1751
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Roberds SL, Filippov I, Alexandrov V, Hanania T, Brunner D. Rapid, computer vision-enabled murine screening system identifies neuropharmacological potential of two new mechanisms. Front Neurosci 2011; 5:103. [PMID: 21927596 PMCID: PMC3169783 DOI: 10.3389/fnins.2011.00103] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 08/18/2011] [Indexed: 11/13/2022] Open
Abstract
The lack of predictive in vitro models for behavioral phenotypes impedes rapid advancement in neuropharmacology and psychopharmacology. In vivo behavioral assays are more predictive of activity in human disorders, but such assays are often highly resource-intensive. Here we describe the successful application of a computer vision-enabled system to identify potential neuropharmacological activity of two new mechanisms. The analytical system was trained using multiple drugs that are used clinically to treat depression, schizophrenia, anxiety, and other psychiatric or behavioral disorders. During blinded testing the PDE10 inhibitor TP-10 produced a signature of activity suggesting potential antipsychotic activity. This finding is consistent with TP-10's activity in multiple rodent models that is similar to that of clinically used antipsychotic drugs. The CK1ε inhibitor PF-670462 produced a signature consistent with anxiolytic activity and, at the highest dose tested, behavioral effects similar to that of opiate analgesics. Neither TP-10 nor PF-670462 was included in the training set. Thus, computer vision-based behavioral analysis can facilitate drug discovery by identifying neuropharmacological effects of compounds acting through new mechanisms.
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Affiliation(s)
- Steven L Roberds
- Indications Discovery Research Unit, Pfizer Inc St. Louis, MO, USA
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1752
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Lone AM, Bachovchin DA, Westwood D, Speers AE, Spicer TP, Fernandez-Vega V, Chase P, Hodder PS, Rosen H, Cravatt BF, Saghatelian A. A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors. J Am Chem Soc 2011; 133:11665-74. [PMID: 21692504 PMCID: PMC3145007 DOI: 10.1021/ja2036095] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidases play vital roles in physiology through the biosynthesis, degradation, and regulation of peptides. Prolyl endopeptidase-like (PREPL) is a newly described member of the prolyl peptidase family, with significant homology to mammalian prolyl endopeptidase and the bacterial peptidase oligopeptidase B. The biochemistry and biology of PREPL are of fundamental interest due to this enzyme's homology to the biomedically important prolyl peptidases and its localization in the central nervous system. Furthermore, genetic studies of patients suffering from hypotonia-cystinuria syndrome (HCS) have revealed a deletion of a portion of the genome that includes the PREPL gene. HCS symptoms thought to be caused by lack of PREPL include neuromuscular and mild cognitive deficits. A number of complementary approaches, ranging from biochemistry to genetics, will be required to understand the biochemical, cellular, physiological, and pathological mechanisms regulated by PREPL. We are particularly interested in investigating physiological substrates and pathways controlled by PREPL. Here, we use a fluorescence polarization activity-based protein profiling (fluopol-ABPP) assay to discover selective small-molecule inhibitors of PREPL. Fluopol-ABPP is a substrate-free approach that is ideally suited for studying serine hydrolases for which no substrates are known, such as PREPL. After screening over 300,000 compounds using fluopol-ABPP, we employed a number of secondary assays to confirm assay hits and characterize a group of 3-oxo-1-phenyl-2,3,5,6,7,8-hexahydroisoquinoline-4-carbonitrile and 1-alkyl-3-oxo-3,5,6,7-tetrahydro-2H-cyclopenta[c]pyridine-4-carbonitrile PREPL inhibitors that are able to block PREPL activity in cells. Moreover, when administered to mice, 1-isobutyl-3-oxo-3,5,6,7-tetrahydro-2H-cyclopenta[c]pyridine-4-carbonitrile distributes to the brain, indicating that it may be useful for in vivo studies. The application of fluopol-ABPP has led to the first reported PREPL inhibitors, and these inhibitors will be of great value in studying the biochemistry of PREPL and in eventually understanding the link between PREPL and HCS.
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Affiliation(s)
- Anna Mari Lone
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Daniel A. Bachovchin
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - David Westwood
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
| | - Anna E. Speers
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Timothy P. Spicer
- Scripps Research Institute Molecular Screening Center, Lead Identification Division, Translational Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Virneliz Fernandez-Vega
- Scripps Research Institute Molecular Screening Center, Lead Identification Division, Translational Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Peter Chase
- Scripps Research Institute Molecular Screening Center, Lead Identification Division, Translational Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Peter S. Hodder
- Scripps Research Institute Molecular Screening Center, Lead Identification Division, Translational Research Institute, 130 Scripps Way, Jupiter, FL 33458
- Department of Molecular Therapeutics, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458
| | - Hugh Rosen
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
- The Scripps Research Institute Molecular Screening Center, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Alan Saghatelian
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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1753
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Abstract
The Paramyxoviridae family comprises of several genera that contain emerging or re-emerging threats for human and animal health with no real specific effective treatment available. Hendra and Nipah virus are members of a newly identified genus of emerging paramyxoviruses, Henipavirus. Since their discovery in the 1990s, henipaviruses outbreaks have been associated with high economic and public health threat potential. When compared to other paramyxoviruses, henipaviruses appear to have unique characteristics. Henipaviruses are zoonotic paramyxoviruses with a broader tropism than most other paramyxoviruses, and can cause severe acute encephalitis with unique features among viral encephalitides. There are currently no approved effective prophylactic or therapeutic treatments for henipavirus infections. Although ribavirin was empirically used and seemed beneficial during the biggest outbreak caused by one of these viruses, the Nipah virus, its efficacy is disputed in light of its lack of efficacy in several animal models of henipavirus infection. Nevertheless, because of its highly pathogenic nature, much effort has been spent in developing anti-henipavirus therapeutics. In this review we describe the unique features of henipavirus infections and the different strategies and animal models that have been developed so far in order to identify and test potential drugs to prevent or treat henipavirus infections. Some of these components have the potential to be broad-spectrum antivirals as they target effectors of viral pathogenecity common to other viruses. We will focus on small molecules or biologics, rather than vaccine strategies, that have been developed as anti-henipaviral therapeutics.
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Affiliation(s)
- Frederic Vigant
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA 90095
| | - Benhur Lee
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA 90095
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA, USA 90095
- UCLA AIDS Institute, UCLA, Los Angeles, CA, USA 90095
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1754
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Steele TWJ, Huang CL, Kumar S, Widjaja E, Chiang Boey FY, Loo JSC, Venkatraman SS. High-throughput screening of PLGA thin films utilizing hydrophobic fluorescent dyes for hydrophobic drug compounds. J Pharm Sci 2011; 100:4317-29. [PMID: 21607953 DOI: 10.1002/jps.22625] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 04/02/2011] [Accepted: 04/26/2011] [Indexed: 01/06/2023]
Abstract
Hydrophobic, antirestenotic drugs such as paclitaxel (PCTX) and rapamycin are often incorporated into thin film coatings for local delivery using implantable medical devices and polymers such as drug-eluting stents and balloons. Selecting the optimum coating formulation through screening the release profile of these drugs in thin films is time consuming and labor intensive. We describe here a high-throughput assay utilizing three model hydrophobic fluorescent compounds: fluorescein diacetate (FDAc), coumarin-6, and rhodamine 6G that were incorporated into poly(d,l-lactide-co-glycolide) (PLGA) and PLGA-polyethylene glycol films. Raman microscopy determined the hydrophobic fluorescent dye distribution within the PLGA thin films in comparison with that of PCTX. Their subsequent release was screened in a high-throughput assay and directly compared with HPLC quantification of PCTX release. It was observed that PCTX controlled-release kinetics could be mimicked by a hydrophobic dye that had similar octanol-water partition coefficient values and homogeneous dissolution in a PLGA matrix as the drug. In particular, FDAc was found to be the optimal hydrophobic dye at modeling the burst release as well as the total amount of PCTX released over a period of 30 days.
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Affiliation(s)
- Terry W J Steele
- Materials and Science Engineering, Division of Materials Technology, Nanyang Technological University, Singapore 639798
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1755
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Hage DS, Anguizola J, Barnaby O, Jackson A, Yoo MJ, Papastavros E, Pfaunmiller E, Sobansky M, Tong Z. Characterization of drug interactions with serum proteins by using high-performance affinity chromatography. Curr Drug Metab 2011; 12:313-28. [PMID: 21395530 PMCID: PMC3174051 DOI: 10.2174/138920011795202938] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 11/23/2010] [Indexed: 11/22/2022]
Abstract
The binding of drugs with serum proteins can affect the activity, distribution, rate of excretion, and toxicity of pharmaceutical agents in the body. One tool that can be used to quickly analyze and characterize these interactions is high-performance affinity chromatography (HPAC). This review shows how HPAC can be used to study drug-protein binding and describes the various applications of this approach when examining drug interactions with serum proteins. Methods for determining binding constants, characterizing binding sites, examining drug-drug interactions, and studying drug-protein dissociation rates will be discussed. Applications that illustrate the use of HPAC with serum binding agents such as human serum albumin, α(1)-acid glycoprotein, and lipoproteins will be presented. Recent developments will also be examined, such as new methods for immobilizing serum proteins in HPAC columns, the utilization of HPAC as a tool in personalized medicine, and HPAC methods for the high-throughput screening and characterization of drug-protein binding.
