51
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Affiliation(s)
| | - Marina Gobbo
- Department of Chemical SciencesUniversity of PadovaPadova35131 Italy
- Institute of Biomolecular Chemistry of CNR, Padova UnitPadova35131 Italy
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52
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Si Y, Bai Y, Qin X, Li J, Zhong W, Xiao Z, Li J, Yin Y. Alkyne–DNA-Functionalized Alloyed Au/Ag Nanospheres for Ratiometric Surface-Enhanced Raman Scattering Imaging Assay of Endonuclease Activity in Live Cells. Anal Chem 2018; 90:3898-3905. [DOI: 10.1021/acs.analchem.7b04735] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yanmei Si
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
| | - Yaocai Bai
- Department of Chemistry, University of California—Riverside, Riverside, California 92521, United States
| | - Xiaojie Qin
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
| | - Jun Li
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
| | - Wenwan Zhong
- Department of Chemistry, University of California—Riverside, Riverside, California 92521, United States
| | - Zhijun Xiao
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
| | - Jishan Li
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha 410082, China
| | - Yadong Yin
- Department of Chemistry, University of California—Riverside, Riverside, California 92521, United States
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53
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Synthesis of fluorescent molecularly imprinted nanoparticles for turn-on fluorescence assay using one-pot synthetic method and a preliminary microfluidic approach. POLYMER 2018. [DOI: 10.1016/j.polymer.2018.01.086] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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54
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Kempf O, Kempf K, Schobert R, Bombarda E. Hydrodabcyl: A Superior Hydrophilic Alternative to the Dark Fluorescence Quencher Dabcyl. Anal Chem 2017; 89:11893-11897. [DOI: 10.1021/acs.analchem.7b03488] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Oxana Kempf
- Department
of Biochemistry and ‡Organic Chemistry Laboratory, University of Bayreuth, Universitaetsstrasse
30, 95440, Bayreuth, Germany
| | - Karl Kempf
- Department
of Biochemistry and ‡Organic Chemistry Laboratory, University of Bayreuth, Universitaetsstrasse
30, 95440, Bayreuth, Germany
| | - Rainer Schobert
- Department
of Biochemistry and ‡Organic Chemistry Laboratory, University of Bayreuth, Universitaetsstrasse
30, 95440, Bayreuth, Germany
| | - Elisa Bombarda
- Department
of Biochemistry and ‡Organic Chemistry Laboratory, University of Bayreuth, Universitaetsstrasse
30, 95440, Bayreuth, Germany
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55
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Bozóki B, Gazda L, Tóth F, Miczi M, Mótyán JA, Tőzsér J. A recombinant fusion protein-based, fluorescent protease assay for high throughput-compatible substrate screening. Anal Biochem 2017; 540-541:52-63. [PMID: 29122614 DOI: 10.1016/j.ab.2017.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 11/25/2022]
Abstract
In connection with the intensive investigation of proteases, several methods have been developed for analysis of the substrate specificity. Due to the great number of proteases and the expected target molecules to be analyzed, time- and cost-efficient high-throughput screening (HTS) methods are preferred. Here we describe the development and application of a separation-based HTS-compatible fluorescent protease assay, which is based on the use of recombinant fusion proteins as substrates of proteases. The protein substrates used in this assay consists of N-terminal (hexahistidine and maltose binding protein) fusion tags, cleavage sequences of the tobacco etch virus (TEV) and HIV-1 proteases, and a C-terminal fluorescent protein (mApple or mTurquoise2). The assay is based on the fluorimetric detection of the fluorescent proteins, which are released from the magnetic bead-attached substrates by the proteolytic cleavage. The protease assay has been applied for activity measurements of TEV and HIV-1 proteases to test the suitability of the system for enzyme kinetic measurements, inhibition studies, and determination of pH optimum. We also found that denatured fluorescent proteins can be renatured after SDS-PAGE of denaturing conditions, but showed differences in their renaturation abilities. After in-gel renaturation both substrates and cleavage products can be identified by in-gel UV detection.
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Affiliation(s)
- Beáta Bozóki
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Biotechnological Analytical Department, Gedeon Richter Plc, 19-21, Gyömrői Rd., Budapest H-1103, Hungary.
| | - Lívia Gazda
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - Ferenc Tóth
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - Márió Miczi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
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56
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Funicello M, Chiummiento L, Tramutola F, Armentano M, Bisaccia F, Miglionico R, Milella L, Benedetti F, Berti F, Lupattelli P. Synthesis and biological evaluation in vitro and in mammalian cells of new heteroaryl carboxyamides as HIV-protease inhibitors. Bioorg Med Chem 2017; 25:4715-4722. [DOI: 10.1016/j.bmc.2017.07.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 11/16/2022]
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57
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Evolution of inhibitor-resistant natural mutant forms of HIV-1 protease probed by pre-steady state kinetic analysis. Biochimie 2017; 142:125-134. [PMID: 28843613 DOI: 10.1016/j.biochi.2017.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/21/2017] [Indexed: 11/23/2022]
Abstract
Pre-steady state kinetic analysis of mechanistic features of substrate binding and processing is crucial for insight into the evolution of inhibitor-resistant forms of HIV-1 protease. These data may provide a correct vector for rational drug design assuming possible intrinsic dynamic effects. These data should also give some clues to the molecular mechanism of protease action and resistance to inhibitors. Here we report pre-steady state kinetics of the interaction of wild type or mutant forms of HIV-1 protease with a FRET-labeled peptide. The three-stage "minimal" kinetic scheme with first and second reversible steps of substrate binding and with following irreversible peptide cleavage step adequately described experimental data. For the first time, a set of "elementary" kinetic parameters of wild type HIV-1 protease and its natural mutant inhibitor-resistant forms MDR-HM, ANAM-11 and prDRV4 were compared. Inhibitors of the first and second generation were used to estimate the inhibitory effects on HIV-1 protease activity. The resulting set of kinetic data supported that the mutant forms are kinetically unaffected by inhibitors of the first generation, proving their functional resistance to these compounds. The second generation inhibitor darunavir inhibited mutant forms MDR-HM and ANAM-11, but was ineffective against prDRV4. Our kinetic data revealed that these inhibitors induced different conformational changes in the enzyme and, thereby they have different mode of binding in the enzyme active site. These data confirmed hypothesis that the driving force of the inhibitor-resistance evolution is disruption of enzyme-inhibitor complex by changing of the contact network in the inhibitor binding site.
