential. The selected examples of PPI modulators encompass those developed for cancer, inflammation and immunomodulation, as well as antiviral applications. This perspective aims to establish a foundation for the effective targeting and modulation of PPIs using PPI modulators and pave the way for future drug development.
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Affiliation(s)
- Hossam Nada
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Republic of Korea
- Department of Radiology, Molecular Imaging Innovations Institute (MI3), Weill Cornell Medicine, New York, USA
| | - Yongseok Choi
- College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Sungdo Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Kwon Su Jeong
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Republic of Korea
| | - Nicholas A Meanwell
- Baruch S. Blumberg Institute, Doylestown, PA, USA
- School of Pharmacy, University of Michigan, Ann Arbor, MI, USA
- Ernest Mario School of Pharmacy, Rutgers University New Brunswick, New Brunswick, NJ, USA
| | - Kyeong Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Republic of Korea.
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3
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Swenson CS, Mandava G, Thomas DM, Moellering RE. Tackling Undruggable Targets with Designer Peptidomimetics and Synthetic Biologics. Chem Rev 2024; 124:13020-13093. [PMID: 39540650 DOI: 10.1021/acs.chemrev.4c00423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
Abstract
The development of potent, specific, and pharmacologically viable chemical probes and therapeutics is a central focus of chemical biology and therapeutic development. However, a significant portion of predicted disease-causal proteins have proven resistant to targeting by traditional small molecule and biologic modalities. Many of these so-called "undruggable" targets feature extended, dynamic protein-protein and protein-nucleic acid interfaces that are central to their roles in normal and diseased signaling pathways. Here, we discuss the development of synthetically stabilized peptide and protein mimetics as an ever-expanding and powerful region of chemical space to tackle undruggable targets. These molecules aim to combine the synthetic tunability and pharmacologic properties typically associated with small molecules with the binding footprints, affinities and specificities of biologics. In this review, we discuss the historical and emerging platforms and approaches to design, screen, select and optimize synthetic "designer" peptidomimetics and synthetic biologics. We examine the inspiration and design of different classes of designer peptidomimetics: (i) macrocyclic peptides, (ii) side chain stabilized peptides, (iii) non-natural peptidomimetics, and (iv) synthetic proteomimetics, and notable examples of their application to challenging biomolecules. Finally, we summarize key learnings and remaining challenges for these molecules to become useful chemical probes and therapeutics for historically undruggable targets.
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Affiliation(s)
- Colin S Swenson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Gunasheil Mandava
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Deborah M Thomas
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Raymond E Moellering
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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4
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Di Lorenzo D. Tau Protein and Tauopathies: Exploring Tau Protein-Protein and Microtubule Interactions, Cross-Interactions and Therapeutic Strategies. ChemMedChem 2024; 19:e202400180. [PMID: 39031682 DOI: 10.1002/cmdc.202400180] [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: 03/07/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/22/2024]
Abstract
Tau, a microtubule-associated protein (MAP), is essential to maintaining neuronal stability and function in the healthy brain. However, aberrant modifications and pathological aggregations of Tau are implicated in various neurodegenerative disorders, collectively known as tauopathies. The most common Tauopathy is Alzheimer's Disease (AD) counting nowadays more than 60 million patients worldwide. This comprehensive review delves into the multifaceted realm of Tau protein, puzzling out its intricate involvement in both physiological and pathological roles. Emphasis is put on Tau Protein-Protein Interactions (PPIs), depicting its interaction with tubulin, microtubules and its cross-interaction with other proteins such as Aβ1-42, α-synuclein, and the chaperone machinery. In the realm of therapeutic strategies, an overview of diverse possibilities is presented with their relative clinical progresses. The focus is mostly addressed to Tau protein aggregation inhibitors including recent small molecules, short peptides and peptidomimetics with specific focus on compounds that showed a double anti aggregative activity on both Tau protein and Aβ amyloid peptide. This review amalgamates current knowledge on Tau protein and evolving therapeutic strategies, providing a comprehensive resource for researchers seeking to deepen their understanding of the Tau protein and for scientists involved in the development of new peptide-based anti-aggregative Tau compounds.
