1
|
Kapitonova AA, Perfilova KV, Cooley RB, Sluchanko NN. Phosphorylation code of human nucleophosmin includes four cryptic sites for hierarchical binding of 14-3-3 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580064. [PMID: 38405961 PMCID: PMC10888825 DOI: 10.1101/2024.02.13.580064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Nucleophosmin (NPM1) is the 46th most abundant human protein with many functions whose dysregulation leads to various cancers. Pentameric NPM1 resides in the nucleolus but can also shuttle to the cytosol. NPM1 is regulated by multisite phosphorylation, yet molecular consequences of site-specific NPM1 phosphorylation remain elusive. Here we identify four 14-3-3 protein binding sites in NPM1 concealed within its oligomerization and α-helical C-terminal domains that are found phosphorylated in vivo. By combining mutagenesis, in-cell phosphorylation and PermaPhos technology for site-directed incorporation of a non-hydrolyzable phosphoserine mimic, we show how phosphorylation promotes NPM1 monomerization and partial unfolding, to recruit 14-3-3 dimers with low-micromolar affinity. Using fluorescence anisotropy we quantified pairwise interactions of all seven human 14-3-3 isoforms with four recombinant NPM1 phosphopeptides and assessed their druggability by fusicoccin. This revealed a complex hierarchy of 14-3-3 affinities toward the primary (S48, S293) and secondary (S106, S260) sites, differentially modulated by the small molecule. As three of these 14-3-3 binding phospho-sites in NPM1 reside within signal sequences, this work highlights a key mechanism of NPM1 regulation by which NPM1 phosphorylation promotes 14-3-3 binding to control nucleocytoplasmic shuttling. It also provides further evidence that phosphorylation-induced structural rearrangements of globular proteins serve to expose otherwise cryptic 14-3-3-binding sites that are important for cellular function.
Collapse
Affiliation(s)
- Anna A. Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Kristina V. Perfilova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Richard B. Cooley
- GCE4All Center, Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, 97331, USA
| | - Nikolai N. Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| |
Collapse
|
2
|
Konstantinidou M, Visser EJ, Vandenboorn E, Chen S, Jaishankar P, Overmans M, Dutta S, Neitz RJ, Renslo AR, Ottmann C, Brunsveld L, Arkin MR. Structure-Based Optimization of Covalent, Small-Molecule Stabilizers of the 14-3-3σ/ERα Protein-Protein Interaction from Nonselective Fragments. J Am Chem Soc 2023; 145:20328-20343. [PMID: 37676236 PMCID: PMC10515640 DOI: 10.1021/jacs.3c05161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 09/08/2023]
Abstract
The stabilization of protein-protein interactions (PPIs) has emerged as a promising strategy in chemical biology and drug discovery. The identification of suitable starting points for stabilizing native PPIs and their subsequent elaboration into selective and potent molecular glues lacks structure-guided optimization strategies. We have previously identified a disulfide fragment that stabilized the hub protein 14-3-3σ bound to several of its clients, including ERα and C-RAF. Here, we show the structure-based optimization of the nonselective fragment toward selective and highly potent small-molecule stabilizers of the 14-3-3σ/ERα complex. The more elaborated molecular glues, for example, show no stabilization of 14-3-3σ/C-RAF up to 150 μM compound. Orthogonal biophysical assays, including mass spectrometry and fluorescence anisotropy, were used to establish structure-activity relationships. The binding modes of 37 compounds were elucidated with X-ray crystallography, which further assisted the concomitant structure-guided optimization. By targeting specific amino acids in the 14-3-3σ/ERα interface and locking the conformation with a spirocycle, the optimized covalent stabilizer 181 achieved potency, cooperativity, and selectivity similar to the natural product Fusicoccin-A. This case study showcases the value of addressing the structure, kinetics, and cooperativity for molecular glue development.