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58
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Nagy-Smith K, Beltramo PJ, Moore E, Tycko R, Furst EM, Schneider JP. Molecular, Local, and Network-Level Basis for the Enhanced Stiffness of Hydrogel Networks Formed from Coassembled Racemic Peptides: Predictions from Pauling and Corey. ACS CENTRAL SCIENCE 2017; 3:586-597. [PMID: 28691070 PMCID: PMC5492410 DOI: 10.1021/acscentsci.7b00115] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Indexed: 05/20/2023]
Abstract
Hydrogels prepared from self-assembling peptides are promising materials for medical applications, and using both l- and d-peptide isomers in a gel's formulation provides an intuitive way to control the proteolytic degradation of an implanted material. In the course of developing gels for delivery applications, we discovered that a racemic mixture of the mirror-image β-hairpin peptides, named MAX1 and DMAX1, provides a fibrillar hydrogel that is four times more rigid than gels formed by either peptide alone-a puzzling observation. Herein, we use transmission electron microscopy, small angle neutron scattering, solid state NMR, diffusing wave, infrared, and fluorescence spectroscopies, and modeling to determine the molecular basis for the increased mechanical rigidity of the racemic gel. We find that enantiomeric peptides coassemble in an alternating fashion along the fibril long axis, forming an extended heterochiral pleat-like β-sheet, a structure predicted by Pauling and Corey in 1953. Hydrogen bonding between enantiomers within the sheet dictates the placement of hydrophobic valine side chains in the fibrils' dry interior in a manner that allows the formation of nested hydrophobic interactions between enantiomers, interactions not accessible within enantiomerically pure fibrils. Importantly, this unique molecular arrangement of valine side chains maximizes inter-residue contacts within the core of the fibrils resulting in their local stiffening, which in turn, gives rise to the significant increase in bulk mechanical rigidity observed for the racemic hydrogel.
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Affiliation(s)
- Katelyn Nagy-Smith
- Chemical
Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
- Department of Chemistry and Biochemistry and Department of Chemical
and Biomolecular
Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Peter J. Beltramo
- Department of Chemistry and Biochemistry and Department of Chemical
and Biomolecular
Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Eric Moore
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
| | - Robert Tycko
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892-0520, United States
| | - Eric M. Furst
- Department of Chemistry and Biochemistry and Department of Chemical
and Biomolecular
Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Joel P. Schneider
- Chemical
Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States
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59
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Sawyer N, Watkins AM, Arora PS. Protein Domain Mimics as Modulators of Protein-Protein Interactions. Acc Chem Res 2017; 50:1313-1322. [PMID: 28561588 DOI: 10.1021/acs.accounts.7b00130] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Protein-protein interactions (PPIs) are ubiquitous in biological systems and often misregulated in disease. As such, specific PPI modulators are desirable to unravel complex PPI pathways and expand the number of druggable targets available for therapeutic intervention. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets. This Account describes our systematic approach using secondary and tertiary protein domain mimics (PDMs) to specifically modulate PPIs. Our strategy focuses on mimicry of regular secondary and tertiary structure elements from one of the PPI partners to inspire rational PDM design. We have compiled three databases (HIPPDB, SIPPDB, and DIPPDB) of secondary and tertiary structures at PPI interfaces to guide our designs and better understand the energetics of PPI secondary and tertiary structures. Our efforts have focused on three of the most common secondary and tertiary structures: α-helices, β-strands, and helix dimers (e.g., coiled coils). To mimic α-helices, we designed the hydrogen bond surrogate (HBS) as an isosteric PDM and the oligooxopiperazine helix mimetic (OHM) as a topographical PDM. The nucleus of the HBS approach is a peptide macrocycle in which the N-terminal i, i + 4 main-chain hydrogen bond is replaced with a covalent carbon-carbon bond. In mimicking a main-chain hydrogen bond, the HBS approach stabilizes the α-helical conformation while leaving all helical faces available for functionalization to tune binding affinity and specificity. The OHM approach, in contrast, envisions a tetrapeptide to mimic one face of a two-turn helix. We anticipated that placement of ethylene bridges between adjacent amides constrains the tetrapeptide backbone to mimic the i, i + 4, and i + 7 side chains on one face of an α-helix. For β-strands, we developed triazolamers, a topographical PDM where the peptide bonds are replaced by triazoles. The triazoles simultaneously stabilize the extended, zigzag conformation of β-strands and transform an otherwise ideal protease substrate into a stable molecule by replacement of the peptide bonds. We turned to a salt bridge surrogate (SBS) approach as a means for stabilizing very short helix dimers. As with the HBS approach, the SBS strategy replaces a noncovalent interaction with a covalent bond. Specifically, we used a bis-triazole linkage that mimics a salt bridge interaction to drive helix association and folding. Using this approach, we were able to stabilize helix dimers that are less than half of the length required to form a coiled coil from two independent strands. In addition to demonstrating the stabilization of desired structures, we have also shown that our designed PDMs specifically modulate target PPIs in vitro and in vivo. Examples of PPIs successfully targeted include HIF1α/p300, p53/MDM2, Bcl-xL/Bak, Ras/Sos, and HIV gp41. The PPI databases and designed PDMs created in these studies will aid development of a versatile set of molecules to probe complex PPI functions and, potentially, PPI-based therapeutics.
