1
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Eck T, Laureano de Souza M, Delvillar M, Ashraf K, Yadav Bheemanaboina RR, Chakrasali R, Kreiss T, Siekierka JJ, Rotella DP, Bhanot P, Goodey NM. Characterization of competitive inhibitors of P. falciparum cGMP‐dependent protein kinase. Chembiochem 2022; 23:e202100704. [PMID: 35044710 PMCID: PMC9132199 DOI: 10.1002/cbic.202100704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/18/2022] [Indexed: 11/09/2022]
Abstract
Plasmodium falciparum cGMP-dependent protein kinase (PfPKG) is an enticing antimalarial drug target. Novel chemotypes are needed because existing inhibitors have safety issues that may prevent further development. This work demonstrates isoxazole-based compounds are potent ATP competitive inhibitors of PfPKG and discloses a new analogue in this series. Isoxazoles 3 and 5 had Ki values that are comparable to a known standard, 4-[2-(4-fluorophenyl)-5-(1-methylpiperidine-4-yl)-1H pyrrol-3-yl] pyridine. They also exhibited excellent selectivity for PfPKG over the human orthologue and the gatekeeper mutant T618Q PfPKG, which mimics the less accessible binding site of the human orthologue. The human orthologue's larger binding site volume is predicted to explain the selectivity of the inhibitors for the P. falciparum enzyme.
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Affiliation(s)
- Tyler Eck
- Montclair State University Chemistry and Biochemistry UNITED STATES
| | - Mariana Laureano de Souza
- Rutgers New Jersey Medical School Department of Microbiology, Biochemistry, and Molecular Genetics UNITED STATES
| | - Melvin Delvillar
- Rutgers New Jersey Medical School Microbiology, Biochemistry and Molecular Genetics UNITED STATES
| | - Kutub Ashraf
- Rutgers New Jersey Medical School Microbiology, Biochemistry and Molecular Genetics UNITED STATES
| | | | | | - Tamara Kreiss
- Montclair State University Chemistry and Biochemistry UNITED STATES
| | - John J Siekierka
- Montclair State University Chemistry and Biochemistry UNITED STATES
| | - David P Rotella
- Montclair State University Chemistry and Biochemistry UNITED STATES
| | - Purnima Bhanot
- Rutgers New Jersey Medical School Department of Microbiology, Biochemistry and Molecular Genetics UNITED STATES
| | - Nina M Goodey
- Montclair State University Chemistry and Biochemistry 1 Normal Avenue 07043 Montclair UNITED STATES
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2
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Mihara K, Nakajima N, Fujii I, Fujiwara D. Generation of inhibitory peptides for
IKKε
from a kinase‐focused phage library of helix‐loop‐helix peptides. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kousuke Mihara
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Natsumi Nakajima
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science Osaka Prefecture University Osaka Japan
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3
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Fujiwara D, Mihara K, Takayama R, Nakamura Y, Ueda M, Tsumuraya T, Fujii I. Chemical Modification of Phage-Displayed Helix-Loop-Helix Peptides to Construct Kinase-Focused Libraries. Chembiochem 2021; 22:3406-3409. [PMID: 34605137 PMCID: PMC9297947 DOI: 10.1002/cbic.202100450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/01/2021] [Indexed: 11/11/2022]
Abstract
Conformationally constrained peptides hold promise as molecular tools in chemical biology and as a new modality in drug discovery. The construction and screening of a target-focused library could be a promising approach for the generation of de novo ligands or inhibitors against target proteins. Here, we have prepared a protein kinase-focused library by chemically modifying helix-loop-helix (HLH) peptides displayed on phage and subsequently tethered to adenosine. The library was screened against aurora kinase A (AurA). The selected HLH peptide Bip-3 retained the α-helical structure and bound to AurA with a KD value of 13.7 μM. Bip-3 and the adenosine-tethered peptide Bip-3-Adc provided IC50 values of 103 μM and 7.7 μM, respectively, suggesting that Bip-3-Adc bivalently inhibited AurA. In addition, the selectivity of Bip-3-Adc to several protein kinases was tested, and was highest against AurA. These results demonstrate that chemical modification can enable the construction of a kinase-focused library of phage-displayed HLH peptides.
