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Kumar V, Chunchagatta Lakshman PK, Prasad TK, Manjunath K, Bairy S, Vasu AS, Ganavi B, Jasti S, Kamariah N. Target-based drug discovery: Applications of fluorescence techniques in high throughput and fragment-based screening. Heliyon 2024; 10:e23864. [PMID: 38226204 PMCID: PMC10788520 DOI: 10.1016/j.heliyon.2023.e23864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024] Open
Abstract
Target-based discovery of first-in-class therapeutics demands an in-depth understanding of the molecular mechanisms underlying human diseases. Precise measurements of cellular and biochemical activities are critical to gain mechanistic knowledge of biomolecules and their altered function in disease conditions. Such measurements enable the development of intervention strategies for preventing or treating diseases by modulation of desired molecular processes. Fluorescence-based techniques are routinely employed for accurate and robust measurements of in-vitro activity of molecular targets and for discovering novel chemical molecules that modulate the activity of molecular targets. In the current review, the authors focus on the applications of fluorescence-based high throughput screening (HTS) and fragment-based ligand discovery (FBLD) techniques such as fluorescence polarization (FP), Förster resonance energy transfer (FRET), fluorescence thermal shift assay (FTSA) and microscale thermophoresis (MST) for the discovery of chemical probe to exploring target's role in disease biology and ultimately, serve as a foundation for drug discovery. Some recent advancements in these techniques for compound library screening against important classes of drug targets, such as G-protein-coupled receptors (GPCRs) and GTPases, as well as phosphorylation- and acetylation-mediated protein-protein interactions, are discussed. Overall, this review presents a landscape of how these techniques paved the way for the discovery of small-molecule modulators and biologics against these targets for therapeutic benefits.
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Affiliation(s)
| | | | - Thazhe Kootteri Prasad
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Kavyashree Manjunath
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Sneha Bairy
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Akshaya S. Vasu
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - B. Ganavi
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Subbarao Jasti
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Neelagandan Kamariah
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
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2
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Gupta R, Singh M, Pathania R. Chemical genetic approaches for the discovery of bacterial cell wall inhibitors. RSC Med Chem 2023; 14:2125-2154. [PMID: 37974958 PMCID: PMC10650376 DOI: 10.1039/d3md00143a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 08/10/2023] [Indexed: 11/19/2023] Open
Abstract
Antimicrobial resistance (AMR) in bacterial pathogens is a worldwide health issue. The innovation gap in discovering new antibiotics has remained a significant hurdle in combating the AMR problem. Currently, antibiotics target various vital components of the bacterial cell envelope, nucleic acid and protein biosynthesis machinery and metabolic pathways essential for bacterial survival. The critical role of the bacterial cell envelope in cell morphogenesis and integrity makes it an attractive drug target. While a significant number of in-clinic antibiotics target peptidoglycan biosynthesis, several components of the bacterial cell envelope have been overlooked. This review focuses on various antibacterial targets in the bacterial cell wall and the strategies employed to find their novel inhibitors. This review will further elaborate on combining forward and reverse chemical genetic approaches to discover antibacterials that target the bacterial cell envelope.
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Affiliation(s)
- Rinki Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Mangal Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
| | - Ranjana Pathania
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee Roorkee - 247 667 Uttarakhand India
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3
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Abstract
In the computational design of antibodies, the interaction analysis between target antigen and antibody is an essential process to obtain feedback for validation and optimization of the design. Kinetic and thermodynamic parameters as well as binding affinity (KD) allow for a more detailed evaluation and understanding of the molecular recognition. In this chapter, we summarize the conventional experimental methods which can calculate KD value (ELISA, FP), analyze a binding activity to actual cells (FCM), and evaluate the kinetic and thermodynamic parameters (ITC, SPR, BLI), including high-throughput analysis and a recently developed experimental technique.