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Affiliation(s)
- Nicholas Sawyer
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Andrew M. Watkins
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
| | - Paramjit S. Arora
- Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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60
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Cecioni S, Vocadlo DJ. Carbohydrate Bis-acetal-Based Substrates as Tunable Fluorescence-Quenched Probes for Monitoring exo-Glycosidase Activity. J Am Chem Soc 2017. [PMID: 28631482 DOI: 10.1021/jacs.7b01948] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tunable Förster resonance energy transfer (FRET)-quenched substrates are useful for monitoring the activity of various enzymes within their relevant physiological environments. Development of FRET-quenched substrates for exo-glycosidases, however, has been hindered by their constrained pocket-shaped active sites. Here we report the design of a new class of substrate that overcomes this problem. These Bis-Acetal-Based Substrates (BABS) bear a hemiacetal aglycon leaving group that tethers fluorochromes in close proximity, also positioning them distant from the active site pocket. Following cleavage of the glycosidic bond, the liberated hemiacetal spontaneously breaks down, leading to separation of the fluorophore and quencher. We detail the synthesis and characterization of GlcNAc-BABS, revealing a striking 99.9% quenching efficiency. These substrates are efficiently turned over by the human exo-glycosidase O-GlcNAcase (OGA). We find the hemiacetal leaving group rapidly breaks down, enabling quantitative monitoring of OGA activity. We expect this strategy to be broadly useful for the development of substrate probes for monitoring exo-glycosidases, as well as a range of other enzymes having constrained pocket-shaped active sites.
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Affiliation(s)
- Samy Cecioni
- Department of Chemistry, Simon Fraser University , Burnaby, British Columbia, Canada
| | - David J Vocadlo
- Department of Chemistry, Simon Fraser University , Burnaby, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University , Burnaby, British Columbia, Canada
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61
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Bai X, Yang Z, Zhu M, Dong B, Zhou L, Zhang G, Wang J, Wang Y. Design and synthesis of potent HIV-1 protease inhibitors with (S)-tetrahydrofuran-tertiary amine-acetamide as P2-ligand: Structure-activity studies and biological evaluation. Eur J Med Chem 2017; 137:30-44. [PMID: 28554091 DOI: 10.1016/j.ejmech.2017.05.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 10/19/2022]
Abstract
The design, synthesis, and SAR study of a new series of HIV-1 protease inhibitors incorporating stereochemically defined tetrahydrofuran-tertiary amine-acetamide P2-ligand are described. Various substituent effects on the tertiary amine P2-ligand and phenylsulfonamide P2'-ligand were investigated to maximize the ligand-binding site interactions in the protease active site. Most of inhibitors displayed low nanomolar to subnanomolar inhibitory potency. Inhibitor 20e containing N-(S-tetrahydrofuran)-N-(2-methoxyethyl)acetamide as P2-ligand along with 4-methoxylphenylsulfonamide as P2'-ligand displayed the most potent enzyme inhibitory activity (IC50 = 0.35 nM) and remarkably low cytotoxicity (CC50 = 305 μM).
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Affiliation(s)
- Xiaoguang Bai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Zhiheng Yang
- Department of Pharmacy, The First Affiliated Hospital, Zhengzhou University, Zhengzhou 450052, China
| | - Mei Zhu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Biao Dong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Lei Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Guoning Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China
| | - Juxian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
| | - Yucheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Science and Peking Union Medical College, Beijing 100050, China.
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62
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Al-Abdullah IH, Bagramyan K, Bilbao S, Qi M, Kalkum M. Fluorogenic Peptide Substrate for Quantification of Bacterial Enzyme Activities. Sci Rep 2017; 7:44321. [PMID: 28287171 PMCID: PMC5347087 DOI: 10.1038/srep44321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/06/2017] [Indexed: 12/18/2022] Open
Abstract
A novel peptide substrate (A G G P L G P P G P G G) was developed for quantifying the activities of bacterial enzymes using a highly sensitive Fluorescence Resonance Energy Transfer (FRET) based assay. The peptide substrate was cleaved by collagenase class I, II, Liberase MTF C/T, collagenase NB1, and thermolysin/neutral protease, which was significantly enhanced in the presence of CaCl2. However, the activities of these enzymes were significantly decreased in the presence of ZnSO4 or ZnCl2. Collagenase I, II, Liberase MTF C/T, thermolysin/neutral protease share similar cleavage sites, L↓G and P↓G. However, collagenase NB1 cleaves the peptide substrate at G↓P and P↓L, in addition to P↓G. The enzyme activity is pH dependent, within a range of 6.8 to 7.5, but was significantly diminished at pH 8.0. Interestingly, the peptide substrate was not cleaved by endogenous pancreatic protease such as trypsin, chymotrypsin, and elastase. In conclusion, the novel peptide substrate is collagenase, thermolysin/neutral protease specific and can be applied to quantify enzyme activities from different microbes. Furthermore, the assay can be used for fine-tuning reaction mixtures of various agents to enhance the overall activity of a cocktail of multiple enzymes and achieve optimal organ/tissue digestion, while protecting the integrity of the target cells.