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Affiliation(s)
- Daisuke Fujiwara
- Department of Biological ScienceGraduate School of ScienceOsaka Prefecture University1-1, Gakuen-cho, Naka-ku, SakaiOsaka599-8531Japan
| | - Kousuke Mihara
- Department of Biological ScienceGraduate School of ScienceOsaka Prefecture University1-1, Gakuen-cho, Naka-ku, SakaiOsaka599-8531Japan
| | - Ryo Takayama
- Department of Biological ScienceGraduate School of ScienceOsaka Prefecture University1-1, Gakuen-cho, Naka-ku, SakaiOsaka599-8531Japan
| | - Yusuke Nakamura
- Department of Biological ScienceGraduate School of ScienceOsaka Prefecture University1-1, Gakuen-cho, Naka-ku, SakaiOsaka599-8531Japan
| | - Mitsuhiro Ueda
- Department of ChemistryGraduate School of ScienceOsaka Prefecture University1-1, Gakuen-cho, Naka-ku, SakaiOsaka599-8531Japan
| | - Takeshi Tsumuraya
- Department of Biological ScienceGraduate School of ScienceOsaka Prefecture University1-1, Gakuen-cho, Naka-ku, SakaiOsaka599-8531Japan
| | - Ikuo Fujii
- Department of Biological ScienceGraduate School of ScienceOsaka Prefecture University1-1, Gakuen-cho, Naka-ku, SakaiOsaka599-8531Japan
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4
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Kim J, Kim D, Jung H, Lee J, Hong VS. Identification and Kinetic Characterization of Serum- and Glucocorticoid-Regulated Kinase Inhibitors Using a Fluorescence Polarization-Based Assay. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:655-662. [PMID: 33783250 DOI: 10.1177/24725552211002465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The serum- and glucocorticoid-regulated kinase (SGK) family consists of three isoforms (SGK1, SGK2, and SGK3) that have been implicated in the regulation of tumor growth, metastasis, autophagy, and epithelial ion transport. SGK1 and SGK3 play essential roles in protein kinase B (AKT or PKB)-independent phosphoinositide 3-kinases (PI3K)-mediated tumorigenesis, as evidenced by the significantly elevated expression levels of SGK1 and SGK3 in many cancers, including prostate cancer, colorectal carcinoma, estrogen-dependent breast cancer, and glioblastoma. Therefore, SGK is a potential target for anticancer therapy. A small kinase-focused library comprising 160 compounds was screened against SGK1 using a fluorescence polarization-based kinase assay that yielded a Z'-factor of 0.82. Among the 39 compounds obtained as initial hits in a primary screen, 12 compounds contained the thiazolidine-2,4-dione scaffold. The inhibitory mechanisms of the most potent hit, KMU010402, were further investigated using kinetic analyses, followed by determination of the inhibition constants for SGK1, SGK2, and SGK3. Molecular modeling was used to propose a potential binding mode of KMU010402 to SGK1.
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Affiliation(s)
- Jeongeun Kim
- Department of Chemistry, College of Natural Sciences, Keimyung University, Daegu, Republic of Korea
| | - Donghee Kim
- Department of Chemistry, College of Natural Sciences, Keimyung University, Daegu, Republic of Korea
| | - Hyunho Jung
- Department of Chemistry, College of Natural Sciences, Keimyung University, Daegu, Republic of Korea
| | - Jinho Lee
- Department of Chemistry, College of Natural Sciences, Keimyung University, Daegu, Republic of Korea
| | - Victor Sukbong Hong
- Department of Chemistry, College of Natural Sciences, Keimyung University, Daegu, Republic of Korea
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5
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Development of a Rapid Mass Spectrometric Determination of AMP and Cyclic AMP for PDE3 Activity Study: Application and Computational Analysis for Evaluating the Effect of a Novel 2-oxo-1,2-dihydropyridine-3-carbonitrile Derivative as PDE-3 Inhibitor. Molecules 2020; 25:molecules25081817. [PMID: 32326556 PMCID: PMC7221589 DOI: 10.3390/molecules25081817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/08/2020] [Accepted: 04/14/2020] [Indexed: 12/16/2022] Open
Abstract
A simple, quick, easy and cheap tandem mass spectrometry (MS/MS) method for the determination of adenosine monophosphate (AMP) and cyclic adenosine monophosphate (cAMP) has been newly developed. This novel MS/MS method was applied for the evaluation of the inhibitory effect of a novel 2-oxo-1,2-dihydropyridine-3-carbonitrile derivative, also named DF492, on PDE3 enzyme activity in comparison to its parent drug milrinone. Molecule DF492, with an IC50 of 409.5 nM, showed an inhibition of PDE3 greater than milrinone (IC50 = 703.1 nM). To explain the inhibitory potential of DF492, molecular docking studies toward the human PDE3A were carried out with the aim of predicting the binding mode of DF492. The presence of different bulkier decorating fragments in DF492 was pursued to shift affinity of this novel molecule toward PDE3A compared to milrinone in accordance with both the theoretical and experimental results. The described mass spectrometric approach could have a wider potential use in kinetic and biomedical studies and could be applied for the determination of other phosphodiesterase inhibitor molecules.
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6
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Dash R, Arifuzzaman M, Mitra S, Abdul Hannan M, Absar N, Hosen SMZ. Unveiling the Structural Insights into the Selective Inhibition of Protein Kinase D1. Curr Pharm Des 2020; 25:1059-1074. [PMID: 31131745 DOI: 10.2174/1381612825666190527095510] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 05/14/2019] [Indexed: 01/06/2023]
Abstract
BACKGROUND Although protein kinase D1 (PKD1) has been proved to be an efficient target for anticancer drug development, lack of structural details and substrate binding mechanisms are the main obstacles for the development of selective inhibitors with therapeutic benefits. OBJECTIVE The present study described the in silico dynamics behaviors of PKD1 in binding with selective and non-selective inhibitors and revealed the critical binding site residues for the selective kinase inhibition. METHODS Here, the three dimensional model of PKD1 was initially constructed by homology modeling along with binding site characterization to explore the non-conserved residues. Subsequently, two known inhibitors were docked to the catalytic site and the detailed ligand binding mechanisms and post binding dyanmics were investigated by molecular dynamics simulation and binding free energy calculations. RESULTS According to the binding site analysis, PKD1 serves several non-conserved residues in the G-loop, hinge and catalytic subunits. Among them, the residues including Leu662, His663, and Asp665 from hinge region made polar interactions with selective PKD1 inhibitor in docking simulation, which were further validated by the molecular dynamics simulation. Both inhibitors strongly influenced the structural dynamics of PKD1 and their computed binding free energies were in accordance with experimental bioactivity data. CONCLUSION The identified non-conserved residues likely to play critical role on molecular reorganization and inhibitor selectivity. Taken together, this study explained the molecular basis of PKD1 specific inhibition, which may help to design new selective inhibitors for better therapies to overcome cancer and PKD1 dysregulated disorders.
