1
|
van Veldhuisen TW, Verwiel MAM, Novosedlik S, Brunsveld L, van Hest JCM. Competitive protein recruitment in artificial cells. Commun Chem 2024; 7:148. [PMID: 38942913 PMCID: PMC11213860 DOI: 10.1038/s42004-024-01229-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024] Open
Abstract
Living cells can modulate their response to environmental cues by changing their sensitivities for molecular signals. Artificial cells are promising model platforms to study intercellular communication, but populations with such differentiated behavior remain underexplored. Here, we show the affinity-regulated exchange of proteins in distinct populations of coacervate-based artificial cells via protein-protein interactions (PPI) of the hub protein 14-3-3. By loading different coacervates with different isoforms of 14-3-3, featuring varying PPI affinities, a client peptide is directed to the more strongly recruiting coacervates. By switching affinity of client proteins through phosphorylation, weaker binding partners can be outcompeted for their 14-3-3 binding, inducing their release from artificial cells. Combined, a communication system between coacervates is constructed, which leads to the transport of client proteins from strongly recruiting coacervates to weakly recruiting ones. The results demonstrate that affinity engineering and competitive binding can provide directed protein uptake and exchange between artificial cells.
Collapse
Affiliation(s)
- Thijs W van Veldhuisen
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Madelief A M Verwiel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Sebastian Novosedlik
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Jan C M van Hest
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
| |
Collapse
|
2
|
Wu D, Li Y, Zheng L, Xiao H, Ouyang L, Wang G, Sun Q. Small molecules targeting protein-protein interactions for cancer therapy. Acta Pharm Sin B 2023; 13:4060-4088. [PMID: 37799384 PMCID: PMC10547922 DOI: 10.1016/j.apsb.2023.05.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/28/2023] [Accepted: 05/22/2023] [Indexed: 10/07/2023] Open
Abstract
Protein-protein interactions (PPIs) are fundamental to many biological processes that play an important role in the occurrence and development of a variety of diseases. Targeting the interaction between tumour-related proteins with emerging small molecule drugs has become an attractive approach for treatment of human diseases, especially tumours. Encouragingly, selective PPI-based therapeutic agents have been rapidly advancing over the past decade, providing promising perspectives for novel therapies for patients with cancer. In this review we comprehensively clarify the discovery and development of small molecule modulators of PPIs from multiple aspects, focusing on PPIs in disease, drug design and discovery strategies, structure-activity relationships, inherent dilemmas, and future directions.
Collapse
Affiliation(s)
- Defa Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Yang Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Lang Zheng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Huan Xiao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Liang Ouyang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Qiu Sun
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
- West China Medical Publishers, West China Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
3
|
Hazegh Nikroo A, Lemmens LJM, Wezeman T, Ottmann C, Merkx M, Brunsveld L. Switchable Control of Scaffold Protein Activity via Engineered Phosphoregulated Autoinhibition. ACS Synth Biol 2022; 11:2464-2472. [PMID: 35765959 PMCID: PMC9295147 DOI: 10.1021/acssynbio.2c00122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Scaffold proteins
operate as organizing hubs to enable high-fidelity
signaling, fulfilling crucial roles in the regulation of cellular
processes. Bottom-up construction of controllable scaffolding platforms
is attractive for the implementation of regulatory processes in synthetic
biology. Here, we present a modular and switchable synthetic scaffolding
system, integrating scaffold-mediated signaling with switchable kinase/phosphatase
input control. Phosphorylation-responsive inhibitory peptide motifs
were fused to 14-3-3 proteins to generate dimeric protein scaffolds
with appended regulatory peptide motifs. The availability of the scaffold
for intermolecular partner protein binding could be lowered up to
35-fold upon phosphorylation of the autoinhibition motifs, as demonstrated
using three different kinases. In addition, a hetero-bivalent autoinhibitory
platform design allowed for dual-kinase input regulation of scaffold
activity. Reversibility of the regulatory platform was illustrated
through phosphatase-controlled abrogation of autoinhibition, resulting
in full recovery of 14-3-3 scaffold activity.
Collapse
Affiliation(s)
- Arjan Hazegh Nikroo
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Lenne J M Lemmens
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Tim Wezeman
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, Eindhoven, 5612AZ Arizona, The Netherlands
| |
Collapse
|
4
|
Tei R, Baskin JM. Induced proximity tools for precise manipulation of lipid signaling. Curr Opin Chem Biol 2021; 65:93-100. [PMID: 34304140 DOI: 10.1016/j.cbpa.2021.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/03/2021] [Accepted: 06/18/2021] [Indexed: 01/07/2023]
Abstract
Lipids are highly dynamic molecules that, due to their hydrophobicity, are spatially confined to membrane environments. From these locations, certain privileged lipids serve as signaling molecules. For understanding the biological functions of subcellular pools of signaling lipids, induced proximity tools have been invaluable. These methods involve controlled heterodimerization, by either small-molecule or light triggers, of functional proteins. In the arena of lipid signaling, induced proximity tools can recruit lipid-metabolizing enzymes to manipulate lipid signaling and create artificial tethers between organelle membranes to control lipid trafficking pathways at membrane contact sites. Here, we review recent advances in methodology development and biological application of chemical-induced and light-induced proximity tools for manipulating lipid metabolism, trafficking, and signaling.
Collapse
Affiliation(s)
- Reika Tei
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853, USA.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
|
7
|
Lemmens LM, Ottmann C, Brunsveld L. Conjugated Protein Domains as Engineered Scaffold Proteins. Bioconjug Chem 2020; 31:1596-1603. [PMID: 32374984 PMCID: PMC7303964 DOI: 10.1021/acs.bioconjchem.0c00183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/05/2020] [Indexed: 01/12/2023]
Abstract
Assembly of proteins into higher-order complexes generates specificity and selectivity in cellular signaling. Signaling complex formation is facilitated by scaffold proteins that use modular scaffolding domains, which recruit specific pathway enzymes. Multimerization and recombination of these conjugated native domains allows the generation of libraries of engineered multidomain scaffold proteins. Analysis of these engineered proteins has provided molecular insight into the regulatory mechanism of the native scaffold proteins and the applicability of these synthetic variants. This topical review highlights the use of engineered, conjugated multidomain scaffold proteins on different length scales in the context of synthetic signaling pathways, metabolic engineering, liquid-liquid phase separation, and hydrogel formation.