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Affiliation(s)
- Ismail H. Al-Abdullah
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, USA
| | - Karine Bagramyan
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, USA
| | - Shiela Bilbao
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, USA
| | - Meirigeng Qi
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, USA
| | - Markus Kalkum
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, USA
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63
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Onagi J, Komatsu T, Ichihashi Y, Kuriki Y, Kamiya M, Terai T, Ueno T, Hanaoka K, Matsuzaki H, Hata K, Watanabe T, Nagano T, Urano Y. Discovery of Cell-Type-Specific and Disease-Related Enzymatic Activity Changes via Global Evaluation of Peptide Metabolism. J Am Chem Soc 2017; 139:3465-3472. [PMID: 28191944 DOI: 10.1021/jacs.6b11376] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Cellular homeostasis is maintained by a complex network of reactions catalyzed by enormous numbers of enzymatic activities (the enzymome), which serve to determine the phenotypes of cells. Here, we focused on the enzymomics of proteases and peptidases because these enzymes are an important class of disease-related proteins. We describe a system that (A) simultaneously evaluates metabolic activities of peptides using a series of exogenous peptide substrates and (B) identifies the enzymes that metabolize the specified peptide substrate with high throughput. We confirmed that the developed system was able to discover cell-type-specific and disease-related exo- and endopeptidase activities and identify the responsible enzymes. For example, we found that the activity of the endopeptidase neurolysin is highly elevated in human colorectal tumor tissue samples. This simple but powerful enzymomics platform should be widely applicable to uncover cell-type-specific reactions and altered enzymatic functions with potential value as biomarkers or drug targets in various disease states and to investigate the mechanisms of the underlying pathologies.
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Affiliation(s)
| | - Toru Komatsu
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | | | | | - Mako Kamiya
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST) , 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | | | | | | | | | | | | | | | - Yasuteru Urano
- Core Research for Evolutional Science and Technology (CREST) Investigator, Japan Agency for Medical Research and Development (AMED) , 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
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64
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Göksel M, Durmuş M, Atilla D. Synthesis and photophysicochemical properties of a set of asymmetrical peptide conjugated zinc(II) phthalocyanines bearing different fluorophore units. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.10.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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65
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Conte MP, Lau KHA, Ulijn RV. Biocatalytic Self-Assembly Using Reversible and Irreversible Enzyme Immobilization. ACS APPLIED MATERIALS & INTERFACES 2017; 9:3266-3271. [PMID: 28080020 DOI: 10.1021/acsami.6b13162] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Biocatalytic control of molecular self-assembly provides an effective approach for developing smart biomaterials, allowing versatile enzyme-mediated tuning of material structure and properties as well as enabling biomedical applications. We functionalized surfaces with bioinspired polydopamine and polyphenol coatings to study the effects of enzyme surface localization and surface release on the self-assembly process. We show how these coatings could be conveniently used to release enzymes for bulk gelation as well as to irreversibly immobilize enzymes for localizing the self-assembly to the surface. The results provide insights to the mode of action of biocatalytic self-assembly relevant to nanofabrication and enzyme-responsive materials.
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Affiliation(s)
- M P Conte
- WestCHEM/Department of Pure & Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - K H A Lau
- WestCHEM/Department of Pure & Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - R V Ulijn
- WestCHEM/Department of Pure & Applied Chemistry, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
- Advanced Science Research Center (ASRC), City University of New York , 85 St Nicholas Terrace, New York, New York 10027, United States
- Department of Chemistry and Biochemistry, City University of New York-Hunter College , 695 Park Avenue, New York, New York 10065, United States
- PhD Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York , New York, New York 10016, United States
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66
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Wei T, Furgal JC, Jung JH, Scott TF. Long, self-assembled molecular ladders by cooperative dynamic covalent reactions. Polym Chem 2017. [DOI: 10.1039/c6py01951j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The dynamic covalent self-assembly of peptoid-based oligomers bearing n complementary functional groups yields molecular ladders with n covalent rungs.