Collapse
Affiliation(s)
- Markella Konstantinidou
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Emira J. Visser
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Edmee Vandenboorn
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Sheng Chen
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Priyadarshini Jaishankar
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Maurits Overmans
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
for Complex Molecular Systems (ICMS), Eindhoven
University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Shubhankar Dutta
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - R. Jeffrey Neitz
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, United States
| | - Adam R. Renslo
- Department
of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, California 94143, 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
| | - 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, California 94143, United States
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Andlovic B, Heilmann G, Ninck S, Andrei SA, Centorrino F, Higuchi Y, Kato N, Brunsveld L, Arkin M, Menninger S, Choidas A, Wolf A, Klebl B, Kaschani F, Kaiser M, Eickhoff J, Ottmann C. IFNα primes cancer cells for Fusicoccin-induced cell death via 14-3-3 PPI stabilization. Cell Chem Biol 2023; 30:573-590.e6. [PMID: 37130519 DOI: 10.1016/j.chembiol.2023.04.005] [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: 07/31/2022] [Revised: 02/02/2023] [Accepted: 04/06/2023] [Indexed: 05/04/2023]
Abstract
The natural product family of the fusicoccanes (FCs) has been shown to display anti-cancer activity, especially when combined with established therapeutic agents. FCs stabilize 14-3-3 protein-protein interactions (PPIs). Here, we tested combinations of a small library of FCs with interferon α (IFNα) on different cancer cell lines and report a proteomics approach to identify the specific 14-3-3 PPIs that are induced by IFNα and stabilized by FCs in OVCAR-3 cells. Among the identified 14-3-3 target proteins are THEMIS2, receptor interacting protein kinase 2 (RIPK2), EIF2AK2, and several members of the LDB1 complex. Biophysical and structural biology studies confirm these 14-3-3 PPIs as physical targets of FC stabilization, and transcriptome as well as pathway analyses suggest possible explanations for the observed synergistic effect of IFNα/FC treatment on cancer cells. This study elucidates the polypharmacological effects of FCs in cancer cells and identifies potential targets from the vast interactome of 14-3-3s for therapeutic intervention in oncology.
Collapse
Affiliation(s)
- Blaž Andlovic
- 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; Lead Discovery Center GmbH, 44227 Dortmund, Germany
| | - Geronimo Heilmann
- Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Sabrina Ninck
- Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Sebastian A Andrei
- 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
| | - Federica Centorrino
- 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
| | - Yusuke Higuchi
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Ibaraki, Japan
| | - Nobuo Kato
- The Institute of Scientific and Industrial Research, Osaka University, Osaka, Ibaraki, Japan
| | - Luc Brunsveld
- 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
| | - Michelle Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Axel Choidas
- Lead Discovery Center GmbH, 44227 Dortmund, Germany
| | | | - Bert Klebl
- Lead Discovery Center GmbH, 44227 Dortmund, Germany
| | - Farnusch Kaschani
- Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Markus Kaiser
- Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Jan Eickhoff
- Lead Discovery Center GmbH, 44227 Dortmund, Germany
| | - 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.
| |
Collapse
|
5
|
Basistyi VS, Frederich JH. A sticky situation for targeted cancer therapy. Cell Chem Biol 2023; 30:569-572. [PMID: 37327777 DOI: 10.1016/j.chembiol.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/18/2023]
Abstract
In this issue of Cell Chemical Biology, Andlovic et al.1 unravel how certain fusicoccin toxins synergize with interferon-α to kill cancer cells. The results suggest that fusicoccins potentiate apoptosis by "sticking together" 14-3-3 protein-protein interactions.
Collapse
Affiliation(s)
- Vitalii S Basistyi
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - James H Frederich
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA.
| |
Collapse
|
6
|
Vinueza-Gavilanes R, Bravo-González JJ, Basurco L, Boncristiani C, Fernández-Irigoyen J, Santamaría E, Marcilla I, Pérez-Mediavilla A, Luquin MR, Vales A, González-Aseguinolaza G, Aymerich MS, Aragón T, Arrasate M. Stabilization of 14-3-3 protein-protein interactions with Fusicoccin-A decreases alpha-synuclein dependent cell-autonomous death in neuronal and mouse models. Neurobiol Dis 2023:106166. [PMID: 37245833 DOI: 10.1016/j.nbd.2023.106166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 05/30/2023] Open
Abstract
Synucleinopathies are a group of neurodegenerative diseases without effective treatment characterized by the abnormal aggregation of alpha-synuclein (aSyn) protein. Changes in levels or in the amino acid sequence of aSyn (by duplication/triplication of the aSyn gene or point mutations in the encoding region) cause familial cases of synucleinopathies. However, the specific molecular mechanisms of aSyn-dependent toxicity remain unclear. Increased aSyn protein levels or pathological mutations may favor abnormal protein-protein interactions (PPIs) that could either promote neuronal death or belong to a coping response program against neurotoxicity. Therefore, the identification and modulation of aSyn-dependent PPIs can provide new therapeutic targets for these diseases. To identify aSyn-dependent PPIs we performed a proximity biotinylation assay based on the promiscuous biotinylase BioID2. When expressed as a fusion protein, BioID2 biotinylates by proximity stable and transient interacting partners, allowing their identification by streptavidin affinity purification and mass spectrometry. The aSyn interactome was analyzed using BioID2-tagged wild-type (WT) and pathological mutant E46K aSyn versions in HEK293 cells. We found the 14-3-3 epsilon isoform as a common protein interactor for WT and E46K aSyn. 14-3-3 epsilon correlates with aSyn protein levels in brain regions of a transgenic mouse model overexpressing WT human aSyn. Using a neuronal model in which aSyn cell-autonomous toxicity is quantitatively scored by longitudinal survival analysis, we found that stabilization of 14-3-3 protein-proteins interactions with Fusicoccin-A (FC-A) decreases aSyn-dependent toxicity. Furthermore, FC-A treatment protects dopaminergic neuronal somas in the substantia nigra of a Parkinson's disease mouse model. Based on these results, we propose that the stabilization of 14-3-3 epsilon interaction with aSyn might reduce aSyn toxicity, and highlight FC-A as a potential therapeutic compound for synucleinopathies.