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Affiliation(s)
- Raju Dash
- Department of Biochemistry and Biotechnology, University of Science and Technology, Chittagong-4202, Bangladesh.,Molecular Modeling and Drug Design Laboratory, Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research, Chittagong-4220, Bangladesh.,Department of Anatomy, Dongguk University Graduate School of Medicine, Gyeongju 38066, Korea
| | - Md Arifuzzaman
- College of Pharmacy, Yeungnam University, Gyeongsan-38541, Korea
| | - Sarmistha Mitra
- Plasma Bioscience Research Center, Plasma-bio display, Kwangwoon University, Seoul, 01897, Korea
| | - Md Abdul Hannan
- Department of Anatomy, Dongguk University Graduate School of Medicine, Gyeongju 38066, Korea.,Department of Biochemistry and Molecular Biology, Bangladesh Agricultural University, Mymensingh-2202, Bangladesh
| | - Nurul Absar
- Department of Biochemistry and Biotechnology, University of Science and Technology, Chittagong-4202, Bangladesh
| | - S M Zahid Hosen
- Molecular Modeling and Drug Design Laboratory, Pharmacology Research Division, Bangladesh Council of Scientific and Industrial Research, Chittagong-4220, Bangladesh
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7
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Imamura RM, Kumagai K, Nakano H, Okabe T, Nagano T, Kojima H. Inexpensive High-Throughput Screening of Kinase Inhibitors Using One-Step Enzyme-Coupled Fluorescence Assay for ADP Detection. SLAS DISCOVERY 2018; 24:284-294. [PMID: 30418800 DOI: 10.1177/2472555218810139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein kinases are attractive targets for both biological research and drug development. Several assay kits, especially for the detection of adenosine diphosphate (ADP), which is universally produced by kinases, are commercially available for high-throughput screening (HTS) of kinase inhibitors, but their cost is quite high for large-scale screening. Here, we report a new enzyme-coupled fluorescence assay for ADP detection, which uses just 10 inexpensive, commercially available components. The assay protocol is very simple, requiring only the mixing of test solutions with ADP detection solution and reading the fluorescence intensity of resorufin produced by coupling reaction. To validate the assay, we focused on CDC2-like kinase 1 (CLK1), a dual-specificity kinase that plays an important role in alternative splicing, and we used the optimized assay to screen an in-house chemical library of about 215,000 compounds for CLK1 inhibitors. We identified and validated 12 potent inhibitors of CLK1, including a novel inhibitory scaffold. The results demonstrate that this assay platform is not only simple and cost-effective, but also sufficiently robust, showing good reproducibility and giving similar results to those obtained with the widely used ADP-Glo bioluminescent assay.
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Affiliation(s)
| | - Kazuo Kumagai
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan.,2 Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Hirofumi Nakano
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
| | - Takayoshi Okabe
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Nagano
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
| | - Hirotatsu Kojima
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
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8
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Jeong EM, Lee MY, Lee JH, Lee BH, Oh KS. A Dual Readout Assay Based on Fluorescence Polarization and Time-Resolved Fluorescence Resonance Energy Transfer to Screen for RSK1 Inhibitors. Biol Pharm Bull 2017; 39:547-55. [PMID: 27040627 DOI: 10.1248/bpb.b15-00808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A dual readout assay based on fluorescence polarization (FP) and time-resolved fluorescence resonance energy transfer (TR-FRET) exhibits many advantages over single assay technology in terms of screening quality and efficiency. In this study, we developed a dual readout assay combining FP and TR-FRET to identify ribosomal S6 kinase 1 (RSK1) inhibitors. This dual readout assay can monitor both FP and TR-FRET signals from a single RSK1 kinase reaction by using the immobilized metal affinity for phosphochemical (IMAP)-based assay. The Z' value and signal to background (S/B) ratio were 0.85 and 4.0 using FP, and 0.79 and 10.6 using TR-FRET, which led to performance of a pilot library screening against the drug repositioning set consisting of 2320 compounds with a reasonable reproducibility. From this screening, we identified 16 compounds showing greater than 50% inhibition against RSK1 for both FP and TR-FRET; 6 compounds with greater than 50% inhibition only for FP; and 4 compounds with greater than 50% inhibition only for TR-FRET. In a cell-based functional assay to validate the hit compounds, 10 compounds identified only in a single assay had little effect on the RSK-mediated phosphorylation of liver kinase B1, whereas 5 compounds showing greater than 80% inhibition for both FP and TR-FRET reduced the phosphorylation of liver kinase B1. These results demonstrate that the dual readout assay can be used to identify hit compounds by subsequently monitoring both FP and TR-FRET signals from one RSK1 reaction.
