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Gray JL, von Delft F, Brennan PE. Targeting the Small GTPase Superfamily through Their Regulatory Proteins. Angew Chem Int Ed Engl 2020; 59:6342-6366. [PMID: 30869179 PMCID: PMC7204875 DOI: 10.1002/anie.201900585] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/11/2019] [Indexed: 12/11/2022]
Abstract
The Ras superfamily of small GTPases are guanine-nucleotide-dependent switches essential for numerous cellular processes. Mutations or dysregulation of these proteins are associated with many diseases, but unsuccessful attempts to target the small GTPases directly have resulted in them being classed as "undruggable". The GTP-dependent signaling of these proteins is controlled by their regulators; guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and in the Rho and Rab subfamilies, guanine nucleotide dissociation inhibitors (GDIs). This review covers the recent small molecule and biologics strategies to target the small GTPases through their regulators. It seeks to critically re-evaluate recent chemical biology practice, such as the presence of PAINs motifs and the cell-based readout using compounds that are weakly potent or of unknown specificity. It highlights the vast scope of potential approaches for targeting the small GTPases in the future through their regulatory proteins.
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Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
| | - Frank von Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
- Department of BiochemistryUniversity of JohannesburgAuckland Park2006South Africa
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of OxfordOxfordOX3 7FZUK
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2
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Kopra K, Vuorinen E, Abreu-Blanco M, Wang Q, Eskonen V, Gillette W, Pulliainen AT, Holderfield M, Härmä H. Homogeneous Dual-Parametric-Coupled Assay for Simultaneous Nucleotide Exchange and KRAS/RAF-RBD Interaction Monitoring. Anal Chem 2020; 92:4971-4979. [PMID: 32106676 PMCID: PMC7143314 DOI: 10.1021/acs.analchem.9b05126] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/28/2020] [Indexed: 02/07/2023]
Abstract
We have developed a rapid and sensitive single-well dual-parametric method introduced in linked RAS nucleotide exchange and RAS/RAF-RBD interaction assays. RAS mutations are frequent drivers of multiple different human cancers, but the development of therapeutic strategies has been challenging. Traditionally, efforts to disrupt the RAS function have focused on nucleotide exchange inhibitors, GTP-RAS interaction inhibitors, and activators increasing GTPase activity of mutant RAS proteins. As the amount of biological knowledge grows, targeted biochemical assays enabling high-throughput screening have become increasingly interesting. We have previously introduced a homogeneous quenching resonance energy transfer (QRET) assay for nucleotide binding studies with RAS and heterotrimeric G proteins. Here, we introduce a novel homogeneous signaling technique called QTR-FRET, which combine QRET technology and time-resolved Förster resonance energy transfer (TR-FRET). The dual-parametric QTR-FRET technique enables the linking of guanine nucleotide exchange factor-induced Eu3+-GTP association to RAS, monitored at 615 nm, and subsequent Eu3+-GTP-loaded RAS interaction with RAF-RBD-Alexa680 monitored at 730 nm. Both reactions were monitored in a single-well assay applicable for inhibitor screening and real-time reaction monitoring. This homogeneous assay enables separable detection of both nucleotide exchange and RAS/RAF interaction inhibitors using low nanomolar protein concentrations. To demonstrate a wider applicability as a screening and real-time reaction monitoring method, the QTR-FRET technique was also applied for G(i)α GTP-loading and pertussis toxin-catalyzed ADP-ribosylation of G(i)α, for which we synthesized a novel γ-GTP-Eu3+ molecule. The study indicates that the QTR-FRET detection technique presented here can be readily applied to dual-parametric assays for various targets.