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Affiliation(s)
- David S Hage
- Department of Chemistry, University of Nebraska, Lincoln, NE 68588-0304, USA.
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1756
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Abstract
Optimizing cell-material interactions is critical for maximizing regeneration in tissue engineering. Combinatorial and high-throughput (CHT) methods can be used to systematically screen tissue scaffolds to identify optimal biomaterial properties. Previous CHT platforms in tissue engineering have involved a two-dimensional (2D) cell culture format where cells were cultured on material surfaces. However, these platforms are inadequate to predict cellular response in a three-dimensional (3D) tissue scaffold. We have developed a simple CHT platform to screen cell-material interactions in 3D culture format that can be applied to screen hydrogel scaffolds. Herein we provide detailed instructions on a method to prepare gradients in elastic modulus of photopolymerizable hydrogels.
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Affiliation(s)
- Kaushik Chatterjee
- Polymers Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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1757
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Mishra A, Mishra KB, Höermiller II, Heyer AG, Nedbal L. Chlorophyll fluorescence emission as a reporter on cold tolerance in Arabidopsis thaliana accessions. Plant Signal Behav 2011; 6:301-10. [PMID: 21427532 PMCID: PMC3121992 DOI: 10.4161/psb.6.2.15278] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Revised: 02/24/2011] [Accepted: 02/24/2011] [Indexed: 05/20/2023]
Abstract
Non-invasive, high-throughput screening methods are valuable tools in breeding for abiotic stress tolerance in plants. Optical signals such as chlorophyll fluorescence emission can be instrumental in developing new screening techniques. In order to examine the potential of chlorophyll fluorescence to reveal plant tolerance to low temperatures, we used a collection of nine Arabidopsis thaliana accessions and compared their fluorescence features with cold tolerance quantified by the well established electrolyte leakage method on detached leaves. We found that, during progressive cooling, the minimal chlorophyll fluorescence emission rose strongly and that this rise was highly dependent on the cold tolerance of the accessions. Maximum quantum yield of PSII photochemistry and steady state fluorescence normalized to minimal fluorescence were also highly correlated to the cold tolerance measured by the electrolyte leakage method. In order to further increase the capacity of the fluorescence detection to reveal the low temperature tolerance, we applied combinatorial imaging that employs plant classification based on multiple fluorescence features. We found that this method, by including the resolving power of several fluorescence features, can be well employed to detect cold tolerance already at mild sub-zero temperatures. Therefore, there is no need to freeze the screened plants to the largely damaging temperatures of around -15°C. This, together with the method's easy applicability, represents a major advantage of the fluorescence technique over the conventional electrolyte leakage method.
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Affiliation(s)
- Anamika Mishra
- Institute of Physical Biology, University of South Bohemia; Nové Hrady, Czech Republic
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1758
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Abstract
It is clear that viral entry, replication, and spread is a complex process involving a dialog between the virus and the targeted host cell. Viruses have evolved highly specific strategies to hijack cellular factors to promote their internalization, initiate their replication, and facilitate their eventual spread. However, the identification of many of these host cell molecules has been hindered by the requirement for robust genome-scale loss-of-function assays that are capable of targeting a wide variety of host factors. The more recent use of genome-scale or genome-wide RNA interference (RNAi) screens have extended our knowledge of the complex interplay between a virus and host and have implicated a wide variety of cellular factors required for infection of a number of viruses. Here, we describe an approach to target mammalian host cell factors involved in regulating viral infections by the use of a genome-scale RNAi library screen.
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Affiliation(s)
- Carolyn B Coyne
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, USA.
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1759
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Cashman JR, MacDonald M, Ghirmai S, Okolotowicz KJ, Sergienko E, Brown B, Garcia X, Zhai D, Dahl R, Reed JC. Inhibition of Bfl-1 with N-aryl maleimides. Bioorg Med Chem Lett 2010; 20:6560-4. [PMID: 20933419 PMCID: PMC2987701 DOI: 10.1016/j.bmcl.2010.09.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/05/2010] [Accepted: 09/08/2010] [Indexed: 10/19/2022]
Abstract
High-throughput screening of 66,000 compounds using competitive binding of peptides comprising the BH3 domain to anti-apoptotic Bfl-1 led to the identification of 14 validated 'hits' as inhibitors of Bfl-1. N-Aryl maleimide 1 was among the validated 'hits'. A chemical library encompassing over 280 analogs of 1 was prepared following a two-step synthesis. Structure-activity studies for inhibition of Bfl-1 by analogs of N-aryl maleimide 1 revealed a preference for electron-withdrawing substituents in the N-aryl ring and hydrophilic amines appended to the maleimide core. Inhibitors of Bfl-1 are potential development candidates for anti-cancer therapeutics.
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Affiliation(s)
- John R Cashman
- Human BioMolecular Research Institute, 5310 Eastgate Mall, San Diego, CA 92121, United States.
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1760
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DeArmond PD, West GM, Anbalagan V, Campa MJ, Patz EF, Fitzgerald MC. Discovery of novel cyclophilin A ligands using an H/D exchange- and mass spectrometry-based strategy. J Biomol Screen 2010; 15:1051-62. [PMID: 20855564 PMCID: PMC3197229 DOI: 10.1177/1087057110382775] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cyclophilin A (CypA) is an overexpressed protein in lung cancer tumors and as a result is a potential therapeutic and diagnostic target. Described here is use of an H/D exchange- and a matrix assisted laser desorption/ionization (MALDI) mass spectrometry-based assay, termed single-point SUPREX (Stability of Unpurified Proteins from Rates of H/D Exchange), to screen 2 chemical libraries, including the 1280-compound LOPAC library and the 9600-compound DIVERSet library, for binding to CypA. This work represents the first application of single-point SUPREX using a pooled ligand approach, which is demonstrated here to yield screening rates as fast as 6 s/ligand. The false-positive and false-negative rates determined in the current work using a set of control samples were 0% and 9%, respectively. A false-positive rate of 20% was found in screening the actual libraries. Eight novel ligands to CypA were discovered, including 2-(α-naphthoyl)ethyltrimethyl-ammonium iodide, (E)-3-(4-t-Butylphenylsulfonyl)-2-propenenitrile, 3-(N-benzyl-N-isopropyl)amino-1-(naphthalen-2-yl)propan-1-one, cis-diammineplatinum (II) chloride, 1-(3,5-dichlorophenyl)-1H-pyrrole-2,5-dione, N-(3-chloro-1, 4-dioxo-1,4-dihydro-2-naphthalenyl)-N-cyclohexylacetamide, 1-[2-(3,4-dimethoxyphenyl)ethyl]-1H-pyrrole-2,5-dione, and 4-(2-methoxy-4-nitrophenyl)-1-methyl-10-oxa-4-azatricyclo[5.2.1.0~2,6~]dec-8-ene-3,5-dione. These compounds, which had moderate binding affinities to CypA (i.e., K(d) values in the low micromolar range), provide new molecular scaffolds that might be useful in the development of CypA-targeted diagnostic imaging or therapeutic agents for lung cancer.