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Affiliation(s)
- Eun-mi Jeong
- Bio-Organic Science Division, Korea Research Institute of Chemical Technology
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9
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Kashem MA, Kennedy CA, Fogarty KE, Dimock JR, Zhang Y, Sanville-Ross ML, Skow DJ, Brunette SR, Swantek JL, Hummel HS, Swindle J, Nelson RM. A High-Throughput Genetic Complementation Assay in Yeast Cells Identified Selective Inhibitors of Sphingosine Kinase 1 Not Found Using a Cell-Free Enzyme Assay. Assay Drug Dev Technol 2016; 14:39-49. [DOI: 10.1089/adt.2015.671] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Mohammed A. Kashem
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Charles A. Kennedy
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Kylie E. Fogarty
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Janice R. Dimock
- Immunology and Respiratory Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Yunlong Zhang
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Mary L. Sanville-Ross
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Donna J. Skow
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Steven R. Brunette
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | - Jennifer L. Swantek
- Immunology and Respiratory Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
| | | | | | - Richard M. Nelson
- Small Molecule Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut
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10
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Lee S, Hong VS. Development and Application of a High-Throughput Fluorescence Polarization Assay to Target Pim Kinases. Assay Drug Dev Technol 2016; 14:50-7. [PMID: 26824666 DOI: 10.1089/adt.2015.685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pim proteins consisting of three isoforms (Pim-1, Pim-2, and Pim-3) are a family of serine/threonine kinases that regulate fundamental cellular responses such as cell growth, differentiation, and apoptosis. Overexpression of the Pim kinases has been linked to a wide variety of hematological and solid tumors. Thus, all three Pim kinases have been studied as promising targets for anticancer therapy. Here, we report on the development and optimization of an immobilized metal ion affinity partitioning (IMAP) fluorescence polarization (FP) method for Pim kinases. In this homogeneous 384-well assay method, fluorescein-labeled phosphopeptides are captured on cationic nanoparticles through interactions with immobilized trivalent metals, resulting in high polarization values. The apparent Km values for adenosine triphosphate (ATP) were determined to be 45 ± 7, 6.4 ± 2, and 29 ± 5 μM for Pim-1, Pim-2, and Pim-3, respectively. The assay yielded robustness with Z'-factors of >0.75 and low day-to-day variability (CV <5%) for all three Pim kinases. The IMAP FP assay was further validated by determining IC50 values for staurosporine and a known Pim inhibitor. We have also used an IMAP FP assay to examine whether compound 1, an ATP mimetic inhibitor designed through structure-based drug design, is indeed an ATP-competitive inhibitor of Pim kinases. Kinetic analysis based on Lineweaver-Burk plots showed that the inhibition mechanism of compound 1 is ATP competitive against all three Pim isoforms. The optimized IMAP assay for Pim kinases not only allows for high-throughput screening but also facilitates the characterization of novel Pim inhibitors for drug development.
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Affiliation(s)
- Seongho Lee
- Department of Chemistry, Keimyung University , Daegu, Korea
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11
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An integrated approach for discovery of highly potent and selective Mnk inhibitors: Screening, synthesis and SAR analysis. Eur J Med Chem 2015; 103:539-50. [DOI: 10.1016/j.ejmech.2015.09.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/07/2014] [Accepted: 09/05/2015] [Indexed: 02/02/2023]
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12
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Lee SH, Rhee HW, van Noort D, Lee HJ, Park HH, Shin IS, Hong JI, Park TH. Microfluidic bead-based sensing platform for monitoring kinase activity. Biosens Bioelectron 2014; 57:1-9. [DOI: 10.1016/j.bios.2014.01.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/18/2014] [Accepted: 01/20/2014] [Indexed: 10/25/2022]
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13
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A sensitive, universal and homogeneous method for determination of biomarkers in biofluids by resonance light scattering correlation spectroscopy (RLSCS). Talanta 2013; 116:501-7. [DOI: 10.1016/j.talanta.2013.07.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 07/09/2013] [Accepted: 07/11/2013] [Indexed: 11/21/2022]
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14
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Grogl M, Hickman M, Ellis W, Hudson T, Lazo JS, Sharlow ER, Johnson J, Berman J, Sciotti RJ. Drug discovery algorithm for cutaneous leishmaniasis. Am J Trop Med Hyg 2013; 88:216-21. [PMID: 23390221 DOI: 10.4269/ajtmh.11-0812] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Cutaneous leishmaniasis is clinically widespread but lacks treatments that are effective and well tolerated. Because all present drugs have been grandfathered into clinical use, there are no examples of a pre-clinical product evaluation scheme that lead to new candidates for formal development. To provide oral agents for development targeting cutaneous leishmaniasis, we have implemented a discovery scheme that incorporates in vitro and in vivo testing of efficacy, toxicity, and pharmacokinetics/metabolism. Particular emphasis is placed on in vivo testing, progression from higher-throughput models to those with most clinical relevance, and efficient use of resources.