Collapse
Affiliation(s)
- Lenne
J. M. Lemmens
- 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
| | - 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
| |
Collapse
|
8
|
Lemmens LJM, Roodhuizen JAL, de Greef TFA, Markvoort AJ, Brunsveld L. Designed Asymmetric Protein Assembly on a Symmetric Scaffold. Angew Chem Int Ed Engl 2020; 59:12113-12121. [PMID: 32333708 PMCID: PMC7383506 DOI: 10.1002/anie.202003626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Indexed: 01/17/2023]
Abstract
Cellular signaling is regulated by the assembly of proteins into higher‐order complexes. Bottom‐up creation of synthetic protein assemblies, especially asymmetric complexes, is highly challenging. Presented here is the design and implementation of asymmetric assembly of a ternary protein complex facilitated by Rosetta modeling and thermodynamic analysis. The wild‐type symmetric CT32–CT32 interface of the 14‐3‐3–CT32 complex was targeted, ultimately favoring asymmetric assembly on the 14‐3‐3 scaffold. Biochemical studies, supported by mass‐balance models, allowed characterization of the parameters driving asymmetric assembly. Importantly, our work reveals that both the individual binding affinities and cooperativity between the assembling components are crucial when designing higher‐order protein complexes. Enzyme complementation on the 14‐3‐3 scaffold highlighted that interface engineering of a symmetric ternary complex generates asymmetric protein complexes with new functions.
Collapse
Affiliation(s)
- Lenne J M Lemmens
- 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
| | - Job A L Roodhuizen
- Computational Biology Group, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600, MB, Eindhoven, The Netherlands
| | - Tom F A de Greef
- Computational Biology Group, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600, MB, Eindhoven, The Netherlands.,Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Albert J Markvoort
- Computational Biology Group, 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
| |
Collapse
|
9
|
Xu X, Lemmens LJM, den Hamer A, Merkx M, Ottmann C, Brunsveld L. Modular bioengineered kinase sensors via scaffold protein-mediated split-luciferase complementation. Chem Sci 2020; 11:5532-5536. [PMID: 32874496 PMCID: PMC7446724 DOI: 10.1039/d0sc00074d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/11/2020] [Indexed: 01/07/2023] Open
Abstract
Phosphorylation is a key regulation event in cellular signaling. To sense the underlying kinase activity, we engineered modular and easy adaptable serine kinase sensors for the exemplary kinases PKA, PKB and CHK1.
Phosphorylation is a key regulation event in cellular signaling. Sensing the underlying kinase activity is of crucial importance for its fundamental understanding and for drug development. For this, modular kinase activity sensing concepts are urgently needed. We engineered modular serine kinase sensors based on complementation of split NanoBiT luciferase on protein assembly platforms generated from the scaffold protein 14-3-3. The bioengineered platforms are modular and easy adaptable as exemplary shown using novel sensors for the kinases PKA, PKB, and CHK1. Two designs were conceptualized, both relying on binding of defined mono- or bivalent kinase recognition motifs to the 14-3-3 platform upon phosphorylation, resulting in reconstitution of active split-luciferase. Especially the design based on double phosphorylation and bivalent 14-3-3 binding exhibits high efficiency for signal amplification (>1000-fold) and sensitivity to specific kinases, including in cellular lysates.
Collapse
Affiliation(s)
- Xiaolu Xu
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Lenne J M Lemmens
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Anniek den Hamer
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Maarten Merkx
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Christian Ottmann
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| | - Luc Brunsveld
- Laboratory of Chemical Biology , Department of Biomedical Engineering , Institute for Complex Molecular Systems (ICMS) , Eindhoven University of Technology , Den Dolech 2 , 5612AZ , Eindhoven , the Netherlands .
| |
Collapse
|
10
|
Kundu A, Shelar S, Ghosh AP, Ballestas M, Kirkman R, Nam H, Brinkley GJ, Karki S, Mobley JA, Bae S, Varambally S, Sudarshan S. 14-3-3 proteins protect AMPK-phosphorylated ten-eleven translocation-2 (TET2) from PP2A-mediated dephosphorylation. J Biol Chem 2020; 295:1754-1766. [PMID: 31901078 PMCID: PMC7008385 DOI: 10.1074/jbc.ra119.011089] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/19/2019] [Indexed: 11/06/2022] Open
Abstract
Ten-eleven translocation-2 (TET2) is a member of the methylcytosine dioxygenase family of enzymes and has been implicated in cancer and aging because of its role as a global epigenetic modifier. TET2 has a large N-terminal domain and a catalytic C-terminal region. Previous reports have demonstrated that the TET2 catalytic domain remains active independently of the N-terminal domain. As such, the function of the N terminus of this large protein remains poorly characterized. Here, using yeast two-hybrid screening, co-immunoprecipitation, and several biochemical assays, we found that several isoforms of the 14-3-3 family of proteins bind TET2. 14-3-3 proteins bound TET2 when it was phosphorylated at Ser-99. In particular, we observed that AMP-activated protein kinase-mediated phosphorylation at Ser-99 promotes TET2 stability and increases global DNA 5-hydroxymethylcytosine levels. The interaction of 14-3-3 proteins with TET2 protected the Ser-99 phosphorylation, and disruption of this interaction both reduced TET2 phosphorylation and decreased TET2 stability. Furthermore, we noted that protein phosphatase 2A can interact with TET2 and dephosphorylate Ser-99. Collectively, these results provide detailed insights into the role of the TET2 N-terminal domain in TET2 regulation. Moreover, they reveal the dynamic nature of TET2 protein regulation that could have therapeutic implications for disease states resulting from reduced TET2 levels or activity.