Collapse
Affiliation(s)
- Rodrigo Vinueza-Gavilanes
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
| | - Jorge Juan Bravo-González
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain.
| | - Leyre Basurco
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; Biochemistry and Genetics Department, School of Sciences, University of Navarra, Pamplona, Spain.
| | | | - Joaquín Fernández-Irigoyen
- Proteored-Institute of Health Carlos III (ISCIII), Clinical Neuroproteomics Unit, Navarrabiomed, Navarra Health Department, Public University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Enrique Santamaría
- Proteored-Institute of Health Carlos III (ISCIII), Clinical Neuroproteomics Unit, Navarrabiomed, Navarra Health Department, Public University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Irene Marcilla
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Alberto Pérez-Mediavilla
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; Biochemistry and Genetics Department, School of Sciences, University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - María Rosario Luquin
- Department of Neurology, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Africa Vales
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Gloria González-Aseguinolaza
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - María Soledad Aymerich
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; Biochemistry and Genetics Department, School of Sciences, University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Tomás Aragón
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| | - Montserrat Arrasate
- Gene Therapy and Regulation of Gene Expression Program, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain; Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain; IdiSNA (Navarra Institute for Health Research), Pamplona, Spain.
| |
Collapse
|
7
|
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.
Collapse
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
| | | |
Collapse
|
8
|
Zhu P, Nguyen KT, Estelle AB, Sluchanko NN, Mehl RA, Cooley RB. Genetic encoding of 3-nitro-tyrosine reveals the impacts of 14-3-3 nitration on client binding and dephosphorylation. Protein Sci 2023; 32:e4574. [PMID: 36691781 PMCID: PMC9926477 DOI: 10.1002/pro.4574] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/25/2023]
Abstract
14-3-3 proteins are central hub regulators of hundreds of phosphorylated "client" proteins. They are subject to over 60 post-translational modifications (PTMs), yet little is known how these PTMs alter 14-3-3 function and its ability to regulate downstream signaling pathways. An often neglected, but well-documented 14-3-3 PTM found under physiological and immune-stimulatory conditions is the conversion of tyrosine to 3-nitro-tyrosine at several Tyr sites, two of which are located at sites considered important for 14-3-3 function: Y130 (β-isoform numbering) is located in the primary phospho-client peptide-binding groove, while Y213 is found on a secondary binding site that engages with clients for full 14-3-3/client complex formation and client regulation. By genetically encoding 3-nitro-tyrosine, we sought to understand if nitration at Y130 and Y213 effectively modulated 14-3-3 structure, function, and client complexation. The 1.5 Å resolution crystal structure of 14-3-3 nitrated at Y130 showed the nitro group altered the conformation of key residues in the primary binding site, while functional studies confirmed client proteins failed to bind this variant of 14-3-3. But, in contrast to other client-binding deficient variants, it did not localize to the nucleus. The 1.9 Å resolution structure of 14-3-3 nitrated at Y213 revealed unusual flexibility of its C-terminal α-helix resulting in domain swapping, suggesting additional structural plasticity though its relevance is not clear as this nitrated form retained its ability to bind clients. Collectively, our data suggest that nitration of 14-3-3 will alter downstream signaling systems, and if uncontrolled could result in global dysregulation of the 14-3-3 interactome.
