1
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Somsen BA, Cossar PJ, Arkin MR, Brunsveld L, Ottmann C. 14-3-3 Protein-Protein Interactions: From Mechanistic Understanding to Their Small-Molecule Stabilization. Chembiochem 2024; 25:e202400214. [PMID: 38738787 DOI: 10.1002/cbic.202400214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/14/2024]
Abstract
Protein-protein interactions (PPIs) are of utmost importance for maintenance of cellular homeostasis. Herein, a central role can be found for 14-3-3 proteins. These hub-proteins are known to bind hundreds of interaction partners, thereby regulating their activity, localization, and/or stabilization. Due to their ability to bind a large variety of client proteins, studies of 14-3-3 protein complexes flourished over the last decades, aiming to gain greater molecular understanding of these complexes and their role in health and disease. Because of their crucial role within the cell, 14-3-3 protein complexes are recognized as highly interesting therapeutic targets, encouraging the discovery of small molecule modulators of these PPIs. We discuss various examples of 14-3-3-mediated regulation of its binding partners on a mechanistic level, highlighting the versatile and multi-functional role of 14-3-3 within the cell. Furthermore, an overview is given on the development of stabilizers of 14-3-3 protein complexes, from initially used natural products to fragment-based approaches. These studies show the potential of 14-3-3 PPI stabilizers as novel agents in drug discovery and as tool compounds to gain greater molecular understanding of the role of 14-3-3-based protein regulation.
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Affiliation(s)
- Bente A Somsen
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
| | - Peter J Cossar
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California, 94143, United States
| | - Luc Brunsveld
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
| | - Christian Ottmann
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, P.O. Box 513, MB Eindhoven, 5600, Eindhoven, The Netherlands
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2
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Kamayirese S, Maity S, Dieckman LM, Hansen LA, Lovas S. Optimizing Phosphopeptide Structures That Target 14-3-3ε in Cutaneous Squamous Cell Carcinoma. ACS OMEGA 2024; 9:2719-2729. [PMID: 38250398 PMCID: PMC10795040 DOI: 10.1021/acsomega.3c07740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024]
Abstract
14-3-3ε is involved in various types of malignancies by increasing cell proliferation, promoting cell invasion, or inhibiting apoptosis. In cutaneous squamous cell carcinoma (cSCC), 14-3-3ε is overexpressed and mislocalized from the nucleus to the cytoplasm where it interacts with the cell division cycle 25 A (CDC25A) and suppresses apoptosis. Hence, inhibition of the 14-3-3ε-CDC25A interaction is an attractive target for promoting apoptosis in cSCC. In this work, we optimized the structure of our previously designed inhibitor of the 14-3-3ε-CDC25A interaction, pT, a phosphopeptide fragment corresponding to one of the two binding regions of CDC25A to 14-3-3ε. Starting from pT, we developed peptide analogs that bind 14-3-3ε with nanomolar affinities. Peptide analogs were designed by shortening the pT peptide and introducing modifications at position 510 of the pT(502-510) analog. Both molecular dynamics (MD) simulations and biophysical methods were used to determine peptide binding to 14-3-3ε. Shortening the pT peptide from 14 to 9 amino acid residues resulted in a peptide (pT(502-510)) that binds 14-3-3ε with a KD value of 45.2 nM. Gly to Phe substitution in position 510 of pT(502-510) led to further improvement in affinity (KD: 22.0 nM) of the peptide for 14-3-3ε. Our results suggest that the designed peptide analogs are potential candidates for inhibiting 14-3-3ε-CDC25A interactions in cSCC cells and thus inducing their apoptosis.
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Affiliation(s)
- Seraphine Kamayirese
- Department
of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, United States
| | - Sibaprasad Maity
- Department
of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, United States
| | - Lynne M. Dieckman
- Department
of Chemistry and Biochemistry, Creighton
University, Omaha, Nebraska 68178, United States
| | - Laura A. Hansen
- Department
of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, United States
| | - Sándor Lovas
- Department
of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, United States
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3
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Wu Q, Centorrino F, Guillory X, Wolter M, Ottmann C, Cossar PJ, Brunsveld L. Discovery of 14-3-3 PPI Stabilizers by Extension of an Amidine-Substituted Thiophene Fragment. Chembiochem 2024; 25:e202300636. [PMID: 37902676 DOI: 10.1002/cbic.202300636] [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: 09/17/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 10/31/2023]
Abstract
Protein-protein interaction (PPI) modulation is a promising approach in drug discovery with the potential to expand the 'druggable' proteome and develop new therapeutic strategies. While there have been significant advancements in methodologies for developing PPI inhibitors, there is a relative scarcity of literature describing the 'bottom-up' development of PPI stabilizers (Molecular Glues). The hub protein 14-3-3 and its interactome provide an excellent platform for exploring conceptual approaches to PPI modulation, including evolution of chemical matter for Molecular Glues. In this study, we employed a fragment extension strategy to discover stabilizers for the complex of 14-3-3 protein and an Estrogen Receptor alpha-derived peptide (ERα). A focused library of analogues derived from an amidine-substituted thiophene fragment enhanced the affinity of the 14-3-3/ERα complex up to 6.2-fold. Structure-activity relationship (SAR) analysis underscored the importance of the newly added, aromatic side chain with a certain degree of rigidity. X-ray structural analysis revealed a unique intermolecular π-π stacking binding mode of the most active analogues, resulting in the simultaneous binding of two molecules to the PPI binding pocket. Notably, analogue 11 displayed selective stabilization of the 14-3-3/ERα complex.
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Affiliation(s)
- Qi Wu
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Federica Centorrino
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
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4
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Kamayirese S, Maity S, Dieckman LM, Hansen LA, Lovas S. Optimizing Phosphopeptide Structures That Target 14-3-3ε in Cutaneous Squamous Cell Carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560749. [PMID: 37873379 PMCID: PMC10592926 DOI: 10.1101/2023.10.03.560749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
14-3-3ε is involved in various types of malignancies by increasing cell proliferation, promoting cell invasion or inhibiting apoptosis. In cutaneous squamous cell carcinoma (cSCC), 14-3-3ε is over expressed and mislocalized from the nucleus to the cytoplasm where it interacts with the cell division cycle 25 A (CDC25A) and suppresses apoptosis. Hence inhibition of the 14-3-3ε - CDC25A interaction is an attractive target for promoting apoptosis in cSCC. In this work, we optimized the structure of our previously designed inhibitor of 14-3-3ε - CDC25A interaction, pT, a phosphopeptide fragment corresponding to one of the two binding regions of CDC25A to 14-3-3ε. Starting from pT, we developed peptide analogs that bind 14-3-3ε with nanomolar affinities. Peptide analogs were designed by shortening the pT peptide, and introducing modifications at position 510 of the pT(502-510) analog. Both molecular dynamics (MD) simulations and biophysical methods were used to determine peptides binding to 14-3-3ε. Shortening the pT peptide from 14 to 9 amino acid residues resulted in a peptide (pT(502-510)) that binds 14-3-3ε with a KD value of 45.2 nM. Gly to Phe substitution in position 510 of pT(502-510) led to further improvement in affinity (KD: 22.0 nM) of the peptide for 14-3-3ε. Our results suggest that the designed peptide analogs are potential candidates for inhibiting 14-3-3ε -CDC25A interactions in cSCC cells; thus, inducing their apoptosis.
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Affiliation(s)
- Seraphine Kamayirese
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, Unites States
| | - Sibaprasad Maity
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, Unites States
| | - Lynne M. Dieckman
- Department of Chemistry and Biochemistry, Creighton University, Omaha, Nebraska 68178, Unites States
| | - Laura A. Hansen
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, Unites States
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska 68178, Unites States
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5
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Ting SI, Snelson DW, Huffman TR, Kuroo A, Sato R, Shenvi RA. Synthesis of (-)-Cotylenol, a 14-3-3 Molecular Glue Component. J Am Chem Soc 2023; 145:20634-20645. [PMID: 37683289 PMCID: PMC11022164 DOI: 10.1021/jacs.3c07849] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
Small molecules that modulate the 14-3-3 protein-protein interaction (PPI) network represent valuable therapeutics and tool compounds. However, access has been lost to 14-3-3 PPI molecular glues of the cotylenin class, leading to investigations into the practical chemical syntheses of congeners and analogues. Here we report a concise synthesis of (-)-cotylenol via a 10-step asymmetric entry into a diversifiable 5-8-5 core. This route features a mild Liebeskind-Srogl fragment coupling that tolerates unprecedented steric hindrance to produce a highly congested ketone, and a tandem Claisen-ene cascade that establishes the 8-membered ring. Late-stage control of stereochemistry and functionality leads to (-)-cotylenol and sets the stage for focused library synthesis.