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Affiliation(s)
- Aki Tanabe
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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4
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Feng C, Huang Y, He W, Cheng X, Liu H, Huang Y, Ma B, Zhang W, Liao C, Wu W, Shao Y, Xu D, Su Z, Lu W. Tanshinones: First-in-Class Inhibitors of the Biogenesis of the Type 3 Secretion System Needle of Pseudomonas aeruginosa for Antibiotic Therapy. ACS CENTRAL SCIENCE 2019; 5:1278-1288. [PMID: 31403076 PMCID: PMC6662154 DOI: 10.1021/acscentsci.9b00452] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Indexed: 05/17/2023]
Abstract
The type 3 secretion system (T3SS) found as cell-surface appendages of many pathogenic Gram-negative bacteria, although nonessential for bacterial survival, is an important therapeutic target for drug discovery and development aimed at inhibiting bacterial virulence without inducing antibiotic resistance. We designed a fluorescence-polarization-based assay for high-throughput screening as a mechanistically well-defined general strategy for antibiotic discovery targeting the T3SS and made a serendipitous discovery of a subset of tanshinones-natural herbal compounds in traditional Chinese medicine widely used for the treatment of cardiovascular and cerebrovascular diseases-as effective inhibitors of the biogenesis of the T3SS needle of multi-drug-resistant Pseudomonas aeruginosa. By inhibiting the T3SS needle assembly and, thus, cytotoxicity and pathogenicity, selected tanshinones reduced the secretion of bacterial virulence factors toxic to macrophages in vitro, and rescued experimental animals challenged with lethal doses of Pseudomonas aeruginosa in a murine model of acute pneumonia. As first-in-class inhibitors with a demonstrable safety profile in humans, tanshinones may be used directly to alleviate Pseudomonas-aeruginosa-associated pulmonary infections without inducing antibiotic resistance. Since the T3SS is highly conserved among Gram-negative bacteria, this antivirulence strategy may be applicable to the discovery and development of novel classes of antibiotics refractory to existing resistance mechanisms for the treatment of many bacterial infections.
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Affiliation(s)
- Chao Feng
- Center
for Translational Medicine, Frontier Institute of Science
and Technology, Shaanxi Institute of Pediatric Diseases, Affiliated Children’s
Hospital, and Key Laboratory of Biomedical Information Engineering of the Ministry
of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710054, China
| | - Yinong Huang
- Center
for Translational Medicine, Frontier Institute of Science
and Technology, Shaanxi Institute of Pediatric Diseases, Affiliated Children’s
Hospital, and Key Laboratory of Biomedical Information Engineering of the Ministry
of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710054, China
| | - Wangxiao He
- Center
for Translational Medicine, Frontier Institute of Science
and Technology, Shaanxi Institute of Pediatric Diseases, Affiliated Children’s
Hospital, and Key Laboratory of Biomedical Information Engineering of the Ministry
of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710054, China
| | - Xiyao Cheng
- Department
of Biological and Food Engineering, Hubei
University of Technology, Wuhan 430068, China
| | - Huili Liu
- State
Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese
Academy of Sciences, Wuhan 430071, China
| | - Yongqi Huang
- Department
of Biological and Food Engineering, Hubei
University of Technology, Wuhan 430068, China
| | - Bohan Ma
- Center
for Translational Medicine, Frontier Institute of Science
and Technology, Shaanxi Institute of Pediatric Diseases, Affiliated Children’s
Hospital, and Key Laboratory of Biomedical Information Engineering of the Ministry
of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710054, China
| | - Wei Zhang
- Center
for Translational Medicine, Frontier Institute of Science
and Technology, Shaanxi Institute of Pediatric Diseases, Affiliated Children’s
Hospital, and Key Laboratory of Biomedical Information Engineering of the Ministry
of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710054, China
| | - Chongbing Liao
- Center
for Translational Medicine, Frontier Institute of Science
and Technology, Shaanxi Institute of Pediatric Diseases, Affiliated Children’s
Hospital, and Key Laboratory of Biomedical Information Engineering of the Ministry
of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710054, China
| | - Weihui Wu
- State Key
Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular
Microbiology and Technology of the Ministry of Education, Department
of Microbiology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Yongping Shao
- Center
for Translational Medicine, Frontier Institute of Science
and Technology, Shaanxi Institute of Pediatric Diseases, Affiliated Children’s
Hospital, and Key Laboratory of Biomedical Information Engineering of the Ministry
of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710054, China
| | - Dan Xu
- Center
for Translational Medicine, Frontier Institute of Science
and Technology, Shaanxi Institute of Pediatric Diseases, Affiliated Children’s
Hospital, and Key Laboratory of Biomedical Information Engineering of the Ministry
of Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710054, China
| | - Zhengding Su
- Department
of Biological and Food Engineering, Hubei
University of Technology, Wuhan 430068, China
| | - Wuyuan Lu
- Institute
of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201, United States
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5
