251
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Bagossi P, Kádas J, Miklóssy G, Boross P, Weber IT, Tözsér J. Development of a microtiter plate fluorescent assay for inhibition studies on the HTLV-1 and HIV-1 proteinases. J Virol Methods 2004; 119:87-93. [PMID: 15158589 DOI: 10.1016/j.jviromet.2004.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2003] [Revised: 10/18/2003] [Accepted: 03/01/2004] [Indexed: 10/26/2022]
Abstract
The proteinase of human T-cell leukemia virus type-1 (HTLV-1), similar to the proteinase of human immunodeficiency virus type-1 (HIV-1), is a potential target for chemotherapy, since the virus is associated with a number of human diseases. A microtiter plate fluorescent assay was developed for the HTLV-1 and HIV-1 proteinases for direct comparison of the inhibition profiles of the enzymes. It was established that, except for Indinavir, none of the inhibitors designed against the HIV-1 proteinase were able to inhibit the HTLV-1 proteinase in the studied concentration range, while two reduced peptide bond-containing peptides having the sequence of HTLV-1 cleavage sites were inhibitors of the HTLV-1 proteinase. One of these was potent enough to be used for active site titration of the HTLV-1 proteinase.
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Affiliation(s)
- Péter Bagossi
- Department of Biochemistry and Molecular Biology, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, H4012 POB 6 Debrecen, Hungary
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252
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Stranix BR, Sauvé G, Bouzide A, Coté A, Sévigny G, Yelle J, Perron V. Lysine sulfonamides as novel HIV-protease inhibitors: Nε-disubstituted ureas. Bioorg Med Chem Lett 2004; 14:3971-4. [PMID: 15225709 DOI: 10.1016/j.bmcl.2004.05.049] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2004] [Revised: 05/21/2004] [Accepted: 05/21/2004] [Indexed: 11/23/2022]
Abstract
A series of lysine sulfonamide analogues bearing a Nepsilon-benzylic ureas was synthesized using both solution-phase and solid-phase approaches. A novel synthetic route of Nalpha-(alkyl)-Nalpha-(sulfonamides)lysinol using alpha-amino-caprolactam was developed. Evaluation of these novel protease inhibitors revealed compounds with high potency against wild-type HIV virus.
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Affiliation(s)
- Brent R Stranix
- Procyon Biopharma Inc., 1650 Trans-Canada Highway, Suite 200, Dorval, Quebec, Canada, H9P 1H7.
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253
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Kuo CJ, Chi YH, Hsu JTA, Liang PH. Characterization of SARS main protease and inhibitor assay using a fluorogenic substrate. Biochem Biophys Res Commun 2004; 318:862-7. [PMID: 15147951 PMCID: PMC7134607 DOI: 10.1016/j.bbrc.2004.04.098] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2004] [Indexed: 12/31/2022]
Abstract
SARS main protease is essential for life cycle of SARS coronavirus and may be a key target for developing anti-SARS drugs. Recently, the enzyme expressed in Escherichia coli was characterized using a HPLC assay to monitor the formation of products from 11 peptide substrates covering the cleavage sites found in the SARS viral genome. This protease easily dissociated into inactive monomer and the deduced Kd of the dimer was 100 μM. In order to detect enzyme activity, the assay needed to be performed at micromolar enzyme concentration. This makes finding the tight inhibitor (nanomolar range IC50) impossible. In this study, we prepared a peptide with fluorescence quenching pair (Dabcyl and Edans) at both ends of a peptide substrate and used this fluorogenic peptide substrate to characterize SARS main protease and screen inhibitors. The fluorogenic peptide gave extremely sensitive signal upon cleavage catalyzed by the protease. Using this substrate, the protease exhibits a significantly higher activity (kcat=1.9 s−1 and Km=17 μM) compared to the previously reported parameters. Under our assay condition, the enzyme stays as an active dimer without dissociating into monomer and reveals a small Kd value (15 nM). This enzyme in conjunction with fluorogenic peptide substrate provides us a suitable tool for identifying potent inhibitors of SARS protease.
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Affiliation(s)
- Chih-Jung Kuo
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan, ROC
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254
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Tanaka F, Mase N, Barbas CF. Design and use of fluorogenic aldehydes for monitoring the progress of aldehyde transformations. J Am Chem Soc 2004; 126:3692-3. [PMID: 15038704 DOI: 10.1021/ja049641a] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the first examples of fluorogenic aldehydes useful for monitoring many types of reactions including aldol reactions, allylations, and reductions. The fluorogenic aldehydes were constructed by covalent combination of a fluorophore and an aldehyde moiety via a linker. In the resulting single molecule, the aldehyde functioned as a quencher of the fluorophore's fluorescence. The reaction product, modified at the aldehyde functionality, no longer served as an effective quencher. The reaction products showed up to approximately 80-fold higher fluorescence than the aldehyde reactants.
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Affiliation(s)
- Fujie Tanaka
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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255
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Abstract
Enzyme assays for high-throughput screening and enzyme engineering, which are often based on derivatives of coumarin, nitrophenol, fluorescein, nitrobenzofurazane or rhodamine dyes, can be divided into two categories: those that depend on labelled substrates, and those that depend on sensing the reactions of unmodified substrates. Labelled substrates include, for example, fluorogenic and chromogenic substrates that generate a reporter molecule by beta-elimination, fluorescence resonance energy transfer (FRET) substrates and isotopic labels for enantioselectivity screening. By contrast, endpoint sensing can be done using amine reagents, fluorescent affinity labels for phosphorylated proteins, or synthetic multifunctional pores. Sensing assays can also be done in real time by using, for example, aldehyde trapping to follow vinyl ester acylation in organic solvent or calcein-copper fluorescence for sensing amino acids. The current trend is to assemble many such assays in parallel for enzyme profiling and enzyme fingerprinting.
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Affiliation(s)
- Jean-Philippe Goddard
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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256
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Sando S, Abe H, Kool ET. Quenched auto-ligating DNAs: multicolor identification of nucleic acids at single nucleotide resolution. J Am Chem Soc 2004; 126:1081-7. [PMID: 14746476 DOI: 10.1021/ja038665z] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the synthesis and study of multicolor quenched autoligating (QUAL) probes for identification and discrimination of closely related RNA and DNA sequences in solution and in bacteria. In these probes, a dabsyl quencher doubles as an activator in the oligonucleotide-joining reaction. The oligonucleotides remain dark until they bind at adjacent sites, and "light up" on nucleophilic displacement of the dabsyl probe by the phosphorothioate probe. Four fluorescent dye conjugates were prepared and tested with probes and targets that differ by one nucleotide. Experiments on polymer beads show clear color-based discrimination of DNAs added in solution. Two-color quenched probe pairs were then tested in the discrimination of 16S rRNA sequences in Escherichia coli. Single nucleotide resolution was achieved in the cells with green/red QUAL probes, allowing identification of a one-base sequencing error in the 16S rRNA database. Finally, QUAL probes were successfully applied in live bacterial cells. The method requires only incubation followed by fluorescence imaging, and requires no enzymes, added reagents, cross-linking, fixing, or washes. Because probes must bind side-by-side to generate signal, there is little or no interference from unintended protein binding, which can occur with other probe types. The results suggest that QUAL probes may be of general use in the detection and identification of sequences in solution, on microarrays, and in microorganisms.