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Affiliation(s)
- Davide Di Lorenzo
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, Universitätsstraße 25, D-33615, Bielefeld, Germany
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5
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Liu Q, Yu Y, Wei G. Oncogenic R248W mutation induced conformational perturbation of the p53 core domain and the structural protection by proteomimetic amyloid inhibitor ADH-6. Phys Chem Chem Phys 2024; 26:20068-20086. [PMID: 39007865 DOI: 10.1039/d4cp02046d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The involvement of p53 aggregation in cancer pathogenesis emphasizes the importance of unraveling the mechanisms underlying mutation-induced p53 destabilization. And understanding how small molecule inhibitors prevent the conversion of p53 into aggregation-primed conformations is pivotal for the development of therapeutics targeting p53-aggregation-associated cancers. A recent experimental study highlights the efficacy of the proteomimetic amyloid inhibitor ADH-6 in stabilizing R248W p53 and inhibiting its aggregation in cancer cells by interacting with the p53 core domain (p53C). However, it remains mostly unclear how R248W mutation induces destabilization of p53C and how ADH-6 stabilizes this p53C mutant and inhibits its aggregation. Herein, we conducted all-atom molecular dynamics simulations of R248W p53C in the absence and presence of ADH-6, as well as that of wild-type (WT) p53C. Our simulations reveal that the R248W mutation results in a shift of helix H2 and β-hairpin S2-S2' towards the mutation site, leading to the destruction of their neighboring β-sheet structure. This further facilitates the formation of a cavity in the hydrophobic core, and reduces the stability of the β-sandwich. Importantly, two crucial aggregation-prone regions (APRs) S9 and S10 are disturbed and more exposed to solvent in R248W p53C, which is conducive to p53C aggregation. Intriguingly, ADH-6 dynamically binds to the mutation site and multiple destabilized regions in R248W p53C, partially inhibiting the shift of helix H2 and β-hairpin S2-S2', thus preventing the disruption of the β-sheets and the formation of the cavity. ADH-6 also reduces the solvent exposure of APRs S9 and S10, which disfavors the aggregation of R248W p53C. Moreover, ADH-6 can preserve the WT-like dynamical network of R248W p53C. Our study elucidates the mechanisms underlying the oncogenic R248W mutation induced p53C destabilization and the structural protection of p53C by ADH-6.
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Affiliation(s)
- Qian Liu
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China.
| | - Yawei Yu
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China.
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China.
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6
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Qian H, Ding CH, Liu F, Chen SJ, Huang CK, Xiao MC, Hong XL, Wang MC, Yan FZ, Ding K, Cui YL, Zheng BN, Ding J, Luo C, Zhang X, Xie WF. SRY-Box transcription factor 9 triggers YAP nuclear entry via direct interaction in tumors. Signal Transduct Target Ther 2024; 9:96. [PMID: 38653754 PMCID: PMC11039692 DOI: 10.1038/s41392-024-01805-4] [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: 08/21/2023] [Revised: 01/27/2024] [Accepted: 03/13/2024] [Indexed: 04/25/2024] Open
Abstract
The translocation of YAP from the cytoplasm to the nucleus is critical for its activation and plays a key role in tumor progression. However, the precise molecular mechanisms governing the nuclear import of YAP are not fully understood. In this study, we have uncovered a crucial role of SOX9 in the activation of YAP. SOX9 promotes the nuclear translocation of YAP by direct interaction. Importantly, we have identified that the binding between Asp-125 of SOX9 and Arg-124 of YAP is essential for SOX9-YAP interaction and subsequent nuclear entry of YAP. Additionally, we have discovered a novel asymmetrical dimethylation of YAP at Arg-124 (YAP-R124me2a) catalyzed by PRMT1. YAP-R124me2a enhances the interaction between YAP and SOX9 and is associated with poor prognosis in multiple cancers. Furthermore, we disrupted the interaction between SOX9 and YAP using a competitive peptide, S-A1, which mimics an α-helix of SOX9 containing Asp-125. S-A1 significantly inhibits YAP nuclear translocation and effectively suppresses tumor growth. This study provides the first evidence of SOX9 as a pivotal regulator driving YAP nuclear translocation and presents a potential therapeutic strategy for YAP-driven human cancers by targeting SOX9-YAP interaction.