Collapse
Affiliation(s)
- Phillip Zhu
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Kyle T. Nguyen
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Aidan B. Estelle
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Nikolai N. Sluchanko
- Federal Research Center of Biotechnology of the Russian Academy of SciencesA.N. Bach Institute of BiochemistryMoscowRussia
| | - Ryan A. Mehl
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| | - Richard B. Cooley
- Department of Biochemistry and Biophysics, 2011 Agricultural and Life SciencesOregon State UniversityCorvallisOregonUSA
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Li F, Aljahdali IAM, Ling X. Molecular Glues: Capable Protein-Binding Small Molecules That Can Change Protein-Protein Interactions and Interactomes for the Potential Treatment of Human Cancer and Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23116206. [PMID: 35682885 PMCID: PMC9181451 DOI: 10.3390/ijms23116206] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 12/29/2022] Open
Abstract
Molecular glue (MG) compounds are a type of unique small molecule that can change the protein–protein interactions (PPIs) and interactomes by degrading, stabilizing, or activating the target protein after their binging. These small-molecule MGs are gradually being recognized for their potential application in treating human diseases, including cancer. Evidence suggests that small-molecule MG compounds could essentially target any proteins, which play critical roles in human disease etiology, where many of these protein targets were previously considered undruggable. Intriguingly, most MG compounds with high efficacy for cancer treatment can glue on and control multiple key protein targets. On the other hand, a single key protein target can also be glued by multiple MG compounds with distinct chemical structures. The high flexibility of MG–protein interaction profiles provides rich soil for the growth and development of small-molecule MG compounds that can be used as molecular tools to assist in unraveling disease mechanisms, and they can also facilitate drug development for the treatment of human disease, especially human cancer. In this review, we elucidate this concept by using various types of small-molecule MG compounds and their corresponding protein targets that have been documented in the literature.
Collapse
Affiliation(s)
- Fengzhi Li
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (I.A.M.A.); (X.L.)
- Developmental Therapeutics (DT) Program, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Gastrointestinal Translational Research Group (GI TRG), Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
- Correspondence: ; Tel.: +1-(716)-845-4398; Fax: +1-(716)-845-8857
| | - Ieman A. M. Aljahdali
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (I.A.M.A.); (X.L.)
- Department of Cellular & Molecular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Xiang Ling
- Department of Pharmacology & Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (I.A.M.A.); (X.L.)
- Canget BioTekpharma LLC, Buffalo, NY 14203, USA
| |
Collapse
|
11
|
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.
Collapse
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.
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Pathways to Parkinson's disease: a spotlight on 14-3-3 proteins. NPJ Parkinsons Dis 2021; 7:85. [PMID: 34548498 PMCID: PMC8455551 DOI: 10.1038/s41531-021-00230-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/23/2021] [Indexed: 02/08/2023] Open
Abstract
14-3-3s represent a family of highly conserved 30 kDa acidic proteins. 14-3-3s recognize and bind specific phospho-sequences on client partners and operate as molecular hubs to regulate their activity, localization, folding, degradation, and protein-protein interactions. 14-3-3s are also associated with the pathogenesis of several diseases, among which Parkinson's disease (PD). 14-3-3s are found within Lewy bodies (LBs) in PD patients, and their neuroprotective effects have been demonstrated in several animal models of PD. Notably, 14-3-3s interact with some of the major proteins known to be involved in the pathogenesis of PD. Here we first provide a detailed overview of the molecular composition and structural features of 14-3-3s, laying significant emphasis on their peculiar target-binding mechanisms. We then briefly describe the implication of 14-3-3s in the central nervous system and focus on their interaction with LRRK2, α-Synuclein, and Parkin, three of the major players in PD onset and progression. We finally discuss how different types of small molecules may interfere with 14-3-3s interactome, thus representing a valid strategy in the future of drug discovery.