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Affiliation(s)
- Stephen I. Ting
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dylan W. Snelson
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tucker R. Huffman
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Akihiro Kuroo
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ryota Sato
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ryan A. Shenvi
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Skaggs Graduate School of Chemical and Biological Sciences, Scripps Research, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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6
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Visser EJ, Jaishankar P, Sijbesma E, Pennings MAM, Vandenboorn EMF, Guillory X, Neitz RJ, Morrow J, Dutta S, Renslo AR, Brunsveld L, Arkin MR, Ottmann C. From Tethered to Freestanding Stabilizers of 14-3-3 Protein-Protein Interactions through Fragment Linking. Angew Chem Int Ed Engl 2023; 62:e202308004. [PMID: 37455289 DOI: 10.1002/anie.202308004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Small-molecule stabilization of protein-protein interactions (PPIs) is a promising strategy in chemical biology and drug discovery. However, the systematic discovery of PPI stabilizers remains a largely unmet challenge. Herein we report a fragment-linking approach targeting the interface of 14-3-3 and a peptide derived from the estrogen receptor alpha (ERα) protein. Two classes of fragments-a covalent and a noncovalent fragment-were co-crystallized and subsequently linked, resulting in a noncovalent hybrid molecule in which the original fragment interactions were largely conserved. Supported by 20 crystal structures, this initial hybrid molecule was further optimized, resulting in selective, 25-fold stabilization of the 14-3-3/ERα interaction. The high-resolution structures of both the single fragments, their co-crystal structures and those of the linked fragments document a feasible strategy to develop orthosteric PPI stabilizers by linking to an initial tethered fragment.
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Affiliation(s)
- Emira J Visser
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Marloes A M Pennings
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Edmee M F Vandenboorn
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - R Jeffrey Neitz
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - John Morrow
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Shubhankar Dutta
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
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7
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Verhoef CJA, Kay DF, van Dijck L, Doveston RG, Brunsveld L, Leney AC, Cossar PJ. Tracking the mechanism of covalent molecular glue stabilization using native mass spectrometry. Chem Sci 2023; 14:6756-6762. [PMID: 37350830 PMCID: PMC10284121 DOI: 10.1039/d3sc01732j] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/30/2023] [Indexed: 06/24/2023] Open
Abstract
Molecular glues are powerful tools for the control of protein-protein interactions. Yet, the mechanisms underlying multi-component protein complex formation remain poorly understood. Native mass spectrometry (MS) detects multiple protein species simultaneously, providing an entry to elucidate these mechanisms. Here, for the first time, covalent molecular glue stabilization was kinetically investigated by combining native MS with biophysical and structural techniques. This approach elucidated the stoichiometry of a multi-component protein-ligand complex, the assembly order, and the contributions of covalent versus non-covalent binding events that govern molecular glue activity. Aldehyde-based molecular glue activity is initially regulated by cooperative non-covalent binding, followed by slow covalent ligation, further enhancing stabilization. This study provides a framework to investigate the mechanisms of covalent small molecule ligation and informs (covalent) molecular glue development.
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Affiliation(s)
- Carlo J A Verhoef
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven 5600 MB The Netherlands
| | - Danielle F Kay
- School of Biosciences, University of Birmingham Birmingham B15 2TT UK
| | - Lars van Dijck
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven 5600 MB The Netherlands
| | - Richard G Doveston
- Leicester Institute of Structural and Chemical Biology and School of Chemistry, University of Leicester Leicester LE1 7RH UK
| | - Luc Brunsveld
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven 5600 MB The Netherlands
| | - Aneika C Leney
- School of Biosciences, University of Birmingham Birmingham B15 2TT UK
| | - Peter J Cossar
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology Eindhoven 5600 MB The Netherlands
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8
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Rui H, Ashton KS, Min J, Wang C, Potts PR. Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction. RSC Chem Biol 2023; 4:192-215. [PMID: 36908699 PMCID: PMC9994104 DOI: 10.1039/d2cb00207h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023] Open
Abstract
Molecular glues are a class of small molecules that stabilize the interactions between proteins. Naturally occurring molecular glues are present in many areas of biology where they serve as central regulators of signaling pathways. Importantly, several clinical compounds act as molecular glue degraders that stabilize interactions between E3 ubiquitin ligases and target proteins, leading to their degradation. Molecular glues hold promise as a new generation of therapeutic agents, including those molecular glue degraders that can redirect the protein degradation machinery in a precise way. However, rational discovery of molecular glues is difficult in part due to the lack of understanding of the protein-protein interactions they stabilize. In this review, we summarize the structures of known molecular glue-induced ternary complexes and the interface properties. Detailed analysis shows different mechanisms of ternary structure formation. Additionally, we also review computational approaches for predicting protein-protein interfaces and highlight the promises and challenges. This information will ultimately help inform future approaches for rational molecular glue discovery.
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Affiliation(s)
- Huan Rui
- Center for Research Acceleration by Digital Innovation, Amgen Research Thousand Oaks CA 91320 USA
| | - Kate S Ashton
- Medicinal Chemistry, Amgen Research Thousand Oaks CA 91320 USA
| | - Jaeki Min
- Induced Proximity Platform, Amgen Research Thousand Oaks CA 91320 USA
| | - Connie Wang
- Digital, Technology & Innovation, Amgen Thousand Oaks CA 91320 USA
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9
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Hu B, Yan W, Jiang P, Jiang L, Yuan X, Lin J, Jiao Y, Jin Y. Switchable synthesis of natural-product-like lawsones and indenopyrazoles through regioselective ring-expansion of indantrione. Commun Chem 2023; 6:17. [PMID: 36697885 PMCID: PMC9849474 DOI: 10.1038/s42004-022-00807-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/29/2022] [Indexed: 01/19/2023] Open
Abstract
Lawsones and indenopyrazoles are the prevalent structural motifs and building blocks in pharmaceuticals and bioactive molecules, but their synthesis has always remained challenging as no comprehensive protocol has been outlined to date. Herein, a metal-free, ring-expansion reaction of indantrione with diazomethanes, generated in situ from the N-tosylhydrazones, has been developed for the synthesis of lawsone and indenopyrazole derivatives in acetonitrile and alcohol solvents, respectively. It provides these valuable lawsone and pyrazole skeletons in good yields and high levels of diastereoselectivity from simple and readily available starting materials. DFT calculations were used to explore the mechanism in different solutions. The synthetic application example also showed the prospects of this method for the preparation of valuable compounds.
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Affiliation(s)
- Bingwei Hu
- grid.440773.30000 0000 9342 2456Key Laboratory of Medicinal for Natural Resource, Ministry of Education and Yunnan Province, School of Pharmacy, Yunnan University, 650091 Kunming, China
| | - Wenxin Yan
- grid.411429.b0000 0004 1760 6172School of Chemistry and Chemical Engineering, Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, 411201 Xiangtan, China
| | - Peiyun Jiang
- grid.440773.30000 0000 9342 2456Key Laboratory of Medicinal for Natural Resource, Ministry of Education and Yunnan Province, School of Pharmacy, Yunnan University, 650091 Kunming, China
| | - Ling Jiang
- grid.440773.30000 0000 9342 2456Key Laboratory of Medicinal for Natural Resource, Ministry of Education and Yunnan Province, School of Pharmacy, Yunnan University, 650091 Kunming, China
| | - Xu Yuan
- grid.440773.30000 0000 9342 2456Key Laboratory of Medicinal for Natural Resource, Ministry of Education and Yunnan Province, School of Pharmacy, Yunnan University, 650091 Kunming, China
| | - Jun Lin
- grid.440773.30000 0000 9342 2456Key Laboratory of Medicinal for Natural Resource, Ministry of Education and Yunnan Province, School of Pharmacy, Yunnan University, 650091 Kunming, China
| | - Yinchun Jiao
- grid.411429.b0000 0004 1760 6172School of Chemistry and Chemical Engineering, Key Laboratory of Theoretical Organic Chemistry and Functional Molecular, Ministry of Education, Hunan University of Science and Technology, 411201 Xiangtan, China
| | - Yi Jin
- grid.440773.30000 0000 9342 2456Key Laboratory of Medicinal for Natural Resource, Ministry of Education and Yunnan Province, School of Pharmacy, Yunnan University, 650091 Kunming, China
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10
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Structure-activity-relationship study of semi-synthetically modified fusicoccins on their stabilization effect for 14-3-3-phospholigand interactions. Bioorg Med Chem 2022; 73:117020. [DOI: 10.1016/j.bmc.2022.117020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022]
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11
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Huang JH, Lv JM, Xiao LY, Xu Q, Lin FL, Wang GQ, Chen GD, Qin SY, Hu D, Gao H. Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme. Beilstein J Org Chem 2022; 18:1396-1402. [PMID: 36262672 PMCID: PMC9551204 DOI: 10.3762/bjoc.18.144] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/19/2022] [Indexed: 01/05/2023] Open
Abstract
Fusicoccane-type terpenoids are a subgroup of diterpenoids featured with a unique 5-8-5 ring system. They are widely distributed in nature and possess a variety of biological activities. Up to date, only five fusicoccane-type diterpene synthases have been identified. Here, we identify a two-gene biosynthetic gene cluster containing a new fusicoccane-type diterpene synthase gene tadA and an associated cytochrome P450 gene tadB from Talaromyces wortmannii ATCC 26942. Heterologous expression reveals that TadA catalyzes the formation of a new fusicoccane-type diterpene talaro-7,13-diene. D2O isotope labeling combined with site-directed mutagenesis indicates that TadA might employ a different C2,6 cyclization strategy from the known fusicoccane-type diterpene synthases, in which a neutral intermediate is firstly formed and then protonated by an environmental proton. In addition, we demonstrate that the associated cytochrome P450 enzyme TadB is able to catalyze multiple oxidation of talaro-7,13-diene to yield talaro-6,13-dien-5,8-dione.