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Affiliation(s)
- Hui Qian
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Chen-Hong Ding
- Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fang Liu
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Shi-Jie Chen
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Chen-Kai Huang
- Department of Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Meng-Chao Xiao
- Department of Gastroenterology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xia-Lu Hong
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Ming-Chen Wang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Fang-Zhi Yan
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Kai Ding
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Ya-Lu Cui
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Bai-Nan Zheng
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jin Ding
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai, China
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
| | - Xin Zhang
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China.
| | - Wei-Fen Xie
- Department of Gastroenterology, Changzheng Hospital, Naval Medical University, Shanghai, China.
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7
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Marciniak M, Mróz P, Napolitano V, Kalel VC, Fino R, Pykacz E, Schliebs W, Plettenburg O, Erdmann R, Sattler M, Popowicz GM, Dawidowski M. Development of novel PEX5-PEX14 protein-protein interaction (PPI) inhibitors based on an oxopiperazine template. Eur J Med Chem 2023; 258:115587. [PMID: 37406382 DOI: 10.1016/j.ejmech.2023.115587] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/10/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
Protein-protein interactions (PPIs) constitute an important but challenging class of molecular targets for small molecules. The PEX5-PEX14 PPI has been shown to play a critical role in glycosome biogenesis and its disruption impairs the metabolism in Trpanosoma parasites, eventually leading to their death. Therefore, this PPI is a potential molecular target for new drugs against diseases caused by Trypanosoma infections. Here, we report a new class of peptidomimetic scaffolds to target the PEX5-PEX14 PPI. The molecular design was based on an oxopiperazine template for the α-helical mimetics. A structural simplification along with modifications of the central oxopiperazine scaffold and addressing the lipophilic interactions led to the development of peptidomimetics that inhibit PEX5-TbPEX14 PPI and display cellular activity against T. b. brucei. This approach provides an alternative approach towards the development of trypanocidal agents and may be generally useful for the design of helical mimetics as PPI inhibitors.
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Affiliation(s)
- Monika Marciniak
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Piotr Mróz
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Valeria Napolitano
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Vishal C Kalel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Roberto Fino
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany
| | - Emilia Pykacz
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Oliver Plettenburg
- Institute of Medicinal Chemistry, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764, Germany; Center of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz Universität Hannover, Schneiderberg 1b, Hannover, 30167, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biochemistry, Faculty of Medicine, Ruhr-University Bochum, 44780, Bochum, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Grzegorz M Popowicz
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764, Neuherberg, Germany; Bavarian NMR Center, Department of Bioscience, School of Natural Sciences, Technical University of Munich, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Maciej Dawidowski
- Department of Drug Technology and Pharmaceutical Biotechnology Medical University of Warsaw, Banacha 1, 02-097, Warszawa, Poland.
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Sola M, Rendon-Angel A, Rojo Martinez V, Sgrignani J, Magrin C, Piovesana E, Cavalli A, Paganetti P, Papin S. Tau protein binds to the P53 E3 ubiquitin ligase MDM2. Sci Rep 2023; 13:10208. [PMID: 37353565 PMCID: PMC10290082 DOI: 10.1038/s41598-023-37046-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/14/2023] [Indexed: 06/25/2023] Open
Abstract
Tau gene mutations cause a progressive dementia and neurotoxic Tau forms deposited in neurofibrillary tangles are hallmarks of neurodegenerative tauopathies. Loss of non-canonical Tau functions may contribute to disease. In fact, Tau depletion affects the cellular response to DNA damage and tauopathies exhibit the accumulation of DNA lesions. Moreover, Tau modulates P53 activity and cell fate. Considering that MDM2 is the main antagonist of P53, we investigated, using orthogonal assays, if Tau interacts with MDM2. We report the existence in cells and brain of a Tau-MDM2 complex that, in vitro, exhibits reduced P53 ubiquitination activity in a manner sensitive to a Tau mutation. The Tau-MDM2 interaction involves the microtubule-binding domain of Tau and the acidic domain of MDM2, reminiscent of the binding of Tau to negatively charged microtubules. Notably, MDM2 accumulates aberrantly in neurofibrillary tangles. Aging-associated insults may expose a novel loss-of-function of Tau in neurodegeneration and cancer.