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Affiliation(s)
- Tao Wei
- Department of Chemical Engineering
- University of Michigan
- Ann Arbor
- USA
| | - Joseph C. Furgal
- Department of Chemical Engineering
- University of Michigan
- Ann Arbor
- USA
| | - Jae Hwan Jung
- Macromolecular Science and Engineering
- University of Michigan
- Ann Arbor
- USA
| | - Timothy F. Scott
- Department of Chemical Engineering
- University of Michigan
- Ann Arbor
- USA
- Macromolecular Science and Engineering
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67
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Castro E, Martinez ZS, Seong CS, Cabrera-Espinoza A, Ruiz M, Hernandez Garcia A, Valdez F, Llano M, Echegoyen L. Characterization of New Cationic N,N-Dimethyl[70]fulleropyrrolidinium Iodide Derivatives as Potent HIV-1 Maturation Inhibitors. J Med Chem 2016; 59:10963-10973. [PMID: 28002960 DOI: 10.1021/acs.jmedchem.6b00994] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
HIV-1 maturation can be impaired by altering protease (PR) activity, the structure of the Gag-Pol substrate, or the molecular interactions of viral structural proteins. Here we report the synthesis and characterization of new cationic N,N-dimethyl[70]fulleropyrrolidinium iodide derivatives that inhibit more than 99% of HIV-1 infectivity at low micromolar concentrations. Analysis of the HIV-1 life cycle indicated that these compounds inhibit viral maturation by impairing Gag and Gag-Pol processing. Importantly, fullerene derivatives 2a-c did not inhibit in vitro PR activity and strongly interacted with HIV immature capsid protein in pull-down experiments. Furthermore, these compounds potently blocked infectivity of viruses harboring mutant PR that are resistant to multiple PR inhibitors or mutant Gag proteins that confer resistance to the maturation inhibitor Bevirimat. Collectively, our studies indicate fullerene derivatives 2a-c as potent and novel HIV-1 maturation inhibitors.
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Affiliation(s)
- Edison Castro
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Zachary S Martinez
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Chang-Soo Seong
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Andrea Cabrera-Espinoza
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Mauro Ruiz
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Andrea Hernandez Garcia
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
| | - Federico Valdez
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Manuel Llano
- Department of Biological Sciences, University of Texas at El Paso , 500 West University Avenue, El Paso, Texas 79968, United States
| | - Luis Echegoyen
- Department of Chemistry, University of Texas at El Paso , 500 West University Avenue, CCSB #3.0302, El Paso, Texas 79968, United States
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Design and Validation of Novel Chikungunya Virus Protease Inhibitors. Antimicrob Agents Chemother 2016; 60:7382-7395. [PMID: 27736770 DOI: 10.1128/aac.01421-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/20/2016] [Indexed: 11/20/2022] Open
Abstract
Chikungunya virus (CHIKV; genus Alphavirus) is the causative agent of chikungunya fever. CHIKV replication can be inhibited by some broad-spectrum antiviral compounds; in contrast, there is very little information about compounds specifically inhibiting the enzymatic activities of CHIKV replication proteins. These proteins are translated in the form of a nonstructural (ns) P1234 polyprotein precursor from the CHIKV positive-strand RNA genome. Active forms of replicase enzymes are generated using the autoproteolytic activity of nsP2. The available three-dimensional (3D) structure of nsP2 protease has made it a target for in silico drug design; however, there is thus far little evidence that the designed compounds indeed inhibit the protease activity of nsP2 and/or suppress CHIKV replication. In this study, a set of 12 compounds, predicted to interact with the active center of nsP2 protease, was designed using target-based modeling. The majority of these compounds were shown to inhibit the ability of nsP2 to process recombinant protein and synthetic peptide substrates. Furthermore, all compounds found to be active in these cell-free assays also suppressed CHIKV replication in cell culture, the 50% effective concentration (EC50) of the most potent inhibitor being ∼1.5 μM. Analysis of stereoisomers of one compound revealed that inhibition of both the nsP2 protease activity and CHIKV replication depended on the conformation of the inhibitor. Combining the data obtained from different assays also indicates that some of the analyzed compounds may suppress CHIKV replication using more than one mechanism.
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69
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Mallidi S, Anbil S, Bulin AL, Obaid G, Ichikawa M, Hasan T. Beyond the Barriers of Light Penetration: Strategies, Perspectives and Possibilities for Photodynamic Therapy. Theranostics 2016; 6:2458-2487. [PMID: 27877247 PMCID: PMC5118607 DOI: 10.7150/thno.16183] [Citation(s) in RCA: 227] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/01/2016] [Indexed: 12/20/2022] Open
Abstract
Photodynamic therapy (PDT) is a photochemistry based treatment modality that involves the generation of cytotoxic species through the interactions of a photosensitizer molecule with light irradiation of an appropriate wavelength. PDT is an approved therapeutic modality for several cancers globally and in several cases has proved to be effective where traditional treatments have failed. The key parameters that determine PDT efficacy are 1. the photosensitizer (nature of the molecules, selectivity, and macroscopic and microscopic localization etc.), 2. light application (wavelength, fluence, fluence rate, irradiation regimes etc.) and 3. the microenvironment (vascularity, hypoxic regions, stromal tissue density, molecular heterogeneity etc.). Over the years, several groups aimed to monitor and manipulate the components of these critical parameters to improve the effectiveness of PDT treatments. However, PDT is still misconstrued to be a surface treatment primarily due to the limited depths of light penetration. In this review, we present the recent advances, strategies and perspectives in PDT approaches, particularly in cancer treatment, that focus on increasing the 'damage zone' beyond the reach of light in the body. This is enabled by a spectrum of approaches that range from innovative photosensitizer excitation strategies, increased specificity of phototoxicity, and biomodulatory approaches that amplify the biotherapeutic effects induced by photodynamic action. Along with the increasing depth of understanding of the underlying physical, chemical and physiological mechanisms, it is anticipated that with the convergence of these strategies, the clinical utility of PDT will be expanded to a powerful modality in the armamentarium for the management of cancer.