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Affiliation(s)
- Max Grogl
- Division Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
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15
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Takagi T, Shum D, Parisi M, Santos RE, Radu C, Calder P, Rizvi Z, Frattini MG, Djaballah H. Comparison of luminescence ADP production assay and radiometric scintillation proximity assay for Cdc7 kinase. Comb Chem High Throughput Screen 2012; 14:669-87. [PMID: 21564015 DOI: 10.2174/138620711796504442] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 03/19/2011] [Accepted: 04/26/2011] [Indexed: 12/20/2022]
Abstract
Several assay technologies have been successfully adapted and used in HTS to screen for protein kinase inhibitors; however, emerging comparative analysis studies report very low hit overlap between the different technologies, which challenges the working assumption that hit identification is not dependent on the assay method of choice. To help address this issue, we performed two screens on the cancer target, Cdc7-Dbf4 heterodimeric protein kinase, using a direct assay detection method measuring [(33)P]-phosphate incorporation into the substrate and an indirect method measuring residual ADP production using luminescence. We conducted the two screens under similar conditions, where in one, we measured [(33)P]-phosphate incorporation using scintillation proximity assay (SPA), and in the other, we detected luminescence signal of the ATP-dependent luciferase after regenerating ATP from residual ADP (LUM). Surprisingly, little or no correlation were observed between the positives identified by the two methods; at a threshold of 30% inhibition, 25 positives were identified in the LUM screen whereas the SPA screen only identified two positives, Tannic acid and Gentian violet, with Tannic acid being common to both. We tested 20 out of the 25 positive compounds in secondary confirmatory study and confirmed 12 compounds including Tannic acid as Cdc7-Dbf4 kinase inhibitors. Gentian violet, which was only positive in the SPA screen, inhibited luminescence detection and categorized as a false positive. This report demonstrates the strong impact in detection format on the success of a screening campaign and the importance of carefully designed confirmatory assays to eliminate those compounds that target the detection part of the assay.
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Affiliation(s)
- Toshimitsu Takagi
- HTS Core Facility, Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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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: 60] [Impact Index Per Article: 5.0] [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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Sharlow ER, Mustata Wilson G, Close D, Leimgruber S, Tandon M, Reed RB, Shun TY, Wang QJ, Wipf P, Lazo JS. Discovery of diverse small molecule chemotypes with cell-based PKD1 inhibitory activity. PLoS One 2011; 6:e25134. [PMID: 21998636 PMCID: PMC3187749 DOI: 10.1371/journal.pone.0025134] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 08/25/2011] [Indexed: 12/21/2022] Open
Abstract
Protein kinase D (PKD) is a novel family of serine/threonine kinases regulated by diacylglycerol, which is involved in multiple cellular processes and various pathological conditions. The limited number of cell-active, selective inhibitors has historically restricted biochemical and pharmacological studies of PKD. We now markedly expand the PKD1 inhibitory chemotype inventory with eleven additional novel small molecule PKD1 inhibitors derived from our high throughput screening campaigns. The in vitro IC(50)s for these eleven compounds ranged in potency from 0.4 to 6.1 µM with all of the evaluated compounds being competitive with ATP. Three of the inhibitors (CID 1893668, (1Z)-1-(3-ethyl-5-methoxy-1,3-benzothiazol-2-ylidene)propan-2-one; CID 2011756, 5-(3-chlorophenyl)-N-[4-(morpholin-4-ylmethyl)phenyl]furan-2-carboxamide; CID 5389142, (6Z)-6-[4-(3-aminopropylamino)-6-methyl-1H-pyrimidin-2-ylidene]cyclohexa-2,4-dien-1-one) inhibited phorbol ester-induced endogenous PKD1 activation in LNCaP prostate cancer cells in a concentration-dependent manner. The specificity of these compounds for PKD1 inhibitory activity was supported by kinase assay counter screens as well as by bioinformatics searches. Moreover, computational analyses of these novel cell-active PKD1 inhibitors indicated that they were structurally distinct from the previously described cell-active PKD1 inhibitors while computational docking of the new cell-active compounds in a highly conserved ATP-binding cleft suggests opportunities for structural modification. In summary, we have discovered novel PKD1 inhibitors with in vitro and cell-based inhibitory activity, thus successfully expanding the structural diversity of small molecule inhibitors available for this important pharmacological target.
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Affiliation(s)
- Elizabeth R Sharlow
- Department of Pharmacology, University of Virginia, Charlottesville, Virginia, United States of America.
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Kim M, Shin DS, Kim J, Lee YS. Substrate screening of protein kinases: detection methods and combinatorial peptide libraries. Biopolymers 2011; 94:753-62. [PMID: 20564046 DOI: 10.1002/bip.21506] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The study of protein kinases has become a matter of great importance in the development of new drugs for the treatment of diseases, including cancer and inflammation. Substrate screening is the first step in the fundamental investigation of protein kinases and the development of inhibitors for use in drug discovery. Towards this goal, various studies have been reported regarding the development of phospho-peptide detection methods and the screening of phosphorylated peptide sites by protein kinases. This review introduces the detection methods for phosphorylation events using the reagents with (γ(32)P)ATP, ligand-linked ATP, phospho-peptide-specific antibodies and metal chelating compounds. Chemical modification methods using β-elimination for the detection of phospho-Ser/Thr peptides are introduced as well. In addition, the implementations of combinatorial peptide libraries for screening peptide substrates of protein kinases are discussed. The phage display approach has been suggested as an alternative method of using synthetic peptides for screening the substrate specificities of protein kinase. However, a solid phase assay using a peptide library-bound polymer resin or a peptide-arrayed glass chip is preferred for high throughput screening (HTS).