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Affiliation(s)
| | - Graham M. West
- Department of Chemistry, Duke University, Durham, North Carolina 27708
| | - Victor Anbalagan
- Department of Chemistry, Duke University, Durham, North Carolina 27708
| | - Michael J. Campa
- Department of Radiology, Duke University Medical Center, Durham, North Carolina, 27710
| | - Edward F. Patz
- Department of Radiology, Duke University Medical Center, Durham, North Carolina, 27710
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1761
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Kecskés M, Kumar TS, Yoo L, Gao ZG, Jacobson KA. Novel Alexa Fluor-488 labeled antagonist of the A(2A) adenosine receptor: Application to a fluorescence polarization-based receptor binding assay. Biochem Pharmacol 2010; 80:506-11. [PMID: 20438717 PMCID: PMC2900413 DOI: 10.1016/j.bcp.2010.04.027] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Revised: 04/23/2010] [Accepted: 04/26/2010] [Indexed: 11/23/2022]
Abstract
Fluorescence polarization (FP) assay has many advantages over the traditional radioreceptor binding studies. We developed an A(2A) adenosine receptor (AR) FP assay using a newly synthesized fluorescent antagonist of the A(2A)AR (MRS5346), a pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidin-5-amine derivative conjugated to the fluorescent dye Alexa Fluor-488. MRS5346 displayed a K(i) value of 111+/-16nM in radioligand binding using [(3)H]CGS21680 and membranes prepared from HEK293 cells stably expressing the human A(2A)AR. In a cyclic AMP functional assay, MRS5346 was shown to be an A(2A)AR antagonist. MRS5346 did not show any effect on A(1) and A(3) ARs in binding or the A(2B)AR in a cyclic AMP assay at 10microM. Its suitability as a fluorescent tracer was indicated in an initial observation of an FP signal following A(2A)AR binding. The FP signal was optimal with 20nM MRS5346 and 150microg protein/mL HEK293 membranes. The association and dissociation kinetic parameters were readily determined using this FP assay. The K(d) value of MRS5346 calculated from kinetic parameters was 16.5+/-4.7nM. In FP competition binding experiments using MRS5346 as a tracer, K(i) values of known AR agonists and antagonists consistently agreed with K(i) values from radioligand binding. Thus, this FP assay, which eliminates using radioisotopes, appears to be appropriate for both routine receptor binding and high-throughput screening with respect to speed of analysis, displaceable signal and precision. The approach used in the present study could be generally applicable to other GPCRs.
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Affiliation(s)
- Miklós Kecskés
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810 USA
| | - T. Santhosh Kumar
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810 USA
| | - Lena Yoo
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810 USA
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810 USA
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810 USA
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1762
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Rusyn I, Daston GP. Computational toxicology: realizing the promise of the toxicity testing in the 21st century. Environ Health Perspect 2010; 118:1047-50. [PMID: 20483702 PMCID: PMC2920091 DOI: 10.1289/ehp.1001925] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 05/18/2010] [Indexed: 05/20/2023]
Abstract
BACKGROUND The National Academies' Standing Committee on Use of Emerging Science for Environmental Health Decisions held a meeting (21-22 September 2009 in Washington, DC) titled "Computational Toxicology: From Data to Analyses to Applications." This commentary reflects on the presentations and roundtable discussions from the meeting that were designed to review the state of the art in the field and the practical applications of the new science and to provide focus to the field. OBJECTIVES The meeting considered two topics: the emerging data streams amenable to computational modeling and data mining, and the emerging data analysis and modeling tools. DISCUSSION Computational toxicology is a subdiscipline of toxicology that aims to use the mathematical, statistical, modeling, and computer science tools to better understand the mechanisms through which a given chemical induces harm and, ultimately, to be able to predict adverse effects of the toxicants on human health and/or the environment. The participants stressed the importance of computational toxicology to the future of environmental health sciences and regulatory decisions in public health; however, many challenges remain to be addressed before the findings from high-throughput screens and in silico models may be considered sufficiently robust and informative. CONCLUSIONS Many scientists, regulators, and the general public believe that new and better ways to assess human toxicity are now needed, and technological breakthroughs are empowering the field of toxicity assessment. Even though the application of computational toxicology to environmental health decisions requires additional efforts, the merger of the power of computers with biological information is poised to deliver new tools and knowledge.
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Affiliation(s)
- Ivan Rusyn
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599-7431, USA.
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1763
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Abid OUR, Babar TM, Ali FI, Ahmed S, Wadood A, Rama NH, Uddin R, Zaheer-ul-Haq, Khan A, Choudhary MI. Identification of novel urease inhibitors by high-throughput virtual and in vitro screening. ACS Med Chem Lett 2010; 1:145-9. [PMID: 24900188 DOI: 10.1021/ml100068u] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 05/03/2010] [Indexed: 11/28/2022] Open
Abstract
Ureases are important in both agriculture and human health. Bacterial ureases are directly involved in many farm-field problems and pathological conditions. Here, we report a structure-based virtual screening of an in-house compound bank of about 6000 molecular entities by computational docking and binding free energy calculations followed by in vitro screening. Applied protocol leads to the identification of novel urease inhibitors, which can serve as starting points for structural optimization.
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Affiliation(s)
| | | | | | - Shahzad Ahmed
- Department of Chemistry, Quaid-i-Azam University, Islamabad-45320, Pakistan
| | - Abdul Wadood
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Nasim Hasan Rama
- Department of Chemistry, Quaid-i-Azam University, Islamabad-45320, Pakistan
| | - Reaz Uddin
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Zaheer-ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Ajmal Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - M. Iqbal Choudhary
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
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1764
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Wager TT, Hou X, Verhoest PR, Villalobos A. Moving beyond rules: the development of a central nervous system multiparameter optimization (CNS MPO) approach to enable alignment of druglike properties. ACS Chem Neurosci 2010; 1:435-49. [PMID: 22778837 DOI: 10.1021/cn100008c] [Citation(s) in RCA: 647] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 03/02/2010] [Indexed: 11/30/2022] Open
Abstract
The interplay among commonly used physicochemical properties in drug design was examined and utilized to create a prospective design tool focused on the alignment of key druglike attributes. Using a set of six physicochemical parameters ((a) lipophilicity, calculated partition coefficient (ClogP); (b) calculated distribution coefficient at pH = 7.4 (ClogD); (c) molecular weight (MW); (d) topological polar surface area (TPSA); (e) number of hydrogen bond donors (HBD); (f) most basic center (pK(a))), a druglikeness central nervous system multiparameter optimization (CNS MPO) algorithm was built and applied to a set of marketed CNS drugs (N = 119) and Pfizer CNS candidates (N = 108), as well as to a large diversity set of Pfizer proprietary compounds (N = 11 303). The novel CNS MPO algorithm showed that 74% of marketed CNS drugs displayed a high CNS MPO score (MPO desirability score ≥ 4, using a scale of 0-6), in comparison to 60% of the Pfizer CNS candidates. This analysis suggests that this algorithm could potentially be used to identify compounds with a higher probability of successfully testing hypotheses in the clinic. In addition, a relationship between an increasing CNS MPO score and alignment of key in vitro attributes of drug discovery (favorable permeability, P-glycoprotein (P-gp) efflux, metabolic stability, and safety) was seen in the marketed CNS drug set, the Pfizer candidate set, and the Pfizer proprietary diversity set. The CNS MPO scoring function offers advantages over hard cutoffs or utilization of single parameters to optimize structure-activity relationships (SAR) by expanding medicinal chemistry design space through a holistic assessment approach. Based on six physicochemical properties commonly used by medicinal chemists, the CNS MPO function may be used prospectively at the design stage to accelerate the identification of compounds with increased probability of success.
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Affiliation(s)
- Travis T. Wager
- Neuroscience Medicinal Chemistry, Pfizer PharmaTherapeutics Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Xinjun Hou
- Neuroscience Medicinal Chemistry, Pfizer PharmaTherapeutics Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Patrick R. Verhoest
- Neuroscience Medicinal Chemistry, Pfizer PharmaTherapeutics Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
| | - Anabella Villalobos
- Neuroscience Medicinal Chemistry, Pfizer PharmaTherapeutics Research and Development, 558 Eastern Point Road, Groton, Connecticut 06340
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1765
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Wager TT, Chandrasekaran RY, Hou X, Troutman MD, Verhoest PR, Villalobos A, Will Y. Defining desirable central nervous system drug space through the alignment of molecular properties, in vitro ADME, and safety attributes. ACS Chem Neurosci 2010; 1:420-34. [PMID: 22778836 PMCID: PMC3368653 DOI: 10.1021/cn100007x] [Citation(s) in RCA: 321] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 03/02/2010] [Indexed: 01/20/2023] Open
Abstract
As part of our effort to increase survival of drug candidates and to move our medicinal chemistry design to higher probability space for success in the Neuroscience therapeutic area, we embarked on a detailed study of the property space for a collection of central nervous system (CNS) molecules. We carried out a thorough analysis of properties for 119 marketed CNS drugs and a set of 108 Pfizer CNS candidates. In particular, we focused on understanding the relationships between physicochemical properties, in vitro ADME (absorption, distribution, metabolism, and elimination) attributes, primary pharmacology binding efficiencies, and in vitro safety data for these two sets of compounds. This scholarship provides guidance for the design of CNS molecules in a property space with increased probability of success and may lead to the identification of druglike candidates with favorable safety profiles that can successfully test hypotheses in the clinic.