Collapse
Affiliation(s)
- Anirban Kundu
- Department of Urology, University of Alabama, Birmingham, Alabama 35294
| | - Sandeep Shelar
- Department of Urology, University of Alabama, Birmingham, Alabama 35294
| | - Arindam P Ghosh
- Department of Urology, University of Alabama, Birmingham, Alabama 35294
| | - Mary Ballestas
- Department of Genetics, University of Alabama, Birmingham, Alabama 35294
| | - Richard Kirkman
- Department of Urology, University of Alabama, Birmingham, Alabama 35294
| | - Hyeyoung Nam
- Department of Urology, University of Alabama, Birmingham, Alabama 35294
| | | | - Suman Karki
- Department of Urology, University of Alabama, Birmingham, Alabama 35294
| | - James A Mobley
- Department of Anesthesiology and Perioperative Medicine, University of Alabama, Birmingham, Alabama 35294
| | - Sejong Bae
- Department of Medicine, University of Alabama, Birmingham, Alabama 35294
| | | | - Sunil Sudarshan
- Department of Urology, University of Alabama, Birmingham, Alabama 35294; Birmingham Veterans Affairs Medical Center, Birmingham, Alabama 35233.
| |
Collapse
|
11
|
Chhetri BK, Lavoie S, Sweeney-Jones AM, Kubanek J. Recent trends in the structural revision of natural products. Nat Prod Rep 2019; 35:514-531. [PMID: 29623331 DOI: 10.1039/c8np00011e] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: 2012 to 2017 This article reviews recent reports on the structural revision of natural products. Through a critical assessment of the original and revised published structures, the article addresses why each structure was targeted for revision, discusses the techniques and key discrepancies that led to the proposal of the revised structure, and offers measures that may have been taken during the original structure determination to prevent error. With the revised structures in hand, weaknesses of original proposals are assessed, providing a better understanding on the logic behind structure determination.
Collapse
Affiliation(s)
- Bhuwan Khatri Chhetri
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| | | | | | | |
Collapse
|
12
|
Aper SJA, den Hamer A, Wouters SFA, Lemmens LJM, Ottmann C, Brunsveld L, Merkx M. Protease-Activatable Scaffold Proteins as Versatile Molecular Hubs in Synthetic Signaling Networks. ACS Synth Biol 2018; 7:2216-2225. [PMID: 30125482 PMCID: PMC6154215 DOI: 10.1021/acssynbio.8b00217] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protease signaling and scaffold-induced control of protein-protein interactions represent two important mechanisms for intracellular signaling. Here we report a generic and modular approach to control the activity of scaffolding proteins by protease activity, creating versatile molecular platforms to construct synthetic signaling networks. Using 14-3-3 proteins as a structurally well-characterized and important class of scaffold proteins, three different architectures were explored to achieve optimal protease-mediated control of scaffold activity, fusing either one or two monovalent inhibitory ExoS peptides or a single bivalent ExoS peptide to T14-3-3 using protease-cleavable linkers. Analysis of scaffolding activity before and after protease-induced cleavage revealed optimal control of 14-3-3 activity for the system that contained monovalent ExoS peptides fused to both the N-and C-terminus, each blocking a single T14-3-3 binding site. The protease-activatable 14-3-3 scaffolds were successfully applied to construct a three-step signaling cascade in which dimerization and activation of FGG-caspase-9 on an orthogonal supramolecular platform resulted in activation of a 14-3-3 scaffold, which in turn allowed 14-3-3-templated complementation of a split-luciferase. In addition, by combining 14-3-3-templated activation of caspase-9 with a caspase-9-activatable 14-3-3 scaffold, the first example of a synthetic self-activating protease signaling network was created. Protease-activatable 14-3-3 proteins thus represent a modular platform whose properties can be rationally engineered to fit different applications, both to create artificial in vitro synthetic molecular networks and as a novel signaling hub to re-engineer intracellular signaling pathways.
Collapse
Affiliation(s)
- Stijn J. A. Aper
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Anniek den Hamer
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Simone F. A. Wouters
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lenne J. M. Lemmens
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| |
Collapse
|
13
|
Zeng G, Wang Y, Bruchez MP, Liang FS. Self-Reporting Chemically Induced Protein Proximity System Based on a Malachite Green Derivative and the L5** Fluorogen Activating Protein. Bioconjug Chem 2018; 29:3010-3015. [PMID: 30016083 DOI: 10.1021/acs.bioconjchem.8b00415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A unique chemically induced proximity method is engineered based on mutant antibody VL domain using a fluorogenic malachite green derivative as the inducer, which gives fluorescent signals upon VL domain dimerization while simultaneously inducing downstream biological effects.
Collapse
Affiliation(s)
- Guihua Zeng
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , United States
| | - Yi Wang
- Department of Chemistry, Department of Biological Sciences, and Molecular Biosensor and Imaging Center , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Marcel P Bruchez
- Department of Chemistry, Department of Biological Sciences, and Molecular Biosensor and Imaging Center , Carnegie Mellon University , Pittsburgh , Pennsylvania 15213 , United States
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , United States
| |
Collapse
|
14
|
Hu Z, Sun W, Li F, Guan J, Lu Y, Liu J, Tang Y, Du G, Xue Y, Luo Z, Wang J, Zhu H, Zhang Y. Fusicoccane-Derived Diterpenoids from Alternaria brassicicola: Investigation of the Structure–Stability Relationship and Discovery of an IKKβ Inhibitor. Org Lett 2018; 20:5198-5202. [DOI: 10.1021/acs.orglett.8b02137] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
15
|
Zhao W, Nguyen H, Zeng G, Gao D, Yan H, Liang FS. A chemically induced proximity system engineered from the plant auxin signaling pathway. Chem Sci 2018; 9:5822-5827. [PMID: 30079194 PMCID: PMC6050582 DOI: 10.1039/c8sc02353k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 06/09/2018] [Indexed: 12/16/2022] Open
Abstract
Methods based on chemically induced proximity (CIP) serve as powerful tools to control cellular processes in a temporally specific manner. To expand the repertoire of CIP systems available for studies of cellular processes, we engineered the plant auxin signaling pathway to create a new indole-3-acetic acid (IAA) based CIP method. Auxin-induced protein degradation that occurs in the natural pathway was eliminated in the system. The new IAA based method is both readily inducible and reversible, and used to control the production of therapeutic proteins that induced the apoptosis of cancer cells. The approach is also orthogonal to existing CIP systems and used to construct a biological Boolean logic gate controlling gene expression system. We believe that the new CIP method will be applicable to the artificial control and dissection of complex cellular functions.