Collapse
|
14
|
The Surprising Story of Fusicoccin: A Wilt-Inducing Phytotoxin, a Tool in Plant Physiology and a 14-3-3-Targeted Drug. Biomolecules 2021; 11:biom11091393. [PMID: 34572605 PMCID: PMC8470340 DOI: 10.3390/biom11091393] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 12/13/2022] Open
Abstract
Fusicoccin is the α glucoside of a carbotricyclic diterpene, produced by the fungus Phomopsis amygdali (previously classified as Fusicoccum amygdali), the causal agent of almond and peach canker disease. A great interest in this molecule started when it was discovered that it brought about an irreversible stomata opening of higher plants, thereby inducing the wilting of their leaves. Since then, several studies were carried out to elucidate its biological activity, biosynthesis, structure, structure-activity relationships and mode of action. After sixty years of research and more than 1800 published articles, FC is still the most studied phytotoxin and one of the few whose mechanism of action has been elucidated in detail. The ability of FC to stimulate several fundamental plant processes depends on its ability to activate the plasma membrane H+-ATPase, induced by eliciting the association of 14-3-3 proteins, a class of regulatory molecules widespread in eukaryotes. This discovery renewed interest in FC and prompted more recent studies aimed to ascertain the ability of the toxin to influence the interaction between 14-3-3 proteins and their numerous client proteins in animals, involved in the regulation of basic cellular processes and in the etiology of different diseases, including cancer. This review covers the different aspects of FC research partially treated in different previous reviews, starting from its discovery in 1964, with the aim to outline the extraordinary pathway which led this very uncommon diterpenoid to evolve from a phytotoxin into a tool in plant physiology and eventually into a 14-3-3-targeted drug.
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Gogl G, Tugaeva KV, Eberling P, Kostmann C, Trave G, Sluchanko NN. Hierarchized phosphotarget binding by the seven human 14-3-3 isoforms. Nat Commun 2021; 12:1677. [PMID: 33723253 PMCID: PMC7961048 DOI: 10.1038/s41467-021-21908-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/17/2021] [Indexed: 02/07/2023] Open
Abstract
The seven 14-3-3 isoforms are highly abundant human proteins encoded by similar yet distinct genes. 14-3-3 proteins recognize phosphorylated motifs within numerous human and viral proteins. Here, we analyze by X-ray crystallography, fluorescence polarization, mutagenesis and fusicoccin-mediated modulation the structural basis and druggability of 14-3-3 binding to four E6 oncoproteins of tumorigenic human papillomaviruses. 14-3-3 isoforms bind variant and mutated phospho-motifs of E6 and unrelated protein RSK1 with different affinities, albeit following an ordered affinity ranking with conserved relative KD ratios. Remarkably, 14-3-3 isoforms obey the same hierarchy when binding to most of their established targets, as supported by literature and a recent human complexome map. This knowledge allows predicting proportions of 14-3-3 isoforms engaged with phosphoproteins in various tissues. Notwithstanding their individual functions, cellular concentrations of 14-3-3 may be collectively adjusted to buffer the strongest phosphorylation outbursts, explaining their expression variations in different tissues and tumors.
Collapse
Affiliation(s)
- Gergo Gogl
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France.
| | - Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Pascal Eberling
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Camille Kostmann
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Gilles Trave
- Equipe Labellisee Ligue 2015, Department of Integrated Structural Biology, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France.
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.
| |
Collapse
|
17
|
Harmange Magnani CS, Maimone TJ. Fusicoccin Keeps Getting Stickier: Modulation of an Adaptor Protein Interactome with a Molecular Glue Leads to Neurite Outgrowth. Cell Chem Biol 2021; 27:635-637. [PMID: 32559498 DOI: 10.1016/j.chembiol.2020.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Many traditional drugs inhibit enzyme function; in contrast, some naturally "sticky" small molecules can stabilize protein-protein interactions. In this issue of Cell Chemical Biology, Kaplan et al. (2020) explore regulation of the 14-3-3 interactome by a small-molecule molecular glue leading to neurite outgrowth through a polypharmacological mechanism.
Collapse
Affiliation(s)
| | - Thomas J Maimone
- Department of Chemistry, University of California-Berkeley, Berkeley, CA 94720, USA.
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Gannon M, Yacoubian TA. 007 (x2)-3-3: 14-3-3 Targeted Compounds as Double Agents. Trends Pharmacol Sci 2020; 41:431-433. [PMID: 32402470 DOI: 10.1016/j.tips.2020.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 05/03/2020] [Indexed: 11/28/2022]
Abstract
14-3-3 Proteins enact a range of cellular functions through protein-protein interactions (PPIs) with client proteins. Kaplan and colleagues recently demonstrated that a semisynthetic compound was able to selectively stabilize or disrupt specific interactions, depending on the binding partner. This finding presents an exciting possibility of designing other 14-3-3 compounds to regulate critical 14-3-3 interactions.
Collapse
Affiliation(s)
- Mary Gannon
- 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.
| |
Collapse
|