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1766
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Abstract
Complex Object Parametric Analyzer and Sorter (COPAS) devices are large-object, fluorescence-capable flow cytometers used for high-throughput analysis of live model organisms, including Drosophila melanogaster, Caenorhabditis elegans, and zebrafish. The COPAS is especially useful in C. elegans high-throughput genome-wide RNA interference (RNAi) screens that utilize fluorescent reporters. However, analysis of data from such screens is relatively labor-intensive and time-consuming. Currently, there are no computational tools available to facilitate high-throughput analysis of COPAS data. We used MATLAB to develop algorithms (COPAquant, COPAmulti, and COPAcompare) to analyze different types of COPAS data. COPAquant reads single-sample files, filters and extracts values and value ratios for each file, and then returns a summary of the data. COPAmulti reads 96-well autosampling files generated with the ReFLX adapter, performs sample filtering, graphs features across both wells and plates, performs some common statistical measures for hit identification, and outputs results in graphical formats. COPAcompare performs a correlation analysis between replicate 96-well plates. For many parameters, thresholds may be defined through a simple graphical user interface (GUI), allowing our algorithms to meet a variety of screening applications. In a screen for regulators of stress-inducible GFP expression, COPAquant dramatically accelerated data analysis and allowed us to rapidly move from raw data to hit identification. Because the COPAS file structure is standardized and our MATLAB code is freely available, our algorithms should be extremely useful for analysis of COPAS data from multiple platforms and organisms. The MATLAB code is freely available at our web site (www.med.upenn.edu/lamitinalab/downloads.shtml).
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Affiliation(s)
- Elizabeth Morton
- Department of Physiology, University of Pennsylvania, Philadelphia, PA 19104, USA
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1767
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Abstract
Substantial interest has focused on the roles of sphingolipid metabolizing enzymes in a variety of hyperproliferative and inflammatory diseases. A key family of enzymes involved in these pathologies is the ceramidases. Ceramidases cleave the pro-apoptotic lipid ceramide into a long-chain fatty acid and sphingosine, which can then be further metabolized to the mitogenic and inflammatory lipid sphingosine 1-phosphate. Consequently, development of ceramidase inhibitors would provide useful pharmacologic probes for further studies of sphingolipid metabolism, as well as lead compounds for drug development. This effort has been hampered by the lack of in vitro and cellular ceramidase assays that are amenable to high-throughput screening. Recently, a fluorogenic ceramide analog has been described as a substrate for use in ceramidase assays. The synthesis of this compound has now been substantially improved in terms of both the required effort and the overall yield of the process. Key improvements include: reduction in number of required steps, use of a hydroboration reaction; incorporation of a Mitsunobu reaction; improved acylation by the addition of triethylamine; together providing a fourfold increase in the overall yield. In addition, it has been demonstrated that the ceramide analog can be used in high-throughput assays to identify ceramidase inhibitors. Overall, the improved efficiency in the preparation of this ceramidase substrate should accelerate discovery efforts relating to sphingolipid metabolism.
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Affiliation(s)
| | | | - Charles D. Smith
- Department of Pharmaceutical and Biomedical Sciences, Medical University of South Carolina, MSC 140, Charleston, SC 29425, United States
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1768
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McDougal NT, Virgil SC, Stoltz BM. High-Throughput Screening of the Asymmetric Decarboxylative Alkylation Reaction of Enolate-Stabilized Enol Carbonates. Synlett 2010; 11:1712-1716. [PMID: 21072327 PMCID: PMC2976558 DOI: 10.1055/s-0030-1258094] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The use of high-throughput screening allowed for the optimization of reaction conditions for the palladium-catalyzed asymmetric decarboxylative alkylation reaction of enolate-stabilized enol carbonates. Changing to a non-polar reaction solvent and to an electron-deficient PHOX derivative as ligand from our standard reaction conditions improved the enantioselectivity for the alkylation of a ketal-protected,1,3-diketone-derived enol carbonate from 28% ee to 84% ee. Similar improvements in enantioselectivity were seen for a β-keto-ester derived- and an α-phenyl cyclohexanone-derived enol carbonate.
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Affiliation(s)
- Nolan T. McDougal
- The Warren and Katharine Schlinger Laboratory of Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Scott C. Virgil
- The Warren and Katharine Schlinger Laboratory of Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Brian M. Stoltz
- The Warren and Katharine Schlinger Laboratory of Chemistry and Chemical Engineering, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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1769
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Jones RL, Giembycz MA, Woodward DF. Prostanoid receptor antagonists: development strategies and therapeutic applications. Br J Pharmacol 2009; 158:104-45. [PMID: 19624532 PMCID: PMC2795261 DOI: 10.1111/j.1476-5381.2009.00317.x] [Citation(s) in RCA: 128] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2009] [Accepted: 04/07/2009] [Indexed: 01/17/2023] Open
Abstract
Identification of the primary products of cyclo-oxygenase (COX)/prostaglandin synthase(s), which occurred between 1958 and 1976, was followed by a classification system for prostanoid receptors (DP, EP(1), EP(2) ...) based mainly on the pharmacological actions of natural and synthetic agonists and a few antagonists. The design of potent selective antagonists was rapid for certain prostanoid receptors (EP(1), TP), slow for others (FP, IP) and has yet to be achieved in certain cases (EP(2)). While some antagonists are structurally related to the natural agonist, most recent compounds are 'non-prostanoid' (often acyl-sulphonamides) and have emerged from high-throughput screening of compound libraries, made possible by the development of (functional) assays involving single recombinant prostanoid receptors. Selective antagonists have been crucial to defining the roles of PGD(2) (acting on DP(1) and DP(2) receptors) and PGE(2) (on EP(1) and EP(4) receptors) in various inflammatory conditions; there are clear opportunities for therapeutic intervention. The vast endeavour on TP (thromboxane) antagonists is considered in relation to their limited pharmaceutical success in the cardiovascular area. Correspondingly, the clinical utility of IP (prostacyclin) antagonists is assessed in relation to the cloud hanging over the long-term safety of selective COX-2 inhibitors. Aspirin apart, COX inhibitors broadly suppress all prostanoid pathways, while high selectivity has been a major goal in receptor antagonist development; more targeted therapy may require an intermediate position with defined antagonist selectivity profiles. This review is intended to provide overviews of each antagonist class (including prostamide antagonists), covering major development strategies and current and potential clinical usage.
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Affiliation(s)
- R L Jones
- Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde, Glasgow, UK.
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1770
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Cardno TS, Poole ES, Mathew SF, Graves R, Tate WP. A homogeneous cell-based bicistronic fluorescence assay for high-throughput identification of drugs that perturb viral gene recoding and read-through of nonsense stop codons. RNA 2009; 15:1614-21. [PMID: 19535460 PMCID: PMC2714747 DOI: 10.1261/rna.1586709] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 04/24/2009] [Indexed: 05/27/2023]
Abstract
Recoding mechanisms are programmed protein synthesis events used commonly by viruses but only very rarely in cells for cellular gene expression. For example, HIV-1 has an absolute reliance on frameshifting to produce the correct ratio of key proteins critical for infectivity. To exploit such recoding sites as therapeutic targets, a simple homogeneous assay capable of detecting small perturbations in these low-frequency (<5%) events is required. Current assays based on dual luciferase reporters use expensive substrates and are labor-intensive, both impediments for high-throughput screening. We have developed a cell-based bifluorophore assay able to measure accurately small recoding changes (<0.1%) with a high Z'-factor in 24- or 96-well formats that could be extended to 384 wells. In cases of nonsense mutations arising within coding regions of genes, the assay is suitable for assessing the potential of screened compounds to increase read-through at these nonprogrammed stop signals of variable termination efficiency.
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Affiliation(s)
- Tony S Cardno
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
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1771
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Lee SH, Lee WG, Chung BG, Park JH, Khademhosseini A. Rapid Formation of Acrylated Microstructures by Microwave-Induced Thermal Crosslinking. Macromol Rapid Commun 2009; 30:1382-1386. [PMID: 20011617 PMCID: PMC2790285 DOI: 10.1002/marc.200900199] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We present a rapid and highly efficient method to form microstructure of poly(ethylene glycol) (PEG)-based acrylates by microwave-induced thermal crosslinking. PEG-based polymeric microstructures such as polymer microarrays and microwells were fabricated on 3-(trimethoxysilyl)propyl methacrylate (TMSPMA)-coated glass slides that were placed on top of a silicon wafer. In comparison to ultraviolet (UV) irradiation curing, microwave-induced thermal crosslinking could be completed within 10 s, without thermal degradation or oxygen inhibition in the presence of ambient oxygen. Furthermore, the activation of surviving free radical impurities by microwave-induced heating enabled crosslinking even without an exogenous radical initiator (e.g., 2,2'-azoisobutyronitrile (AIBN)). This approach can be beneficial for fabricating various PEG-based microstructures for high-throughput screening assays, cell-based biosensors, and biomedical microdevices.