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Affiliation(s)
- Shinsuke Sando
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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257
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Rodems SM, Hamman BD, Lin C, Zhao J, Shah S, Heidary D, Makings L, Stack JH, Pollok BA. A FRET-based assay platform for ultra-high density drug screening of protein kinases and phosphatases. Assay Drug Dev Technol 2004; 1:9-19. [PMID: 15090152 DOI: 10.1089/154065802761001266] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Protein phosphorylation is one of the major regulatory mechanisms involved in signal-induced cellular events, including cell proliferation, apoptosis, and metabolism. Because many facets of biology are regulated by protein phosphorylation, aberrant kinase and/or phosphatase activity forms the basis for many different types of pathology. The disease relevance of protein kinases and phosphatases has led many pharmaceutical and biotechnology companies to expend significant resources in lead discovery programs for these two target classes. The existence of >500 kinases and phosphatases encoded by the human genome necessitates development of methodologies for the rapid screening for novel and specific compound inhibitors. We describe here a fluorescence-based, molecular assay platform that is compatible with robotic, ultra-high throughput screening systems and can be applied to virtually all tyrosine and serine/threonine protein kinases and phosphatases. The assay has a coupled-enzyme format, utilizing the differential protease sensitivity of phosphorylated versus nonphosphorylated peptide substrates. In addition to screening individual kinases, the assay can be formatted such that kinase pathways are re-created in vitro to identify compounds that specifically interact with inactive kinases. Miniaturization of this assay format to the 1-microl scale allows for the rapid and accurate compound screening of a host of kinase and phosphatase targets, thereby facilitating the hunt for new leads for these target classes.
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Affiliation(s)
- Steven M Rodems
- Aurora Biosciences Corp, and Vertex Pharmaceuticals, Inc, San Diego, CA, USA
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258
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Ingr M, Uhlíková T, Strísovský K, Majerová E, Konvalinka J. Kinetics of the dimerization of retroviral proteases: the "fireman's grip" and dimerization. Protein Sci 2004; 12:2173-82. [PMID: 14500875 PMCID: PMC2366921 DOI: 10.1110/ps.03171903] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
All retroviral proteases belong to the family of aspartic proteases. They are active as homodimers, each unit contributing one catalytic aspartate to the active site dyad. An important feature of all aspartic proteases is a conserved complex scaffold of hydrogen bonds supporting the active site, called the "fireman's grip," which involves the hydroxyl groups of two threonine (serine) residues in the active site Asp-Thr(Ser)-Gly triplets. It was shown previously that the fireman's grip is indispensable for the dimer stability of HIV protease. The retroviral proteases harboring Ser in their active site triplet are less active and, under natural conditions, are expressed in higher enzyme/substrate ratio than those having Asp-Thr-Gly triplet. To analyze whether this observation can be attributed to the different influence of Thr or Ser on dimerization, we prepared two pairs of the wild-type and mutant proteases from HIV and myeloblastosis-associated virus harboring either Ser or Thr in their Asp-Thr(Ser)-Gly triplet. The equilibrium dimerization constants differed by an order of magnitude within the relevant pairs. The proteases with Thr in their active site triplets were found to be approximately 10 times more thermodynamically stable. The dimer association contributes to this difference more than does the dissociation. We propose that the fireman's grip might be important in the initial phases of dimer formation to help properly orientate the two subunits of a retroviral protease. The methyl group of threonine might contribute significantly to fixing such an intermediate conformation.
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Affiliation(s)
- Marek Ingr
- Institute of Organic Chemistry and Biochemistry, Academy of Science of the Czech Republic, 166 10 Praha 6, Czech Republic
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259
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Tompa P, Buzder-Lantos P, Tantos A, Farkas A, Szilágyi A, Bánóczi Z, Hudecz F, Friedrich P. On the sequential determinants of calpain cleavage. J Biol Chem 2004; 279:20775-85. [PMID: 14988399 DOI: 10.1074/jbc.m313873200] [Citation(s) in RCA: 251] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The structural clues of substrate recognition by calpain are incompletely understood. In this study, 106 cleavage sites in substrate proteins compiled from the literature have been analyzed to dissect the signal for calpain cleavage and also to enable the design of an ideal calpain substrate and interfere with calpain action via site-directed mutagenesis. In general, our data underline the importance of the primary structure of the substrate around the scissile bond in the recognition process. Significant amino acid preferences were found to extend over 11 residues around the scissile bond, from P(4) to P(7)'. In compliance with earlier data, preferred residues in the P(2) position are Leu, Thr, and Val, and in P(1) Lys, Tyr, and Arg. In position P(1) ', small hydrophilic residues, Ser and to a lesser extent Thr and Ala, occur most often. Pro dominates the region flanking the P(2)-P(1)' segment, i.e. positions P(3) and P(2)'-P(4)'; most notable is its occurrence 5.59 times above chance in P(3)'. Intriguingly, the segment C-terminal to the cleavage site resembles the consensus inhibitory region of calpastatin, the specific inhibitor of the enzyme. Further, the position of the scissile bond correlates with certain sequential attributes, such as secondary structure and PEST score, which, along with the amino acid preferences, suggests that calpain cleaves within rather disordered segments of proteins. The amino acid preferences were confirmed by site-directed mutagenesis of the autolysis sites of Drosophila calpain B; when amino acids at key positions were changed to less preferred ones, autolytic cleavage shifted to other, adjacent sites. Based on these preferences, a new fluorogenic calpain substrate, DABCYLTPLKSPPPSPR-EDANS, was designed and synthesized. In the case of micro- and m-calpain, this substrate is kinetically superior to commercially available ones, and it can be used for the in vivo assessment of the activity of these ubiquitous mammalian calpains.
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Affiliation(s)
- Peter Tompa
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, P.O. Box 7, H-1518 Budapest, Hungary
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260
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Kiyonaka S, Sada K, Yoshimura I, Shinkai S, Kato N, Hamachi I. Semi-wet peptide/protein array using supramolecular hydrogel. NATURE MATERIALS 2004; 3:58-64. [PMID: 14661016 DOI: 10.1038/nmat1034] [Citation(s) in RCA: 362] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2003] [Accepted: 10/10/2003] [Indexed: 05/22/2023]
Abstract
The protein microarray is a crucial biomaterial for the rapid and high-throughput assay of many biological events where proteins are involved. In contrast to the DNA microarray, it has not been sufficiently established because of protein instability under the conventional dry conditions. Here we report a novel semi-wet peptide/protein microarray using a supramolecular hydrogel composed of glycosylated amino acetate. The spontaneous gel-formation and amphiphilic properties of this supramolecular hydrogel have been applied to a new type of peptide/protein gel array that is compatible with enzyme assays. Aqueous cavities created in the gel matrix are a suitable semi-wet reaction medium for enzymes, whereas the hydrophobic domains of the fibre are useful as a unique site for monitoring the reaction. This array system overcomes several drawbacks of conventional protein chips, and thus can have potential applications in pharmaceutical research and diagnosis.
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Affiliation(s)
- Shigeki Kiyonaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka, 812-8581, Japan
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261
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Pattanaik P, Jain B, Ravindra G, Gopi HN, Pal PP, Balaram H, Balaram P. Stage-specific profiling of Plasmodium falciparum proteases using an internally quenched multispecificity protease substrate. Biochem Biophys Res Commun 2003; 309:974-9. [PMID: 13679069 DOI: 10.1016/j.bbrc.2003.08.108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Novel internally quenched fluorescence peptide substrates containing sequence specific sites for cleavage by multiple proteases were designed and synthesized. The 28 and 29 residue peptides contain an N-terminal fluorescence acceptor group, 4-(4-dimethylaminophenylazo)benzoic acid (DABCYL), and a C-terminal fluorescence donor group, 5-(2-aminoethylamino)naphthalene-1-sulfonic acid (EDANS). Efficient energy transfer between the donor and acceptor groups flanking the peptide sequence was achieved by incorporation of a central DPro-Gly segment, which serves as a conformation nucleating site, inducing hairpin formation. This multispecificity protease substrate was used to profile the proteolytic activities in the malarial parasite Plasmodium falciparum in a stage dependent manner using a combination of fluorescence and MALDI mass spectrometry. Cysteine protease activity was shown to be dominating at neutral pH, whereas aspartic protease activity contributed predominantly to the proteolytic repertoire at acidic pH. Maximum proteolysis was observed at the trophozoite stage followed by the schizonts and the rings.