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Affiliation(s)
- Kari Kopra
- Materials
Chemistry and Chemical Analysis, University
of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Emmiliisa Vuorinen
- Materials
Chemistry and Chemical Analysis, University
of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Maria Abreu-Blanco
- Leidos
Biomedical Research, Inc., Frederick National
Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Qi Wang
- Institute
of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Ville Eskonen
- Materials
Chemistry and Chemical Analysis, University
of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - William Gillette
- Leidos
Biomedical Research, Inc., Frederick National
Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Arto T. Pulliainen
- Institute
of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Matthew Holderfield
- Leidos
Biomedical Research, Inc., Frederick National
Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Harri Härmä
- Materials
Chemistry and Chemical Analysis, University
of Turku, Vatselankatu 2, 20500 Turku, Finland
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3
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Detection of the in vitro modulation of Plasmodium falciparum Arf1 by Sec7 and ArfGAP domains using a colorimetric plate-based assay. Sci Rep 2020; 10:4193. [PMID: 32144363 PMCID: PMC7061341 DOI: 10.1038/s41598-020-61101-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/09/2019] [Indexed: 11/18/2022] Open
Abstract
The regulation of human Arf1 GTPase activity by ArfGEFs that stimulate GDP/GTP exchange and ArfGAPs that mediate GTP hydrolysis has attracted attention for the discovery of Arf1 inhibitors as potential anti-cancer agents. The malaria parasite Plasmodium falciparum encodes a Sec7 domain-containing protein - presumably an ArfGEF - and two putative ArfGAPs, as well as an Arf1 homologue (PfArf1) that is essential for blood-stage parasite viability. However, ArfGEF and ArfGAP-mediated activation/deactivation of PfArf1 has not been demonstrated. In this study, we established an in vitro colorimetric microtiter plate-based assay to detect the activation status of truncated human and P. falciparum Arf1 and used it to demonstrate the activation of both proteins by the Sec7 domain of ARNO, their deactivation by the GAP domain of human ArfGAP1 and the inhibition of the respective reactions by the compounds SecinH3 and QS11. In addition, we found that the GAP domains of both P. falciparum ArfGAPs have activities equivalent to that of human ArfGAP1, but are insensitive to QS11. Library screening identified a novel inhibitor which selectively inhibits one of the P. falciparum GAP domains (IC50 4.7 µM), suggesting that the assay format is suitable for screening compound collections for inhibitors of Arf1 regulatory proteins.
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4
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Gray JL, Delft F, Brennan PE. Targeting der kleinen GTPasen über ihre regulatorischen Proteine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201900585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
| | - Frank Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
- Department of BiochemistryUniversity of Johannesburg Auckland Park 2006 Südafrika
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of Oxford Oxford OX3 7FZ Großbritannien
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5
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Mayoral MJ, Serrano-Molina D, Camacho-García J, Magdalena-Estirado E, Blanco-Lomas M, Fadaei E, González-Rodríguez D. Understanding complex supramolecular landscapes: non-covalent macrocyclization equilibria examined by fluorescence resonance energy transfer. Chem Sci 2018; 9:7809-7821. [PMID: 30429990 PMCID: PMC6194488 DOI: 10.1039/c8sc03229g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/16/2018] [Indexed: 12/13/2022] Open
Abstract
As molecular self-assembled systems increase in complexity, due to a large number of participating entities and/or the establishment of multiple competing equilibria, their full understanding becomes likewise more complicated, and the use of diverse analytical techniques that can afford complementary information is required. We demonstrate in this work that resonance excitation energy transfer phenomena, measured by fluorescence spectroscopy in combination with other optical spectroscopies, can be a valuable tool to obtain supplementary thermodynamic data about complex supramolecular landscapes that other methods fail to provide. In particular, noncovalent macrocyclization processes of lipophilic dinucleosides are studied here by setting up a competition between intra- and intermolecular association processes of Watson-Crick H-bonding pairs. Multiwavelength analysis of the monomer emission changes allowed us to determine cyclotetramerization constants and to quantify chelate cooperativity, which was confirmed to be substantially larger for the G-C than for the A-U pair. Furthermore, when bithiophene-BODIPY donor-acceptor energy transfer probes are employed in these competition experiments, fluorescence and circular dichroism spectroscopy measurements in different regions of the visible spectrum additionally reveal intermolecular interactions occurring simultaneously at both sides of the macrocyclization reaction: the cyclic product, acting as a host for the competitor, and the monomer reactant, ultimately leading to macrocycle denaturation.