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Affiliation(s)
- Jia-Hua Huang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Liang-Yan Xiao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Qian Xu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Fu-Long Lin
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Gao-Qian Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Guo-Dong Chen
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Sheng-Ying Qin
- Clinical Experimental Center, First Affiliated Hospital of Jinan University, Guangzhou 510630, China,
| | - Dan Hu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
- Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Hao Gao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy / Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research / International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
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12
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Sluchanko NN. Recent advances in structural studies of 14-3-3 protein complexes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:289-324. [PMID: 35534110 DOI: 10.1016/bs.apcsb.2021.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Being phosphopeptide-binding hubs, 14-3-3 proteins coordinate multiple cellular processes in eukaryotes, including the regulation of apoptosis, cell cycle, ion channels trafficking, transcription, signal transduction, and hormone biosynthesis. Forming constitutive α-helical dimers, 14-3-3 proteins predominantly recognize specifically phosphorylated Ser/Thr sites within their partners; this generally stabilizes phosphotarget conformation and affects its activity, intracellular distribution, dephosphorylation, degradation and interactions with other proteins. Not surprisingly, 14-3-3 complexes are involved in the development of a range of diseases and are considered promising drug targets. The wide interactome of 14-3-3 proteins encompasses hundreds of different phosphoproteins, for many of which the interaction is well-documented in vitro and in vivo but lack the structural data that would help better understand underlying regulatory mechanisms and develop new drugs. Despite obtaining structural information on 14-3-3 complexes is still lagging behind the research of 14-3-3 interactions on a proteome-wide scale, recent works provided some advances, including methodological improvements and accumulation of new interesting structural data, that are discussed in this review.
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Affiliation(s)
- Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow, Russian Federation.
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13
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Tang R, Chen P, Wang Z, Wang L, Hao H, Hou T, Sun H. Characterizing the stabilization effects of stabilizers in protein-protein systems with end-point binding free energy calculations. Brief Bioinform 2022; 23:6565618. [PMID: 35395683 DOI: 10.1093/bib/bbac127] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/10/2022] [Accepted: 03/15/2022] [Indexed: 02/06/2023] Open
Abstract
Drug design targeting protein-protein interactions (PPIs) associated with the development of diseases has been one of the most important therapeutic strategies. Besides interrupting the PPIs with PPI inhibitors/blockers, increasing evidence shows that stabilizing the interaction between two interacting proteins may also benefit the therapy, such as the development of various types of molecular glues/stabilizers that mostly work by stabilizing the two interacting proteins to regulate the downstream biological effects. However, characterizing the stabilization effect of a stabilizer is usually hard or too complicated for traditional experiments since it involves ternary interactions [protein-protein-stabilizer (PPS) interaction]. Thus, developing reliable computational strategies will facilitate the discovery/design of molecular glues or PPI stabilizers. Here, by fully analyzing the energetic features of the binary interactions in the PPS ternary complex, we systematically investigated the performance of molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics generalized Born surface area (MM/GBSA) methods on characterizing the stabilization effects of stabilizers in 14-3-3 systems. The results show that both MM/PBSA and MM/GBSA are powerful tools in distinguishing the stabilizers from the decoys (with area under the curves of 0.90-0.93 for all tested cases) and are reasonable for ranking protein-peptide interactions in the presence or absence of stabilizers as well (with the average Pearson correlation coefficient of ~0.6 at a relatively high dielectric constant for both methods). Moreover, to give a detailed picture of the stabilization effects, the stabilization mechanism is also analyzed from the structural and energetic points of view for individual systems containing strong or weak stabilizers. This study demonstrates a potential strategy to accelerate the discovery of PPI stabilizers.
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Affiliation(s)
- Rongfan Tang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Pengcheng Chen
- Institute of Big Data and Artificial Intelligence in Medicine, School of Electronics and Information Engineering, Taizhou University, Taizhou 318000, Zhejiang, P. R. China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Lingling Wang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, 210009 Nanjing, China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
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14
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Fragment-based exploration of the 14-3-3/Amot-p130 interface. Curr Res Struct Biol 2022; 4:21-28. [PMID: 35036934 PMCID: PMC8743172 DOI: 10.1016/j.crstbi.2021.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 02/06/2023] Open
Abstract
The modulation of protein-protein interactions (PPIs) has developed into a well-established field of drug discovery. Despite the advances achieved in the field, many PPIs are still deemed as ‘undruggable’ targets and the design of PPIs stabilizers remains a significant challenge. The application of fragment-based methods for the identification of drug leads and to evaluate the ‘tractability’ of the desired protein target has seen a remarkable development in recent years. In this study, we explore the molecular characteristics of the 14-3-3/Amot-p130 PPI and the conceptual possibility of targeting this interface using X-ray crystallography fragment-based screening. We report the first structural elucidation of the 14-3-3 binding motif of Amot-p130 and the characterization of the binding mode and affinities involved. We made use of fragments to probe the ‘ligandability’ of the 14-3-3/Amot-p130 composite binding pocket. Here we disclose initial hits with promising stabilizing activity and an early-stage selectivity toward the Amot-p130 motifs over other representatives 14-3-3 partners. Our findings highlight the potential of using fragments to characterize and explore proteins' surfaces and might provide a starting point toward the development of small molecules capable of acting as molecular glues. Phosphorylation of Ser 175 mediates binding of Amot-p130 to 14-3-3. The crystal structure of the 14-3-3σΔC/Amot-p130 peptide complex describes the interface. A fragment-based exploration of the interface assesses ‘ligandability’. Fragments binding at the 14-3-3/Amot-p130 interface display an initial stabilizing activity.
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Key Words
- 14-3-3 /protein-protein interactions stabilizers
- AIP4, Atrophin-1 interacting protein 4
- Amot, Angiomotin
- Amot-p130
- AmotL1/2, Angiomotin-like 1/2
- FBDD, Fragment-based drug discovery
- FP, Fluorescence polarization
- Fragment-based drug discovery
- Lats 1/2, Large tumor suppressor 1/2
- Ligandability
- MST, Microscale thermophoresis
- PPI, Protein-protein interaction
- PTMs, post-translational modifications
- X-ray crystallography
- YAP1, Yes-associated protein 1
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15
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Wu XD, Ding LF, Li WY, Cheng B, Lei T, Zhou HF, Zhao QS. Hypoestins A−D: highly modified fusicoccane diterpenoids with promising Cav3.1 calcium channel inhibitory activity from Hypoestes purpurea. Org Chem Front 2022. [DOI: 10.1039/d2qo00265e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hypoestins A–D (1–4), four highly modified fusicoccane diterpenoids with two unreported carbon skeletons, and hypoestins E (5) and F (6), two prviously undescribed fusicoccane diterpenoids, were isolated from aerial parts...
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16
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Falcicchio M, Ward JA, Chothia SY, Basran J, Mohindra A, Macip S, Roversi P, Doveston RG. Cooperative stabilisation of 14-3-3σ protein-protein interactions via covalent protein modification. Chem Sci 2021; 12:12985-12992. [PMID: 34745529 PMCID: PMC8513901 DOI: 10.1039/d1sc02120f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/05/2021] [Indexed: 12/19/2022] Open
Abstract
14-3-3 proteins are an important family of hub proteins that play important roles in many cellular processes via a large network of interactions with partner proteins. Many of these protein-protein interactions (PPI) are implicated in human diseases such as cancer and neurodegeneration. The stabilisation of selected 14-3-3 PPIs using drug-like 'molecular glues' is a novel therapeutic strategy with high potential. However, the examples reported to date have a number of drawbacks in terms of selectivity and potency. Here, we report that WR-1065, the active species of the approved drug amifostine, covalently modifies 14-3-3σ at an isoform-unique cysteine residue, Cys38. This modification leads to isoform-specific stabilisation of two 14-3-3σ PPIs in a manner that is cooperative with a well characterised molecular glue, fusicoccin A. Our findings reveal a novel stabilisation mechanism for 14-3-3σ, an isoform with particular involvement in cancer pathways. This mechanism can be exploited to harness the enhanced potency conveyed by covalent drug molecules and dual ligand cooperativity. This is demonstrated in two cancer cell lines whereby the cooperative behaviour of fusicoccin A and WR-1065 leads to enhanced efficacy for inducing cell death and attenuating cell growth.