Collapse
Affiliation(s)
- Weiye Zhao
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
| | - Huong Nguyen
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
| | - Guihua Zeng
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
| | - Dan Gao
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
| | - Hao Yan
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
| | - Fu-Sen Liang
- Department of Chemistry and Chemical Biology , University of New Mexico , 300 Terrace Street NE , Albuquerque , New Mexico 87131 , USA .
| |
Collapse
|
16
|
Salvati AE, Law JA, Liriano J, Frederich JH. Modular access to functionalized 5-8-5 fused ring systems via a photoinduced cycloisomerization reaction. Chem Sci 2018; 9:5389-5393. [PMID: 30009010 PMCID: PMC6009507 DOI: 10.1039/c8sc00999f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/22/2018] [Indexed: 12/13/2022] Open
Abstract
A 5-8-5 carbocyclic ring system forms the core of over 30 distinct natural products. Several members of this family have gained attention for their diverse activity in cell culture. In these cases, biological function is mediated by the arrangement of substituents around a conserved 5-8-5 nucleus. Despite the potential applications of this privileged substructure in medicinal chemistry, modular strategies for its assembly are underdeveloped. Herein, we describe a cycloisomerization reaction that forms the 5-8-5 framework directly. This strategy uniquely allows access to gram quantities of this valuable scaffold in four steps.
Collapse
Affiliation(s)
- Anna E Salvati
- Department of Chemistry and Biochemistry , Florida State University , 95 Cheiftan Way , Tallahassee , FL 32306 , USA .
| | - James A Law
- Department of Chemistry and Biochemistry , Florida State University , 95 Cheiftan Way , Tallahassee , FL 32306 , USA .
| | - Josue Liriano
- Department of Chemistry and Biochemistry , Florida State University , 95 Cheiftan Way , Tallahassee , FL 32306 , USA .
| | - James H Frederich
- Department of Chemistry and Biochemistry , Florida State University , 95 Cheiftan Way , Tallahassee , FL 32306 , USA .
| |
Collapse
|
17
|
Ehlers M, Grad JN, Mittal S, Bier D, Mertel M, Ohl L, Bartel M, Briels J, Heimann M, Ottmann C, Sanchez-Garcia E, Hoffmann D, Schmuck C. Rational Design, Binding Studies, and Crystal-Structure Evaluation of the First Ligand Targeting the Dimerization Interface of the 14-3-3ζ Adapter Protein. Chembiochem 2018; 19:591-595. [DOI: 10.1002/cbic.201700588] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Martin Ehlers
- Institute of Organic Chemistry; University of Duisburg-Essen (Germany); Universitätsstrasse 7 45141 Essen Germany
| | - Jean-Noël Grad
- Department of Bioinformatics and Computational Biophysics; ZMB/Faculty of Biology; University of Duisburg-Essen; 45117 Essen Germany
| | - Sumit Mittal
- Computational Biochemistry; University of Duisburg-Essen; Universitätsstrasse 3 45141 Essen Germany
| | - David Bier
- Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45141 Essen Germany
| | - Marcel Mertel
- Institute of Organic Chemistry; University of Duisburg-Essen (Germany); Universitätsstrasse 7 45141 Essen Germany
| | - Ludwig Ohl
- Department of Bioinformatics and Computational Biophysics; ZMB/Faculty of Biology; University of Duisburg-Essen; 45117 Essen Germany
| | - Maria Bartel
- Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45141 Essen Germany
- Department of Biomedical Engineering and; Institute for Complex Molecular Systems; Technische Universiteit Eindhoven; P. O. Box 513 5600 MB Eindhoven Netherlands
| | - Jeroen Briels
- Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45141 Essen Germany
- Department of Biomedical Engineering and; Institute for Complex Molecular Systems; Technische Universiteit Eindhoven; P. O. Box 513 5600 MB Eindhoven Netherlands
| | - Marius Heimann
- Institute of Organic Chemistry; University of Duisburg-Essen (Germany); Universitätsstrasse 7 45141 Essen Germany
| | - Christian Ottmann
- Department of Chemistry; University of Duisburg-Essen; Universitätsstrasse 7 45141 Essen Germany
- Department of Biomedical Engineering and; Institute for Complex Molecular Systems; Technische Universiteit Eindhoven; P. O. Box 513 5600 MB Eindhoven Netherlands
| | - Elsa Sanchez-Garcia
- Computational Biochemistry; University of Duisburg-Essen; Universitätsstrasse 3 45141 Essen Germany
| | - Daniel Hoffmann
- Department of Bioinformatics and Computational Biophysics; ZMB/Faculty of Biology; University of Duisburg-Essen; 45117 Essen Germany
| | - Carsten Schmuck
- Institute of Organic Chemistry; University of Duisburg-Essen (Germany); Universitätsstrasse 7 45141 Essen Germany
| |
Collapse
|
18
|
Guduru SKR, Arya P. Synthesis and biological evaluation of rapamycin-derived, next generation small molecules. MEDCHEMCOMM 2018; 9:27-43. [PMID: 30108899 PMCID: PMC6072512 DOI: 10.1039/c7md00474e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/21/2017] [Indexed: 12/20/2022]
Abstract
Over the years, rapamycin has attracted serious attention due to its remarkable biological properties and as a potent inhibitor of the mammalian target of rapamycin (mTOR) protein through its binding with FKBP-12. Several efficient strategies that utilize synthetic and biosynthetic approaches have been utilized to develop small molecule rapamycin analogs or for synthesizing hybrid compounds containing a partial rapamycin structure to improve pharmacokinetic properties. Herein, we report selected case studies related to the synthesis of rapamycin-derived compounds and hybrid molecules to explore their biological properties.