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Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex. Proc Natl Acad Sci U S A 2018; 115:12973-12978. [PMID: 30514815 DOI: 10.1073/pnas.1806438115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Promoter-proximal pausing by RNA polymerase II (Pol II) is a key regulatory step in human immunodeficiency virus-1 (HIV-1) transcription and thus in the reversal of HIV latency. By binding to the nascent transactivating response region (TAR) RNA, HIV-1 Tat recruits the human super elongation complex (SEC) to the promoter and releases paused Pol II. Structural studies of TAR interactions have been largely focused on interactions between the TAR bulge and the arginine-rich motif (ARM) of Tat. Here, the crystal structure of the TAR loop in complex with Tat and the SEC core was determined at a 3.5-Å resolution. The bound TAR loop is stabilized by cross-loop hydrogen bonds. It makes structure-specific contacts with the side chains of the Cyclin T1 Tat-TAR recognition motif (TRM) and the zinc-coordinating loop of Tat. The TAR loop phosphate backbone forms electrostatic and VDW interactions with positively charged side chains of the CycT1 TRM. Mutational analysis showed that these interactions contribute importantly to binding affinity. The Tat ARM was present in the crystallized construct; however, it was not visualized in the electron density, and the TAR bulge was not formed in the RNA construct used in crystallization. Binding assays showed that TAR bulge-Tat ARM interactions contribute less to TAR binding affinity than TAR loop interactions with the CycT1 TRM and Tat core. Thus, the TAR loop evolved to make high-affinity interactions with the TRM while Tat has three roles: scaffolding and stabilizing the TRM, making specific interactions through its zinc-coordinating loop, and making electrostatic interactions through its ARM.
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Joachim I, Rikker S, Hauck D, Ponader D, Boden S, Sommer R, Hartmann L, Titz A. Development and optimization of a competitive binding assay for the galactophilic low affinity lectin LecA from Pseudomonas aeruginosa. Org Biomol Chem 2018; 14:7933-48. [PMID: 27488655 DOI: 10.1039/c6ob01313a] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Infections with the Gram-negative bacterium Pseudomonas aeruginosa result in a high mortality among immunocompromised patients and those with cystic fibrosis. The pathogen can switch from planktonic life to biofilms, and thereby shields itself against antibiotic treatment and host immune defense to establish chronic infections. The bacterial protein LecA, a C-type lectin, is a virulence factor and an integral component for biofilm formation. Inhibition of LecA with its carbohydrate ligands results in reduced biofilm mass, a potential Achilles heel for treatment. Here, we report the development and optimization of a fluorescence polarization-based competitive binding assay with LecA for application in screening of potential inhibitors. As a consequence of the low affinity of d-galactose for LecA, the fluorescent ligand was optimized to reduce protein consumption in the assay. The assay was validated using a set of known inhibitors of LecA and IC50 values in good agreement with the known Kd values were obtained. Finally, we employed the optimized assay to screen sets of synthetic thio-galactosides and natural blood group antigens and report their structure-activity relationship. In addition, we evaluated a multivalent fluorescent assay probe for LecA and report its applicability in an inhibition assay.
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Affiliation(s)
- Ines Joachim
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany. and Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover, Braunschweig, Germany and Department of Chemistry and Graduate School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Sebastian Rikker
- Department of Chemistry and Graduate School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Dirk Hauck
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany. and Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover, Braunschweig, Germany
| | - Daniela Ponader
- Max Planck Institute of Colloids and Interfaces, Department of Biomolecular Systems, Research Campus Golm, 14424 Potsdam, Germany
| | - Sophia Boden
- Heinrich-Heine-University Duesseldorf, Institute of Organic Chemistry and Macromolecular Chemistry, D-40225 Düsseldorf, Germany
| | - Roman Sommer
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany. and Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover, Braunschweig, Germany
| | - Laura Hartmann
- Heinrich-Heine-University Duesseldorf, Institute of Organic Chemistry and Macromolecular Chemistry, D-40225 Düsseldorf, Germany
| | - Alexander Titz
- Chemical Biology of Carbohydrates, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), D-66123 Saarbrücken, Germany. and Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover, Braunschweig, Germany and Department of Chemistry and Graduate School Chemical Biology, University of Konstanz, D-78457 Konstanz, Germany
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7
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Wagner T, Greschik H, Burgahn T, Schmidtkunz K, Schott AK, McMillan J, Baranauskienė L, Xiong Y, Fedorov O, Jin J, Oppermann U, Matulis D, Schüle R, Jung M. Identification of a small-molecule ligand of the epigenetic reader protein Spindlin1 via a versatile screening platform. Nucleic Acids Res 2016; 44:e88. [PMID: 26893353 PMCID: PMC4872087 DOI: 10.1093/nar/gkw089] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/30/2016] [Accepted: 02/03/2016] [Indexed: 12/14/2022] Open
Abstract
Epigenetic modifications of histone tails play an essential role in the regulation of eukaryotic transcription. Writer and eraser enzymes establish and maintain the epigenetic code by creating or removing posttranslational marks. Specific binding proteins, called readers, recognize the modifications and mediate epigenetic signalling. Here, we present a versatile assay platform for the investigation of the interaction between methyl lysine readers and their ligands. This can be utilized for the screening of small-molecule inhibitors of such protein-protein interactions and the detailed characterization of the inhibition. Our platform is constructed in a modular way consisting of orthogonal in vitro binding assays for ligand screening and verification of initial hits and biophysical, label-free techniques for further kinetic characterization of confirmed ligands. A stability assay for the investigation of target engagement in a cellular context complements the platform. We applied the complete evaluation chain to the Tudor domain containing protein Spindlin1 and established the in vitro test systems for the double Tudor domain of the histone demethylase JMJD2C. We finally conducted an exploratory screen for inhibitors of the interaction between Spindlin1 and H3K4me3 and identified A366 as the first nanomolar small-molecule ligand of a Tudor domain containing methyl lysine reader.