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Affiliation(s)
- Marta Falcicchio
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,School of Chemistry, University of Leicester University Road Leicester LE1 7RH UK
| | - Jake A Ward
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,Mechanisms of Cancer and Aging Laboratory, Department of Molecular and Cell Biology, University of Leicester University Road Leicester LE1 7RH UK
| | - Sara Y Chothia
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,School of Chemistry, University of Leicester University Road Leicester LE1 7RH UK
| | - Jaswir Basran
- Department of Molecular and Cell Biology, University of Leicester University Road Leicester LE1 7RH UK
| | - Alisha Mohindra
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,School of Chemistry, University of Leicester University Road Leicester LE1 7RH UK
| | - Salvador Macip
- Mechanisms of Cancer and Aging Laboratory, Department of Molecular and Cell Biology, University of Leicester University Road Leicester LE1 7RH UK.,FoodLab, Faculty of Health Sciences, Universitat Oberta de Catalunya Barcelona Spain
| | - Pietro Roversi
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,Department of Molecular and Cell Biology, University of Leicester University Road Leicester LE1 7RH UK.,Institute of Agricultural Biology and Biotechnology, IBBA-CNR Unit of Milano Via Bassini 15 I-20133 Milan Italy
| | - Richard G Doveston
- Leicester Institute for Structural and Chemical Biology, University of Leicester University Road Leicester LE1 7RH UK .,School of Chemistry, University of Leicester University Road Leicester LE1 7RH UK
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17
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Sijbesma E, Hallenbeck KK, Andrei SA, Rust RR, Adriaans JMC, Brunsveld L, Arkin MR, Ottmann C. Exploration of a 14-3-3 PPI Pocket by Covalent Fragments as Stabilizers. ACS Med Chem Lett 2021; 12:976-982. [PMID: 34136078 PMCID: PMC8201753 DOI: 10.1021/acsmedchemlett.1c00088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/04/2021] [Indexed: 12/20/2022] Open
Abstract
![]()
The systematic discovery
of functional fragments binding to the
composite interface of protein complexes is a first critical step
for the development of orthosteric stabilizers of protein–protein
interactions (PPIs). We have previously shown that disulfide trapping
successfully yielded covalent stabilizers for the PPI of 14-3-3 with
the estrogen receptor ERα. Here we provide an assessment of
the composite PPI target pocket and the molecular characteristics
of various fragments binding to a specific subpocket. Evaluating structure–activity
relationships highlights the basic principles for PPI stabilization
by these covalent fragments that engage a relatively large and exposed
binding pocket at the protein/peptide interface with a “molecular
glue” mode of action.
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Affiliation(s)
- Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Kenneth K. Hallenbeck
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94134, United States
| | - Sebastian A. Andrei
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Reanne R. Rust
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Joris M. C. Adriaans
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Michelle R. Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco 94134, United States
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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18
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Tang C, Mo X, Niu Q, Wahafu A, Yang X, Qui M, Ivanov AA, Du Y, Fu H. Hypomorph mutation-directed small-molecule protein-protein interaction inducers to restore mutant SMAD4-suppressed TGF-β signaling. Cell Chem Biol 2021; 28:636-647.e5. [PMID: 33326750 PMCID: PMC10053325 DOI: 10.1016/j.chembiol.2020.11.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 10/05/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023]
Abstract
Tumor suppressor genes represent a major class of oncogenic drivers. However, direct targeting of loss-of-function tumor suppressors remains challenging. To address this gap, we explored a variant-directed chemical biology approach to reverse the lost function of tumor suppressors using SMAD4 as an example. SMAD4, a central mediator of the TGF-β pathway, is recurrently mutated in many tumors. Here, we report the development of a TR-FRET technology that recapitulated the dynamic differential interaction of SMAD4 and SMAD4R361H with SMAD3 and identified Ro-31-8220, a bisindolylmaleimide derivative, as a SMAD4R361H/SMAD3 interaction inducer. Ro-31-8220 reactivated the dormant SMAD4R361H-mediated transcriptional activity and restored TGF-β-induced tumor suppression activity in SMAD4 mutant cancer cells. Thus, demonstration of Ro-31-8220 as a SMAD4R361H/SMAD3 interaction inducer illustrates a general strategy to reverse the lost function of tumor suppressors with hypomorph mutations and supports a systematic approach to develop small-molecule protein-protein interaction (PPI) molecular glues for biological insights and therapeutic discovery.
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Affiliation(s)
- Cong Tang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shannxi 710061, P.R.China
| | - Xiulei Mo
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Qiankun Niu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alafate Wahafu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; The First Affiliated Hospital, Medical School of Xi'an Jiaotong University, Xi'an, Shannxi 710061, P.R.China
| | - Xuan Yang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Min Qui
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrey A Ivanov
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA; Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Hematology and Medical Oncology and Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA.
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19
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Pair FS, Yacoubian TA. 14-3-3 Proteins: Novel Pharmacological Targets in Neurodegenerative Diseases. Trends Pharmacol Sci 2021; 42:226-238. [PMID: 33518287 PMCID: PMC8011313 DOI: 10.1016/j.tips.2021.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/17/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022]
Abstract
14-3-3 proteins are a family of proteins expressed throughout the body and implicated in many diseases, from cancer to neurodegenerative disorders. While these proteins do not have direct enzymatic activity, they form a hub for many signaling pathways via protein-protein interactions (PPIs). 14-3-3 interactions have proven difficult to target with traditional pharmacological methods due to the unique nature of their binding. However, recent advances in compound development utilizing a range of tools, from thermodynamic binding site analysis to computational molecular modeling techniques, have opened the door to targeting these interactions. Compounds are already being developed targeting 14-3-3 interactions with potential therapeutic implication for neurodegenerative disorders, but challenges still remain in optimizing specificity and target engagement to avoid unintended negative consequences arising from targeting 14-3-3 signaling networks.
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Affiliation(s)
- F Sanders Pair
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Talene A Yacoubian
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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20
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Ruks T, Loza K, Heggen M, Ottmann C, Bayer P, Beuck C, Epple M. Targeting the Surface of the Protein 14-3-3 by Ultrasmall (1.5 nm) Gold Nanoparticles Carrying the Specific Peptide CRaf. Chembiochem 2021; 22:1456-1463. [PMID: 33275809 PMCID: PMC8248332 DOI: 10.1002/cbic.202000761] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 12/04/2020] [Indexed: 12/11/2022]
Abstract
The surface of ultrasmall gold nanoparticles with an average diameter of 1.55 nm was conjugated with a 14-3-3 protein-binding peptide derived from CRaf. Each particle carries 18 CRaf peptides, leading to an overall stoichiometry of Au(115)Craf(18). The binding to the protein 14-3-3 was probed by isothermal titration calorimetry (ITC) and fluorescence polarization spectroscopy (FP). The dissociation constant (KD ) was measured as 5.0 μM by ITC and 0.9 μM by FP, which was close to the affinity of dissolved CRaf to 14-3-3σ. In contrast to dissolved CRaf, which alone did not enter HeLa cells, CRAF-conjugated gold nanoparticles were well taken up by HeLa cells, opening the opportunity to target the protein inside a cell.
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Affiliation(s)
- Tatjana Ruks
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstrasse 5-7, 45117, Essen, Germany
| | - Kateryna Loza
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstrasse 5-7, 45117, Essen, Germany
| | - Marc Heggen
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Peter Bayer
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117, Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117, Essen, Germany
| | - Matthias Epple
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), University of Duisburg-Essen, Universitätsstrasse 5-7, 45117, Essen, Germany
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21
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Aljabal G, Yap BK. 14-3-3σ and Its Modulators in Cancer. Pharmaceuticals (Basel) 2020; 13:ph13120441. [PMID: 33287252 PMCID: PMC7761676 DOI: 10.3390/ph13120441] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 01/19/2023] Open
Abstract
14-3-3σ is an acidic homodimer protein with more than one hundred different protein partners associated with oncogenic signaling and cell cycle regulation. This review aims to highlight the crucial role of 14-3-3σ in controlling tumor growth and apoptosis and provide a detailed discussion on the structure-activity relationship and binding interactions of the most recent 14-3-3σ protein-protein interaction (PPI) modulators reported to date, which has not been reviewed previously. This includes the new fusicoccanes stabilizers (FC-NAc, DP-005), fragment stabilizers (TCF521-123, TCF521-129, AZ-003, AZ-008), phosphate-based inhibitors (IMP, PLP), peptide inhibitors (2a-d), as well as inhibitors from natural sources (85531185, 95911592). Additionally, this review will also include the discussions of the recent efforts by a different group of researchers for understanding the binding mechanisms of existing 14-3-3σ PPI modulators. The strategies and state-of-the-art techniques applied by various group of researchers in the discovery of a different chemical class of 14-3-3σ modulators for cancer are also briefly discussed in this review, which can be used as a guide in the development of new 14-3-3σ modulators in the near future.