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Affiliation(s)
- Priyaranjan Pattanaik
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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262
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Stranix BR, Sauvé G, Bouzide A, Coté A, Sévigny G, Yelle J. Lysine sulfonamides as novel HIV-Protease inhibitors: optimization of the Nε -acyl-phenyl spacer. Bioorg Med Chem Lett 2003; 13:4289-92. [PMID: 14643311 DOI: 10.1016/j.bmcl.2003.09.058] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A series of Nalpha-isobutyl-Nalpha-arylsulfonamido-(Nepsilon acyl) lysine and lysinol derivatives were prepared and evaluated as inhibitors of HIV protease and wild type virus. A simple original synthesis was devised to form Nalpha-(arylsulfonamide)-Nalpha-isobutyl lysine, which could be easily acylated with carboxylic acids at the Nepsilon position. A two-atom spacer was found to be optimal between this acyl group and a phenyl yielding compounds of sub-nanomolar potency on purified enzyme.
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Affiliation(s)
- Brent R Stranix
- Pharmacor Inc, 535 Cartier West, blvd, Laval, Quebec, Canada H7V 3S8.
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263
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Hossain MA, Mihara H, Ueno A. Fluorescence resonance energy transfer in a novel cyclodextrin–Peptide conjugate for detecting steroid molecules. Bioorg Med Chem Lett 2003; 13:4305-8. [PMID: 14643314 DOI: 10.1016/j.bmcl.2003.09.051] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
A novel cyclodextrin conjugated peptide, 1, having two different fluorophores, coumarin and pyrene, in the side chains has been designed and synthesized. The circular dichroism study reveals that 1 shows typical alpha-helix pattern, and forms intramolecular inclusion complex with coumarin. The fluorescence emission study shows that the peptide exhibits intramolecular fluorescence resonance energy transfer (FRET) without quenching of two fluorophores. We have determined the binding constants of 1 for various biologically important steroid molecules as guests using the guest-responsive variation in the fluorescence emission intensity of coumarin.
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Affiliation(s)
- Mohammed Akhter Hossain
- Department of Bioengineering, Tokyo Institute of Technology, 4259Nagatsuta, Midori, Yokohama 226-8501, Japan
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264
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Bouzide A, Sauvé G, Sévigny G, Yelle J. 1,2,5,6-Tetra- O -benzyl- d -mannitol derivatives as novel HIV protease inhibitors. Bioorg Med Chem Lett 2003; 13:3601-5. [PMID: 14505679 DOI: 10.1016/s0960-894x(03)00677-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The synthesis and structure-activity relationships of HIV protease inhibitors derived from carbohydrate alditols are discussed. We disclose a new series of 1,2,5,6-tetra-O-alkyl-D-mannitol exhibiting sub-micromolar activity against HIV-protease. This series of inhibitors are non-nitrogen containing HIV-protease inhibitors and they are readily prepared in a few chemical steps from inexpensive commercially available starting materials.
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265
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Murata CE, Goldberg DE. Plasmodium falciparum falcilysin: a metalloprotease with dual specificity. J Biol Chem 2003; 278:38022-8. [PMID: 12876284 DOI: 10.1074/jbc.m306842200] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The malaria parasite Plasmodium falciparum degrades host cell hemoglobin within an acidic food vacuole. The metalloprotease falcilysin has previously been identified as an important component of this catabolic process. Using random peptide substrate analysis, we confirm that recombinant falcilysin is highly active at acidic pH, consistent with its role in hemoglobin degradation. Unexpectedly, the enzyme is also robustly active at neutral pH, but with a substantially different substrate specificity. Imaging studies confirm the location of falcilysin in the food vacuole and reveal association with vesicular structures elsewhere within the parasite. These data suggest that falcilysin may have an expanded role beyond globin catabolism and may function as two different proteases in its two locations.
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Affiliation(s)
- Christina E Murata
- Howard Hughes Medical Institute, Washington University, Department of Molecular Microbiology, St. Louis, Missouri 63110, USA
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266
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Mittoo S, Sundstrom LE, Bradley M. Synthesis and evaluation of fluorescent probes for the detection of calpain activity. Anal Biochem 2003; 319:234-8. [PMID: 12871716 DOI: 10.1016/s0003-2697(03)00324-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Two new probes for the detection of calpain I activity based on fluorescence resonance energy transfer technology have been synthesized and evaluated. The probes incorporated the cleavage site present in alpha-spectrin, a naturally occurring substrate of calpain I. The design of the internally quenched substrates is such that the calpain-sensitive bond of the peptides (between the Tyr-Gly residues) is located centrally between the donor and the quencher chromophores. The calpain assay protocol is capable of detecting enzymatic activity in the nanomolar region.
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Affiliation(s)
- Stifun Mittoo
- Department of Chemistry, University of Southampton, Highfield, UK
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267
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Kennedy ME, Wang W, Song L, Lee J, Zhang L, Wong G, Wang L, Parker E. Measuring human beta-secretase (BACE1) activity using homogeneous time-resolved fluorescence. Anal Biochem 2003; 319:49-55. [PMID: 12842106 DOI: 10.1016/s0003-2697(03)00253-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The human beta-secretase enzyme, BACE1, mediates a critical step in the production of A beta(40) and A beta(42) peptides which are responsible for the severe neuronal cell death and insoluble amyloid plaques of Alzheimer's disease (AD). Several lines of evidence suggest that potent BACE1 inhibitors represent an attractive A beta-lowering strategy for AD. We designed a simple homogeneous time-resolved fluorescence (HTRF) assay which utilizes the fluorescence resonance energy transfer (FRET) pair europium and allophycocyanin for measuring BACE1 enzymatic activity in a high-throughput manner. Robust FRET was observed when an 18-amino-acid APP Swedish-synthetic peptide that was N-terminally labeled with europium cryptate and C-terminally biotinylated was incubated with streptavidin-coupled cross-linked allophycocyanin (SA-XL665). Purified BACE1 enzyme caused a time- and concentration-dependent linear change in FRET at low nanomolar enzyme concentrations. This assay was used to compare the autoprocessed "mature" BACE1 enzyme (sautoBACe1) and the soluble proBACE1 for activity and inhibition by selected peptidic BACE inhibitors. sautoBACE1 displayed only a modest increase in activity compared to sproBACE1 and this activity was uninhibited by the BACE1 prodomain peptide. Interestingly, the BACE1 prodomain peptide was able to partially inhibit sproBACE1 activity. IC(50s) for a P10-P4' statine BACE1 inhibitor, OM99-2, and OM-003 determined using the HTRF assay were in good agreement with those reported in the literature. The primary advantages of the HTRF-formatted BACE1 protease assay include appropriate reflection of native BACE1 activity, high sensitivity, low variability, and intrinsic quench correction afforded by ratiometric measurements made between EuK and SA-XL665 fluorophores.
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Affiliation(s)
- Matthew E Kennedy
- CNS/Cardiovascular Research, Schering Plough Research Institute, Kenilworth, NJ 07033, USA.
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268
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Mueller R, Huerzeler M, Boss C. Synthesis of Plasmepsin II Inhibitors – Potential Antimalarial Agents. Molecules 2003. [PMCID: PMC6146960 DOI: 10.3390/80700556] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A new series of plasmepsin II (PM II) inhibitors has been prepared based on 4-aminopiperidine-tert-butyl-carbamate (1). These compounds might be useful as antimalarial drugs acting via a new mechanism, and therefore be less susceptible to parasite resistance now often observed with current antimalarial therapies. Some of the final compounds prepared exhibited encouraging inhibitory activity towards PM II.