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Affiliation(s)
- Tobias Wagner
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg 79104, Germany
| | - Holger Greschik
- Department of Urology and Center for Clinical Research, University Freiburg Medical Center, Freiburg 79106, Germany
| | - Teresa Burgahn
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg 79104, Germany
| | - Karin Schmidtkunz
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg 79104, Germany
| | - Anne-Kathrin Schott
- Department of Urology and Center for Clinical Research, University Freiburg Medical Center, Freiburg 79106, Germany
| | - Joel McMillan
- Department of Urology and Center for Clinical Research, University Freiburg Medical Center, Freiburg 79106, Germany
| | - Lina Baranauskienė
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius 02241, Lithuania
| | - Yan Xiong
- Department of Structural and Chemical Biology, Department of Oncological Sciences, Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Target Discovery Institute (TDI), Oxford OX3 7FZ, UK
| | - Jian Jin
- Department of Structural and Chemical Biology, Department of Oncological Sciences, Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Udo Oppermann
- Structural Genomics Consortium, Botnar Research Center, NIHR Oxford BRU, University of Oxford, Oxford OX3 7LD, UK
| | - Daumantas Matulis
- Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius 02241, Lithuania
| | - Roland Schüle
- Department of Urology and Center for Clinical Research, University Freiburg Medical Center, Freiburg 79106, Germany German Cancer Consortium (DKTK), Freiburg, Germany BIOSS Centre of Biological Signalling Studies, University of Freiburg, 79106 Freiburg, Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg 79104, Germany BIOSS Centre of Biological Signalling Studies, University of Freiburg, 79106 Freiburg, Germany German Cancer Research Centre (DKFZ), Heidelberg, Germany
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8
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Hall MD, Yasgar A, Peryea T, Braisted JC, Jadhav A, Simeonov A, Coussens NP. Fluorescence polarization assays in high-throughput screening and drug discovery: a review. Methods Appl Fluoresc 2016; 4:022001. [PMID: 28809163 DOI: 10.1088/2050-6120/4/2/022001] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The sensitivity of fluorescence polarization (FP) and fluorescence anisotropy (FA) to molecular weight changes has enabled the interrogation of diverse biological mechanisms, ranging from molecular interactions to enzymatic activity. Assays based on FP/FA technology have been widely utilized in high-throughput screening (HTS) and drug discovery due to the homogenous format, robust performance and relative insensitivity to some types of interferences, such as inner filter effects. Advancements in assay design, fluorescent probes, and technology have enabled the application of FP assays to increasingly complex biological processes. Herein we discuss different types of FP/FA assays developed for HTS, with examples to emphasize the diversity of applicable targets. Furthermore, trends in target and fluorophore selection, as well as assay type and format, are examined using annotated HTS assays within the PubChem database. Finally, practical considerations for the successful development and implementation of FP/FA assays for HTS are provided based on experience at our center and examples from the literature, including strategies for flagging interference compounds among a list of hits.