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22
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Ballone A, Picarazzi F, Prosser C, Davis J, Ottmann C, Mori M. Experimental and Computational Druggability Exploration of the 14-3-3ζ/SOS1pS 1161 PPI Interface. J Chem Inf Model 2020; 60:6555-6565. [PMID: 33138374 DOI: 10.1021/acs.jcim.0c00722] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The exploration of the druggability of certain protein-protein interactions (PPIs) still remains a challenging task in drug discovery. Here, we present a case study using the 14-3-3-PPI, showing how small molecules can be located that are able to modulate this key oncogenic pathway. A workflow embracing biophysical techniques and MD simulations was developed to evaluate the potential of a 14-3-3ζ PPI system to bind new tool compounds. The significance of the use of computational approaches to compensate for the limitations of experimental techniques is demonstrated.
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Affiliation(s)
- Alice Ballone
- Department of Biochemical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, University of Technology Eindhoven, 5600 MB, Eindhoven, The Netherlands.,Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy.,Department of Chemistry, UCB Pharma SPRL, 216 Bath Rd., Slough SL1 3WE, United Kingdom
| | - Francesca Picarazzi
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Christine Prosser
- Department of Chemistry, UCB Pharma SPRL, 216 Bath Rd., Slough SL1 3WE, United Kingdom
| | - Jeremy Davis
- Department of Chemistry, UCB Pharma SPRL, 216 Bath Rd., Slough SL1 3WE, United Kingdom
| | - Christian Ottmann
- Department of Biochemical Engineering and Institute for Complex Molecular Systems, Laboratory of Chemical Biology, University of Technology Eindhoven, 5600 MB, Eindhoven, The Netherlands
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy, Department of Excellence 2018-2022, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
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23
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Sengupta A, Liriano J, Bienkiewicz EA, Miller BG, Frederich JH. Probing the 14-3-3 Isoform-Specificity Profile of Protein-Protein Interactions Stabilized by Fusicoccin A. ACS OMEGA 2020; 5:25029-25035. [PMID: 33043180 PMCID: PMC7542595 DOI: 10.1021/acsomega.0c01454] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
Fusicoccin A (FC) is a fungal phytotoxin that stabilizes protein-protein interactions (PPIs) between 14-3-3 adapter proteins and their phosphoprotein interaction partners. Recently, FC has emerged as an important chemical probe of human 14-3-3 PPIs involved in cancer and neurobiology. These previous studies have established the structural requirements for FC-induced stabilization of 14-3-3·client phosphoprotein complexes; however, the effect of 14-3-3 isoforms on FC activity remains underexplored. This is a relevant question for the continued development of FC variants because there are seven isoforms of 14-3-3 in humans. Despite their sequence and structural similarities, a growing body of experimental evidence supports both tissue-specific expression of 14-3-3 isoforms and isoform-specific functions in vivo. Herein, we interrogate the isoform-specificity profile of FC in vitro using recombinant 14-3-3 isoforms and a library of fluorescein-labeled hexaphosphopeptides mimicking the C-terminal recognition domains of client proteins that are characterized targets of FC in vivo. Our results reveal modest isoform preferences for individual client phospholigands and demonstrate that FC differentially stabilizes PPIs involving 14-3-3σ. Together, these data support the feasibility of developing FC variants with enhanced isoform selectivity.
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Affiliation(s)
- Ananya Sengupta
- Department
of Chemistry and Biochemistry, Florida State
University, 95 Chieftan Way, Tallahassee, Florida 32306, United
States
| | - Josue Liriano
- Department
of Chemistry and Biochemistry, Florida State
University, 95 Chieftan Way, Tallahassee, Florida 32306, United
States
| | - Ewa A. Bienkiewicz
- Department
of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, Florida 32306, United
States
| | - Brian G. Miller
- Department
of Chemistry and Biochemistry, Florida State
University, 95 Chieftan Way, Tallahassee, Florida 32306, United
States
| | - James H. Frederich
- Department
of Chemistry and Biochemistry, Florida State
University, 95 Chieftan Way, Tallahassee, Florida 32306, United
States
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24
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Ballone A, Lau RA, Zweipfenning FPA, Ottmann C. A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes. Acta Crystallogr F Struct Biol Commun 2020; 76:501-507. [PMID: 33006579 PMCID: PMC7531243 DOI: 10.1107/s2053230x2001122x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/16/2020] [Indexed: 11/29/2022] Open
Abstract
Interactions between a protein and a peptide motif of its protein partner are prevalent in nature. Often, a protein also has multiple interaction partners. X-ray protein crystallography is commonly used to examine these interactions in terms of bond distances and angles as well as to describe hotspots within protein complexes. However, the crystallization process presents a significant bottleneck in structure determination since it often requires notably time-consuming screening procedures, which involve testing a broad range of crystallization conditions via a trial-and-error approach. This difficulty is also increased as each protein-peptide complex does not necessarily crystallize under the same conditions. Here, a new co-crystallization/peptide-soaking method is presented which circumvents the need to return to the initial lengthy crystal screening and optimization processes for each consequent new complex. The 14-3-3σ protein, which has multiple interacting partners with specific peptidic motifs, was used as a case study. It was found that co-crystals of 14-3-3σ and a low-affinity peptide from one of its partners, c-Jun, could easily be soaked with another interacting peptide to quickly and easily generate new structures at high resolution. Not only does this significantly reduce the production time, but new 14-3-3-peptide structures that were previously not accessible with the 14-3-3σ isoform, despite screening hundreds of other different conditions, were now also able to be resolved. The findings achieved in this study may be considered as a supporting and practical guide to potentially enable the acceleration of the crystallization process of any protein-peptide system.
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Affiliation(s)
- Alice Ballone
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Roxanne A. Lau
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Fabian P. A. Zweipfenning
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117 Essen, Germany
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25
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Wolter M, Valenti D, Cossar PJ, Levy LM, Hristeva S, Genski T, Hoffmann T, Brunsveld L, Tzalis D, Ottmann C. Fragment-Based Stabilizers of Protein-Protein Interactions through Imine-Based Tethering. Angew Chem Int Ed Engl 2020; 59:21520-21524. [PMID: 32816380 PMCID: PMC7756862 DOI: 10.1002/anie.202008585] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/16/2020] [Indexed: 12/22/2022]
Abstract
Small‐molecule stabilization of protein–protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a “bottom‐up” approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine‐forming fragments. The imine bond offers a covalent anchor for site‐directed fragment targeting, whereas its transient nature enables efficient analysis of structure–activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65‐subunit‐derived peptide of NF‐κB with the adapter protein 14‐3‐3. Those fragments that subsequently establish contacts with the p65‐derived peptide, rather than with 14‐3‐3, efficiently stabilize the 14‐3‐3/p65 complex and offer novel starting points for molecular glues.
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Affiliation(s)
- Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Dario Valenti
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Peter J Cossar
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Laura M Levy
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Stanimira Hristeva
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Thorsten Genski
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Torsten Hoffmann
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Dimitrios Tzalis
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Straße 76a, 44227, Dortmund, Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical, Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.,Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45117, Essen, Germany
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26
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Wolter M, Valenti D, Cossar PJ, Levy LM, Hristeva S, Genski T, Hoffmann T, Brunsveld L, Tzalis D, Ottmann C. Fragment‐Based Stabilizers of Protein–Protein Interactions through Imine‐Based Tethering. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Madita Wolter
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Dario Valenti
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Peter J. Cossar
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Laura M. Levy
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Stanimira Hristeva
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Thorsten Genski
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Torsten Hoffmann
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Luc Brunsveld
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Dimitrios Tzalis
- Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany
| | - Christian Ottmann
- Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
- Department of Chemistry University of Duisburg-Essen Universitätsstrasse 7 45117 Essen Germany
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27
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Computational methods-guided design of modulators targeting protein-protein interactions (PPIs). Eur J Med Chem 2020; 207:112764. [PMID: 32871340 DOI: 10.1016/j.ejmech.2020.112764] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/09/2020] [Accepted: 08/16/2020] [Indexed: 12/15/2022]
Abstract
Protein-protein interactions (PPIs) play a pivotal role in extensive biological processes and are thus crucial to human health and the development of disease states. Due to their critical implications, PPIs have been spotlighted as promising drug targets of broad-spectrum therapeutic interests. However, owing to the general properties of PPIs, such as flat surfaces, featureless conformations, difficult topologies, and shallow pockets, previous attempts were faced with serious obstacles when targeting PPIs and almost portrayed them as "intractable" for decades. To date, rapid progress in computational chemistry and structural biology methods has promoted the exploitation of PPIs in drug discovery. These techniques boost their cost-effective and high-throughput traits, and enable the study of dynamic PPI interfaces. Thus, computational methods represent an alternative strategy to target "undruggable" PPI interfaces and have attracted intense pharmaceutical interest in recent years, as exemplified by the accumulating number of successful cases. In this review, we first introduce a diverse set of computational methods used to design PPI modulators. Herein, we focus on the recent progress in computational strategies and provide a comprehensive overview covering various methodologies. Importantly, a list of recently-reported successful examples is highlighted to verify the feasibility of these computational approaches. Finally, we conclude the general role of computational methods in targeting PPIs, and also discuss future perspectives on the development of such aids.