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Affiliation(s)
- Reto Mueller
- University of Applied Sciences Basel, Gründenstrasse 40, CH-4132 Muttenz, Switzerland; E-mail:
| | - Marianne Huerzeler
- University of Applied Sciences Basel, Gründenstrasse 40, CH-4132 Muttenz, Switzerland; E-mail:
| | - Christoph Boss
- Actelion Pharmaceuticals Ltd, Gewerbestrasse 16, CH-4123 Allschwil, Switzerland; Tel.: (+41)-61-487-4561; Fax: (+41)-61-487-4500
- Author to whom correspondence should be addressed; E-Mail:
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269
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Hoffmann D, Assfalg-Machleidt I, Nitschko H, von der Helm K, Koszinowski U, Machleidt W. Rapid enzymatic test for phenotypic HIV protease drug resistance. Biol Chem 2003; 384:1109-17. [PMID: 12956428 DOI: 10.1515/bc.2003.124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A phenotypic resistance test based on recombinant expression of the active HIV protease in E. coli from patient blood samples was developed. The protease is purified in a rapid one-step procedure as active enzyme and tested for inhibition by five selected synthetic inhibitors (amprenavir, indinavir, nelfinavir, ritonavir, and saquinavir) used presently for chemotherapy of HIV-infected patients. The HPLC system used in a previous approach was replaced by a continuous fluorogenic assay suitable for high-throughput screening on microtiter plates. This reduces significantly the total assay time and allows the determination of inhibition constants (Ki). The Michaelis constant (Km) and the inhibition constant (Ki) of recombinant wild-type protease agree well with published data for cloned HIV protease. The enzymatic test was evaluated with recombinant HIV protease derived from eight HIV-positive patients scored from 'sensitive' to 'highly resistant' according to mutations detected by genotypic analysis. The measured Ki values correlate well with the genotypic resistance scores, but allow a higher degree of differentiation. The non-infectious assay enables a more rapid yet sensitive detection of HIV protease resistance than other phenotypic assays.
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Affiliation(s)
- Dieter Hoffmann
- Max von Pettenkofer-Institut, Abteilung für Virologie der Ludwig-Maximilians-Universität, Pettenkoferstr. 9a, D-80336 München, Germany
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270
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Lee TG, Yeum DM. Isolation of HIV-1 Pretense Inhibiting Peptide from Thermolysin Hydrolysate of Manila Clam Proteins. Prev Nutr Food Sci 2003. [DOI: 10.3746/jfn.2003.8.2.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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271
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Abstract
Many cellular and viral processes depend on site-specific proteolysis. Here, a genetic system for the identification of such proteases and inhibitors is described. The system utilizes the temperature- sensitive Saccharomyces cerevisiae CDC25-2 mutant strain and exploits the strict requirement of membrane localization of a constitutively active Ras mutant for the complementation of the yeast growth defect at the non-permissive temperature. Expression of a fusion protein in which a substrate peptide of the TEV protease separates a myristoylation signal from a constitutively active human Ras protein confers temperature insensitivity. Co-expression of the protease results in release of the Ras mutant from the membrane and growth arrest at the non-permissive temperature. This non-transcriptional assay represents a new approach to the in vivo analysis of site-specific proteases and may be a valuable alternative to existing methods. It has significant potential for the selection of inhibitors of cytoplasmic and membrane-associated proteases of biotechnical and clinical relevance.
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Affiliation(s)
- Fabian Köhler
- Institut für Biologie III, Albert-Ludwigs-Universität, Schänzlestrasse 1, 79104 Freiburg, Germany.
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272
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273
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Gopi HN, Ravindra G, Pal PP, Pattanaik P, Balaram H, Balaram P. Proteolytic stability of beta-peptide bonds probed using quenched fluorescent substrates incorporating a hemoglobin cleavage site. FEBS Lett 2003; 535:175-8. [PMID: 12560099 DOI: 10.1016/s0014-5793(02)03885-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A set of designed internally quenched fluorescence peptide substrates has been used to probe the effects of insertion of beta-peptide bonds into peptide sequences. The test sequence chosen corresponds to a proteolytically susceptible site in hemoglobin alpha-chain, residues 32-37. Fluorescence and mass spectral measurements demonstrate that the insertion of an beta-residues at the potential cleavage sites completely abolishes the action of proteases; in addition, the rate of cleavage of the peptide bond preceding the site of modification is also considerably reduced.
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Affiliation(s)
- Hosahudya N Gopi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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274
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Saghatelian A, Guckian KM, Thayer DA, Ghadiri MR. DNA detection and signal amplification via an engineered allosteric enzyme. J Am Chem Soc 2003; 125:344-5. [PMID: 12517141 PMCID: PMC2453066 DOI: 10.1021/ja027885u] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rapid, sensitive, and sequence-specific DNA detection can be achieved in one step using an engineered intrasterically regulated enzyme. The semi-synthetic inhibitor-DNA-enzyme (IDE) construct (left) rests in the inactive state but upon exposure to a complementary DNA sequence undergoes a DNA hybridization-triggered allosteric enzyme activation (right). The ensuing rapid substrate turnover provides the built-in signal amplification mechanism for detecting approximately 10 fmol DNA in less than 3 min under physiological conditions.
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Affiliation(s)
- Alan Saghatelian
- Contribution from the Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Kevin M. Guckian
- Contribution from the Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Desiree A. Thayer
- Contribution from the Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037
| | - M. Reza Ghadiri
- Contribution from the Departments of Chemistry and Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037.
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275
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Yan ZH, Ren KJ, Wang Y, Chen S, Brock TA, Rege AA. Development of intramolecularly quenched fluorescent peptides as substrates of angiotensin-converting enzyme 2. Anal Biochem 2003; 312:141-7. [PMID: 12531198 DOI: 10.1016/s0003-2697(02)00461-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Angiotensin-converting enzyme 2 (ACE2 or ACEH) is a novel angiotensin-converting enzyme-related carboxypeptidase that cleaves a single amino acid from angiotensin I, des-Arg bradykinin, and many other bioactive peptides. Using des-Arg bradykinin as a template, we designed a series of intramolecularly quenched fluorogenic peptide substrates for ACE2. The general structure of the substrates was F-X-Q, in which F was the fluorescent group, Abz, Q was the quenching group (either Phe(NO(2)) or Tyr(NO(2))), and X was the intervening peptide. These substrates were selectively cleaved by recombinant human ACE2, as shown by MS and HPLC. Quenching efficiency increased as the peptide sequence was shortened from 8 to 3 aa, and also when Tyr(NO(2)) was used as a quenching group instead of Phe(NO(2)). Two of the optimized substrates, TBC5180 and TBC5182, produced a signal:noise ratio of better than 20 when hydrolyzed by ACE2. Kinetic measurements with ACE2 were as follows: TBC5180, K(m)=58 microM and k(cat)/K(m)=1.3x10(5)M(-1)s(-1); TBC5182, K(m)=23 microM and k(cat)/K(m)=3.5 x 10(4)M(-1)s(-1). Thus, based on hydrolysis rate, TBC5180 was a better substrate than TBC5182. However, TBC5180 was also hydrolyzed by ACE, whereas TBC5182 was not cleaved, suggesting that TBC5182 was a selective for ACE2. We conclude that these two peptides can be used as fluorescent substrates for high-throughput screening for selective inhibitors of ACE2 enzyme.