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Affiliation(s)
- Martina Sola
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
- PhD Program in Neurosciences, Faculty of Biomedical Sciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Azucena Rendon-Angel
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
| | - Viviana Rojo Martinez
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Computational Structural Biology, Institute for Research in Biomedicine, Università Della Svizzera Italiana, Bellinzona, Switzerland
| | - Claudia Magrin
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
- PhD Program in Neurosciences, Faculty of Biomedical Sciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Ester Piovesana
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
- PhD Program in Neurosciences, Faculty of Biomedical Sciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Andrea Cavalli
- Computational Structural Biology, Institute for Research in Biomedicine, Università Della Svizzera Italiana, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paolo Paganetti
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland.
- PhD Program in Neurosciences, Faculty of Biomedical Sciences, Università Della Svizzera Italiana, Lugano, Switzerland.
- Neurocentro Della Svizzera Italiana, Ente Ospedaliero Cantonale, Lugano, Switzerland.
| | - Stéphanie Papin
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
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9
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Dewis LI, Rudrakshula M, Williams C, Chiarparin E, Myers EL, Butts CP, Aggarwal VK. Conformationally Controlled sp 3 -Hydrocarbon-Based α-Helix Mimetics. Angew Chem Int Ed Engl 2023; 62:e202301209. [PMID: 37017133 PMCID: PMC10953326 DOI: 10.1002/anie.202301209] [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: 01/30/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/06/2023]
Abstract
With over 60 % of protein-protein interfaces featuring an α-helix, the use of α-helix mimetics as inhibitors of these interactions is a prevalent therapeutic strategy. However, methods to control the conformation of mimetics, thus enabling maximum efficacy, can be restrictive. Alternatively, conformation can be controlled through the introduction of destabilizing syn-pentane interactions. This tactic, which is often adopted by Nature, is not a common feature of lead optimization owing to the significant synthetic effort required. Through assembly-line synthesis with NMR and computational analysis, we have shown that alternating syn-anti configured contiguously substituted hydrocarbons, by avoiding syn-pentane interactions, adopt well-defined conformations that present functional groups in an arrangement that mimics the α-helix. The design of a p53 mimetic that binds to Mdm2 with moderate to good affinity, demonstrates the therapeutic promise of these scaffolds.
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Affiliation(s)
- Lydia I. Dewis
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
| | | | | | | | - Eddie L. Myers
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
- School of Biological and Chemical SciencesUniversity of GalwayUniversity RoadGalwayIreland
| | - Craig P. Butts
- School of ChemistryUniversity of BristolCantock's CloseBristolBS8 1TSUK
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10
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Persico M, Galatello P, Ferraro MG, Irace C, Piccolo M, Abduvakhidov A, Tkachuk O, d'Aulisio Garigliota ML, Campiglia P, Iannece P, Varra M, Ramunno A, Fattorusso C. Tetrasubstituted Pyrrole Derivative Mimetics of Protein-Protein Interaction Hot-Spot Residues: A Promising Class of Anticancer Agents Targeting Melanoma Cells. Molecules 2023; 28:molecules28104161. [PMID: 37241902 DOI: 10.3390/molecules28104161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
A new series of tetrasubstituted pyrrole derivatives (TSPs) was synthesized based on a previously developed hypothesis on their ability to mimic hydrophobic protein motifs. The resulting new TSPs were endowed with a significant toxicity against human epithelial melanoma A375 cells, showing IC50 values ranging from 10 to 27 μM, consistent with the IC50 value of the reference compound nutlin-3a (IC50 = 15 μM). In particular, compound 10a (IC50 = 10 μM) resulted as both the most soluble and active among the previous and present TSPs. The biological investigation evidenced that the anticancer activity is related to the activation of apoptotic cell-death pathways, supporting our rational design based on the ability of TSPs to interfere with PPI involved in the cell cycle regulation of cancer cells and, in particular, the p53 pathway. A reinvestigation of the TSP pharmacophore by using DFT calculations showed that the three aromatic substituents on the pyrrole core are able to mimic the hydrophobic side chains of the hot-spot residues of parallel and antiparallel coiled coil structures suggesting a possible molecular mechanism of action. A structure-activity relationship (SAR) analysis which includes solubility studies allows us to rationalize the role of the different substituents on the pyrrole core.