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Affiliation(s)
- Mira Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 151-744 Korea
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19
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Iliuk A, Martinez JS, Hall MC, Tao WA. Phosphorylation assay based on multifunctionalized soluble nanopolymer. Anal Chem 2011; 83:2767-74. [PMID: 21395237 DOI: 10.1021/ac2000708] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantitative phosphorylation analysis is essential to understanding cellular signal transductions. Here we present a novel technology for the highly efficient assay of protein phosphorylation in high-throughput format without the use of phospho-specific antibodies. The technique is based on a water-soluble, nanosize polymer, termed pIMAGO, that is multifunctionalized with titanium(IV) ions for specific binding to phosphoproteins and with biotin groups that allow for enzyme-linked spectrometric detection. The sensitivity, specificity, and quantitative nature of pIMAGO for phosphorylation assays were examined with standard phosphoproteins and with purified phosphoproteins from whole cell extracts. As low as 100 pg of phosphoprotein can be measured quantitatively with the pIMAGO chemiluminescence assay. The pIMAGO assay was applied to an in vitro kinase assay, kinase inhibitor screening, and measurement of endogenous phosphorylation events. The technique provides a universal, quantitative method for global phosphorylation analysis with high sensitivity and specificity.
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Affiliation(s)
- Anton Iliuk
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, USA
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20
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Lan T, Dong C, Huang X, Ren J. Single particle technique for one-step homogeneous detection of cancer marker using gold nanoparticle probes. Analyst 2011; 136:4247-53. [DOI: 10.1039/c1an15497d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Abstract
IMPORTANCE OF THE FIELD Fluorescence polarization (FP) is a homogeneous method that allows rapid and quantitative analysis of diverse molecular interactions and enzyme activities. This technique has been widely utilized in clinical and biomedical settings, including the diagnosis of certain diseases and monitoring therapeutic drug levels in body fluids. Recent developments in the field have been symbolized by the facile adoption of FP in high-throughput screening and small molecule drug discovery of an increasing range of target classes. AREAS COVERED IN THIS REVIEW The article provides a brief overview of the theoretical foundation of FP, followed by updates on recent advancements in its application for various drug target classes, including GPCRs, enzymes and protein-protein interactions. The strengths and weaknesses of this method, practical considerations in assay design, novel applications and future directions are also discussed. WHAT THE READER WILL GAIN The reader is informed of the most recent advancements and future directions of FP application to small molecule screening. TAKE HOME MESSAGE In addition to its continued utilization in high-throughput screening, FP has expanded into new disease and target areas and has been marked by increased use of labeled small molecule ligands for receptor-binding studies.
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Affiliation(s)
- Wendy A. Lea
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-3370, U.S.A
| | - Anton Simeonov
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-3370, U.S.A
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22
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Shun TY, Lazo JS, Sharlow ER, Johnston PA. Identifying actives from HTS data sets: practical approaches for the selection of an appropriate HTS data-processing method and quality control review. ACTA ACUST UNITED AC 2010; 16:1-14. [PMID: 21160066 DOI: 10.1177/1087057110389039] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
High-throughput screening (HTS) has achieved a dominant role in drug discovery over the past 2 decades. The goal of HTS is to identify active compounds (hits) by screening large numbers of diverse chemical compounds against selected targets and/or cellular phenotypes. The HTS process consists of multiple automated steps involving compound handling, liquid transfers, and assay signal capture, all of which unavoidably contribute to systematic variation in the screening data. The challenge is to distinguish biologically active compounds from assay variability. Traditional plate controls-based and non-controls-based statistical methods have been widely used for HTS data processing and active identification by both the pharmaceutical industry and academic sectors. More recently, improved robust statistical methods have been introduced, reducing the impact of systematic row/column effects in HTS data. To apply such robust methods effectively and properly, we need to understand their necessity and functionality. Data from 6 HTS case histories are presented to illustrate that robust statistical methods may sometimes be misleading and can result in more, rather than less, false positives or false negatives. In practice, no single method is the best hit detection method for every HTS data set. However, to aid the selection of the most appropriate HTS data-processing and active identification methods, the authors developed a 3-step statistical decision methodology. Step 1 is to determine the most appropriate HTS data-processing method and establish criteria for quality control review and active identification from 3-day assay signal window and DMSO validation tests. Step 2 is to perform a multilevel statistical and graphical review of the screening data to exclude data that fall outside the quality control criteria. Step 3 is to apply the established active criterion to the quality-assured data to identify the active compounds.
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Affiliation(s)
- Tong Ying Shun
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA, USA.
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Rhee HW, Lee SH, Shin IS, Choi SJ, Park HH, Han K, Park TH, Hong JI. Detection of kinase activity using versatile fluorescence quencher probes. Angew Chem Int Ed Engl 2010; 49:4919-23. [PMID: 20540130 DOI: 10.1002/anie.201000879] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hyun-Woo Rhee
- Department of Chemistry, School of Chemical & Biological Engineering, Seoul National University, Seoul 151-747, Korea
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24
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Rhee HW, Lee S, Shin IS, Choi S, Park H, Han K, Park T, Hong JI. Detection of Kinase Activity Using Versatile Fluorescence Quencher Probes. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000879] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Gangoiti P, Camacho L, Arana L, Ouro A, Granado MH, Brizuela L, Casas J, Fabriás G, Abad JL, Delgado A, Gómez-Muñoz A. Control of metabolism and signaling of simple bioactive sphingolipids: Implications in disease. Prog Lipid Res 2010; 49:316-34. [PMID: 20193711 DOI: 10.1016/j.plipres.2010.02.004] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Revised: 02/18/2010] [Accepted: 02/22/2010] [Indexed: 01/05/2023]
Abstract
Simple bioactive sphingolipids include ceramide, sphingosine and their phosphorylated forms sphingosine 1-phosphate and ceramide 1-phosphate. These molecules are crucial regulators of cell functions. In particular, they play important roles in the regulation of angiogenesis, apoptosis, cell proliferation, differentiation, migration, and inflammation. Decoding the mechanisms by which these cellular functions are regulated requires detailed understanding of the signaling pathways that are implicated in these processes. Most importantly, the development of inhibitors of the enzymes involved in their metabolism may be crucial for establishing new therapeutic strategies for treatment of disease.