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Affiliation(s)
- Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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9
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Cromm PM, Schaubach S, Spiegel J, Fürstner A, Grossmann TN, Waldmann H. Orthogonal ring-closing alkyne and olefin metathesis for the synthesis of small GTPase-targeting bicyclic peptides. Nat Commun 2016; 7:11300. [PMID: 27075966 PMCID: PMC4834642 DOI: 10.1038/ncomms11300] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/11/2016] [Indexed: 02/06/2023] Open
Abstract
Bicyclic peptides are promising scaffolds for the development of inhibitors of biological targets that proved intractable by typical small molecules. So far, access to bioactive bicyclic peptide architectures is limited due to a lack of appropriate orthogonal ring-closing reactions. Here, we report chemically orthogonal ring-closing olefin (RCM) and alkyne metathesis (RCAM), which enable an efficient chemo- and regioselective synthesis of complex bicyclic peptide scaffolds with variable macrocycle geometries. We also demonstrate that the formed alkyne macrocycle can be functionalized subsequently. The orthogonal RCM/RCAM system was successfully used to evolve a monocyclic peptide inhibitor of the small GTPase Rab8 into a bicyclic ligand. This modified peptide shows the highest affinity for an activated Rab GTPase that has been reported so far. The RCM/RCAM-based formation of bicyclic peptides provides novel opportunities for the design of bioactive scaffolds suitable for the modulation of challenging protein targets. Bicyclic peptides can inhibit biological targets hard to address with small molecules. Here, the authors combine two orthogonal ring-closing reactions to produce bicyclic peptides with improved bioactivity thereby providing a strategy that can greatly improve the structural diversity of such peptides.
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Affiliation(s)
- Philipp M Cromm
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Sebastian Schaubach
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim/Ruhr, Germany
| | - Jochen Spiegel
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Alois Fürstner
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim/Ruhr, Germany
| | - Tom N Grossmann
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany.,Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
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10
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Janzen WP. Screening technologies for small molecule discovery: the state of the art. ACTA ACUST UNITED AC 2015; 21:1162-70. [PMID: 25237860 DOI: 10.1016/j.chembiol.2014.07.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 01/24/2023]
Abstract
Screening, high-throughput screening, and ultra-high-throughput screening are all really just points on a spectrum that represent differing applications of the same process: the creation of biologically relevant assays that are relevant, reproducible, reliable, and robust. Whether the discovery program is developing a pharmaceutical, an academic probe, cosmetics, pesticides, or a toxicity monitoring assay, the development of a screen focuses on generating a method that will reliably deliver reproducible results over a period of weeks, months, or years and that will generate consistent results for every test along the way. This review provides both historical perspective on how this unique scientific discipline evolved and commentary on the current state of the art technologies and techniques.
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Affiliation(s)
- William P Janzen
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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11
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A small-molecule mimic of a peptide docking motif inhibits the protein kinase PDK1. Proc Natl Acad Sci U S A 2014; 111:18590-5. [PMID: 25518860 DOI: 10.1073/pnas.1415365112] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
There is great interest in developing selective protein kinase inhibitors by targeting allosteric sites, but these sites often involve protein-protein or protein-peptide interfaces that are very challenging to target with small molecules. Here we present a systematic approach to targeting a functionally conserved allosteric site on the protein kinase PDK1 called the PDK1-interacting fragment (PIF)tide-binding site, or PIF pocket. More than two dozen prosurvival and progrowth kinases dock a conserved peptide tail into this binding site, which recruits them to PDK1 to become activated. Using a site-directed chemical screen, we identified and chemically optimized ligand-efficient, selective, and cell-penetrant small molecules (molecular weight ∼ 380 Da) that compete with the peptide docking motif for binding to PDK1. We solved the first high-resolution structure of a peptide docking motif (PIFtide) bound to PDK1 and mapped binding energy hot spots using mutational analysis. We then solved structures of PDK1 bound to the allosteric small molecules, which revealed a binding mode that remarkably mimics three of five hot-spot residues in PIFtide. These allosteric small molecules are substrate-selective PDK1 inhibitors when used as single agents, but when combined with an ATP-competitive inhibitor, they completely suppress the activation of the downstream kinases. This work provides a promising new scaffold for the development of high-affinity PIF pocket ligands, which may be used to enhance the anticancer activity of existing PDK1 inhibitors. Moreover, our results provide further impetus for exploring the helix αC patches of other protein kinases as potential therapeutic targets even though they involve protein-protein interfaces.