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Affiliation(s)
- Seung Hwan Lee
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Won Gu Lee
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Bong Geun Chung
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jae Hong Park
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ali Khademhosseini
- Center for Biomedical Engineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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1772
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KAINKARYAM RAGHUNANDANM, WOOLF PETERJ. Pooling in high-throughput drug screening. Curr Opin Drug Discov Devel 2009; 12:339-50. [PMID: 19396735 PMCID: PMC3204799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Pooling in HTS refers to the act of testing mixtures of compounds in a primary screen to accurately identify hits for secondary screening. The reduction in the number of tests needed to screen a compound library by pooling can also be extended to achieve much-needed error tolerance in HTS. Despite the success of HTS in other biological experiments, pooling in high-throughput drug screening has been a controversial and often marginalized paradigm. At first appearance, pooling appears to promise gains from reduced effort, or possibly could create more problems than solutions. However, this article demonstrates that pooling is a practical and necessary part of HTS: discussions include the rationale for pooling compounds in HTS, a unifying view of pooling design theory, a review of past attempts at pooling and their success, and recent advances in the field.
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Affiliation(s)
| | - PETER J. WOOLF
- Department of Chemical Engineering, University of Michigan, Ann Arbor
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1773
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Hong K, Gao AH, Xie QY, Gao H, Zhuang L, Lin HP, Yu HP, Li J, Yao XS, Goodfellow M, Ruan JS. Actinomycetes for marine drug discovery isolated from mangrove soils and plants in China. Mar Drugs 2009; 7:24-44. [PMID: 19370169 PMCID: PMC2666887 DOI: 10.3390/md7010024] [Citation(s) in RCA: 233] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Revised: 01/20/2009] [Accepted: 01/21/2009] [Indexed: 02/05/2023] Open
Abstract
The mangrove ecosystem is a largely unexplored source for actinomycetes with the potential to produce biologically active secondary metabolites. Consequently, we set out to isolate, characterize and screen actinomycetes from soil and plant material collected from eight mangrove sites in China. Over 2,000 actinomycetes were isolated and of these approximately 20%, 5%, and 10% inhibited the growth of Human Colon Tumor 116 cells, Candida albicans and Staphylococcus aureus, respectively, while 3% inhibited protein tyrosine phosphatase 1B (PTP1B), a protein related to diabetes. In addition, nine isolates inhibited aurora kinase A, an anti-cancer related protein, and three inhibited caspase 3, a protein related to neurodegenerative diseases. Representative bioactive isolates were characterized using genotypic and phenotypic procedures and classified to thirteen genera, notably to the genera Micromonospora and Streptomyces. Actinomycetes showing cytotoxic activity were assigned to seven genera whereas only Micromonospora and Streptomyces strains showed anti-PTP1B activity. We conclude that actinomycetes isolated from mangrove habitats are a potentially rich source for the discovery of anti-infection and anti-tumor compounds, and of agents for treating neurodegenerative diseases and diabetes.
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Affiliation(s)
- Kui Hong
- Author to whom correspondence should be addressed; E-mail:
| | - An-Hui Gao
- National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai 201203, China E-mails:
;
;
| | - Qing-Yi Xie
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, P.R.China;;
;
| | - Hao Gao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, P.R. China; E-mail:
,
| | - Ling Zhuang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, P.R.China;;
;
| | - Hai-Peng Lin
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, P.R.China;;
;
| | - Hai-Ping Yu
- National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai 201203, China E-mails:
;
;
| | - Jia Li
- National Center for Drug Screening, Shanghai Institute of Materia Medica, Shanghai 201203, China E-mails:
;
;
| | - Xin-Sheng Yao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Jinan University, Guangzhou 510632, P.R. China; E-mail:
,
| | | | - Ji-Sheng Ruan
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agriculture Sciences, Haikou 571101, P.R.China;;
;
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100081, P.R. China; E-mail:
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1774
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Abstract
Living cells are remarkably complex. To unravel this complexity, living-cell assays have been developed that allow delivery of experimental stimuli and measurement of the resulting cellular responses. High-throughput adaptations of these assays, known as living-cell microarrays, which are based on microtiter plates, high-density spotting, microfabrication, and microfluidics technologies, are being developed for two general applications: (a) to screen large-scale chemical and genomic libraries and (b) to systematically investigate the local cellular microenvironment. These emerging experimental platforms offer exciting opportunities to rapidly identify genetic determinants of disease, to discover modulators of cellular function, and to probe the complex and dynamic relationships between cells and their local environment.
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Affiliation(s)
- Martin L Yarmush
- Center for Engineering in Medicine and Surgical Services, Massachusetts General Hospital, Harvard Medical School, Massachusetts 02139, USA.
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1775
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Abstract
Non-viral gene delivery systems are promising as they avoid many problems of viral gene therapy by having increased design flexibility, high safety, large DNA cargo capacity, and ease of manufacture. Here, we describe the use of polymeric vectors, in particular biodegradable poly(beta-amino esters) (PBAEs), for non-viral gene delivery. These polymers are able to self-assemble with DNA and form positively charged gene delivery nanoparticles. Methods for synthesis of these polymers, particle self-assembly, and transfection using these particles are delineated. A standard protocol is presented as well as a high-throughput screening technique that can be used to more quickly optimize transfection parameters for efficient delivery.
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Affiliation(s)
- Jordan J Green
- Department of Biological Engineering, Department of Chemical Engineering, and Center for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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1776
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Rabinowitz JR, Goldsmith MR, Little SB, Pasquinelli MA. Computational molecular modeling for evaluating the toxicity of environmental chemicals: prioritizing bioassay requirements. Environ Health Perspect 2008; 116:573-7. [PMID: 18470285 PMCID: PMC2367647 DOI: 10.1289/ehp.11077] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Accepted: 02/01/2008] [Indexed: 05/05/2023]
Abstract
BACKGROUND The human health risk from exposure to environmental chemicals often must be evaluated when relevant elements of the preferred data are unavailable. Therefore, strategies are needed that can predict this information and prioritize the outstanding data requirements for the risk evaluation. Many modes of molecular toxicity require the chemical or one of its biotransformation products to interact with specific biologic macromolecules (i.e., proteins and DNA). Molecular modeling approaches may be adapted to study the interactions of environmental chemicals with biomolecular targets. OBJECTIVE In this commentary we provide an overview of the challenges that arise from applying molecular modeling tools developed and commonly used for pharmaceutical discovery to the problem of predicting the potential toxicities of environmental chemicals. DISCUSSION The use of molecular modeling tools to predict the unintended health and environmental consequences of environmental chemicals differs strategically from the use of the same tools in the pharmaceutical discovery process in terms of the goals and potential applications. It also requires consideration of the greater diversity of chemical space and binding affinity domains than is covered by pharmaceuticals. CONCLUSION Molecular modeling methods offer one of several complementary approaches to evaluate the risk to human health and the environment as a result of exposure to environmental chemicals. These tools can streamline the hazard assessment process by simulating possible modes of action and providing virtual screening tools that can help prioritize bioassay requirements. Tailoring these strategies to the particular challenges presented by environmental chemical interactions make them even more effective.
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Affiliation(s)
| | | | | | - Melissa A. Pasquinelli
- Address correspondence to M.A. Pasquinelli, North Carolina State University, Fiber and Polymer Science/Department of TECS, Campus Box 8301, 2401 Research Dr., Raleigh, NC 27695 USA. Telephone: (919) 515-9426. Fax: (919) 515-6532. E-mail:
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1777
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Zhu H, Rusyn I, Richard A, Tropsha A. Use of cell viability assay data improves the prediction accuracy of conventional quantitative structure-activity relationship models of animal carcinogenicity. Environ Health Perspect 2008; 116:506-13. [PMID: 18414635 PMCID: PMC2291015 DOI: 10.1289/ehp.10573] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Accepted: 01/03/2008] [Indexed: 05/02/2023]
Abstract
BACKGROUND To develop efficient approaches for rapid evaluation of chemical toxicity and human health risk of environmental compounds, the National Toxicology Program (NTP) in collaboration with the National Center for Chemical Genomics has initiated a project on high-throughput screening (HTS) of environmental chemicals. The first HTS results for a set of 1,408 compounds tested for their effects on cell viability in six different cell lines have recently become available via PubChem. OBJECTIVES We have explored these data in terms of their utility for predicting adverse health effects of the environmental agents. METHODS AND RESULTS Initially, the classification k nearest neighbor (kNN) quantitative structure-activity relationship (QSAR) modeling method was applied to the HTS data only, for a curated data set of 384 compounds. The resulting models had prediction accuracies for training, test (containing 275 compounds together), and external validation (109 compounds) sets as high as 89%, 71%, and 74%, respectively. We then asked if HTS results could be of value in predicting rodent carcinogenicity. We identified 383 compounds for which data were available from both the Berkeley Carcinogenic Potency Database and NTP-HTS studies. We found that compounds classified by HTS as "actives" in at least one cell line were likely to be rodent carcinogens (sensitivity 77%); however, HTS "inactives" were far less informative (specificity 46%). Using chemical descriptors only, kNN QSAR modeling resulted in 62.3% prediction accuracy for rodent carcinogenicity applied to this data set. Importantly, the prediction accuracy of the model was significantly improved (72.7%) when chemical descriptors were augmented by HTS data, which were regarded as biological descriptors. CONCLUSIONS Our studies suggest that combining NTP-HTS profiles with conventional chemical descriptors could considerably improve the predictive power of computational approaches in toxicology.