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Affiliation(s)
- Patricia Gangoiti
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
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26
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Xie C, Xu F, Huang X, Dong C, Ren J. Single gold nanoparticles counter: an ultrasensitive detection platform for one-step homogeneous immunoassays and DNA hybridization assays. J Am Chem Soc 2009; 131:12763-70. [PMID: 19678640 DOI: 10.1021/ja903873n] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, we present for the first time a single gold nanoparticle counter (SGNPC) in solution based on the photon bursting in a highly focused laser beam (less than 1 fL) due to the plasmon resonance scattering and Brownian motion of gold nanoparticles (GNPs). The photon burst intensity of single 36 nm GNPs is several tens to hundreds times stronger than that of quantum dots (QDs) and organic dyes. The relationship between the photon burst counts and GNPs concentration shows an excellent linearity. The linear range is over 4 orders of magnitude, and the detection limit of GNPs (36 nm) is 17 fM. On the basis of this single nanoparticle technique, we developed an ultrasensitive and highly selective detection platform for homogeneous immunoassay and DNA hybridization assays using GNPs as probes, which were 2-5 orders of magnitude more sensitive than current homogeneous methods. We used this technology to construct homogeneous sandwich immunoassays for cancer biomarkers, such as carcinoembryonic antigen (CEA) and alpha fetal protein (AFP), and aptamer recognition for thrombin. The detection limits are 130 fM for CEA, 714 fM for AFP and 2.72 pM for thrombin. Our method was successfully applied for direct determination of CEA, AFP and thrombin levels in sera from healthy subjects and cancer patients. In homogeneous DNA hybridization detection, we chose methylenetetrahydrofolate reductase (MTHFR) gene as a target. This assay successfully distinguished DNA sequences with single base mismatches, and the detection limits for the target were at 1 fM level.
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Affiliation(s)
- Chao Xie
- College of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, PR China
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27
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Sharlow ER, Close D, Shun T, Leimgruber S, Reed R, Mustata G, Wipf P, Johnson J, O'Neil M, Grögl M, Magill AJ, Lazo JS. Identification of potent chemotypes targeting Leishmania major using a high-throughput, low-stringency, computationally enhanced, small molecule screen. PLoS Negl Trop Dis 2009; 3:e540. [PMID: 19888337 PMCID: PMC2765639 DOI: 10.1371/journal.pntd.0000540] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 10/02/2009] [Indexed: 11/21/2022] Open
Abstract
Patients with clinical manifestations of leishmaniasis, including cutaneous leishmaniasis, have limited treatment options, and existing therapies frequently have significant untoward liabilities. Rapid expansion in the diversity of available cutaneous leishmanicidal chemotypes is the initial step in finding alternative efficacious treatments. To this end, we combined a low-stringency Leishmania major promastigote growth inhibition assay with a structural computational filtering algorithm. After a rigorous assay validation process, we interrogated ∼200,000 unique compounds for L. major promastigote growth inhibition. Using iterative computational filtering of the compounds exhibiting >50% inhibition, we identified 553 structural clusters and 640 compound singletons. Secondary confirmation assays yielded 93 compounds with EC50s ≤ 1 µM, with none of the identified chemotypes being structurally similar to known leishmanicidals and most having favorable in silico predicted bioavailability characteristics. The leishmanicidal activity of a representative subset of 15 chemotypes was confirmed in two independent assay formats, and L. major parasite specificity was demonstrated by assaying against a panel of human cell lines. Thirteen chemotypes inhibited the growth of a L. major axenic amastigote-like population. Murine in vivo efficacy studies using one of the new chemotypes document inhibition of footpad lesion development. These results authenticate that low stringency, large-scale compound screening combined with computational structure filtering can rapidly expand the chemotypes targeting in vitro and in vivo Leishmania growth and viability. Leishmaniasis is a parasitic disease with cutaneous, mucocutaneous and visceral clinical manifestations, depending on the Leishmania spp. and human host. Globally, there are 350 million people at risk of leishmaniasis, but current treatment options rely predominantly on ancient pentavalent antimonials, which have the potential to cause serious systemic toxicity. Our research focuses on the rapid expansion of potential anti-leishmanial compounds that could function as novel chemical structures for future drug development and offer additional therapeutic options to patients with leishmaniasis. We combined high throughput screening methodologies with computational algorithms and multiple confirmatory assay formats to identify and characterize new potent L. major promastigote growth inhibitors, including one that displays in vivo activity without toxicity to human cells. Our use of a large, broadly distributed compound library enabled the identification of these new chemotypes. In addition, since this chemical library is publicly available and annotated, we were able to cross-query archived bioassays and to identify new molecular targets that may be involved in L. major growth and viability as well as identify new protein targets for future leishmanicidal drug discovery.