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Affiliation(s)
- María J Mayoral
- Nanostructured Molecular Systems and Materials Group , Departamento de Química Orgánica , Facultad de Ciencias , Universidad Autónoma de Madrid , 28049 Madrid , Spain . ;
| | - David Serrano-Molina
- Nanostructured Molecular Systems and Materials Group , Departamento de Química Orgánica , Facultad de Ciencias , Universidad Autónoma de Madrid , 28049 Madrid , Spain . ;
| | - Jorge Camacho-García
- Nanostructured Molecular Systems and Materials Group , Departamento de Química Orgánica , Facultad de Ciencias , Universidad Autónoma de Madrid , 28049 Madrid , Spain . ;
| | - Eva Magdalena-Estirado
- Nanostructured Molecular Systems and Materials Group , Departamento de Química Orgánica , Facultad de Ciencias , Universidad Autónoma de Madrid , 28049 Madrid , Spain . ;
| | - Marina Blanco-Lomas
- Nanostructured Molecular Systems and Materials Group , Departamento de Química Orgánica , Facultad de Ciencias , Universidad Autónoma de Madrid , 28049 Madrid , Spain . ;
| | - Elham Fadaei
- Nanostructured Molecular Systems and Materials Group , Departamento de Química Orgánica , Facultad de Ciencias , Universidad Autónoma de Madrid , 28049 Madrid , Spain . ;
| | - David González-Rodríguez
- Nanostructured Molecular Systems and Materials Group , Departamento de Química Orgánica , Facultad de Ciencias , Universidad Autónoma de Madrid , 28049 Madrid , Spain . ;
- Institute for Advanced Research in Chemical Sciences (IAdChem) , Universidad Autónoma de Madrid , 28049 Madrid , Spain
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6
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Mayoral MJ, Camacho-García J, Magdalena-Estirado E, Blanco-Lomas M, Fadaei E, Montoro-García C, Serrano-Molina D, González-Rodríguez D. Dye-conjugated complementary lipophilic nucleosides as useful probes to study association processes by fluorescence resonance energy transfer. Org Biomol Chem 2017; 15:7558-7565. [DOI: 10.1039/c7ob01930k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Resonance energy transfer is used here to study the association and self-sorting events between lipophilic nucleosides in apolar aromatic solvents.
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Affiliation(s)
- M. J. Mayoral
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
| | - J. Camacho-García
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
| | - E. Magdalena-Estirado
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
| | - M. Blanco-Lomas
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
| | - E. Fadaei
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
| | - C. Montoro-García
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
| | - D. Serrano-Molina
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
| | - D. González-Rodríguez
- Nanostructured Molecular Systems and Materials Group
- Departamento de Química Orgánica
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- 28049 Madrid
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7
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Hu R, Yap HK, Fung YH, Wang Y, Cheong WL, So LY, Tsang CS, Lee LYS, Lo WKC, Yuan J, Sun N, Leung YC, Yang G, Wong KY. ‘Light up’ protein–protein interaction through bioorthogonal incorporation of a turn-on fluorescent probe into β-lactamase. MOLECULAR BIOSYSTEMS 2016; 12:3544-3549. [DOI: 10.1039/c6mb00566g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aggregation induced emissive compound EPB can detect protein–protein interaction.
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8
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Lahtinen S, Wang Q, Soukka T. Long-Lifetime Luminescent Europium(III) Complex as an Acceptor in an Upconversion Resonance Energy Transfer Based Homogeneous Assay. Anal Chem 2015; 88:653-8. [DOI: 10.1021/acs.analchem.5b02228] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Satu Lahtinen
- Department of Biochemistry/Biotechnology, University of Turku, Tykistökatu 6 A, 20520 Turku, Finland
| | - Qi Wang
- Department of Biochemistry/Biotechnology, University of Turku, Tykistökatu 6 A, 20520 Turku, Finland
| | - Tero Soukka
- Department of Biochemistry/Biotechnology, University of Turku, Tykistökatu 6 A, 20520 Turku, Finland
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9
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Xie S, Bao S, Ouyang J, Zhou X, Kuang Q, Xie Z, Zheng L. Organic-Inorganic Interface-Induced Multi-Fluorescence of MgO Nanocrystal Clusters and Their Applications in Cellular Imaging. Chemistry 2014; 20:5244-52. [DOI: 10.1002/chem.201303927] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Indexed: 12/12/2022]
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10
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Wei ZH, Chen H, Zhang C, Ye BC. FRET-based system for probing protein-protein interactions between σR and RsrA from Streptomyces coelicolor in response to the redox environment. PLoS One 2014; 9:e92330. [PMID: 24651617 PMCID: PMC3961337 DOI: 10.1371/journal.pone.0092330] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 02/21/2014] [Indexed: 11/26/2022] Open
Abstract
Protein-protein interactions between sigma factor σ(R) and its corresponding zinc-binding anti-sigma (ZAS) protein RsrA trigger the thioredoxin system for maintaining cellular redox homeostasis in S. coelicolor. RsrA bound to zinc associates with σ(R), inhibiting its transcriptional activity in a reducing environment. During disulfide stress it forms intramolecular disulfide bonds, leading to zinc release and dissociation from σ(R), which initiates transcription to produce reductase and thioredoxin. We designed a fluorescence resonance energy transfer (FRET) based system for monitoring protein-protein interactions between σ(R) and RsrA to further understand how this redox switch regulates the thioredoxin system in S. coelicolor in response to its redox environment, especially various reactive oxygen species (ROS) derived from different metabolic pathways, and clarify the different response mechanisms between Zn-RsrA and apo-RsrA. By the use of the FRET approach described here, we showed that zinc protected thiols in RsrA and causes the σ(R)-RsrA complex to form a more compact structure. This system was also utilized to detect changes in redox status induced by ROS and diamide in real time in E. coli cells.