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Affiliation(s)
- Hao Zhu
- Carolina Environmental Bioinformatics Research Center
- Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products, School of Pharmacy and
| | - Ivan Rusyn
- Carolina Environmental Bioinformatics Research Center
- Department of Environmental Sciences and Engineering, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina USA
| | - Ann Richard
- National Center for Computational Toxicology, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA
| | - Alexander Tropsha
- Carolina Environmental Bioinformatics Research Center
- Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products, School of Pharmacy and
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1778
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Brenk R, Schipani A, James D, Krasowski A, Gilbert IH, Frearson J, Wyatt PG. Lessons learnt from assembling screening libraries for drug discovery for neglected diseases. ChemMedChem 2008; 3:435-44. [PMID: 18064617 PMCID: PMC2628535 DOI: 10.1002/cmdc.200700139] [Citation(s) in RCA: 317] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Revised: 09/21/2007] [Indexed: 11/11/2022]
Abstract
To enable the establishment of a drug discovery operation for neglected diseases, out of 2.3 million commercially available compounds 222 552 compounds were selected for an in silico library, 57 438 for a diverse general screening library, and 1 697 compounds for a focused kinase set. Compiling these libraries required a robust strategy for compound selection. Rules for unwanted groups were defined and selection criteria to enrich for lead-like compounds which facilitate straightforward structure-activity relationship exploration were established. Further, a literature and patent review was undertaken to extract key recognition elements of kinase inhibitors ("core fragments") to assemble a focused library for hit discovery for kinases. Computational and experimental characterisation of the general screening library revealed that the selected compounds 1) span a broad range of lead-like space, 2) show a high degree of structural integrity and purity, and 3) demonstrate appropriate solubility for the purposes of biochemical screening. The implications of this study for compound selection, especially in an academic environment with limited resources, are considered.
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Affiliation(s)
- Ruth Brenk
- University of Dundee, College of Life Sciences, James Black Centre, Dow Street, Dundee DD1 5EH, UK.
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1779
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Li Y, Schellhorn HE. Rapid kinetic microassay for catalase activity. J Biomol Tech 2007; 18:185-187. [PMID: 17916790 PMCID: PMC2062561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Catalase is a commonly assayed enzyme found in many bacteria and eukaryotes. In this report, we examined the applicability of a kinetic microassay to quantify catalase from two different sources. The assay was found to be linear over a wide range (0.1-1.0 units), but was limited at high values (>1 unit) by oxygen evolution. Nonetheless, the microassay allows simultaneous evaluation of many samples (up to 96) in a short time (<5 min) and is thus well-suited to applications, such as high-throughput screening, where many parallel assays are required.
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Affiliation(s)
| | - Herb E. Schellhorn
- Address correspondence and reprint requests to: Herb E. Schellhorn, Life Sciences Building 433, 1280 Main Street West, Hamilton, ON Canada L8S 4K1 (phone: 905-525-9140 ext. 27316; fax: 905-522-6066;
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1780
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Mestas SP, Sholders AJ, Peersen OB. A fluorescence polarization-based screening assay for nucleic acid polymerase elongation activity. Anal Biochem 2007; 365:194-200. [PMID: 17475199 PMCID: PMC2713175 DOI: 10.1016/j.ab.2007.03.039] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Revised: 03/09/2007] [Accepted: 03/22/2007] [Indexed: 11/22/2022]
Abstract
We have devised a simple high-throughput screening compatible fluorescence polarization-based assay that can be used to detect the elongation activity of nucleic acid polymerase enzymes. The assay uses a 5' end-labeled template strand and relies on an increase in the polarization signal from the fluorescent label as it is drawn in toward the active site by the action of the enzyme. If the oligonucleotide is sufficiently short, the fluorescence polarization signal can also be used to detect binding prior to elongation activity. We refer to the nucleic acid substrate as a polymerase elongation template element (PETE) and demonstrate the utility of this PETE assay in a microtiter plate format using the RNA-dependent RNA polymerase from poliovirus to extend a self-priming hairpin RNA. The PETE assay provides an efficient method for screening compounds that may inhibit the nucleic acid binding or elongation activities of polymerases.
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Affiliation(s)
- Santano P Mestas
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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1781
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Thakur CS, Jha BK, Dong B, Das Gupta J, Silverman KM, Mao H, Sawai H, Nakamura AO, Banerjee AK, Gudkov A, Silverman RH. Small-molecule activators of RNase L with broad-spectrum antiviral activity. Proc Natl Acad Sci U S A 2007; 104:9585-90. [PMID: 17535916 PMCID: PMC1877983 DOI: 10.1073/pnas.0700590104] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Indexed: 11/18/2022] Open
Abstract
RNase L, a principal mediator of innate immunity to viral infections in higher vertebrates, is required for a complete IFN antiviral response against certain RNA stranded viruses. dsRNA produced during viral infections activates IFN-inducible synthetases that produce 5'-phosphorylated, 2',5'-oligoadenylates (2-5A) from ATP. 2-5A activates RNase L in a wide range of different mammalian cell types, thus blocking viral replication. However, 2-5A has unfavorable pharmacologic properties; it is rapidly degraded, does not transit cell membranes, and leads to apoptosis. To obtain activators of RNase L with improved drug-like properties, high-throughput screening was performed on chemical libraries by using fluorescence resonance energy transfer. Seven compounds were obtained that activated RNase L at micromolar concentrations, and structure-activity relationship studies resulted in identification of an additional four active compounds. Two lead compounds were shown to have a similar mechanistic path toward RNase L activation as the natural activator 2-5A. The compounds bound to the 2-5A-binding domain of RNase L (as determined by surface plasmon resonance and confirmed by computational docking), and the compounds induced RNase L dimerization and activation. Interestingly, the low-molecular-weight activators of RNase L had broad-spectrum antiviral activity against diverse types of RNA viruses, including the human pathogen human parainfluenza virus type 3, yet these compounds by themselves were not cytotoxic at the effective concentrations. Therefore, these RNase L activators are prototypes for a previously uncharacterized class of broad-spectrum antiviral agents.
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Affiliation(s)
- Chandar S. Thakur
- Departments of *Cancer Biology and
- Department of Chemistry, Cleveland State University, Euclid Avenue at East 24th Street, Cleveland, OH 44115; and
| | | | | | | | | | - Hongxia Mao
- Molecular Genetics, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195
| | - Hiro Sawai
- Department of Applied Chemistry, Faculty of Engineering, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Akiko O. Nakamura
- Department of Applied Chemistry, Faculty of Engineering, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Amiya K. Banerjee
- Molecular Genetics, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195
| | - Andrei Gudkov
- Molecular Genetics, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195
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1782
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Coecke S, Goldberg AM, Allen S, Buzanska L, Calamandrei G, Crofton K, Hareng L, Hartung T, Knaut H, Honegger P, Jacobs M, Lein P, Li A, Mundy W, Owen D, Schneider S, Silbergeld E, Reum T, Trnovec T, Monnet-Tschudi F, Bal-Price A. Workgroup report: incorporating in vitro alternative methods for developmental neurotoxicity into international hazard and risk assessment strategies. Environ Health Perspect 2007; 115:924-31. [PMID: 17589601 PMCID: PMC1892131 DOI: 10.1289/ehp.9427] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2006] [Accepted: 02/06/2007] [Indexed: 05/16/2023]
Abstract
This is the report of the first workshop on Incorporating In Vitro Alternative Methods for Developmental Neurotoxicity (DNT) Testing into International Hazard and Risk Assessment Strategies, held in Ispra, Italy, on 19-21 April 2005. The workshop was hosted by the European Centre for the Validation of Alternative Methods (ECVAM) and jointly organized by ECVAM, the European Chemical Industry Council, and the Johns Hopkins University Center for Alternatives to Animal Testing. The primary aim of the workshop was to identify and catalog potential methods that could be used to assess how data from in vitro alternative methods could help to predict and identify DNT hazards. Working groups focused on two different aspects: a) details on the science available in the field of DNT, including discussions on the models available to capture the critical DNT mechanisms and processes, and b) policy and strategy aspects to assess the integration of alternative methods in a regulatory framework. This report summarizes these discussions and details the recommendations and priorities for future work.
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Affiliation(s)
- Sandra Coecke
- ECVAM-European Centre for the Validation of Alternative Methods, Institute for Health and Consumer Protection, European Commission, Joint Research Center, Ispra, Italy.