Collapse
Affiliation(s)
- Shiva Krishna Reddy Guduru
- Center for Drug Discovery , Department of Pharmacology and Chemical Biology , Baylor College of Medicine , One Baylor Plaza , Houston , Texas 77030 , USA . ; ; Tel: +1 713 798 8794
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , One Baylor Plaza , Houston , Texas 77030 , USA
| | - Prabhat Arya
- Chemistry and Chemical Biology , Dr. Reddy's Institute of Life Sciences (DRILS) , University of Hyderabad Campus , Hyderabad 500046 , India
| |
Collapse
|
19
|
Hellinger R, Thell K, Vasileva M, Muhammad T, Gunasekera S, Kümmel D, Göransson U, Becker CW, Gruber CW. Chemical Proteomics for Target Discovery of Head-to-Tail Cyclized Mini-Proteins. Front Chem 2017; 5:73. [PMID: 29075625 PMCID: PMC5641551 DOI: 10.3389/fchem.2017.00073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/19/2017] [Indexed: 11/24/2022] Open
Abstract
Target deconvolution is one of the most challenging tasks in drug discovery, but a key step in drug development. In contrast to small molecules, there is a lack of validated and robust methodologies for target elucidation of peptides. In particular, it is difficult to apply these methods to cyclic and cysteine-stabilized peptides since they exhibit reduced amenability to chemical modification and affinity capture; however, such ribosomally synthesized and post-translationally modified peptide natural products are rich sources of promising drug candidates. For example, plant-derived circular peptides called cyclotides have recently attracted much attention due to their immunosuppressive effects and oral activity in the treatment of multiple sclerosis in mice, but their molecular target has hitherto not been reported. In this study, a chemical proteomics approach using photo-affinity crosslinking was developed to determine a target for the circular peptide [T20K]kalata B1. Using this prototypic nature-derived peptide enabled the identification of a possible functional modulation of 14-3-3 proteins. This biochemical interaction was validated via competition pull down assays as well as a cellular reporter assay indicating an effect on 14-3-3-dependent transcriptional activity. As proof of concept, the presented approach may be applicable for target elucidation of various cyclic peptides and mini-proteins, in particular cyclotides, which represent a promising class of molecules in drug discovery and development.
Collapse
Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Kathrin Thell
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Mina Vasileva
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Taj Muhammad
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Sunithi Gunasekera
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Daniel Kümmel
- School of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Christian W Becker
- Department of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.,School of Biomedical Sciences, Faculty of Medicine, University of Queensland, St. Lucia, QLD, Australia
| |
Collapse
|
20
|
Sijbesma E, Skora L, Leysen S, Brunsveld L, Koch U, Nussbaumer P, Jahnke W, Ottmann C. Identification of Two Secondary Ligand Binding Sites in 14-3-3 Proteins Using Fragment Screening. Biochemistry 2017; 56:3972-3982. [PMID: 28681606 PMCID: PMC5543393 DOI: 10.1021/acs.biochem.7b00153] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Proteins
typically interact with multiple binding partners, and
often different parts of their surfaces are employed to establish
these protein–protein interactions (PPIs). Members of the class
of 14-3-3 adapter proteins bind to several hundred other proteins
in the cell. Multiple small molecules for the modulation of 14-3-3
PPIs have been disclosed; however, they all target the conserved phosphopeptide
binding channel, so that selectivity is difficult to achieve. Here
we report on the discovery of two individual secondary binding sites
that have been identified by combining nuclear magnetic resonance-based
fragment screening and X-ray crystallography. The two pockets that
these fragments occupy are part of at least three physiologically
relevant and structurally characterized 14-3-3 PPI interfaces, including
those with serotonin N-acetyltransferase and plant
transcription factor FT. In addition, the high degree of conservation
of the two sites implies their relevance for 14-3-3 PPIs. This first
identification of secondary sites on 14-3-3 proteins bound by small
molecule ligands might facilitate the development of new chemical
tool compounds for more selective PPI modulation.
Collapse
Affiliation(s)
- Eline Sijbesma
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lukasz Skora
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research , 4002 Basel, Switzerland
| | - Seppe Leysen
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Luc Brunsveld
- Department of Biomedical Engineering, Laboratory of Chemical Biology, and Institute for Complex Molecular Systems, Eindhoven University of Technology , P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Uwe Koch
- Lead Discovery Center GmbH , Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Peter Nussbaumer
- Lead Discovery Center GmbH , Otto-Hahn-Straße 15, 44227 Dortmund, Germany
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research , 4002 Basel, Switzerland
| | - Christian Ottmann
- Department of Biomedical Engineering, Laboratory of Chemical Biology, 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 , Essen, Germany
| |
Collapse
|
21
|
Tachibana R, Terai T, Boncompain G, Sugiyama S, Saito N, Perez F, Urano Y. Improving the Solubility of Artificial Ligands of Streptavidin to Enable More Practical Reversible Switching of Protein Localization in Cells. Chembiochem 2017; 18:358-362. [PMID: 27905160 DOI: 10.1002/cbic.201600640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Indexed: 12/21/2022]
Abstract
Chemical inducers that can control target-protein localization in living cells are powerful tools to investigate dynamic biological systems. We recently reported the retention using selective hook or "RUSH" system for reversible localization change of proteins of interest by addition/washout of small-molecule artificial ligands of streptavidin (ALiS). However, the utility of previously developed ALiS was restricted by limited solubility in water. Here, we overcame this problem by X-ray crystal structure-guided design of a more soluble ALiS derivative (ALiS-3), which retains sufficient streptavidin-binding affinity for use in the RUSH system. The ALiS-3-streptavidin interaction was characterized in detail. ALiS-3 is a convenient and effective tool for dynamic control of α-mannosidase II localization between ER and Golgi in living cells.