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28
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Guillory X, Wolter M, Leysen S, Neves JF, Kuusk A, Genet S, Somsen B, Morrow JK, Rivers E, van Beek L, Patel J, Goodnow R, Schoenherr H, Fuller N, Cao Q, Doveston RG, Brunsveld L, Arkin MR, Castaldi P, Boyd H, Landrieu I, Chen H, Ottmann C. Fragment-based Differential Targeting of PPI Stabilizer Interfaces. J Med Chem 2020; 63:6694-6707. [PMID: 32501690 PMCID: PMC7356319 DOI: 10.1021/acs.jmedchem.9b01942] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Stabilization of protein-protein interactions (PPIs) holds great potential for therapeutic agents, as illustrated by the successful drugs rapamycin and lenalidomide. However, how such interface-binding molecules can be created in a rational, bottom-up manner is a largely unanswered question. We report here how a fragment-based approach can be used to identify chemical starting points for the development of small-molecule stabilizers that differentiate between two different PPI interfaces of the adapter protein 14-3-3. The fragments discriminately bind to the interface of 14-3-3 with the recognition motif of either the tumor suppressor protein p53 or the oncogenic transcription factor TAZ. This X-ray crystallography driven study shows that the rim of the interface of individual 14-3-3 complexes can be targeted in a differential manner with fragments that represent promising starting points for the development of specific 14-3-3 PPI stabilizers.
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Affiliation(s)
- Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Seppe Leysen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - João Filipe Neves
- CNRS ERL9002 Integrative Structural Biology F-59000 Lille, France.,Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE, Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - Ave Kuusk
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands.,Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Gothenburg, 431 50 Mölndal, Sweden
| | - Sylvia Genet
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Bente Somsen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - John Kenneth Morrow
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Emma Rivers
- Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Gothenburg, 431 50 Mölndal, Sweden
| | - Lotte van Beek
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Joe Patel
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Robert Goodnow
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Heike Schoenherr
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Nathan Fuller
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Qing Cao
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Richard G Doveston
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Paola Castaldi
- Oncology and Discovery Sciences, IMED Biotech Unit, AstraZeneca, Gatehouse Park, Waltham, Massachusetts 02451, United States
| | - Helen Boyd
- Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Gothenburg, 431 50 Mölndal, Sweden
| | - Isabelle Landrieu
- CNRS ERL9002 Integrative Structural Biology F-59000 Lille, France.,Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE, Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
| | - Hongming Chen
- Hit Discovery, Discovery Sciences, Biopharmaceutical R&D, AstraZeneca, Gothenburg, 431 50 Mölndal, Sweden
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, The Netherlands.,Department of Organic Chemistry, University of Duisburg-Essen, 47057 Duisburg, Germany
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29
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Wolter M, de Vink P, Neves JF, Srdanović S, Higuchi Y, Kato N, Wilson A, Landrieu I, Brunsveld L, Ottmann C. Selectivity via Cooperativity: Preferential Stabilization of the p65/14-3-3 Interaction with Semisynthetic Natural Products. J Am Chem Soc 2020; 142:11772-11783. [PMID: 32501683 PMCID: PMC8022324 DOI: 10.1021/jacs.0c02151] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Natural
compounds are an important class of potent drug molecules
including some retrospectively found to act as stabilizers of protein–protein
interactions (PPIs). However, the design of synthetic PPI stabilizers
remains an understudied approach. To date, there are limited examples
where cooperativity has been utilized to guide the optimization of
a PPI stabilizer. The 14-3-3 scaffold proteins provide an excellent
platform to explore PPI stabilization because these proteins mediate
several hundred PPIs, and a class of natural compounds, the fusicoccanes,
are known to stabilize a subset of 14-3-3 protein interactions. 14-3-3
has been reported to negatively regulate the p65 subunit of the NF-κB
transcription factor, which qualifies this protein complex as a potential
target for drug discovery to control cell proliferation. Here, we
report the high-resolution crystal structures of two 14-3-3 binding
motifs of p65 in complex with 14-3-3. A semisynthetic natural product
derivative, DP-005, binds to an interface pocket of the p65/14-3-3
complex and concomitantly stabilizes it. Cooperativity analyses of
this interaction, and other disease relevant 14-3-3-PPIs, demonstrated
selectivity of DP-005 for the p65/14-3-3 complex. The adaptation of
a cooperative binding model provided a general approach to characterize
stabilization and to assay for selectivity of PPI stabilizers.
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Affiliation(s)
- Madita Wolter
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Pim de Vink
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - João Filipe Neves
- U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Université de Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille F-59000, France.,CNRS ERL9002 Integrative Structural Biology, Lille F-59000, France
| | - Sonja Srdanović
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Yusuke Higuchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Nobuo Kato
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan
| | - Andrew Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, United Kingdom
| | - Isabelle Landrieu
- U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Université de Lille, Inserm, CHU Lille, Institut Pasteur de Lille, Lille F-59000, France.,CNRS ERL9002 Integrative Structural Biology, Lille F-59000, France
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, P.O. Box 513, Eindhoven 5600 MB, The Netherlands.,Department of Organic Chemistry, University of Duisburg-Essen, 45117, Essen, Germany
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30
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Kaplan A, Andrei SA, van Regteren Altena A, Simas T, Banerjee SL, Kato N, Bisson N, Higuchi Y, Ottmann C, Fournier AE. Polypharmacological Perturbation of the 14-3-3 Adaptor Protein Interactome Stimulates Neurite Outgrowth. Cell Chem Biol 2020; 27:657-667.e6. [PMID: 32220335 DOI: 10.1016/j.chembiol.2020.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/05/2020] [Accepted: 02/28/2020] [Indexed: 10/24/2022]
Abstract
Targeting protein-protein interactions (PPIs) is a promising approach in the development of drugs for many indications. 14-3-3 proteins are a family of phosphoprotein-binding molecules with critical functions in dozens of cell signaling networks. 14-3-3s are abundant in the central nervous system, and the small molecule fusicoccin-A (FC-A), a tool compound that can be used to manipulate 14-3-3 PPIs, enhances neurite outgrowth in cultured neurons. New semisynthetic FC-A derivatives with improved binding affinity for 14-3-3 complexes have recently been developed. Here, we use a series of screens that identify these compounds as potent inducers of neurite outgrowth through a polypharmacological mechanism. Using proteomics and X-ray crystallography, we discover that these compounds extensively regulate the 14-3-3 interactome by stabilizing specific PPIs, while disrupting others. These results provide new insights into the development of drugs to target 14-3-3 PPIs, a potential therapeutic strategy for CNS diseases.
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Affiliation(s)
- Andrew Kaplan
- Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, QC, Canada.
| | - Sebastian A Andrei
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Anna van Regteren Altena
- Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Tristan Simas
- Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Sara L Banerjee
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Centre de Recherche sur le Cancer, Université Laval, Québec, QC, Canada
| | - Nobuo Kato
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
| | - Nicolas Bisson
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Centre de Recherche sur le Cancer, Université Laval, Québec, QC, Canada
| | - Yusuke Higuchi
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, Japan
| | - Christian Ottmann
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands; Department of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Alyson E Fournier
- Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, QC, Canada.