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Affiliation(s)
- Srivalleesha Mallidi
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114
| | - Sriram Anbil
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815
- The University of Texas School of Medicine at San Antonio, San Antonio, TX 78229
| | - Anne-Laure Bulin
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114
| | - Girgis Obaid
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114
| | - Megumi Ichikawa
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114
| | - Tayyaba Hasan
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114
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70
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Suchý M, Ettles C, Wisner JA, Matarazzo A, Hudson RHE. Unusual C7- versus Normal 5′-O-Dimethoxytritylation of 6-Arylpyrrolocytidine Analogs. J Org Chem 2016; 81:8415-25. [DOI: 10.1021/acs.joc.6b01584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Mojmír Suchý
- Department
of Chemistry and ‡The Centre for Advanced Materials and Biomaterials
Research, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Christie Ettles
- Department
of Chemistry and ‡The Centre for Advanced Materials and Biomaterials
Research, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - James A. Wisner
- Department
of Chemistry and ‡The Centre for Advanced Materials and Biomaterials
Research, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Augusto Matarazzo
- Department
of Chemistry and ‡The Centre for Advanced Materials and Biomaterials
Research, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Robert H. E. Hudson
- Department
of Chemistry and ‡The Centre for Advanced Materials and Biomaterials
Research, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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71
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Matrix Metalloproteinases in the Interstitial Space. Protein Sci 2016. [DOI: 10.1201/9781315374307-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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72
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Chuang EY, Lin CC, Chen KJ, Wan DH, Lin KJ, Ho YC, Lin PY, Sung HW. A FRET-guided, NIR-responsive bubble-generating liposomal system for in vivo targeted therapy with spatially and temporally precise controlled release. Biomaterials 2016; 93:48-59. [DOI: 10.1016/j.biomaterials.2016.03.040] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 03/07/2016] [Accepted: 03/28/2016] [Indexed: 11/26/2022]
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73
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Cozens R, Bold G, Capraro HG, Fässler A, Mestan J, Lang M, Poncioni B, Stover D, Rösel J. Synthesis and Pharmacological Evaluation of CGP 57813 and CGP 61755, HIV-1 Protease Inhibitors from the Phe-c-Phe Peptidomimetic Class. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029600700602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this report we describe the enzyme inhibitory, antiviral and pharmacokinetic properties of CGP 57813 and CGP 61755, structural analogues of CGP 53437 that were synthesized in an attempt to obtain human immunodeficiency virus type 1 (HIV-1) protease inhibitors with improved selectivity and oral bioavailability. CGP 57813 inhibited HIV-1 protease with an IC50 of 11 nM (similar to CGP 53437). CGP 61755, on the other hand, was c.a. 10-fold more potent (IC50 = 1 nM; similar to saquinavir and indinavir). The selectivity profile of CGP 57813 was comparable to that of CGP 53437 while CGP 61755 clearly had improved selectivity for HIV-1 protease over human aspartic proteases. All three compounds had similar antiviral activity in HIV-1/MN infected MT-2 cells; ED50s were c.a. 5 nM and ED90s were 30 nM. Compared to CGP 53437, both CGP 57813 and CGP 61755 had markedly better bioavailability in mice after oral administration in a DMSO-hydroxypropyl-β-cyclodextrin formulation. However, when CGP 57813 was administered in a sesame oil-based formulation to either mice or dogs no useful plasma concentrations could be measured. In contrast, CGP 61755 was clearly bioavailable in dogs after oral administration of the compound in the same formulation; 1.2 g per dog resulted in a mean AUC0-8 h = 21.06 ± 3.53 μM.h, a mean Cmax = 4.8 ± 0.52 μM and compound was detectable for at least 8 h after administration. The potent antiviral activity of CGP 61755 together with improved selectivity and oral bioavailability holds promise for efficacy in AIDS therapy.
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Affiliation(s)
- R.M. Cozens
- Ciba, Pharmaceutical Division, Research Department Cancer and Infectious Diseases, CH 4002 Basel, Switzerland
| | - G. Bold
- Ciba, Pharmaceutical Division, Research Department Cancer and Infectious Diseases, CH 4002 Basel, Switzerland
| | - H-G. Capraro
- Ciba, Pharmaceutical Division, Research Department Cancer and Infectious Diseases, CH 4002 Basel, Switzerland
| | - A. Fässler
- Ciba, Pharmaceutical Division, Research Department Cancer and Infectious Diseases, CH 4002 Basel, Switzerland
| | - J. Mestan
- Ciba, Pharmaceutical Division, Research Department Cancer and Infectious Diseases, CH 4002 Basel, Switzerland
| | - M. Lang
- Ciba, Pharmaceutical Division, Research Department Cancer and Infectious Diseases, CH 4002 Basel, Switzerland
| | - B. Poncioni
- Ciba, Pharmaceutical Division, Research Department Cancer and Infectious Diseases, CH 4002 Basel, Switzerland
| | - D. Stover
- Ciba, Pharmaceutical Division, Research Department Cancer and Infectious Diseases, CH 4002 Basel, Switzerland
| | - J.L. Rösel
- Ciba, Pharmaceutical Division, Research Department Cancer and Infectious Diseases, CH 4002 Basel, Switzerland
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74
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Wang QM, Johnson RB, Cohen JD, Voy GT, Richardson JM, Jungheim LN. Development of a Continuous Fluorescence Assay for Rhinovirus 14 3C Protease Using Synthetic Peptides. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029700800402] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Rhinovirus 3C protease is an attractive target for therapeutic intervention owing to its important role in virion maturation and infectivity. In order to facilitate the identification of potential 3C protease inhibitors, we have developed a continuous fluorescence assay using 5-[(2-aminoethyl)amino]naphthalene-1-sulphonic acid (Edans) as a fluorescent donor and 4-(4-dimethylaminophenylazo)benzoic acid (Dabcyl) as a quenching acceptor. Several fluorogenic peptide substrates for 3C protease were synthesized by both solution chemistry and solid phase peptide synthesis. One of the synthetic Edans/Dabcyl substrates, with an amino acid sequence derived from the 2C/3A site of the virus polyprotein, yielded a 24-fold increase in fluorescence intensity after 3C cleavage. Data regarding substrate cleavage kinetics, assay sensitivity and optimization are presented. The application of this assay to the evaluation of 3C protease inhibitors is also shown.