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1783
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Holloway GA, Baell JB, Fairlamb AH, Novello PM, Parisot JP, Richardson J, Watson KG, Street IP. Discovery of 2-iminobenzimidazoles as a new class of trypanothione reductase inhibitor by high-throughput screening. Bioorg Med Chem Lett 2007; 17:1422-7. [PMID: 17194585 PMCID: PMC3428904 DOI: 10.1016/j.bmcl.2006.11.090] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 11/21/2006] [Accepted: 11/30/2006] [Indexed: 11/26/2022]
Abstract
A high-throughput screening campaign of a library of 100,000 lead-like compounds identified 2-iminobenzimidazoles as a novel class of trypanothione reductase inhibitors. These 2-iminobenzimidazoles display potent trypanocidal activity against Trypanosoma brucei rhodesiense, do not inhibit closely related human glutathione reductase and have low cytotoxicity against mammalian cells.
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Affiliation(s)
- Georgina A. Holloway
- The Walter and Eliza Hall Institute of Medical Research, Biotechnology Centre, 4 Research Avenue, La Trobe Research and Development Park, Bundoora, Vic. 3086, Australia
| | - Jonathan B. Baell
- The Walter and Eliza Hall Institute of Medical Research, Biotechnology Centre, 4 Research Avenue, La Trobe Research and Development Park, Bundoora, Vic. 3086, Australia
| | - Alan H. Fairlamb
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, Scotland, UK
| | - Patrizia M. Novello
- The Walter and Eliza Hall Institute of Medical Research, Biotechnology Centre, 4 Research Avenue, La Trobe Research and Development Park, Bundoora, Vic. 3086, Australia
| | - John P. Parisot
- The Walter and Eliza Hall Institute of Medical Research, Biotechnology Centre, 4 Research Avenue, La Trobe Research and Development Park, Bundoora, Vic. 3086, Australia
| | - John Richardson
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, Wellcome Trust Biocentre, University of Dundee, Dundee, Scotland, UK
| | - Keith G. Watson
- The Walter and Eliza Hall Institute of Medical Research, Biotechnology Centre, 4 Research Avenue, La Trobe Research and Development Park, Bundoora, Vic. 3086, Australia
| | - Ian P. Street
- The Walter and Eliza Hall Institute of Medical Research, Biotechnology Centre, 4 Research Avenue, La Trobe Research and Development Park, Bundoora, Vic. 3086, Australia
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1784
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Galam L, Hadden MK, Ma Z, Ye Q, Yun BG, Blagg BSJ, Matts RL. High-throughput assay for the identification of Hsp90 inhibitors based on Hsp90-dependent refolding of firefly luciferase. Bioorg Med Chem 2007; 15:1939-46. [PMID: 17223347 PMCID: PMC1906718 DOI: 10.1016/j.bmc.2007.01.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2006] [Revised: 12/20/2006] [Accepted: 01/01/2007] [Indexed: 10/23/2022]
Abstract
Previously, we have demonstrated that the renaturation of heat denatured firefly luciferase is dependent upon the activity of Hsp90 in rabbit reticulocyte lysate. Here, we demonstrate that this assay may identify inhibitors that obstruct the chaperone activity of Hsp90 either by direct binding to its N-terminal or C-terminal nucleotide binding sites or by interference with the ability of the chaperone to switch conformations. The assay was adapted and optimized for high-throughput screening. Greater than 20,000 compounds were screened to demonstrate the feasibility of using this assay on a large scale. The assay was reproducible (av Z-factor=0.62) and identified 120 compounds that inhibited luciferase renaturation by greater than 70% at a concentration of 12.5 microg/mL. IC50 values for twenty compounds with varying structures were determined for inhibition of luciferase refolding and in cell-based assays for Hsp90 inhibition. Several compounds had IC50 values <10 microM and represent a number of new lead structures with the potential for further development and optimization as potent Hsp90 inhibitors.
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Affiliation(s)
- Lakshmi Galam
- Department of Biochemistry and Molecular Biology, NRC 246, Oklahoma State University, Stillwater, Oklahoma, U.S.A. 74078
| | - M. Kyle Hadden
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, Kansas, U.S.A. 66045-7563
| | - Zeqiang Ma
- High-Throughput Screening Laboratory, The University of Kansas, 1501 Wakarusa Drive, Lawrence, Kansas, U.S.A. 66047
| | - Qi–Zhuang Ye
- High-Throughput Screening Laboratory, The University of Kansas, 1501 Wakarusa Drive, Lawrence, Kansas, U.S.A. 66047
| | - Bo-Geon Yun
- Department of Biochemistry and Molecular Biology, NRC 246, Oklahoma State University, Stillwater, Oklahoma, U.S.A. 74078
| | - Brian S. J. Blagg
- Department of Medicinal Chemistry, 1251 Wescoe Hall Drive, Malott 4070, The University of Kansas, Lawrence, Kansas, U.S.A. 66045-7563
| | - Robert L. Matts
- Department of Biochemistry and Molecular Biology, NRC 246, Oklahoma State University, Stillwater, Oklahoma, U.S.A. 74078
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1785
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Schwartz MP, Derfus AM, Alvarez SD, Bhatia SN, Sailor MJ. The smart Petri dish: a nanostructured photonic crystal for real-time monitoring of living cells. Langmuir 2006; 22:7084-90. [PMID: 16863264 PMCID: PMC3530423 DOI: 10.1021/la060420n] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The intensity of light scattered from a porous Si photonic crystal is used to monitor physiological changes in primary rat hepatocytes. The cells are seeded on the surface of a porous Si photonic crystal that has been filled with polystyrene and treated with an O2 plasma. Light resonant with the photonic crystal is scattered by the cell layer and detected as an optical peak with a charge-coupled-device spectrometer. It is demonstrated that exposure of hepatocytes to the toxins cadmium chloride or acetaminophen leads to morphology changes that cause a measurable increase in scattered intensity. The increase in signal occurs before traditional assays are able to detect a decrease in viability, demonstrating the potential of the technique as a complementary tool for cell viability studies. The scattering method presented here is noninvasive and can be performed in real time, representing a significant advantage compared to other techniques for in vitro monitoring of cell morphology.
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Affiliation(s)
- Michael P Schwartz
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, Department 0358, La Jolla, CA 92093-0358, USA
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1786
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Griswold KE, Kawarasaki Y, Ghoneim N, Benkovic SJ, Iverson BL, Georgiou G. Evolution of highly active enzymes by homology-independent recombination. Proc Natl Acad Sci U S A 2005; 102:10082-7. [PMID: 16009931 PMCID: PMC1177412 DOI: 10.1073/pnas.0504556102] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The theta-class GST enzymes hGSTT1-1 (human GSTTheta-1-1) and rGSTT2-2 (rat GSTTheta-2-2) share 54.3% amino acid identity and exhibit different substrate specificities. Homology-independent techniques [incremental truncation for the creation of hybrid enzymes (ITCHY) and SCRATCHY] and low-homology techniques (recombination-dependent exponential amplification PCR) were used to create libraries of chimeric enzymes containing crossovers (C/Os) at positions not accessible by DNA family shuffling. High-throughput flow cytometric screening using the fluorogenic rGSTT2-2-specific substrate 7-amino-4-chloromethyl coumarin led to the isolation of active variants with either one or two C/Os. One of these enzymes, SCR23 (83% identity to hGSTT1-1), was encoded by a gene that exchanged helices 4 and 5 of hGSTT1-1 with the corresponding sequence from rGSTT2-2. Compared with either parent, this variant was found to have an improved k(cat) with the selection substrate and also exhibited activity for the conjugation of glutathione to ethacrynic acid, a compound that is not recognized by either parental enzyme. These results highlight the power of combinatorial homology-independent and low-homology recombination methods for the generation of unique, highly active enzymes and also suggest a possible means of enzyme "humanization."
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Affiliation(s)
- Karl E Griswold
- Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA
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1787
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Wood SJ, Miller KA, David SA. Anti-endotoxin agents. 2. Pilot high-throughput screening for novel lipopolysaccharide-recognizing motifs in small molecules. Comb Chem High Throughput Screen 2004; 7:733-47. [PMID: 15578935 PMCID: PMC1360204 DOI: 10.2174/1386207043328229] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lipopolysaccharides (LPS), otherwise termed 'endotoxins', are an integral part of the outer leaflet of the outer-membrane of Gram-negative bacteria. Lipopolysaccharides play a pivotal role in the pathogenesis of 'Septic Shock', a major cause of mortality in the critically ill patient, worldwide. The sequestration of circulatory endotoxin may be a viable therapeutic strategy for the prophylaxis and treatment of Gram-negative sepsis. We have earlier shown that the pharmacophore necessary for small molecules to bind LPS is simple, comprising of two protonatable cationic functions separated by about 15 A, permitting the simultaneous interaction with the negatively charged phosphates on lipid A, the toxically active center of endotoxin. In this report, we employ high-throughput screening methods, using a novel fluorescent probe displacement method. Searches in three-dimensional structure databases yielded about approximately 4000 commercially available small molecules, each possessing two cationic functions spaced approximately 15 A apart. Approximately 400 such compounds have been screened in an effort to validate the method by which high-affinity endotoxin binders can be identified. We show that the IC50 values that are obtained from the fluorescence-based primary screen are correlated both to the enthalpy of binding, as measured by isothermal titration calorimetry, as well as to biological potency in vitro assays. By performing rapid toxicity screens in tandem with the bioassays, lead compounds of interest can be easily identified for further systematic structural modifications and SAR studies.