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12
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Preidl JJ, Gnanapragassam VS, Lisurek M, Saupe J, Horstkorte R, Rademann J. Fluoreszente Mimetika von CMP-Neu5Ac sind hochaffine, zellgängige Polarisationssonden eukaryotischer und bakterieller Sialyltransferasen und inhibieren die zelluläre Sialylierung. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201400394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Preidl JJ, Gnanapragassam VS, Lisurek M, Saupe J, Horstkorte R, Rademann J. Fluorescent mimetics of CMP-Neu5Ac are highly potent, cell-permeable polarization probes of eukaryotic and bacterial sialyltransferases and inhibit cellular sialylation. Angew Chem Int Ed Engl 2014; 53:5700-5. [PMID: 24737687 DOI: 10.1002/anie.201400394] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Indexed: 12/23/2022]
Abstract
Oligosaccharides of the glycolipids and glycoproteins at the outer membranes of human cells carry terminal neuraminic acids, which are responsible for recognition events and adhesion of cells, bacteria, and virus particles. The synthesis of neuraminic acid containing glycosides is accomplished by intracellular sialyl transferases. Therefore, the chemical manipulation of cellular sialylation could be very important to interfere with cancer development, inflammations, and infections. The development and applications of the first nanomolar fluorescent inhibitors of sialyl transferases are described herein. The obtained carbohydrate-nucleotide mimetics were found to bind all four commercially available and tested eukaryotic and bacterial sialyl transferases in a fluorescence polarization assay. Moreover, it was observed that the anionic mimetics intruded rapidly and efficiently into cells in vesicles and translocated to cellular organelles surrounding the nucleus of CHO cells. The new compounds inhibit cellular sialylation in two cell lines and open new perspectives for investigations of cellular sialylation.
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Affiliation(s)
- Johannes J Preidl
- Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195 Berlin (Germany) http://www.bcp.fu-berlin.de/ag-rademann; Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin (Germany)
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14
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Kopra K, Shweta, Martikkala E, Hänninen P, Petäjä-Repo U, Härmä H. A homogeneous single-label quenching resonance energy transfer assay for a δ-opioid receptor–ligand using intact cells. Analyst 2013; 138:4907-14. [DOI: 10.1039/c3an00736g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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zhang Y, Yang X, Liu L, Huang X, Huang Z, Pu J, Long G, Zhang L, Liu D, Xu B, Liao J, Liao F. Comparison of Förster-resonance-energy-transfer acceptors for tryptophan and tyrosine residues in native proteins as donors. J Fluoresc 2012; 23:147-57. [PMID: 23001429 DOI: 10.1007/s10895-012-1128-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2012] [Accepted: 09/05/2012] [Indexed: 11/28/2022]
Abstract
Homogenous bioaffinity analysis with tryptophan/tyrosine residues in native proteins as FÖrster-resonance-energy-transfer (FRET) donors is feasible when suitable fluorophors can act as FRET acceptors in ligands (FRET probes) and FRET efficiency in complexes of proteins and FRET probes is high enough. In complexes of proteins and FRET probes, suitable acceptors should have excitation peaks around 335 nm and high rotation freedom, are preferred to have sufficient quantum yields and excitation valleys around 280 nm. In protein binding sites mimicked with mixtures of neutral phosphate buffer and organic solvents, quantum yields of candidate acceptors are altered inconsistently but their excitation peaks show tiny changes. Fluorophores as acceptors in such FRET probes are buried inside glutathione-S-transferase and have low rotation freedom, but are localized on streptavidin surface and display high rotation freedom; FRET efficiency in complexes of streptavidin and its FRET probes is much stronger than that in complexes of glutathione-S-transferase and its FRET probes. Specially, the quantum yield is about 0.70 for free 1-naphthylamine probe in neutral phosphate buffer, about 0.50 for 1-naphthylamine probe bound by streptavidin, and about 0.15 for that bound by glutathione-S-transferase. The quantum yield is about 0.06 for free dansylamide probe, about 0.11 for dansylamide probe bound by streptavidin and about 0.27 for that bound by glutathione-S-transferase. Therefore, 1-naphthylamine and dansylamide are effective acceptors when they localize on surfaces of complexes of proteins and FRET probes.