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31
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Gigante A, Sijbesma E, Sánchez‐Murcia PA, Hu X, Bier D, Bäcker S, Knauer S, Gago F, Ottmann C, Schmuck C. A Supramolecular Stabilizer of the 14-3-3ζ/ERα Protein-Protein Interaction with a Synergistic Mode of Action. Angew Chem Int Ed Engl 2020; 59:5284-5287. [PMID: 31814236 PMCID: PMC7155037 DOI: 10.1002/anie.201914517] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Indexed: 12/27/2022]
Abstract
We report on a stabilizer of the interaction between 14-3-3ζ and the Estrogen Receptor alpha (ERα). ERα is a driver in the majority of breast cancers and 14-3-3 proteins are negative regulators of this nuclear receptor, making the stabilization of this protein-protein interaction (PPI) an interesting strategy. The stabilizer (1) consists of three symmetric peptidic arms containing an arginine mimetic, previously described as the GCP motif. 1 stabilizes the 14-3-3ζ/ERα interaction synergistically with the natural product Fusicoccin-A and was thus hypothesized to bind to a different site. This is supported by computational analysis of 1 binding to the binary complex of 14-3-3 and an ERα-derived phosphopeptide. Furthermore, 1 shows selectivity towards 14-3-3ζ/ERα interaction over other 14-3-3 client-derived phosphomotifs. These data provide a solid support of a new binding mode for a supramolecular 14-3-3ζ/ERα PPI stabilizer.
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Affiliation(s)
- Alba Gigante
- Department of Organic ChemistryUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
| | - Eline Sijbesma
- Department of Biomedical EngineeringEindhoven University of TechnologyP.O. Box 5135600 MBEindhovenThe Netherlands
| | - Pedro A. Sánchez‐Murcia
- Departamento de Ciencias BiomédicasUniversidad de Alcalá28805Alcalá de HenaresSpain
- Present address: Institute of Theoretical ChemistryFaculty of ChemistryUniversity of ViennaWähringer Str. 171090ViennaAustria
| | - Xiaoyu Hu
- Department of Organic ChemistryUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
| | - David Bier
- Department of Organic ChemistryUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
- Department of Biomedical EngineeringEindhoven University of TechnologyP.O. Box 5135600 MBEindhovenThe Netherlands
| | - Sandra Bäcker
- Centre for Medical BiotechnologyUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
| | - Shirley Knauer
- Centre for Medical BiotechnologyUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
| | - Federico Gago
- Departamento de Ciencias BiomédicasUniversidad de Alcalá28805Alcalá de HenaresSpain
| | - Christian Ottmann
- Department of Organic ChemistryUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
- Department of Biomedical EngineeringEindhoven University of TechnologyP.O. Box 5135600 MBEindhovenThe Netherlands
| | - Carsten Schmuck
- Department of Organic ChemistryUniversity of Duisburg EssenUniversitätstr. 745141EssenGermany
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32
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Gigante A, Sijbesma E, Sánchez‐Murcia PA, Hu X, Bier D, Bäcker S, Knauer S, Gago F, Ottmann C, Schmuck C. A Supramolecular Stabilizer of the 14‐3‐3ζ/ERα Protein‐Protein Interaction with a Synergistic Mode of Action. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Alba Gigante
- Department of Organic ChemistryUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
| | - Eline Sijbesma
- Department of Biomedical EngineeringEindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Pedro A. Sánchez‐Murcia
- Departamento de Ciencias BiomédicasUniversidad de Alcalá 28805 Alcalá de Henares Spain
- Present address: Institute of Theoretical ChemistryFaculty of ChemistryUniversity of Vienna Währinger Str. 17 1090 Vienna Austria
| | - Xiaoyu Hu
- Department of Organic ChemistryUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
| | - David Bier
- Department of Organic ChemistryUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
- Department of Biomedical EngineeringEindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Sandra Bäcker
- Centre for Medical BiotechnologyUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
| | - Shirley Knauer
- Centre for Medical BiotechnologyUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
| | - Federico Gago
- Departamento de Ciencias BiomédicasUniversidad de Alcalá 28805 Alcalá de Henares Spain
| | - Christian Ottmann
- Department of Organic ChemistryUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
- Department of Biomedical EngineeringEindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands
| | - Carsten Schmuck
- Department of Organic ChemistryUniversity of Duisburg Essen Universitätstr. 7 45141 Essen Germany
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Sengupta A, Liriano J, Miller BG, Frederich JH. Analysis of Interactions Stabilized by Fusicoccin A Reveals an Expanded Suite of Potential 14-3-3 Binding Partners. ACS Chem Biol 2020; 15:305-310. [PMID: 31971771 DOI: 10.1021/acschembio.9b00795] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Fusicoccin A (FC) is a diterpene glycoside that stabilizes protein-protein interactions (PPIs) between 14-3-3 adapter proteins and their phosphoprotein interaction partners. Recently, FC has gained attention for its pro-apoptotic and neuroprotective properties in cell culture. Although the exact molecular mechanism(s) is (are) unresolved, 14-3-3 PPIs are central to this activity. With the goal of refining the pharmacology of this chemotype, we conducted a systematic analysis of the structural features that govern FC-induced stabilization of 14-3-3 PPIs utilizing a C-terminal phosphorylation recognition motif. This study confirmed that a C-terminal amino acid with a small alkyl group is required for the interaction of FC at canonical C-terminal 14-3-3 PPI interfaces. Using bioinformatics, this structural insight was leveraged to assemble a database of 119 candidate 14-3-3 PPIs that can serve as targets for FC. This group includes a subset of proteins with experimentally determined C-terminal phosphosites that have not been explored as potential targets of FC.
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Affiliation(s)
- Ananya Sengupta
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
| | - Josue Liriano
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
| | - Brian G. Miller
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
| | - James H. Frederich
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, Florida 32306, United States
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Valenti D, Neves JF, Cantrelle FX, Hristeva S, Lentini Santo D, Obšil T, Hanoulle X, Levy LM, Tzalis D, Landrieu I, Ottmann C. Set-up and screening of a fragment library targeting the 14-3-3 protein interface. MEDCHEMCOMM 2019; 10:1796-1802. [PMID: 31814953 PMCID: PMC6839876 DOI: 10.1039/c9md00215d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/20/2019] [Indexed: 12/16/2022]
Abstract
Protein-protein interactions (PPIs) are at the core of regulation mechanisms in biological systems and consequently became an attractive target for therapeutic intervention. PPIs involving the adapter protein 14-3-3 are representative examples given the broad range of partner proteins forming a complex with one of its seven human isoforms. Given the challenges represented by the nature of these interactions, fragment-based approaches offer a valid alternative for the development of PPI modulators. After having assembled a fragment set tailored on PPIs' modulation, we started a screening campaign on the sigma isoform of 14-3-3 adapter proteins. Through the use of both mono- and bi-dimensional nuclear magnetic resonance spectroscopy measurements, coupled with differential scanning fluorimetry, three fragment hits were identified. These molecules bind the protein at two different regions distant from the usual binding groove highlighting new possibilities for selective modulation of 14-3-3 complexes.
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Affiliation(s)
- Dario Valenti
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 , Dortmund , Germany .
- Department of Biomedical Engineering and Institute for Complex Molecular Systems , Technische Universiteit Eindhoven , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands .
| | | | | | - Stanimira Hristeva
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 , Dortmund , Germany .
| | - Domenico Lentini Santo
- Department of Physical and Macromolecular Chemistry , Faculty of Science , Charles University , 12843 Prague , Czech Republic
| | - Tomáš Obšil
- Department of Physical and Macromolecular Chemistry , Faculty of Science , Charles University , 12843 Prague , Czech Republic
- Department of Structural Biology of Signaling Proteins , Division BIOCEV , Institute of Physiology of the Czech Academy of Sciences , Prumyslova 595, 252 50 Vestec , Czech Republic
| | - Xavier Hanoulle
- Univ. Lille , CNRS , UMR 8576 - UGSF , F-59000 Lille , France .
| | - Laura M Levy
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 , Dortmund , Germany .
| | - Dimitrios Tzalis
- Medicinal Chemistry , Taros Chemicals GmbH & Co. KG , Emil-Figge-Straße 76a , 44227 , Dortmund , Germany .
| | | | - Christian Ottmann
- Department of Biomedical Engineering and Institute for Complex Molecular Systems , Technische Universiteit Eindhoven , Den Dolech 2 , 5612 AZ Eindhoven , The Netherlands .
- Department of Chemistry , University of Duisburg-Essen , Universitätsstraße 7 , 45117 , Essen , Germany
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Lalle M, Fiorillo A. The protein 14-3-3: A functionally versatile molecule in Giardia duodenalis. ADVANCES IN PARASITOLOGY 2019; 106:51-103. [PMID: 31630760 DOI: 10.1016/bs.apar.2019.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Giardia duodenalis is a cosmopolitan zoonotic protozoan parasite causing giardiasis, one of the most common diarrhoeal diseases in human and animals. Beyond its public health relevance, Giardia represents a valuable and fascinating model microorganism. The deep-branching phylogenetic position of Giardia, its simple life cycle and its minimalistic genomic and cellular organization provide a unique opportunity to define basal and "ancestral" eukaryotic functions. The eukaryotic 14-3-3 protein family represents a distinct example of phosphoserine/phosphothreonine-binding proteins. The extended network of protein-protein interactions established by 14-3-3 proteins place them at the crossroad of multiple signalling pathways that regulate physiological and pathological cellular processes. Despite the remarkable insight on 14-3-3 protein in different organisms, from yeast to humans, so far little attention was given to the study of this protein in protozoan parasites. However, in the last years, research efforts have provided evidences on unique properties of the single 14-3-3 protein of Giardia and on its association in key aspects of Giardia life cycle. In the first part of this chapter, a general overview of the features commonly shared among 14-3-3 proteins in different organisms (i.e. structure, target recognition, mode of action and regulatory mechanisms) is included. The second part focus on the current knowledge on the biochemistry and biology of the Giardia 14-3-3 protein and on the possibility to use this protein as target to propose new strategies for developing innovative antigiardial therapy.