Collapse
Affiliation(s)
- Ryo Tachibana
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takuya Terai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Present address: Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama City, Saitama, 338-8570, Japan
| | - Gaelle Boncompain
- Institut Curie, Centre de Recherche, PSL Research University, 26, rue d'Ulm, Paris, 75248, France.,CNRS, UMR144, PSL Research University, 26, rue d'Ulm, Paris, 75248, France
| | - Shigeru Sugiyama
- Graduate School of Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nae Saito
- Drug Discovery Initiative, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Franck Perez
- Institut Curie, Centre de Recherche, PSL Research University, 26, rue d'Ulm, Paris, 75248, France.,CNRS, UMR144, PSL Research University, 26, rue d'Ulm, Paris, 75248, France
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,CREST, JST, 7 Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan
| |
Collapse
|
22
|
den Hamer A, Lemmens LJM, Nijenhuis MAD, Ottmann C, Merkx M, de Greef TFA, Brunsveld L. Small-Molecule-Induced and Cooperative Enzyme Assembly on a 14-3-3 Scaffold. Chembiochem 2017; 18:331-335. [PMID: 27897387 PMCID: PMC5299510 DOI: 10.1002/cbic.201600631] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Indexed: 12/23/2022]
Abstract
Scaffold proteins regulate cell signalling by promoting the proximity of putative interaction partners. Although they are frequently applied in cellular settings, fundamental understanding of them in terms of, amongst other factors, quantitative parameters has been lagging behind. Here we present a scaffold protein platform that is based on the native 14-3-3 dimeric protein and is controllable through the action of a small-molecule compound, thus permitting study in an in vitro setting and mathematical description. Robust small-molecule regulation of caspase-9 activity through induced dimerisation on the 14-3-3 scaffold was demonstrated. The individual parameters of this system were precisely determined and used to develop a mathematical model of the scaffolding concept. This model was used to elucidate the strong cooperativity of the enzyme activation mediated by the 14-3-3 scaffold. This work provides an entry point for the long-needed quantitative insights into scaffold protein functioning and paves the way for the optimal use of reengineered 14-3-3 proteins as chemically inducible scaffolds in synthetic systems.
Collapse
Affiliation(s)
- Anniek den Hamer
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Lenne J. M. Lemmens
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Minke A. D. Nijenhuis
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Christian Ottmann
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Maarten Merkx
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Tom F. A. de Greef
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| | - Luc Brunsveld
- Laboratory of Chemical BiologyDepartment of Biomedical Engineering andInstitute of Complex Molecular SystemsEindhoven University of TechnologyDen Dolech 25612AZ EindhovenNetherlands
| |
Collapse
|
23
|
Tang Y, Xue Y, Du G, Wang J, Liu J, Sun B, Li XN, Yao G, Luo Z, Zhang Y. Structural Revisions of a Class of Natural Products: Scaffolds of Aglycon Analogues of Fusicoccins and Cotylenins Isolated from Fungi. Angew Chem Int Ed Engl 2016; 55:4069-73. [PMID: 26916098 DOI: 10.1002/anie.201600313] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 01/22/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Ying Tang
- Tongji Hospital, Tongji Medical College; Huazhong University of Science and Technology; Wuhan China
| | - Yongbo Xue
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Guang Du
- Tongji Hospital, Tongji Medical College; Huazhong University of Science and Technology; Wuhan China
| | - Jianping Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Junjun Liu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Bin Sun
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Xiao-Nian Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China; Chinese Academy of Sciences; Kunming China
| | - Guangmin Yao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Zengwei Luo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| |
Collapse
|
24
|
Tang Y, Xue Y, Du G, Wang J, Liu J, Sun B, Li XN, Yao G, Luo Z, Zhang Y. Structural Revisions of a Class of Natural Products: Scaffolds of Aglycon Analogues of Fusicoccins and Cotylenins Isolated from Fungi. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600313] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ying Tang
- Tongji Hospital, Tongji Medical College; Huazhong University of Science and Technology; Wuhan China
| | - Yongbo Xue
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Guang Du
- Tongji Hospital, Tongji Medical College; Huazhong University of Science and Technology; Wuhan China
| | - Jianping Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Junjun Liu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Bin Sun
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Xiao-Nian Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China; Chinese Academy of Sciences; Kunming China
| | - Guangmin Yao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Zengwei Luo
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation; School of Pharmacy, Tongji Medical College; Huazhong University of Science and Technology; Wuhan 430030 China
| |
Collapse
|
25
|
Kim AK, DeRose R, Ueno T, Lin B, Komatsu T, Nakamura H, Inoue T. Toward total synthesis of cell function: Reconstituting cell dynamics with synthetic biology. Sci Signal 2016; 9:re1. [DOI: 10.1126/scisignal.aac4779] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Allen K. Kim
- Department of Cell Biology, School of Medicine, Johns Hopkins University, 855 N. Wolfe Street, Baltimore, MD 21205, USA
- Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Robert DeRose
- Department of Cell Biology, School of Medicine, Johns Hopkins University, 855 N. Wolfe Street, Baltimore, MD 21205, USA
- Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Tasuku Ueno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Benjamin Lin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Systems Biology Institute, Yale University, 840 West Campus Drive, West Haven, CT 06516, USA
- Department of Biomedical Engineering, Yale University, West Haven, CT 06516, USA
| | - Toru Komatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Hideki Nakamura
- Department of Cell Biology, School of Medicine, Johns Hopkins University, 855 N. Wolfe Street, Baltimore, MD 21205, USA
- Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Takanari Inoue
- Department of Cell Biology, School of Medicine, Johns Hopkins University, 855 N. Wolfe Street, Baltimore, MD 21205, USA
- Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
26
|
van Bergeijk P, Hoogenraad CC, Kapitein LC. Right Time, Right Place: Probing the Functions of Organelle Positioning. Trends Cell Biol 2015; 26:121-134. [PMID: 26541125 DOI: 10.1016/j.tcb.2015.10.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/30/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
Abstract
The proper spatial arrangement of organelles underlies many cellular processes including signaling, polarization, and growth. Despite the importance of local positioning, the precise connection between subcellular localization and organelle function is often not fully understood. To address this, recent studies have developed and employed different strategies to directly manipulate organelle distributions, such as the use of (light-sensitive) heterodimerization to control the interaction between selected organelles and specific motor proteins, adaptor molecules, or anchoring factors. We review here the importance of subcellular localization as well as tools to control local organelle positioning. Because these approaches allow spatiotemporal control of organelle distribution, they will be invaluable tools to unravel local functioning and the mechanisms that control positioning.