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Affiliation(s)
- Yi zhang
- Unit for analytical probes and protein biotechnology, Key laboratory of medical laboratory diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
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16
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Baughman BM, Jake Slavish P, DuBois RM, Boyd VA, White SW, Webb TR. Identification of influenza endonuclease inhibitors using a novel fluorescence polarization assay. ACS Chem Biol 2012; 7:526-34. [PMID: 22211528 DOI: 10.1021/cb200439z] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Influenza viruses have been responsible for the largest pandemics in the previous century. Although vaccination and prophylactic antiviral therapeutics are the primary defense against influenza virus, there is a pressing need to develop new antiviral agents to circumvent the limitations of current therapies. The endonuclease activity of the influenza virus PA(N) protein is essential for virus replication and is a promising target for novel anti-influenza drugs. To facilitate the discovery of endonuclease inhibitors, we have developed a high-throughput fluorescence polarization (FP) assay, utilizing a novel fluorescein-labeled compound (K(d) = 0.378 μM) and a PA(N) construct, to identify small molecules that bind to the PA(N) endonuclease active site. Several known 4-substituted 2,4-dioxobutanoic acid inhibitors with high and low affinities have been evaluated in this FP-based competitive binding assay, and there was a general correlation between binding and the reported inhibition of endonuclease activity. Additionally, we have demonstrated the utility of this assay for identifying endonuclease inhibitors in a small diverse targeted fragment library. These fragment hits were used to build a follow-up library that that led to new active compounds that demonstrate FP binding and anti-influenza activities in plaque inhibition assays. The assay offers significant advantages over previously reported assays and is suitable for high-throughput and fragment-based screening studies. Additionally the demonstration of the applicability of a mechanism-based "targeted fragment" library supports the general potential of this novel approach for other enzyme targets. These results serve as a sound foundation for the development of new therapeutic leads targeting influenza endonuclease.
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Affiliation(s)
- Brandi M. Baughman
- Integrated Program in Biomedical
Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | | | | | | | - Stephen W. White
- Integrated Program in Biomedical
Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Thomas R. Webb
- Integrated Program in Biomedical
Sciences, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
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17
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Geurink PP, El Oualid F, Jonker A, Hameed DS, Ovaa H. A general chemical ligation approach towards isopeptide-linked ubiquitin and ubiquitin-like assay reagents. Chembiochem 2012; 13:293-7. [PMID: 22213387 PMCID: PMC3488293 DOI: 10.1002/cbic.201100706] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Indexed: 11/26/2022]
Affiliation(s)
- Paul P Geurink
- Division of Cell Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
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18
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Tian W, Xu Y, Han X, Duggineni S, Han X, Huang Z, An J. Development of a Novel Fluorescence Polarization–Based Assay for Studying the β-Catenin/Tcf4 Interaction. ACTA ACUST UNITED AC 2011; 17:530-4. [DOI: 10.1177/1087057111429745] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aberrant activation of the Wnt/β-catenin signaling pathway is associated with a wide range of human cancers. The interaction of β-catenin with T cell factor (Tcf) is a key step in activation of proliferative genes in this pathway. Interruption of this interaction would be a valuable strategy as a tumor therapy. In this study, we developed a novel fluorescein isothiocyanate (FITC)–labeled Tcf4-derived probe for identification of inhibitors of the β-catenin/Tcf4 interaction using a fluorescence polarization assay. This assay shows high potential for use in high-throughput screening for the discovery of inhibitors of the β-catenin/Tcf4 interaction.
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Affiliation(s)
- Wang Tian
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Yan Xu
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Xiaofeng Han
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Srinivas Duggineni
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Xiaobing Han
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Ziwei Huang
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
| | - Jing An
- Department of Pharmacology, State University of New York, Upstate Medical University, Syracuse, NY, USA
- Upstate Cancer Research Institute, State University of New York, Upstate Medical University, Syracuse, NY, USA
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Xie Y, Yang X, Pu J, Zhao Y, Zhang Y, Xie G, Zheng J, Yuan H, Liao F. Homogeneous competitive assay of ligand affinities based on quenching fluorescence of tyrosine/tryptophan residues in a protein via Főrster-resonance-energy-transfer. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 77:869-76. [PMID: 20822950 DOI: 10.1016/j.saa.2010.08.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2010] [Accepted: 08/05/2010] [Indexed: 05/13/2023]
Abstract
A new homogeneous competitive assay of ligand affinities was proposed based on quenching the fluorescence of tryptophan/tyrosine residues in a protein via Főrster-resonance-energy-transfer using a fluorescent reference ligand as the acceptor. Under excitation around 280 nm, the fluorescence of a protein or a bound acceptor was monitored upon competitive binding against a nonfluorescent candidate ligand. Chemometrics for deriving the binding ratio of the acceptor with either fluorescence signal was discussed; the dissociation constant (K(d)) of a nonfluorescent candidate ligand was calculated from its concentration to displace 50% binding of the acceptor. N-biotinyl-N'-(1-naphthyl)-ethylenediamine (BNEDA) and N-biotinyl-N'-dansyl-ethylenediamine (BDEDA) were used as the reference ligands and acceptors to streptavidin to test this new homogeneous competitive assay. Upon binding of an acceptor to streptavidin, there were the quench of streptavidin fluorescence at 340 nm and the characteristic fluorescence at 430 nm for BNEDA or at 525 nm for BDEDA. K(d) of BNEDA and BDEDA was obtained via competitive binding against biotin. By quantifying BNEDA fluorescence, K(d) of each tested nonfluorescent biotin derivative was consistent with that by quantifying streptavidin fluorescence using BNEDA or BDEDA as the acceptor. The overall coefficients of variation were about 10%. Therefore, this homogeneous competitive assay was effective and promising to high-throughput-screening.