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Affiliation(s)
- Zhong-Hua Yan
- Department of Pharmacology, Texas Biotechnology Corporation, 7000 Fannin Street, Houston 77030, USA
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276
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Barrios AM, Craik CS. Scanning the prime-site substrate specificity of proteolytic enzymes: a novel assay based on ligand-enhanced lanthanide ion fluorescence. Bioorg Med Chem Lett 2002; 12:3619-23. [PMID: 12443789 DOI: 10.1016/s0960-894x(02)00786-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A novel method for assaying the substrate specificity of proteolytic enzymes has been developed utilizing ligand-enhanced lanthanide ion fluorescence. This approach was used to develop peptide libraries to probe substrate specificity in the prime sites of proteolytic enzymes. A positional scanning synthetic combinatorial library of fluorogenic peptides was synthesized and used to determine the extended prime site specificity of bovine alpha-chymotrypsin. The enzyme showed a preference for Lys and Arg in the P1' position, rather broad specificity in the P2' position, and a slight Arg specificity in the P3' position. The specificity profile of bovine alpha-chymotrypsin agrees well with previously reported data, and the substrate library reported herein should provide valuable information about the prime site substrate specificities of other proteolytic enzymes as well. Furthermore, the continuous fluorogenic assay described may prove useful in analyzing the activity of other hydrolytic enzymes.
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Affiliation(s)
- Amy M Barrios
- Department of Pharmaceutical Chemistry, University of California, San Francisco 94143, USA
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277
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Rockwell NC, Krysan DJ, Komiyama T, Fuller RS. Precursor processing by kex2/furin proteases. Chem Rev 2002; 102:4525-48. [PMID: 12475200 DOI: 10.1021/cr010168i] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nathan C Rockwell
- Department of Biological Chemistry, University of Michigan Medical Center, Room 5413 Med Sci I, 1301 East Catherine, Ann Arbor Michigan 48109, USA
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278
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Marras SAE, Kramer FR, Tyagi S. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res 2002; 30:e122. [PMID: 12409481 PMCID: PMC135848 DOI: 10.1093/nar/gnf121] [Citation(s) in RCA: 475] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An important consideration in the design of oligonucleotide probes for homogeneous hybridization assays is the efficiency of energy transfer between the fluorophore and quencher used to label the probes. We have determined the efficiency of energy transfer for a large number of combinations of commonly used fluorophores and quenchers. We have also measured the quenching effect of nucleotides on the fluorescence of each fluorophore. Quenching efficiencies were measured for both the resonance energy transfer and the static modes of quenching. We found that, in addition to their photochemical characteristics, the tendency of the fluorophore and the quencher to bind to each other has a strong influence on quenching efficiency. The availability of these measurements should facilitate the design of oligonucleotide probes that contain interactive fluorophores and quenchers, including competitive hybridization probes, adjacent probes, TaqMan probes and molecular beacons.
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279
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Iga M, Matsuda Z, Okayama A, Sugiura W, Hashida S, Morishita K, Nagai Y, Tsubouchi H. Rapid phenotypic assay for human immunodeficiency virus type 1 protease using in vitro translation. J Virol Methods 2002; 106:25-37. [PMID: 12367727 DOI: 10.1016/s0166-0934(02)00133-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A rapid in vitro phenotyping method for human immunodeficiency virus type 1 (HIV-1) protease was developed. In this system, both HIV-1 protease and substrates are prepared using a rabbit reticulocyte based coupled in vitro transcription/translation system. The activity of protease is evaluated by the amount of cleaved substrate measured by ELISA. In this system, wild-type protease derived from strain HXB2 was specifically inhibited in a dose-dependent manner by the protease inhibitors, indinavir and nelfinavir. Three drug-resistant proteases carrying a single mutation, D30N, L90M, and V82F, were analyzed in the absence of the inhibitors. Reflecting their impaired fitness, they exhibited decreased protease activity compared with the wild type. The apparent protease activity was greater for a Gag-Pol substrate encompassing the Gag-protease-reverse transcriptase junctions than for a substrate only covering the Gag region. Using the Gag-Pol substrate as the target, the indinavir-resistant mutant V82F was evaluated further. V82F showed 9-fold resistance to its cognitive protease inhibitor, indinavir; however, it manifested only moderate (2-fold) resistance to a non-cognitive inhibitor, nelfinavir. This simple and rapid method may be useful for phenotyping of drug-resistant HIV-1 protease as well as for screening new inhibitors of HIV-1 protease.
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Affiliation(s)
- Mutsunori Iga
- Department of Internal Medicine II, Miyazaki Medical College, 5200 Kihara, Kiyotake, Miyazaki 889-1601, Japan
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280
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Anderson RD, Zhou J, Hecht SM. Fluorescence resonance energy transfer between unnatural amino acids in a structurally modified dihydrofolate reductase. J Am Chem Soc 2002; 124:9674-5. [PMID: 12175203 DOI: 10.1021/ja0205939] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cleavage of a substrate protein by HIV-1 protease has been monitored in real time by the use of a dihydrofolate reductase fusion protein in which a fluorescence donor and a fluorescence acceptor were introduced into sites flanking the HIV-1 protease cleavage site. The amino acids 7-azatryptophan and dabcyl-1,2-diaminopropionic acid were introduced into specific sites of the DHFR fusion protein in an in vitro protein biosynthesizing system using two misacylated suppressor tRNAs, each of which recognized a specific, unique codon introduced into the mRNA. Excitation of the fluorescence acceptor in the initially expressed protein afforded no light production, consistent with quenching by fluorescence resonance energy transfer. Treatment of the elaborated protein with HIV-1 protease cleaved the protein between the fluorescence donor and acceptor, affording a time-dependent increase in fluorescence that was equal in magnitude to that produced by admixture of a stoichiometric amount of free 7-azatryptophan to the solution containing the intact protein.
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Affiliation(s)
- Raymond D Anderson
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, USA
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281
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Gutiérrez OA, Salas E, Hernández Y, Lissi EA, Castrillo G, Reyes O, Garay H, Aguilar A, García B, Otero A, Chavez MA, Duarte CA. An immunoenzymatic solid-phase assay for quantitative determination of HIV-1 protease activity. Anal Biochem 2002; 307:18-24. [PMID: 12137774 DOI: 10.1016/s0003-2697(02)00009-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A novel immunoenzymatic procedure for the quantitative determination of HIV protease activity is provided. An N-terminal biotinylated peptide (DU1) that comprises an HIV-1 protease (HIV-PR) cleavage sequence was bound to streptavidin-coated microtiter plates. The bound peptide can be quantified by an immunoenzymatic procedure (enzyme-linked immunosorbent assay, ELISA) that includes a monoclonal antibody (Mab 332) against the peptide (DU1) C-terminal. The incubation of the bound peptide with HIV-PR in solution resulted in a signal decrement, as the peptide was hydrolyzed and the released C-terminal segment washed away. An equation that relates the amount of added enzyme to the kinetics of the reaction was written in order to describe this heterogeneous enzyme-quasi-saturable system. This equation allows quantitative determination of protease activity, a feature widely underrated in previous similar assays. The assay also allows evaluation of the inhibitory activity of HIV-PR inhibitors. Due to the intrinsic advantages of the ELISA format, this method could be used in high-throughput screening of HIV protease inhibitors. The assay can be extended to other proteolytic enzymes.
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Affiliation(s)
- Omar A Gutiérrez
- Facultad de Biología, Centro de Estudios de la Proteínas, Universidad de la Habana, Ciudad Habana, Cuba.
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282
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Ahn T, Kim JS, Choi HI, Yun CH. Development of peptide substrates for trypsin based on monomer/excimer fluorescence of pyrene. Anal Biochem 2002; 306:247-51. [PMID: 12123662 DOI: 10.1006/abio.2002.5717] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An assay using fluorogenic peptides based on the monomer/excimer fluorescence features of pyrene was developed to measure the proteolytic activity of trypsin, a serine protease. Two pyrene moieties were incorporated into the respective N- and C-terminus of the peptides as (pyrene)-C-Xaa-C-(pyrene), where Xaa represents amino acid residues of 5-, 6-, 7-, or 8-mer containing the cleavage site of trypsin. The proteolytic cleavage of the substrates led to an increase in monomer fluorescence and a decrease in excimer fluorescence of pyrene. Kinetic parameters (k(cat) and K(m)) for the enzymatic hydrolysis of the substrates were successfully determined. The parameters are dependent on the chain length of the substrate and optimal catalytic activity was obtained with substrates that consisted of 9 or 10 amino acid residues. The present assay system is sensitive and the preparation of the substrate is very simple. We suggest that this method may be suitable for high-throughput screening and also applicable to the characterization of other proteases.