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Affiliation(s)
- Marco Lalle
- Department of Infectious Diseases, European Union Reference Laboratory for Parasites, Istituto Superiore di Sanità, Rome, Italy.
| | - Annarita Fiorillo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
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Valeur E, Narjes F, Ottmann C, Plowright AT. Emerging modes-of-action in drug discovery. MEDCHEMCOMM 2019; 10:1550-1568. [PMID: 31673315 PMCID: PMC6786009 DOI: 10.1039/c9md00263d] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022]
Abstract
An increasing focus on complex biology to cure diseases rather than merely treat symptoms has transformed how drug discovery can be approached. Instead of activating or blocking protein function, a growing repertoire of drug modalities can be leveraged or engineered to hijack cellular processes, such as translational regulation or degradation mechanisms. Drug hunters can therefore access a wider arsenal of modes-of-action to modulate biological processes and this review summarises these emerging strategies by highlighting the most representative examples of these approaches.
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Affiliation(s)
- Eric Valeur
- Medicinal Chemistry , Research and Early Development, Cardiovascular, Renal & Metabolism , BioPharmaceuticals R&D , AstraZeneca, Gothenburg , 43183 Mölndal , Sweden .
| | - Frank Narjes
- Medicinal Chemistry , Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA) , BioPharmaceuticals R&D , AstraZeneca, Gothenburg , 43183 Mölndal , Sweden
| | - Christian Ottmann
- Department of Biomedical Engineering and Institute for Complex Molecular Systems , Technische Universiteit Eindhoven , Den Dolech 2 , 5612 , AZ , Eindhoven , the Netherlands
- Department of Chemistry , University of Duisburg-Essen , Universitätsstraße 7 , 45117 , Essen , Germany
| | - Alleyn T Plowright
- Integrated Drug Discovery , Sanofi-Aventis Deutschland GmbH , Industriepark Höchst , D-65926 Frankfurt am Main , Germany
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Rational modulator design by exploitation of protein-protein complex structures. Future Med Chem 2019; 11:1015-1033. [PMID: 31141413 DOI: 10.4155/fmc-2018-0433] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The horizon of drug discovery is currently expanding to target and modulate protein-protein interactions (PPIs) in globular proteins and intrinsically disordered proteins that are involved in various diseases. To either interrupt or stabilize PPIs, the 3D structure of target protein-protein (or protein-peptide) complexes can be exploited to rationally design PPI modulators (inhibitors or stabilizers) through structure-based molecular design. In this review, we present an overview of experimental and computational methods that can be used to determine 3D structures of protein-protein complexes. Several approaches including rational and in silico methods that can be applied to design peptides, peptidomimetics and small compounds by utilization of determined 3D protein-protein/peptide complexes are summarized and illustrated.
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Wu G, Zhao T, Kang D, Zhang J, Song Y, Namasivayam V, Kongsted J, Pannecouque C, De Clercq E, Poongavanam V, Liu X, Zhan P. Overview of Recent Strategic Advances in Medicinal Chemistry. J Med Chem 2019; 62:9375-9414. [PMID: 31050421 DOI: 10.1021/acs.jmedchem.9b00359] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introducing novel strategies, concepts, and technologies that speed up drug discovery and the drug development cycle is of great importance both in the highly competitive pharmaceutical industry as well as in academia. This Perspective aims to present a "big-picture" overview of recent strategic innovations in medicinal chemistry and drug discovery.
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Affiliation(s)
- Gaochan Wu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Yuning Song
- Department of Clinical Pharmacy , Qilu Hospital of Shandong University , 250012 Ji'nan , China
| | - Vigneshwaran Namasivayam
- Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , 53121 Bonn , Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy , K.U. Leuven , Herestraat 49 Postbus 1043 (09.A097) , B-3000 Leuven , Belgium
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry, and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , 44 West Culture Road , 250012 Ji'nan , Shandong , P. R. China
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de Vink PJ, Andrei SA, Higuchi Y, Ottmann C, Milroy LG, Brunsveld L. Cooperativity basis for small-molecule stabilization of protein-protein interactions. Chem Sci 2019; 10:2869-2874. [PMID: 30996864 PMCID: PMC6429609 DOI: 10.1039/c8sc05242e] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 01/25/2019] [Indexed: 12/14/2022] Open
Abstract
A cooperativity framework to describe and interpret small-molecule stabilization of protein–protein interactions (PPI) is presented, which allows elucidating structure–activity relationships regarding cooperativity and intrinsic affinity.
A cooperativity framework to describe and interpret small-molecule stabilization of protein–protein interactions (PPI) is presented. The stabilization of PPIs is a versatile and emerging therapeutic strategy to target specific combinations of protein partners within the protein interactome. Currently, the potency of PPI stabilizers is typically expressed by their apparent affinity or EC50. Here, we propose that the effect of a PPI stabilizer be best described involving the cooperativity factor, α, between the stabilizer and binding partners in addition to the intrinsic affinity, KDII, of the stabilizer for one of the apo-proteins. By way of illustration, we combine fluorescence polarization measurements with thermodynamic modeling to determine the α and KDII for the PPI stabilization of 14-3-3 and TASK3 by fusicoccin-A (FC-A) and validate our approach by studying other PPI-partners of 14-3-3 proteins. Finally, we characterize a library of different stabilizer compounds, and perform structure–activity relationship studies in which molecular changes could be attributed to either changes in cooperativity or intrinsic affinity. Such insights should aid in the development of more effective protein–protein stabilizer drugs.
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Affiliation(s)
- Pim J de Vink
- Laboratory of Chemical Biology , Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600MB , Eindhoven , The Netherlands .
| | - Sebastian A Andrei
- Laboratory of Chemical Biology , Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600MB , Eindhoven , The Netherlands .
| | - Yusuke Higuchi
- The Institute of Scientific and Industrial Research , Osaka University , Ibaraki , Japan
| | - Christian Ottmann
- Laboratory of Chemical Biology , Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600MB , Eindhoven , The Netherlands . .,Department of Organic Chemistry , University of Duisburg-Essen , Germany
| | - Lech-Gustav Milroy
- Laboratory of Chemical Biology , Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600MB , Eindhoven , The Netherlands .
| | - Luc Brunsveld
- Laboratory of Chemical Biology , Department of Biomedical Engineering and Institute for Complex Molecular Systems , Eindhoven University of Technology , P. O. Box 513 , 5600MB , Eindhoven , The Netherlands .
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Camoni L, Visconti S, Aducci P, Marra M. From plant physiology to pharmacology: fusicoccin leaves the leaves. PLANTA 2019; 249:49-57. [PMID: 30467630 DOI: 10.1007/s00425-018-3051-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/14/2018] [Indexed: 06/09/2023]
Abstract
This review highlights 50 years of research on the fungal diterpene fusicoccin, during which the molecule went from a tool in plant physiology research to a pharmacological agent in treating animal diseases. Fusicoccin is a phytotoxic glycosylated diterpene produced by the fungus Phomopsis amygdali, a pathogen of almond and peach plants. Widespread interest in this molecule started when it was discovered that it is capable of causing stomate opening in all higher plants, thereby inducing wilting of leaves. Thereafter, FC became, and still is, a tool in plant physiology, due to its ability to influence a number of fundamental processes, which are dependent on the activation of the plasma membrane H+-ATPase. Molecular studies carried out in the last 20 years clarified details of the mechanism of proton pump stimulation, which involves the fusicoccin-mediated irreversible stabilization of the complex between the H+-ATPase and activatory 14-3-3 proteins. More recently, FC has been shown to influence cellular processes involving 14-3-3 binding to client proteins both in plants and animals. In this review, we report the milestones achieved in more than 50 years of research in plants and highlight recent advances in animals that have allowed this diterpene to be used as a 14-3-3 targeted drug.
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Affiliation(s)
- Lorenzo Camoni
- Department of Biology, University of Rome Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy.
| | - Sabina Visconti
- Department of Biology, University of Rome Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Patrizia Aducci
- Department of Biology, University of Rome Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
| | - Mauro Marra
- Department of Biology, University of Rome Tor Vergata, via della Ricerca Scientifica, 00133, Rome, Italy
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