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Affiliation(s)
- QM Wang
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - RB Johnson
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - JD Cohen
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - GT Voy
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - JM Richardson
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | - LN Jungheim
- Infectious Diseases Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
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75
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Billich A, Billich S, Rosenwirth B. Assay Systems for HIV-1 Proteinase and Their Use for Evaluation of Inhibitors. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029100200201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- A. Billich
- Sandoz Forschungsinstitut GmbH, Department of AntiRetroviral Therapy, Brunnerstr. 59, A-1235 Vienna, Austria
| | - S. Billich
- Sandoz Forschungsinstitut GmbH, Department of AntiRetroviral Therapy, Brunnerstr. 59, A-1235 Vienna, Austria
| | - B. Rosenwirth
- Sandoz Forschungsinstitut GmbH, Department of AntiRetroviral Therapy, Brunnerstr. 59, A-1235 Vienna, Austria
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76
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Samizadeh M, Zhang X, Gunaseelan S, Nelson AG, Palombo MS, Myers DR, Singh Y, Ganapathi U, Szekely Z, Sinko PJ. Colorectal delivery and retention of PEG-Amprenavir-Bac7 nanoconjugates--proof of concept for HIV mucosal pre-exposure prophylaxis. Drug Deliv Transl Res 2016; 6:1-16. [PMID: 26712122 DOI: 10.1007/s13346-015-0269-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Local delivery of anti-HIV drugs to the colorectal mucosa, a major site of HIV replication, and their retention within mucosal tissue would allow for a reduction in dose administered, reduced dosing frequency and minimal systemic exposure. The current report describes a mucosal pre-exposure prophylaxis (mPrEP) strategy that utilizes nanocarrier conjugates (NC) consisting of poly(ethylene glycol) (PEG), amprenavir (APV), and a cell-penetrating peptide (CPP; namely Bac7, a fragment derived from bactenecin 7). APV-PEG NCs with linear PEGs (2, 5, 10, and 30 kDa) exhibited reduced (52-21%) anti-HIV-1 protease (PR) activity as compared to free APV in an enzyme-based FRET assay. In MT-2 T cells, APV-PEG3.4 kDa-FITC (APF) anti-HIV-1 activity was significantly reduced (160-fold, IC50 = 8064 nM) due to poor cell uptake, whereas it was restored (IC50 = 78.29 nM) and similar to APV (IC50 = 50.29 nM) with the addition of Bac7 to the NC (i.e., APV-PEG3.4 kDa-Bac7, APB). Flow cytometry and confocal microscopy demonstrated Bac7-PEG3.4 kDa-FITC (BPF) uptake was two- and fourfold higher than APF in MT-2 T cells and Caco-2 intestinal epithelial cells, respectively. There was no detectable punctate fluorescence in either cell line suggesting that BPF directly enters the cytosol thus avoiding endosomal entrapment. After colorectal administration in mice, BPF mucosal concentrations were 21-fold higher than APF concentrations. BPF concentrations also remained constant for the 5 days of the study suggesting that (1) the NC's structural characteristics (i.e., the size of the PEG carrier and the presence of a CPP) significantly influenced tissue persistence, and (2) the NCs were probably lodged in the lamina propria since the average rodent colon mucosal cell turnover time is 2-3 days. These encouraging results suggest that Bac7 functionalized NCs delivered locally to the colorectal mucosa may form drug delivery depots that are capable of sustaining colorectal drug concentrations. Although the exact mechanisms for tissue persistence are unclear and will require further study, these results provide proof-of-concept feasibility for mPrEP.
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Affiliation(s)
- Mahta Samizadeh
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Xiaoping Zhang
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Simi Gunaseelan
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Antoinette G Nelson
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Matthew S Palombo
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Daniel R Myers
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Yashveer Singh
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Usha Ganapathi
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Zoltan Szekely
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA
| | - Patrick J Sinko
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ, 08854, USA.