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Affiliation(s)
- Zi-Han Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Huan Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Chang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bang-Ce Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
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11
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Syafrizayanti, Betzen C, Hoheisel JD, Kastelic D. Methods for analyzing and quantifying protein–protein interaction. Expert Rev Proteomics 2014; 11:107-20. [DOI: 10.1586/14789450.2014.875857] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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12
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Bajorath J. Molecular crime scene investigation - dusting for fingerprints. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 10:e491-e498. [PMID: 24451639 DOI: 10.1016/j.ddtec.2012.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In chemoinformatics and drug design, fingerprints (FPs) are defined as string representations of molecular structure and properties and are popular descriptors for similarity searching. FPs are generally characterized by the simplicity of their design and ease of use. Despite a long history in chemoinformatics, the potential and limitations of FP searching are often not well under- stood. Standard FPs can also be subjected to engineering techniques to tune them for specific search applications.
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13
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Rouhana J, Hoh F, Estaran S, Henriquet C, Boublik Y, Kerkour A, Trouillard R, Martinez J, Pugnière M, Padilla A, Chavanieu A. Fragment-based identification of a locus in the Sec7 domain of Arno for the design of protein-protein interaction inhibitors. J Med Chem 2013; 56:8497-511. [PMID: 24112024 DOI: 10.1021/jm4009357] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
By virtual screening using a fragment-based drug design (FBDD) approach, 33 fragments were selected within small pockets around interaction hot spots on the Sec7 surface of the nucleotide exchange factor Arno, and then their ability to interfere with the Arno-catalyzed nucleotide exchange on the G-protein Arf1 was evaluated. By use of SPR, NMR, and fluorescence assays, the direct binding of three of the identified fragments to Arno Sec7 domain was demonstrated and the promiscuous aggregate behavior evaluated. Then the binding mode of one fragment and of a more active analogue was solved by X-ray crystallography. This highlighted the role of stable and transient pockets at the Sec7 domain surface in the discovery and binding of interfering compounds. These results provide structural information on how small organic compounds can interfere with the Arf1-Arno Sec7 domain interaction and may guide the rational drug design of competitive inhibitors of Arno enzymatic activity.
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Affiliation(s)
- Jad Rouhana
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247, CNRS, Universités Montpellier 1 et 2, Faculté de Pharmacie, 15 Avenue Charles Flahault BP14491, 34093 Montpellier Cedex 5, France
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14
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Hussein M, Bettio M, Schmitz A, Hannam JS, Theis J, Mayer G, Dosa S, Gütschow M, Famulok M. Kovalente Inhibition der Pleckstrin-Homologiedomäne von Cytohesinen durch Cyplecksine. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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15
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Hussein M, Bettio M, Schmitz A, Hannam JS, Theis J, Mayer G, Dosa S, Gütschow M, Famulok M. Cyplecksins Are Covalent Inhibitors of the Pleckstrin Homology Domain of Cytohesin. Angew Chem Int Ed Engl 2013; 52:9529-33. [DOI: 10.1002/anie.201302207] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Indexed: 01/06/2023]
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16
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Stender AS, Marchuk K, Liu C, Sander S, Meyer MW, Smith EA, Neupane B, Wang G, Li J, Cheng JX, Huang B, Fang N. Single cell optical imaging and spectroscopy. Chem Rev 2013; 113:2469-527. [PMID: 23410134 PMCID: PMC3624028 DOI: 10.1021/cr300336e] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Anthony S. Stender
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Kyle Marchuk
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Chang Liu
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Suzanne Sander
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Matthew W. Meyer
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Emily A. Smith
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
| | - Bhanu Neupane
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Gufeng Wang
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Junjie Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Ji-Xin Cheng
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907
| | - Bo Huang
- Department of Pharmaceutical Chemistry and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158
| | - Ning Fang
- Department of Chemistry, Iowa State University and Ames Laboratory, U. S. Department of Energy, Ames, IA 50011, USA
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17