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Affiliation(s)
- Marco Persico
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Paola Galatello
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84100 Fisciano, SA, Italy
| | - Maria Grazia Ferraro
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Carlo Irace
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Marialuisa Piccolo
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Avazbek Abduvakhidov
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Oleh Tkachuk
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Napoli, NA, Italy
| | | | - Pietro Campiglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84100 Fisciano, SA, Italy
| | - Patrizia Iannece
- Department of Chemistry and Biology, University of Salerno, Via G. Paolo II 132, 84100 Fisciano, SA, Italy
| | - Michela Varra
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Napoli, NA, Italy
| | - Anna Ramunno
- Department of Pharmacy, University of Salerno, Via G. Paolo II 132, 84100 Fisciano, SA, Italy
| | - Caterina Fattorusso
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131 Napoli, NA, Italy
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11
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Haque M, Flack T, Singh R, Wall A, de Castro GV, Jiang L, White AJP, Barnard A. Aromatic oligoesters as novel helix mimetic scaffolds. Bioorg Med Chem 2023; 87:117311. [PMID: 37182518 DOI: 10.1016/j.bmc.2023.117311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/16/2023]
Abstract
The design, synthesis, and conformational analysis of a novel aromatic oligoester helix mimetic scaffold is reported. A range of amino acid-type side-chain functionality can be readily incorporated into monomer building blocks over three facile synthetic steps. Analysis of representative dimers revealed a stable conformer capable of effective mimicry of a canonical α-helix and the scaffold was found to be surprisingly stable to degradation in aqueous solutions at acidic and neutral pH.
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Affiliation(s)
- Muhammed Haque
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Theo Flack
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Ravi Singh
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Archie Wall
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | | | - Lishen Jiang
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Andrew J P White
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Anna Barnard
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK.
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12
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A novel mRNA decay inhibitor abolishes pathophysiological cellular transition. Cell Death Dis 2022; 8:278. [PMID: 35672286 PMCID: PMC9174231 DOI: 10.1038/s41420-022-01076-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022]
Abstract
In cells, mRNA synthesis and decay are influenced by each other, and their balance is altered by either external or internal cues, resulting in changes in cell dynamics. We previously reported that it is important that an array of mRNAs that shape a phenotype are degraded before cellular transitions, such as cellular reprogramming and differentiation. In adipogenesis, the interaction between DDX6 and 4E-T had a definitive impact on the pathway in the processing body (PB). We screened a library of α-helix analogs with an alkaloid-like backbone to identify compounds that inhibit the binding between DDX6 and 4E-T proteins, which occurs between the α-helix of structured and internally disordered proteins. IAMC-00192 was identified as a lead compound. This compound directly inhibited the interaction between DDX6 and 4E-T. IAMC-00192 inhibited the temporal increase in PB formation that occurs during adipogenesis and epithelial-mesenchymal transition (EMT) and significantly suppressed these cellular transitions. In the EMT model, the half-life of preexisting mRNAs in PBs was extended twofold by the compound. The novel inhibitor of RNA decay not only represents a potentially useful tool to analyze in detail the pathological conditions affected by RNA decay and how it regulates the pathological state. The identification of this inhibitor may lead to the discovery of a first-in-class RNA decay inhibitor drug. ![]()
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13
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Minisini M, Di Giorgio E, Kerschbamer E, Dalla E, Faggiani M, Franforte E, Meyer-Almes FJ, Ragno R, Antonini L, Mai A, Fiorentino F, Rotili D, Chinellato M, Perin S, Cendron L, Weichenberger CX, Angelini A, Brancolini C. Transcriptomic and genomic studies classify NKL54 as a histone deacetylase inhibitor with indirect influence on MEF2-dependent transcription. Nucleic Acids Res 2022; 50:2566-2586. [PMID: 35150567 PMCID: PMC8934631 DOI: 10.1093/nar/gkac081] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 01/25/2022] [Indexed: 12/23/2022] Open
Abstract
In leiomyosarcoma class IIa HDACs (histone deacetylases) bind MEF2 and convert these transcription factors into repressors to sustain proliferation. Disruption of this complex with small molecules should antagonize cancer growth. NKL54, a PAOA (pimeloylanilide o-aminoanilide) derivative, binds a hydrophobic groove of MEF2, which is used as a docking site by class IIa HDACs. However, NKL54 could also act as HDAC inhibitor (HDACI). Therefore, it is unclear which activity is predominant. Here, we show that NKL54 and similar derivatives are unable to release MEF2 from binding to class IIa HDACs. Comparative transcriptomic analysis classifies these molecules as HDACIs strongly related to SAHA/vorinostat. Low expressed genes are upregulated by HDACIs, while abundant genes are repressed. This transcriptional resetting correlates with a reorganization of H3K27 acetylation around the transcription start site (TSS). Among the upregulated genes there are several BH3-only family members, thus explaining the induction of apoptosis. Moreover, NKL54 triggers the upregulation of MEF2 and the downregulation of class IIa HDACs. NKL54 also increases the binding of MEF2D to promoters of genes that are upregulated after treatment. In summary, although NKL54 cannot outcompete MEF2 from binding to class IIa HDACs, it supports MEF2-dependent transcription through several actions, including potentiation of chromatin binding.