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Affiliation(s)
| | | | - Sunil A. David
- University of Kansas Life Sciences Research Laboratories 1501 Wakarusa Drive, Lawrence, KS – 66049
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1788
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Peng C, Unger SW, Filipp FV, Sattler M, Szalma S. Automated evaluation of chemical shift perturbation spectra: New approaches to quantitative analysis of receptor-ligand interaction NMR spectra. J Biomol NMR 2004; 29:491-504. [PMID: 15243180 PMCID: PMC5003417 DOI: 10.1023/b:jnmr.0000034351.37982.9e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
This paper presents new methods designed for quantitative analysis of chemical shift perturbation NMR spectra. The methods automatically trace the displacements of cross peaks between a perturbed test spectrum and the reference spectrum (or among a series of titration spectra), and measure the changes of chemical shifts, heights, and widths of the altered peaks. The methods are primary aimed at the (1)H-(15)N HSQC spectra of relatively small proteins (<15 kDa) assuming fast exchange between free and ligand-bound states on the chemical shift time scale, or for comparing spectra of free and fully bound states in the slow exchange situation. Using the (1)H-(15)N HSQC spectra from a titration experiment of the 74-residue Pex13p SH3 domain with a Pex14p peptide ligand (14 residues, K (d)= approximately 40 microM), we demonstrate the scope and limits of our automatic peak tracing (APET) algorithm for efficient scoring of high-throughput SAR by NMR type HSQC spectra, and progressive peak tracing (PROPET) algorithm for detailed analysis of ligand titration spectra. Simulated spectra with low signal-to-noise ratios (S/N ranged from 20 to 1) were used to demonstrate the reliability and reproducibility of the results when dealing with poor quality spectra. These algorithms have been implemented in a new software module, FELIX-Autoscreen, for streamlined processing, analysis and visualization of SAR by NMR and other high-throughput receptor/ligand interaction experiments.
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Affiliation(s)
- Chen Peng
- Accelrys Inc., 9685 Scranton Road, San Diego, CA 92121, U.S.A
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1789
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Wood SJ, Miller KA, David SA. Anti-endotoxin agents. 1. Development of a fluorescent probe displacement method optimized for the rapid identification of lipopolysaccharide-binding agents. Comb Chem High Throughput Screen 2004; 7:239-49. [PMID: 15134530 PMCID: PMC1540690 DOI: 10.2174/1386207043328832] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Lipopolysaccharides (LPS), otherwise termed 'endotoxins', are outer-membrane constituents of Gram-negative bacteria. Lipopolysaccharides play a key role in the pathogenesis of 'Septic Shock', a major cause of mortality in the critically ill patient. Therapeutic options aimed at limiting downstream systemic inflammatory processes by targeting lipopolysaccharide do not exist at the present time. We have defined the pharmacophore necessary for small molecules to specifically bind and neutralize LPS, and have shown using animal models of sepsis that the sequestration of circulatory LPS by small molecules is a therapeutically viable strategy. Assays reported previously in the literature do not lend themselves well to the rapid screening of large numbers of structurally diverse compounds. In this report, we describe a highly sensitive and robust fluorescent displacement assay using BODIPY TR cadaverine (BC), which binds specifically to the toxic center of LPS, lipid A, and is competitively displaced by compounds displaying an affinity for lipid A. The assay clearly discriminates subtle differences in the binding of polymyxin B, and its nonapeptide derivative, with LPS. The spectral properties of the BODIPY fluorophore are ideally suited for screening diverse structural classes of compounds, including those with conjugated aromatic groups, or with chromophores in the 260-500 nm range. The fluorescent probe: LPS complex is stable under physiologically relevant salt concentrations, resulting in the rapid rejection of spurious binders interacting via non-specific electrostatic interactions, and, therefore, in greatly improved dispersion of ED(50)values.
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Affiliation(s)
- Stewart J. Wood
- University of Kansas Life Sciences Research Laboratories 1501 Wakarusa Drive, Lawrence, KS – 66049
| | - Kelly A. Miller
- University of Kansas Life Sciences Research Laboratories 1501 Wakarusa Drive, Lawrence, KS – 66049
| | - Sunil A. David
- University of Kansas Life Sciences Research Laboratories 1501 Wakarusa Drive, Lawrence, KS – 66049
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1790
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Iourgenko V, Zhang W, Mickanin C, Daly I, Jiang C, Hexham JM, Orth AP, Miraglia L, Meltzer J, Garza D, Chirn GW, McWhinnie E, Cohen D, Skelton J, Terry R, Yu Y, Bodian D, Buxton FP, Zhu J, Song C, Labow MA. Identification of a family of cAMP response element-binding protein coactivators by genome-scale functional analysis in mammalian cells. Proc Natl Acad Sci U S A 2003; 100:12147-52. [PMID: 14506290 PMCID: PMC218727 DOI: 10.1073/pnas.1932773100] [Citation(s) in RCA: 292] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2003] [Indexed: 11/18/2022] Open
Abstract
This report describes an unbiased method for systematically determining gene function in mammalian cells. A total of 20,704 predicted human full-length cDNAs were tested for induction of the IL-8 promoter. A number of genes, including those for cytokines, receptors, adapters, kinases, and transcription factors, were identified that induced the IL-8 promoter through known regulatory sites. Proteins that acted through a cooperative interaction between an AP-1 and an unrecognized cAMP response element (CRE)-like site were also identified. A protein, termed transducer of regulated cAMP response element-binding protein (CREB) (TORC1), was identified that activated expression through the variant CRE and consensus CRE sites. TORC1 potently induced known CREB1 target genes, bound CREB1, and activated expression through a potent transcription activation domain. A functional Drosophila TORC gene was also identified. Thus, TORCs represent a family of highly conserved CREB coactivators that may control the potency and specificity of CRE-mediated responses.
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Affiliation(s)
- Vadim Iourgenko
- Department of Functional Genomics, Novartis Institute for Biomedical Research, 100 Technology Square, Cambridge, MA 02139, USA
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1791
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Affiliation(s)
- C M Snively
- School of Chemical Engineering, Purdue University West Lafayette, IN 47907-1283, USA, Fax: (+1) 765-494-0805
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1792
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Aherne GW, McDonald E, Workman P. Finding the needle in the haystack: why high-throughput screening is good for your health. Breast Cancer Res 2002; 4:148-54. [PMID: 12100740 PMCID: PMC138735 DOI: 10.1186/bcr440] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2002] [Revised: 05/02/2002] [Accepted: 05/09/2002] [Indexed: 11/10/2022] Open
Abstract
High-throughput screening is an essential component of the toolbox of modern technologies that improve speed and efficiency in contemporary cancer drug development. This is particularly important as we seek to exploit, for maximum therapeutic benefit, the large number of new molecular targets emerging from the Human Genome Project and cancer genomics. Screening of diverse collections of low molecular weight compounds plays a key role in providing chemical starting points for iterative optimisation by medicinal chemistry. Examples of successful drug discovery programmes based on high-throughput screening are described, and these offer potential in the treatment of breast cancer and other malignancies.
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Affiliation(s)
- G Wynne Aherne
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Sutton, UK
| | - Edward McDonald
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Sutton, UK
| | - Paul Workman
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Sutton, UK
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1793
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Abstract
A continuous assay method, such as one that utilizes an increase in fluorescence upon hydrolysis, allows for rapid and convenient kinetic evaluation of proteases. To better understand MMP behaviors and to aid in the design of MMP inhibitors, a variety of sequence specificity, phage display, and combinatorial chemistry studies have been performed. Results of these studies have been valuable for defining the differences in MMPs and for creating quenched fluorescent substrates that utilize fluorescence resonance energy transfer (FRET)/intramolecular fluorescence energy transfer (IFET). FRET triple-helical substrates have been constructed to examine the collagenolytic activity of MMP family members. The present chapter provides an overview of MMP and related FRET substrates and describes how to construct and utilize these substrates.
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Affiliation(s)
- Gregg B. Fields
- Department of Chemistry & Biochemistry, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431 U.S.A. Phone 561-297-2093, Fax 561-297-2759
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