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Ponterini G. Fluorescence Observables and Enzyme Kinetics in the Investigation of PPI Modulation by Small Molecules: Detection, Mechanistic Insight, and Functional Consequences. DISRUPTION OF PROTEIN-PROTEIN INTERFACES 2013. [PMCID: PMC7123529 DOI: 10.1007/978-3-642-37999-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The potential of fluorescence-based methods and kinetic analysis in the screening and molecular-scale mechanistic investigation of PPI modulation by small molecules is discussed through several representative examples collected and commented. These experimental approaches take advantage of a variety of observables. Changes in the protein aggregation pattern have been monitored through fluorescence properties such as spectra, intensities (related to quantum yields), time-decays, and anisotropies of intrinsic protein fluorophores, of extrinsic fluorescent tags and, even, of the same small molecules added to modulate PPIs, as well as through bimolecular excited-state processes such as static and collisional quenching, including electron and excitation-energy transfer, or exciton interaction, whose efficiencies are crucially structure dependent. Besides allowing for qualitative and quantitative information on the small-molecule induced PPI modulation, these approaches can take advantage from the sensitivity of fluorescence observables on fine structural details to shed light on the molecular-scale mechanisms of action and their functional consequences. Direct investigation of the latter by kinetic inhibition analysis represents a useful change in perspective whenever PPI are relevant for enzyme activity. Dissociative inhibition, that is, the ability of some small molecules to inhibit enzymes by disrupting their active oligomeric assembly is shortly reviewed.
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18
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Thompson AD, Dugan A, Gestwicki JE, Mapp AK. Fine-tuning multiprotein complexes using small molecules. ACS Chem Biol 2012; 7:1311-20. [PMID: 22725693 DOI: 10.1021/cb300255p] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Multiprotein complexes such as the transcriptional machinery, signaling hubs, and protein folding machines are typically composed of at least one enzyme combined with multiple non-enzymes. Often the components of these complexes are incorporated in a combinatorial manner, in which the ultimate composition of the system helps dictate the type, location, or duration of cellular activities. Although drugs and chemical probes have traditionally targeted the enzyme components, emerging strategies call for controlling the function of protein complexes by modulation of protein-protein interactions (PPIs). However, the challenges of targeting PPIs have been well documented, and the diversity of PPIs makes a "one-size-fits-all" solution highly unlikely. These hurdles are particularly daunting for PPIs that encompass large buried surface areas and those with weak affinities. In this Review, we discuss lessons from natural systems, in which allostery and other mechanisms are used to overcome the challenge of regulating the most difficult PPIs. These systems may provide a blueprint for identifying small molecules that target challenging PPIs and affecting molecular decision-making within multiprotein systems.
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Affiliation(s)
- Andrea D. Thompson
- Program
in Chemical Biology, ‡Departments of Pathology and Biological Chemistry and the Life Sciences
Institute, and §Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amanda Dugan
- Program
in Chemical Biology, ‡Departments of Pathology and Biological Chemistry and the Life Sciences
Institute, and §Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jason E. Gestwicki
- Program
in Chemical Biology, ‡Departments of Pathology and Biological Chemistry and the Life Sciences
Institute, and §Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anna K. Mapp
- Program
in Chemical Biology, ‡Departments of Pathology and Biological Chemistry and the Life Sciences
Institute, and §Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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Abstract
Small GTP-binding proteins of the ADP-ribosylation factor (Arf) family control various cell functional responses including protein transport and recycling between different cellular compartments, phagocytosis, proliferation, cytoskeletal remodelling, and migration. The activity of Arfs is tightly regulated. GTPase-activating proteins (GAPs) inactivate Arfs by stimulating GTP hydrolysis, and guanine nucleotide exchange factors (GEFs) stimulate the conversion of inactive GDP-bound Arf to the active GTP-bound conformation. There is increasing evidence that Arf small GTPases contribute to cancer growth and invasion. Increased expression of Arf6 and of Arf-GEPs, or deregulation Arf-GAP functions have been correlated with enhanced invasive capacity of tumor cells and metastasis. The spatiotemporal specificity of Arf activation is dictated by their GEFs that integrate various signals in stimulated cells. Brefeldin A (BFA), which inactivates a subset of Arf-GEFs, has been very useful for assessing the function of Golgi-localized Arfs. However, specific inhibitors to investigate the individual function of BFA-sensitive and insensitive Arf-GEFs are lacking. In recent years, specific screens have been developed, and new inhibitors with improved selectivity and potency to study cell functional responses regulated by BFA-sensitive and BFA-insensitive Arf pathways have been identified. These inhibitors have been instrumental for our understanding of the spatiotemporal activation of Arf proteins in cells and demonstrate the feasibility of developing small molecules interfering with Arf activation to prevent tumor invasion and metastasis.