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Affiliation(s)
- Taeho Ahn
- Research Institute of Natural Science, Pai-Chai University, Taejon 302-735, Korea.
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283
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Karvinen J, Hurskainen P, Gopalakrishnan S, Burns D, Warrior U, Hemmilä I. Homogeneous time-resolved fluorescence quenching assay (LANCE) for caspase-3. JOURNAL OF BIOMOLECULAR SCREENING 2002; 7:223-31. [PMID: 12097185 DOI: 10.1177/108705710200700306] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In addition to kinases and G protein-coupled receptors, proteases are one of the main targets in modern drug discovery. Caspases and viral proteases, for instance, are potential targets for new drugs. To satisfy the current need for fast and sensitive high-throughput screening for inhibitors, new homogeneous protease assays are needed. We used a caspase-3 assay as a model to develop a homogeneous time-resolved fluorescence quenching assay technology. The assay utilizes a peptide labeled with both a luminescent europium chelate and a quencher. Cleavage of the peptide by caspase-3 separates the quencher from the chelate and thus recovers europium fluorescence. The sensitivity of the assay was 1 pg/microl for active caspase-3 and 200 pM for the substrate. We evaluated the assay for high-throughput usage by screening 9600 small-molecule compounds. We also evaluated this format for absorption/distribution/metabolism/excretion assays with cell lysates. Additionally, the assay was compared to a commercial fluorescence caspase-3 assay.
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284
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Lebon F, Boggetto N, Ledecq M, Durant F, Benatallah Z, Sicsic S, Lapouyade R, Kahn O, Mouithys-Mickalad A, Deby-Dupont G, Reboud-Ravaux M. Metal-organic compounds: a new approach for drug discovery. N1-(4-methyl-2-pyridyl)-2,3,6-trimethoxybenzamide copper(II) complex as an inhibitor of human immunodeficiency virus 1 protease. Biochem Pharmacol 2002; 63:1863-73. [PMID: 12034371 DOI: 10.1016/s0006-2952(02)00918-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The use of metal-organic complexes is a potentially fruitful approach for the development of novel enzyme inhibitors. They hold the attractive promise of forming stronger attachments with the target by combining the co-ordination ability of metals with the unique stereoelectronic properties of the ligand. We demonstrated that this approach can be successfully used to inhibit the protease of the human immunodeficiency virus (type 1). Several ligands bearing substituents designed to interact with the catalytic site of the enzyme when complexed to Cu(2+) were synthesised. The inhibition pattern of the resulting copper(II) complexes was analysed. We showed that the copper(II) complex of N1-(4-methyl-2-pyridyl)-2,3,6-trimethoxybenzamide (C1) interacts with the active site of the enzyme leading to competitive inhibition. On the other hand, N2-pyridine-amide ligands and oxazinane carboxamide ligand were found to be poor chelators of the cupric ion under the enzymatic assay conditions. In these cases, the observed inhibition was attributed to released cupric ions which react with cysteine residues on the surface of the protease. While unchelated metal cations are not likely to be useful agents, metal chelates such as C1 should be considered as promising lead compounds for the development of targeted drugs.
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Affiliation(s)
- Florence Lebon
- Facultés Universitaires Notre-Dame de la Paix, Laboratoire de Chimie Moléculaire Structurale, 61 rue de Bruxelles, 5000 Namur, Belgium
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285
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Hua DH, Tamura M, Huang X, Stephany HA, Helfrich BA, Perchellet EM, Sperfslage BJ, Perchellet JP, Jiang S, Kyle DE, Chiang PK. Syntheses and bioactivities of substituted 9,10-dihydro-9,10-[1,2]benzenoanthracene-1,4,5,8-tetrones. Unusual reactivities with amines. J Org Chem 2002; 67:2907-12. [PMID: 11975545 DOI: 10.1021/jo010958s] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A number of substituted 9,10-dihydro-9,10-[1,2]benzenoanthracene-1,4,5,8-tetrones have been synthesized and their anticancer and antimalarial activities evaluated. A one-pot synthesis of 2,5,8-trimethoxy-9,10-dihydro-9,10-[1,2]benzenoanthracene-1,4-dione (4) was achieved by heating a mixture of 1,4-dimethoxyanthracene, methoxyhydroquinone, silver oxide, and zinc iodide in toluene. Regioselective bromination of 4 and 2-methoxy-9,10-dihydro-9,10-[1,2]benzenoanthracene-1,4,5,8-tetrone (7) with N-bromosuccinimide provided 2-bromo-3,5,8-trimethoxy-9,10-dihydro-9,10-[1,2]benzenoanthracene-1,4-dione and 2-bromo-3-methoxy-9,10-dihydro-9,10-[1,2]benzenoanthracene-1,4,5,8-tetrone (1), respectively. The reactions of 1 with aliphatic primary amines and secondary amines, respectively, produced different products, a result most likely attributed to the different basicities (or nucleophilicities) and steric effects of the two kinds of amines. The structure of the displacement product, 2-bromo-3-[2-(tert-butoxycarbonyl)ethylamino]-9,10-dihydro-9,10-[1,2]benzenoanthracene-1,4,5,8-tetrone, from the reaction of 1 with tert-butyl 3-aminopropanoate was unequivocally determined by a single-crystal X-ray analysis. IC(50) values of triptycene bisquinones for the inhibition of L1210 leukemia cell viability are in the 0.11-0.27 microM range and for the inhibition of Plasmodium falciparum 3D7 are in the 4.7-8.0 microM range.
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Affiliation(s)
- Duy H Hua
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, USA.
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286
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Ha JJ, Gaul DA, Mariani VL, Ding YS, Ikeda RA, Shuker SB. HTLV-I protease cleavage of P19/24 substrates is not dependent on NaCl concentration. Bioorg Chem 2002; 30:138-44. [PMID: 12020138 DOI: 10.1006/bioo.2001.1230] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Understanding the factors that affect the activity of Human T-cell Leukemia Virus type I (HTLV-I) protease is essential for the discovery of inhibitors to be used for the treatment of HTLV-I infection, but little has been reported on the protease to date. Here we report the production of HTLV-I protease in purified yields greater than 150 mg/L, determination of its extinction coefficient, and determination of the optimum conditions for cleavage of the p19/24 substrates (DABCYL)-(GABA)-PQVL-Nph-VMH-(EDANS), (DABSYL)-(GABA)-PQVL-Nph-VMH-(EDANS), and (DABSYL)-(GABA)-PQVLPVMH-(EDANS). The highest activity was found at pH 5.2-5.3 and 37 degrees C. There was no effect on activity upon change in sodium chloride concentration from 0 to 1500 mM. The values of K(m) and k(cat) for cleavage of these substrates by the protease with and without the histidine tag were determined.
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Affiliation(s)
- Julie J Ha
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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287
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Boyer V, Fort S, Frandsen TP, Schülein M, Cottaz S, Driguez H. Chemoenzymatic synthesis of a bifunctionalized cellohexaoside as a specific substrate for the sensitive assay of cellulase by fluorescence quenching. Chemistry 2002; 8:1389-94. [PMID: 11921222 DOI: 10.1002/1521-3765(20020315)8:6<1389::aid-chem1389>3.0.co;2-#] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A new bifunctionalized cellohexaose derivative was synthesized as a specific substrate for continuous assay of cellulases by resonance energy transfer. This cellohexaoside has a naphthalene moiety (EDANS) as a fluorescent energy donor at the reducing end and a 4-(4'-dimethylaminobenzeneazo)-benzene derivative as an acceptor chromophore at the non-reducing end. The key steps for the preparation of the target molecule involved transglycosylation reactions of cellobiosyl and cellotetraosyl fluoride donors onto cellobiosyl acceptors catalysed by the E197A mutant of cellulase Cel7B from Humicola insolens. Upon digestion with various cellulases, the energy transfer was disrupted and an increase of fluorescence was observed.