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Affiliation(s)
- Martina Minisini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Eros Di Giorgio
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Emanuela Kerschbamer
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck. Via Galvani 31, 39100 Bolzano, Italy
| | - Emiliano Dalla
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Massimo Faggiani
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Elisa Franforte
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
| | - Franz-Josef Meyer-Almes
- Department of Chemical Engineering and Biotechnology, University of Applied Science, Haardtring 100, 64295 Darmstadt, Germany
| | - Rino Ragno
- Rome Center for Molecular Design, Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Lorenzo Antonini
- Rome Center for Molecular Design, Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Antonello Mai
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Francesco Fiorentino
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Dante Rotili
- Department of Chemistry and Technology of Drugs, "Sapienza" University of Rome, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Monica Chinellato
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121 Padova, Italy
| | - Stefano Perin
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy.,European Centre for Living Technology (ECLT), Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Laura Cendron
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121 Padova, Italy
| | - Christian X Weichenberger
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck. Via Galvani 31, 39100 Bolzano, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Mestre, Italy.,European Centre for Living Technology (ECLT), Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Claudio Brancolini
- Department of Medicine, Università degli Studi di Udine. P.le Kolbe 4, 33100 Udine Italy
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14
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Mihara K, Nakajima N, Fujii I, Fujiwara D. Generation of inhibitory peptides for
IKKε
from a kinase‐focused phage library of helix‐loop‐helix peptides. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kousuke Mihara
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Natsumi Nakajima
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
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15
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Santi S, Bisello A, Cardena R, Tomelleri S, Schiesari R, Biondi B, Crisma M, Formaggio F. Flat, C α,β -Didehydroalanine Foldamers with Ferrocene Pendants: Assessing the Role of α-Peptide Dipolar Moments. Chempluschem 2021; 86:723-730. [PMID: 33825347 DOI: 10.1002/cplu.202100072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/22/2021] [Indexed: 12/28/2022]
Abstract
The foldamer field is continuously expanding as it allows to produce molecules endowed with 3D-structures and functions never observed in nature. We synthesized flat foldamers based on the natural, but non-coded, Cα,β -didehydroalanine α-amino acid, and covalently linked to them two ferrocene (Fc) moieties, as redox probes. These conjugates retain the flat and extended conformation of the 2.05 -helix, both in solution and in the crystal state (X-ray diffraction). Cyclic voltammetry measurements agree with the adoption of the 2.05 -helix, characterized by a negligible dipole moment. Thus, elongated α-peptide stretches of this type are insulators rather than charge conductors, the latter being constituted by peptide α-helices. Also, our homo-tetrapeptide has a N-to-C length of about 18.2 Å, almost double than that (9.7 Å) of an α-helical α-tetrapeptide.
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Affiliation(s)
- Saverio Santi
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Annalisa Bisello
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Roberta Cardena
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Silvia Tomelleri
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Renato Schiesari
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, via Marzolo 1, 35131, Padova, Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, via Marzolo 1, 35131, Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR, via Marzolo 1, 35131, Padova, Italy
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