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Vinkenborg JL, Mayer G, Famulok M. Aptamer-based affinity labeling of proteins. Angew Chem Int Ed Engl 2012; 51:9176-80. [PMID: 22865679 DOI: 10.1002/anie.201204174] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Indexed: 12/20/2022]
Abstract
A most able label: Labeled aptamers can be cross-linked to their target structures in a light-dependent and highly specific manner as a result of a new strategy termed aptamer-based affinity labeling (ABAL) of proteins. The aptamer-protein complexes can be enriched in vitro, from a cellular lysate and from the surface of living cells, opening new ways to study aptamer interactions in biological contexts.
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Vinkenborg JL, Mayer G, Famulok M. Aptamer-basierte Affinitätsmarkierung von Proteinen. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204174] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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22
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Abstract
Virtual screening (VS) methods are applied in both academia and drug discovery, and can be divided into ligand- and target structure-based approaches. The VS field is still evolving and is characterized by scientific heterogeneity. The value of virtual compound screening for drug discovery is often debated, in particular, given the large investments made in experimental high-throughput screening technologies. The current state-of-the-art in the VS field is discussed. Despite its limitations, VS applications have often succeeded in identifying novel hits including first-in-class active compounds and novel chemotypes. VS has its place in pharmaceutical research, but there is still much room for further improvements including method evaluation and drug discovery applications. The potential of VS is currently underutilized because its complementarity to high-throughput screening is not sufficiently exploited. Building close interfaces between computational and experimental screening would further streamline the hit identification process.
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Bill A, Schmitz A, König K, Heukamp LC, Hannam JS, Famulok M. Anti-proliferative effect of cytohesin inhibition in gefitinib-resistant lung cancer cells. PLoS One 2012; 7:e41179. [PMID: 22815959 PMCID: PMC3399819 DOI: 10.1371/journal.pone.0041179] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 06/18/2012] [Indexed: 11/18/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI), such as gefitinib, have been proven to efficiently inhibit the proliferation of a subset of non small-cell lung cancers (NSCLC). Unfortunately, the majority of NSCLC expressing wild type EGFR is primarily resistant to EGFR-TKI treatment. Here, we show that the proliferation of the gefitinib-resistant NSCLC cell lines H460 and A549 is reduced by the small molecule SecinH3 which indirectly attenuates EGFR activation by inhibition of cytohesins, a class of recently discovered cytoplasmic EGFR activators. SecinH3 and gefitinib showed a synergistic antiproliferative effect, which correlated with a profound inhibition of Akt activation and survivin expression. Treating mice bearing H460 xenografts with SecinH3 showed the antiproliferative and pro-apoptotic effect of SecinH3 in vivo. Our data suggest that targeting the EGFR indirectly by inhibiting its cytoplasmic activators, the cytohesins, has the potential to improve the treatment of primarily EGFR-TKI resistant lung cancers.
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Affiliation(s)
- Anke Bill
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Anton Schmitz
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Katharina König
- Institute of Pathology, University of Cologne, Köln, Germany
| | | | - Jeffrey S. Hannam
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Michael Famulok
- Chemical Biology and Medicinal Chemistry Unit, Life and Medical Sciences (LIMES) Institute, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- * E-mail:
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24
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Hons M, Niebel B, Karnowski N, Weiche B, Famulok M. Pan-selective aptamers for the family of small GTPases. Chembiochem 2012; 13:1433-7. [PMID: 22689339 DOI: 10.1002/cbic.201200164] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Michael Hons
- Life and Medical Sciences (LIMES) Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Strasse 1,53121 Bonn, Germany
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25
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Niebel B, Weiche B, Mueller AL, Li DY, Karnowski N, Famulok M. A luminescent oxygen channeling biosensor that measures small GTPase activation. Chem Commun (Camb) 2011; 47:7521-3. [PMID: 21625685 DOI: 10.1039/c1cc11944c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We established a homogeneous luminescent oxygen channeling sensor for measuring activation states of small GTPases. The assay quantifies activated GTPases in cell lysates, can be applied to different GTPases, and can be used for multiplex screening. The study will provide guidelines for determining activation states of diverse GTPases in various biological contexts.
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Affiliation(s)
- Björn Niebel
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, 53121 Bonn, Germany
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