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Affiliation(s)
- Viviane Boyer
- Centre de Recherches sur les Macromolécules Végétales, CERMAV-CNRS, Université Joseph Fourier B.P. 53, 38041 Grenoble cedex 9, France
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288
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Jin G, Huang X, Black R, Wolfson M, Rauch C, McGregor H, Ellestad G, Cowling R. A continuous fluorimetric assay for tumor necrosis factor-alpha converting enzyme. Anal Biochem 2002; 302:269-75. [PMID: 11878807 DOI: 10.1006/abio.2001.5549] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fluorogenic peptide substrates with fluorophore/quencher-capped ends have found extensive use in monitoring protease activity in the screening of small-molecule libraries for protease inhibitors. We report here the identification and characterization of a fluorogenic substrate for tumor necrosis factor-alpha converting enzyme (TACE). This substrate is a 10-amino-acid peptide (LAQAVRSSSR) capped with an o-aminobenzoyl group on the N-terminal end and with a 3-(2,4-dinitrophenyl)-L-2,3-diaminopropionic amide group on the C-terminal end. Exhaustive enzymatic conversion of the substrate to products resulted in a fluorescence enhancement of -11-fold. A single cleavage occurred at the A-V scissile bond of the peptide. The validity of this fluorimetric assay for TACE was corroborated by an independent HPLC method. Interestingly, the hydrolysis of the substrate displayed positive cooperativity with a Hill coefficient of 1.5, while the hydrolysis of the corresponding uncapped peptide displayed Michaelis-Menten kinetics. A k(cat) value of 21.6 s(-1) and an S(0.5) value of 342 microM were obtained for the fluorogenic substrate. The addition of the two capping groups on the two ends of the peptide enhanced the k(cat) value by 64-fold. Nine additional decapeptides that contained the same capping groups on the two ends and substitutions at the P1 and P1' sites were also tested. TACE appears to slightly prefer the A-V scissile bond. The enzyme also cleaves scissile bonds such as F-V, A-I, and A-L efficiently.
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Affiliation(s)
- Guixian Jin
- Department of Biological Chemistry, Wyeth-Ayerst Research, 401 North Middletown Road, Pearl River, New York 10965, USA
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289
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Yamaguchi K, Honda M, Ikigai H, Hara Y, Shimamura T. Inhibitory effects of (-)-epigallocatechin gallate on the life cycle of human immunodeficiency virus type 1 (HIV-1). Antiviral Res 2002; 53:19-34. [PMID: 11684313 DOI: 10.1016/s0166-3542(01)00189-9] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Epigallocatechin gallate (EGCg), the major tea catechin, is known as a potent anti-bacterial agent. In addition, anti-tumor promoting, anti-inflammatory, anti-oxidative and antiviral activities have been reported. In the present study, we investigated possible anti-human immunodeficiency virus type-1 (HIV-1) activity of EGCg and its mechanisms of action in the viral life cycle. EGCg impinges on each step of the HIV life cycle. Thus, destruction of the viral particles, viral attachment to cells, post-adsorption entry into cells, reverse transcription (RT), viral production from chronically-infected cells, and the level of expression of viral mRNA, were analyzed using T-lymphoid (H9) and monocytoid (THP-1) cell systems, and antiviral protease activity was measured using a cell-free assay. Inhibitory effects of EGCg on specific binding of the virions to the cellular surfaces and changes in the steady state viral regulation (mRNA expression) due to EGCg were not observed. However, EGCg had a destructive effect on the viral particles, and post-adsorption entry and RT in acutely infected monocytoid cells were significantly inhibited at concentrations of EGCg greater than 1 microM, and protease kinetics were suppressed at a concentration higher than 10 microM in the cell-free study. Viral production by THP-1 cells chronically-infected with HIV-1 was also inhibited in a dose-dependent manner and the inhibitory effect was enhanced by liposome modification of EGCg. As expected, increased viral mRNA production was observed in lipopolysaccharide (LPS)-activated chronically HIV-1-infected cells. This production was significantly inhibited by EGCg treatment of THP-1 cells. In contrast, production of HIV-1 viral mRNA in unstimulated or LPS-stimulated T-lymphoid cells (H9) was not inhibited by EGCg. Anti-HIV viral activity of EGCg may thus result from an interaction with several steps in the HIV-1 life cycle.
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Affiliation(s)
- Koushi Yamaguchi
- Department of Microbiology and Immunology, Showa University School of Medicine, 1-5-8, Hatanodai, Shinagawa-ku, 142-8555, Tokyo, Japan.
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290
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Bazin H, Trinquet E, Mathis G. Time resolved amplification of cryptate emission: a versatile technology to trace biomolecular interactions. J Biotechnol 2002; 82:233-50. [PMID: 11999692 DOI: 10.1016/s1389-0352(01)00040-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fluorescence resonance energy transfer (FRET) in association with a time-resolved fluorescence mode of detection was used to design a new homogeneous technology suitable to monitor biomolecular interactions. A lanthanide cryptate characterised by a long lived fluorescence emission was used as donor and a cross-linked allophycocyanine was used as acceptor. This new donor/acceptor pair displayed an exceptionally large Forster radius of 9 nm. This allowed to build up a set of labelling strategies to probe the interactions between biomolecules with an emphasis on fully indirect cassette formats particularly suitable for high throughput screening applications. Herein we describe the basics of the technology, review the latest applications to the study of molecular interactions involved in cells and new oligonucleotides based assays.
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Affiliation(s)
- H Bazin
- CIS bio international, Bagnols sur Céze, France
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291
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Boonacker E, Van Noorden CJ. Enzyme cytochemical techniques for metabolic mapping in living cells, with special reference to proteolysis. J Histochem Cytochem 2001; 49:1473-86. [PMID: 11724895 DOI: 10.1177/002215540104901201] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Specific enzymes play key roles in many pathophysiological processes and therefore are targets for therapeutic strategies. The activity of most enzymes is largely determined by many factors at the post-translational level. Therefore, it is essential to study the activity of target enzymes in living cells and tissues in a quantitative manner in relation to pathophysiological processes to understand its relevance and the potential impact of its targeting by drugs. Proteases, in particular, are crucial in every aspect of life and death of an organism and are therefore important targets. Enzyme activity in living cells can be studied with various tools. These can be endogenous fluorescent metabolites or synthetic chromogenic or fluorogenic substrates. The use of endogenous metabolites is rather limited and nonspecific because they are involved in many biological processes, but novel chromogenic and fluorogenic substrates have been developed to monitor activity of enzymes, and particularly proteases, in living cells and tissues. This review discusses these substrates and the methods in which they are applied, as well as their advantages and disadvantages for metabolic mapping in living cells.
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Affiliation(s)
- E Boonacker
- Academic Medical Center, University of Amsterdam, Department of Cell Biology and Histology, Amsterdam, The Netherlands
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292
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Abstract
Recent progress in high-throughput enzyme assays includes new examples of fluorogenic and chromogenic substrates, fluorescence resonance energy transfer substrates, and applications of the pH and pM indicator methods. Recent developments of Horeau's pseudo-enantiomer derivatisation method to screen enantioselectivities in high-throughput have also been reported.