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Affiliation(s)
- Elizabeth R. Sharlow
- University of Pittsburgh Drug Discovery Institute and the Pittsburgh Molecular Library Screening Center, Pittsburgh, Pennsylvania, United States of America
- Departments of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - David Close
- University of Pittsburgh Drug Discovery Institute and the Pittsburgh Molecular Library Screening Center, Pittsburgh, Pennsylvania, United States of America
| | - Tongying Shun
- University of Pittsburgh Drug Discovery Institute and the Pittsburgh Molecular Library Screening Center, Pittsburgh, Pennsylvania, United States of America
| | - Stephanie Leimgruber
- University of Pittsburgh Drug Discovery Institute and the Pittsburgh Molecular Library Screening Center, Pittsburgh, Pennsylvania, United States of America
| | - Robyn Reed
- University of Pittsburgh Drug Discovery Institute and the Pittsburgh Molecular Library Screening Center, Pittsburgh, Pennsylvania, United States of America
| | - Gabriela Mustata
- Department of Computational Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Peter Wipf
- University of Pittsburgh Drug Discovery Institute and the Pittsburgh Molecular Library Screening Center, Pittsburgh, Pennsylvania, United States of America
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jacob Johnson
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Michael O'Neil
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Max Grögl
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - Alan J. Magill
- Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America
| | - John S. Lazo
- University of Pittsburgh Drug Discovery Institute and the Pittsburgh Molecular Library Screening Center, Pittsburgh, Pennsylvania, United States of America
- Departments of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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28
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Habig M, Blechschmidt A, Dressler S, Hess B, Patel V, Billich A, Ostermeier C, Beer D, Klumpp M. Efficient elimination of nonstoichiometric enzyme inhibitors from HTS hit lists. ACTA ACUST UNITED AC 2009; 14:679-89. [PMID: 19470716 DOI: 10.1177/1087057109336586] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-throughput screening often identifies not only specific, stoichiometrically binding inhibitors but also undesired compounds that unspecifically interfere with the targeted activity by nonstoichiometrically binding, unfolding, and/or inactivating proteins. In this study, the effect of such unwanted inhibitors on several different enzyme targets was assessed based on screening results for over a million compounds. In particular, the shift in potency on variation of enzyme concentration was used as a means to identify nonstoichiometric inhibitors among the screening hits. These potency shifts depended on both compound structure and target enzyme. The approach was confirmed by statistical analysis of thousands of dose-response curves, which showed that the potency of competitive and therefore clearly stoichiometric inhibitors was not affected by increasing enzyme concentration. Light-scattering measurements of thermal protein unfolding further verified that compounds that stabilize protein structure by stoichiometric binding show the same potency irrespective of enzyme concentration. In summary, measuring inhibitor IC(50) values at different enzyme concentrations is a simple, cost-effective, and reliable method to identify and eliminate compounds that inhibit a specific target enzyme via nonstoichiometric mechanisms.
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Affiliation(s)
- Michael Habig
- Lead Finding Platform, Protein Structure Unit, Novartis Institutes for Biomedical Research, Center for Proteomic Chemistry, Basel, Switzerland
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29
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Sharlow ER, Giridhar KV, LaValle CR, Chen J, Leimgruber S, Barrett R, Bravo-Altamirano K, Wipf P, Lazo JS, Wang QJ. Potent and selective disruption of protein kinase D functionality by a benzoxoloazepinolone. J Biol Chem 2008; 283:33516-26. [PMID: 18829454 PMCID: PMC2586241 DOI: 10.1074/jbc.m805358200] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 09/30/2008] [Indexed: 11/06/2022] Open
Abstract
Protein kinase D (PKD) is a novel family of serine/threonine kinases targeted by the second messenger diacylglycerol. It has been implicated in many important cellular processes and pathological conditions. However, further analysis of PKD in these processes is severely hampered by the lack of a PKD-specific inhibitor that can be readily applied to cells and in animal models. We now report the discovery of the first potent and selective cell-active small molecule inhibitor for PKD, benzoxoloazepinolone (CID755673). This inhibitor was identified from the National Institutes of Health small molecule repository library of 196,173 compounds using a human PKD1 (PKCmu)-based fluorescence polarization high throughput screening assay. CID755673 suppressed half of the PKD1 enzyme activity at 182 nm and exhibited selective PKD1 inhibition when compared with AKT, polo-like kinase 1 (PLK1), CDK activating kinase (CAK), CAMKIIalpha, and three different PKC isoforms. Moreover, it was not competitive with ATP for enzyme inhibition. In cell-based assays, CID755673 blocked phorbol ester-induced endogenous PKD1 activation in LNCaP cells in a concentration-dependent manner. Functionally, CID755673 inhibited the known biological actions of PKD1 including phorbol ester-induced class IIa histone deacetylase 5 nuclear exclusion, vesicular stomatitis virus glycoprotein transport from the Golgi to the plasma membrane, and the ilimaquinone-induced Golgi fragmentation. Moreover, CID755673 inhibited prostate cancer cell proliferation, cell migration, and invasion. In summary, our findings indicate that CID755673 is a potent and selective PKD1 inhibitor with valuable pharmacological and cell biological potential.
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Affiliation(s)
- Elizabeth R Sharlow
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
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