Collapse
Affiliation(s)
- Petra van Bergeijk
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Casper C Hoogenraad
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Lukas C Kapitein
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, 3584 CH Utrecht, The Netherlands.
| |
Collapse
|
27
|
Terai T, Kohno M, Boncompain G, Sugiyama S, Saito N, Fujikake R, Ueno T, Komatsu T, Hanaoka K, Okabe T, Urano Y, Perez F, Nagano T. Artificial Ligands of Streptavidin (ALiS): Discovery, Characterization, and Application for Reversible Control of Intracellular Protein Transport. J Am Chem Soc 2015; 137:10464-7. [DOI: 10.1021/jacs.5b05672] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | | | - Shigeru Sugiyama
- Graduate
School of Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Bier D, Thiel P, Briels J, Ottmann C. Stabilization of Protein-Protein Interactions in chemical biology and drug discovery. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:10-9. [PMID: 26093250 DOI: 10.1016/j.pbiomolbio.2015.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 05/26/2015] [Accepted: 05/28/2015] [Indexed: 01/08/2023]
Abstract
More than 300,000 Protein-Protein Interactions (PPIs) can be found in human cells. This number is significantly larger than the number of single proteins, which are the classical targets for pharmacological intervention. Hence, specific and potent modulation of PPIs by small, drug-like molecules would tremendously enlarge the "druggable genome" enabling novel ways of drug discovery for essentially every human disease. This strategy is especially promising in diseases with difficult targets like intrinsically disordered proteins or transcription factors, for example neurodegeneration or metabolic diseases. Whereas the potential of PPI modulation has been recognized in terms of the development of inhibitors that disrupt or prevent a binary protein complex, the opposite (or complementary) strategy to stabilize PPIs has not yet been realized in a systematic manner. This fact is rather surprising given the number of impressive natural product examples that confer their activity by stabilizing specific PPIs. In addition, in recent years more and more examples of synthetic molecules are being published that work as PPI stabilizers, despite the fact that in the majority they initially have not been designed as such. Here, we describe examples from both the natural products as well as the synthetic molecules advocating for a stronger consideration of the PPI stabilization approach in chemical biology and drug discovery.
Collapse
Affiliation(s)
- David Bier
- 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
| | - Philipp Thiel
- Applied Bioinformatics, Center for Bioinformatics, and Dept. of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Jeroen Briels
- 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
| | - 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
|
29
|
Small molecules, peptides and natural products: getting a grip on 14-3-3 protein-protein modulation. Future Med Chem 2015; 6:903-21. [PMID: 24962282 DOI: 10.4155/fmc.14.47] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
One of the proteins that is found in a diverse range of eukaryotic protein-protein interactions is the adaptor protein 14-3-3. As 14-3-3 is a hub protein with very diverse interactions, it is a good model to study various protein-protein interactions. A wide range of classes of molecules, peptides, small molecules or natural products, has been used to modify the protein interactions, providing both stabilization or inhibition of the interactions of 14-3-3 with its binding partners. The first protein crystal structures were solved in 1995 and gave molecular insights for further research. The plant analog of 14-3-3 binds to a plant plasma membrane H(+)-ATPase and this protein complex is stabilized by the fungal phytotoxin fusicoccin A. The knowledge gained from the process in plants was transferred to and applied in human models to find stabilizers or inhibitors of 14-3-3 interaction in human cellular pathways.
Collapse
|
30
|
Barnard A, Miles JA, Burslem GM, Barker AM, Wilson AJ. Multivalent helix mimetics for PPI-inhibition. Org Biomol Chem 2015; 13:258-64. [DOI: 10.1039/c4ob02066a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A multivalent helix mimetic is developed that inhibits the p53/hDM2 and induces dimerization/aggregation of its target – hDM2.
Collapse
Affiliation(s)
- Anna Barnard
- School of Chemistry
- University of Leeds
- Leeds
- UK
- Astbury Centre for Structural and Molecular Biology
| | - Jennifer A. Miles
- School of Chemistry
- University of Leeds
- Leeds
- UK
- Astbury Centre for Structural and Molecular Biology
| | - George M. Burslem
- School of Chemistry
- University of Leeds
- Leeds
- UK
- Astbury Centre for Structural and Molecular Biology
| | - Amy M. Barker
- Astbury Centre for Structural and Molecular Biology
- University of Leeds
- Leeds
- UK
- School of Molecular and Cellular Biology
| | - Andrew J. Wilson
- School of Chemistry
- University of Leeds
- Leeds
- UK
- Astbury Centre for Structural and Molecular Biology
| |
Collapse
|
31
|
Adjobo-Hermans MJW. Fast reversibility of dimeriser system enables quantification of signal molecule turnover. Chembiochem 2014; 15:2037-9. [PMID: 25145328 DOI: 10.1002/cbic.201402294] [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: 06/08/2014] [Indexed: 11/10/2022]
Abstract
The design of a brake: Chemical induced dimerisation systems have revolutionised signal transduction research by allowing fast activation of specific proteins. A recent report describes the design of tools that enable the rapid switching off of the induced signal, thereby enabling quantification of signal molecule turnover.