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Affiliation(s)
- D Wahler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
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293
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Wang L, Hall JG, Lu M, Liu Q, Smith LM. A DNA computing readout operation based on structure-specific cleavage. Nat Biotechnol 2001; 19:1053-9. [PMID: 11689851 DOI: 10.1038/nbt1101-1053] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a structure-specific cleavage-based READOUT strategy for surface-based DNA computing. The strategy was demonstrated in the solution of a 4-variable/3-satisfiability (SAT) problem. The READOUT step identifies the DNA molecules present at the end of the computational process. The specificity of the sequence detection used here derives from the sequence specificity of DNA hybridization coupled with the structure specificity of the enzymatic cleavage. The process is linear, yielding a higher uniformity of detection of the DNA computing products compared to that obtained with PCR amplification. The structure-specific cleavage-based readout is simple, accurate, and compatible with multiple-word DNA computing.
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Affiliation(s)
- L Wang
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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294
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Todd MJ, Gomez J. Enzyme kinetics determined using calorimetry: a general assay for enzyme activity? Anal Biochem 2001; 296:179-87. [PMID: 11554713 DOI: 10.1006/abio.2001.5218] [Citation(s) in RCA: 233] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two techniques for determining enzyme kinetic constants using isothermal titration microcalorimetry are presented. The methods are based on the proportionality between the rate of a reaction and the thermal power (heat/time) generated. (i) An enzyme can be titrated with increasing amounts of substrate, while pseudo-first-order conditions are maintained. (ii) Following a single injection, the change in thermal power as substrate is depleted can be continuously monitored. Both methods allow highly precise kinetic characterization in a single experiment and can be used to measure enzyme inhibition. Applicability is demonstrated using a representative enzyme from each EC classification, including (i) oxidation-reduction activity of DHFR (EC 1.5.1.3); (ii) transferase activity of creatine phosphokinase (EC 2.7.3.2) and hexokinase (EC 2.7.1.1); (iii) hydrolytic activity of Helicobacter pylori urease (EC 3.5.1.5), trypsin (EC 3.4.21.4), and the HIV-1 protease (EC 3.4.21.16); (iv) lyase activity of heparinase (EC 4.1.1.7); and (v) ligase activity of pyruvate carboxylate (EC 6.4.1.1). This nondestructive method is completely general, enabling precise analysis of reactions in spectroscopically opaque solutions, using physiological substrates. Such a universal assay may have wide applicability in functional genomics.
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Affiliation(s)
- M J Todd
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA.
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295
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Bazin H, Préaudat M, Trinquet E, Mathis G. Homogeneous time resolved fluorescence resonance energy transfer using rare earth cryptates as a tool for probing molecular interactions in biology. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2001; 57:2197-2211. [PMID: 11603838 DOI: 10.1016/s1386-1425(01)00493-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A homogeneous assay technology using time resolved fluorescence and fluorescence resonance energy transfer is described. A new class of fluorescent complexes, the cryptates, have been used as fluorescent donor with cross-linked allophycocyanin as acceptor. This new donor/acceptor shows an exceptionally high Förster distance R0 of 9 nm. This allows to build up a set of strategies to probe the interactions of biomolecules in biology, particularly for high throughput screening applications. In this article, we describe the basics of the technology and review applications developed for studying different key molecular interactions involved in cellular processes.
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Affiliation(s)
- H Bazin
- CIS Bio International, Bagnols sur Céze, France
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296
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Lindsten K, Uhlíková T, Konvalinka J, Masucci MG, Dantuma NP. Cell-based fluorescence assay for human immunodeficiency virus type 1 protease activity. Antimicrob Agents Chemother 2001; 45:2616-22. [PMID: 11502538 PMCID: PMC90701 DOI: 10.1128/aac.45.9.2616-2622.2001] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) protease is essential for production of infectious virus and is therefore a major target for the development of drugs against AIDS. Cellular proteins are also cleaved by the protease, which explains its cytotoxic activity and the consequent failure to establish convenient cell-based protease assays. We have exploited this toxicity to develop a new protease assay that relies on transient expression of an artificial protease precursor harboring the green fluorescent protein (GFP-PR). The precursor is activated in vivo by autocatalytic cleavage, resulting in rapid elimination of protease-expressing cells. Treatment with therapeutic doses of HIV-1 protease inhibitors results in a dose-dependent accumulation of the fluorescent precursor that can be easily detected and quantified by flow cytometric and fluorimetric assays. The precursor provides a convenient and noninfectious model for high-throughput screenings of substances that can interfere with the activity of the protease in living cells.
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Affiliation(s)
- K Lindsten
- Microbiology and Tumor Biology Center, Karolinska Institutet, S-171 77 Stockholm, Sweden
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297
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Jiang S, Prigge ST, Wei L, Hudson TH, Gerena L, Dame JB, Kyle DE. New class of small nonpeptidyl compounds blocks Plasmodium falciparum development in vitro by inhibiting plasmepsins. Antimicrob Agents Chemother 2001; 45:2577-84. [PMID: 11502532 PMCID: PMC90695 DOI: 10.1128/aac.45.9.2577-2584.2001] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Malarial parasites rely on aspartic proteases called plasmepsins to digest hemoglobin during the intraerythrocytic stage. Plasmepsins from Plasmodium falciparum and Plasmodium vivax have been cloned and expressed for a variety of structural and enzymatic studies. Recombinant plasmepsins possess kinetic similarity to the native enzymes, indicating their suitability for target-based antimalarial drug development. We developed an automated assay of P. falciparum plasmepsin II and P. vivax plasmepsin to quickly screen compounds in the Walter Reed chemical database. A low-molecular-mass (346 Da) diphenylurea derivative (WR268961) was found to inhibit plasmepsins with a K(i) of 1 to 6 microM. This compound appears to be selective for plasmepsin, since it is a poor inhibitor of the human aspartic protease cathepsin D (K(i) greater than 280 microM). WR268961 inhibited the growth of P. falciparum strains W2 and D6, with 50% inhibitory concentrations ranging from 0.03 to 0.16 microg/ml, but was much less toxic to mammalian cells. The Walter Reed chemical database contains over 1,500 compounds with a diphenylurea core structure, 9 of which inhibit the plasmepsins, with K(i) values ranging from 0.05 to 0.68 microM. These nine compounds show specificity for the plasmepsins over human cathepsin D, but they are poor inhibitors of P. falciparum growth in vitro. Computational docking experiments indicate how diphenylurea compounds bind to the plasmepsin active site and inhibit the enzyme.
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Affiliation(s)
- S Jiang
- Department of Parasitology, Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910-7500, USA.
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298
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Ilangovan U, Ton-That H, Iwahara J, Schneewind O, Clubb RT. Structure of sortase, the transpeptidase that anchors proteins to the cell wall of Staphylococcus aureus. Proc Natl Acad Sci U S A 2001; 98:6056-61. [PMID: 11371637 PMCID: PMC33421 DOI: 10.1073/pnas.101064198] [Citation(s) in RCA: 235] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2001] [Indexed: 01/30/2023] Open
Abstract
Surface proteins of Gram-positive bacteria play important roles during the pathogenesis of human infections and require sortase for anchoring to the cell-wall envelope. Sortase cleaves surface proteins at the LPXTG motif and catalyzes the formation of an amide bond between the carboxyl group of threonine (T) and the amino group of cell-wall crossbridges. The NMR structure of sortase reveals a unique beta-barrel structure, in which the active-site sulfhydryl of cysteine-184 is poised for ionization by histidine-120, presumably enabling the resultant thiolate to attack the LPXTG peptide. Calcium binding near the active site stimulates catalysis, possibly by altering the conformation of a surface loop that recognizes newly translocated polypeptides. The structure suggests a mechanistic relationship to the papain/cathepsin proteases and should facilitate the design of new antiinfective agents.
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Affiliation(s)
- U Ilangovan
- Department of Chemistry and Biochemistry and University of California at Los Angeles, CA 90095, USA
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299
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300
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