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Affiliation(s)
- Yanling Xie
- Unit for Biotransformation and Protein Biotechnology, Chongqing Key Laboratory of Biochemical & Molecular Pharmacology, Chongqing Medical University, Chongqing 400016, China
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20
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Wilder PT, Charpentier TH, Liriano MA, Gianni K, Varney KM, Pozharski E, Coop A, Toth EA, Mackerell AD, Weber DJ. In vitro screening and structural characterization of inhibitors of the S100B-p53 interaction. ACTA ACUST UNITED AC 2010; 2010:109-126. [PMID: 21132089 DOI: 10.2147/ijhts.s8210] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
S100B is highly over-expressed in many cancers, including malignant melanoma. In such cancers, S100B binds wild-type p53 in a calcium-dependent manner, sequestering it, and promoting its degradation, resulting in the loss of p53-dependent tumor suppression activities. Therefore, S100B inhibitors may be able to restore wild-type p53 levels in certain cancers and provide a useful therapeutic strategy. In this regard, an automated and sensitive fluorescence polarization competition assay (FPCA) was developed and optimized to screen rapidly for lead compounds that bind Ca(2+)-loaded S100B and inhibit S100B target complex formation. A screen of 2000 compounds led to the identification of 26 putative S100B low molecular weight inhibitors. The binding of these small molecules to S100B was confirmed by nuclear magnetic resonance spectroscopy, and additional structural information was provided by x-ray crystal structures of several compounds in complexes with S100B. Notably, many of the identified inhibitors function by chemically modifying Cys84 in protein. These results validate the use of high-throughput FPCA to facilitate the identification of compounds that inhibit S100B. These lead compounds will be the subject of future optimization studies with the ultimate goal of developing a drug with therapeutic activity for the treatment of malignant melanoma and/or other cancers with elevated S100B.
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Affiliation(s)
- Paul T Wilder
- Department of Biochemistry and Molecular Biology, The University of Maryland School of Medicine, Maryland, USA
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21
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Xi XG, Deprez E. Monitoring helicase-catalyzed DNA unwinding by fluorescence anisotropy and fluorescence cross-correlation spectroscopy. Methods 2010; 51:289-94. [PMID: 20219681 DOI: 10.1016/j.ymeth.2010.02.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2010] [Revised: 02/23/2010] [Accepted: 02/24/2010] [Indexed: 11/28/2022] Open
Abstract
In order to elucidate molecular mechanism of helicases, we have developed two new rapid and sensitive fluorescence assays to measure helicase-mediated DNA unwinding. The fluorescence anisotropy (FA) assay takes the advantage of the substantial change in fluorescence polarization upon helicase binding to DNA and DNA unwinding. The extent of depolarization depends on the rate of tumbling of the fluorescently labeled DNA molecule, which decreases with increasing size. This assay therefore can simultaneously monitor the DNA binding of helicase and the subsequent helicase-catalyzed DNA unwinding in real-time. For size limitation reasons, the FA approach is more suitable for single-turnover kinetic studies. A fluorescence cross-correlation spectroscopy method (FCCS) is also described for measuring DNA unwinding. This assay is based on the degree of concomitant diffusion of the two complementary DNA strands in a small excitation volume, each labeled by a different color. The decrease in the amplitude of the cross-correlation signal is then directly related to the unwinding activity. By contrast with FA, the FCCS-based assay can be used to measure the unwinding activity under both single- and multiple-turnover conditions, with no limitation related to the size of the DNA strands constituting the DNA substrate. These methods used together have proven to be useful for studying molecular mechanism underlying efficient motor function of helicases. Here, we describe the theoretical basis and framework of FA and FCCS and some practical implications for measuring DNA binding and unwinding. We discuss sample preparation and potential troubleshooting. Special attention is paid to instrumentation, data acquisition and analysis.
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Affiliation(s)
- Xu Guang Xi
- Laboratoire de Stress Génotoxiques et Cancer, CNRS UMR3348, Institut Curie-Section de Recherche, Centre Universitaire, Bat 110, 91405 Orsay, France.
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