Collapse
Affiliation(s)
- Merel J W Adjobo-Hermans
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Geert Grooteplein 28, 6525 GA, Nijmegen (The Netherlands).
| |
Collapse
|
32
|
Pastuszka MK, Okamoto CT, Hamm-Alvarez SF, MacKay JA. Flipping the Switch on Clathrin-Mediated Endocytosis using Thermally Responsive Protein Microdomains. ADVANCED FUNCTIONAL MATERIALS 2014; 24:5340-5347. [PMID: 25419208 PMCID: PMC4235962 DOI: 10.1002/adfm.201400715] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A ubiquitous approach to study protein function is to knock down activity (gene deletions, siRNA, small molecule inhibitors, etc) and study the cellular effects. Using a new methodology, this manuscript describes how to rapidly and specifically switch off cellular pathways using thermally responsive protein polymers. A small increase in temperature stimulates cytosolic elastin-like polypeptides (ELPs) to assemble microdomains. We hypothesize that ELPs fused to a key effector in a target macromolecular complex will sequester the complex within these microdomains, which will bring the pathway to a halt. To test this hypothesis, we fused ELPs to clathrin-light chain (CLC), a protein associated with clathrin-mediated endocytosis. Prior to thermal stimulation, the ELP fusion is soluble and clathrin-mediated endocytosis remains 'on.' Increasing the temperature induces the assembly of ELP fusion proteins into organelle-sized microdomains that switches clathrin-mediated endocytosis 'off.' These microdomains can be thermally activated and inactivated within minutes, are reversible, do not require exogenous chemical stimulation, and are specific for components trafficked within the clathrin-mediated endocytosis pathway. This temperature-triggered cell switch system represents a new platform for the temporal manipulation of trafficking mechanisms in normal and disease cell models and has applications for manipulating other intracellular pathways.
Collapse
Affiliation(s)
- Martha K. Pastuszka
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California. 1985 Zonal Avenue, Los Angeles 90033-9121
| | - Curtis T. Okamoto
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California. 1985 Zonal Avenue, Los Angeles 90033-9121
| | - Sarah F. Hamm-Alvarez
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California. 1985 Zonal Avenue, Los Angeles 90033-9121
| | - J. Andrew MacKay
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California. 1985 Zonal Avenue, Los Angeles 90033-9121
| |
Collapse
|
33
|
Liu P, Calderon A, Konstantinidis G, Hou J, Voss S, Chen X, Li F, Banerjee S, Hoffmann JE, Theiss C, Dehmelt L, Wu YW. A Bioorthogonal Small-Molecule-Switch System for Controlling Protein Function in Live Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403463] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
34
|
Liu P, Calderon A, Konstantinidis G, Hou J, Voss S, Chen X, Li F, Banerjee S, Hoffmann JE, Theiss C, Dehmelt L, Wu YW. A bioorthogonal small-molecule-switch system for controlling protein function in live cells. Angew Chem Int Ed Engl 2014; 53:10049-55. [PMID: 25065762 DOI: 10.1002/anie.201403463] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/23/2014] [Indexed: 12/13/2022]
Abstract
Chemically induced dimerization (CID) has proven to be a powerful tool for modulating protein interactions. However, the traditional dimerizer rapamycin has limitations in certain in vivo applications because of its slow reversibility and its affinity for endogenous proteins. Described herein is a bioorthogonal system for rapidly reversible CID. A novel dimerizer with synthetic ligand of FKBP' (SLF') linked to trimethoprim (TMP). The SLF' moiety binds to the F36V mutant of FK506-binding protein (FKBP) and the TMP moiety binds to E. coli dihydrofolate reductase (eDHFR). SLF'-TMP-induced heterodimerization of FKBP(F36V) and eDHFR with a dissociation constant of 0.12 μM. Addition of TMP alone was sufficient to rapidly disrupt this heterodimerization. Two examples are presented to demonstrate that this system is an invaluable tool, which can be widely used to rapidly and reversibly control protein function in vivo.
Collapse
Affiliation(s)
- Peng Liu
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Str. 15, 44227 Dortmund (Germany) http://www.cgc.mpg.de/index.php/research-groups/rg-dr-yaowen-wu/research; Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Str. 11, 44227, Dortmund (Germany)
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C. A rapidly reversible chemical dimerizer system to study lipid signaling in living cells. Angew Chem Int Ed Engl 2014; 53:6720-3. [PMID: 24841150 DOI: 10.1002/anie.201402294] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Indexed: 01/11/2023]
Abstract
Chemical dimerizers are powerful tools for non-invasive manipulation of enzyme activities in intact cells. Here we introduce the first rapidly reversible small-molecule-based dimerization system and demonstrate a sufficiently fast switch-off to determine kinetics of lipid metabolizing enzymes in living cells. We applied this new method to induce and stop phosphatidylinositol 3-kinase (PI3K) activity, allowing us to quantitatively measure the turnover of phosphatidylinositol 3,4,5-trisphosphate (PIP3) and its downstream effectors by confocal fluorescence microscopy as well as standard biochemical methods.
Collapse
Affiliation(s)
- Suihan Feng
- Cell Biology & Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg (Germany)
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C. A Rapidly Reversible Chemical Dimerizer System to Study Lipid Signaling in Living Cells. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201402294] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
37
|
Ishida M, Watanabe H, Takigawa K, Kurishita Y, Oki C, Nakamura A, Hamachi I, Tsukiji S. Synthetic Self-Localizing Ligands That Control the Spatial Location of Proteins in Living Cells. J Am Chem Soc 2013; 135:12684-9. [DOI: 10.1021/ja4046907] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | | | | | - Yasutaka Kurishita
- Department of Synthetic Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
| | | | | | - Itaru Hamachi
- Department of Synthetic Chemistry
and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510,
Japan
- Core Research for Evolutional
Science and Technology (CREST), Japan Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | | |
Collapse
|