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77
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Gandhi S, Arami H, Krishnan KM. Detection of Cancer-Specific Proteases Using Magnetic Relaxation of Peptide-Conjugated Nanoparticles in Biological Environment. NANO LETTERS 2016; 16:3668-3674. [PMID: 27219521 DOI: 10.1021/acs.nanolett.6b00867] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protease expression is closely linked to malignant phenotypes of different solid tumors; as such, their detection is promising for diagnosis and treatment of cancers, Alzheimer's, and vascular diseases. Here, we describe a new method for detecting proteases by sensitively monitoring the magnetic relaxation of monodisperse iron oxide nanoparticles (IONPs) using magnetic particle spectrometer (MPS). In this assay, tailored peptides functioning as activatable nanosensors link magnetic nanoparticles and possess selective sites that are recognizeable and cleaveable by specific proteases. When these linker peptides, labeled with biotin at N- and C-terminals, are added to the neutravidin functionalized IONPs, nanoparticles aggregate, resulting in well-defined changes in the MPS signal. However, as designed, in the presence of proteases these peptides are cleaved at predetermined sites, redispersing IONPs, and returning the MPS signal(s) close to its preaggregation state. These changes observed in all aspects of the MPS signal (peak intensity, its position as a function of field amplitude, and full width at half-maximum-when combined, these three also eliminate false positives), help to detect specific proteases, relying only on the magnetic relaxation characteristics of the functionalized nanoparticles. We demonstrate the general utility of this assay by detecting one each from the two general classes of proteases: trypsin (digestive serine protease, involved in various cancers, promoting proliferation, invasion, and metastasis) and matrix metalloproteinase (MMP-2, observed through metastasis and tumor angiogenesis). This MPS based protease-assay is rapid, reproducible, and highly sensitive and can form the basis of a feasible, high-throughput method for detection of various other proteases.
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Affiliation(s)
- Sonu Gandhi
- Materials Science & Engineering Department, University of Washington , Seattle, Washington 98195-2120 United States
| | - Hamed Arami
- Materials Science & Engineering Department, University of Washington , Seattle, Washington 98195-2120 United States
| | - Kannan M Krishnan
- Materials Science & Engineering Department, University of Washington , Seattle, Washington 98195-2120 United States
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78
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Ye G, Deng F, Shen Z, Luo R, Zhao L, Xiao S, Fu ZF, Peng G. Structural basis for the dimerization and substrate recognition specificity of porcine epidemic diarrhea virus 3C-like protease. Virology 2016; 494:225-35. [PMID: 27128350 PMCID: PMC7111274 DOI: 10.1016/j.virol.2016.04.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 04/14/2016] [Accepted: 04/15/2016] [Indexed: 01/16/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus, has caused significant damage to the Asian and American pork industries. Coronavirus 3C-like protease (3CLpro), which is involved in the processing of viral polyproteins for viral replication, is an appealing antiviral drug target. Here, we present the crystal structures of PEDV 3CLpro and a molecular complex between an inactive PEDV 3CLpro variant C144A bound to a peptide substrate. Structural characterization, mutagenesis and biochemical analysis reveal the substrate-binding pockets and the residues that comprise the active site of PEDV 3CLpro. The dimerization of PEDV 3CLpro is similar to that of other Alphacoronavirus 3CLpros but has several differences from that of SARS-CoV 3CLpro from the genus Betacoronavirus. Furthermore, the non-conserved motifs in the pockets cause different cleavage of substrate between PEDV and SARS-CoV 3CLpros, which may provide new insights into the recognition of substrates by 3CLpros in various coronavirus genera. The substrate binding mechanism of PEDV 3CLpro has been characterized. The large buried surface area is responsible for dimerization of PEDV 3CLpro. Non-conserved motifs cause different cleavage between PEDV and SARS-CoV 3CLpros.
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Affiliation(s)
- Gang Ye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Feng Deng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhou Shen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ling Zhao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China; The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China.
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79
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Sloniec-Myszk J, Resch-Genger U, Hennig A. Chiral, J-Aggregate-Forming Dyes for Alternative Signal Modulation Mechanisms in Self-Immolative Enzyme-Activatable Optical Probes. J Phys Chem B 2016; 120:877-85. [DOI: 10.1021/acs.jpcb.5b10526] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jagoda Sloniec-Myszk
- BAM Federal Institute
for Materials Research and Testing, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
| | - Ute Resch-Genger
- BAM Federal Institute
for Materials Research and Testing, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
| | - Andreas Hennig
- BAM Federal Institute
for Materials Research and Testing, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
- Department
of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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80
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Dunyak BM, Nakamura RL, Frankel AD, Gestwicki JE. Selective Targeting of Cells via Bispecific Molecules That Exploit Coexpression of Two Intracellular Proteins. ACS Chem Biol 2015; 10:2441-7. [PMID: 26322864 DOI: 10.1021/acschembio.5b00426] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In drug discovery, small molecules must often discriminate between healthy and diseased cells. This feat is usually accomplished by binding to a protein that is preferentially expressed in the target cell or on its surface. However, in many cases, the expression of an individual protein may not generate sufficient cyto-selectivity. Here, we demonstrate that bispecific molecules can better discriminate between similar cell types by exploiting their simultaneous affinity for two proteins. Inspired by the natural product FK506, we designed molecules that have affinity for both FKBP12 and HIV protease. Using cell-based reporters and live virus assays, we observed that these compounds preferentially accumulated in cells that express both targets, mimicking an infected lymphocyte. Treatment with FKBP12 inhibitors reversed this partitioning, while overexpression of FKBP12 protein further promoted it. The partitioning into the target cell type could be tuned by controlling the properties of the linker and the affinities for the two proteins. These results show that bispecific molecules create significantly better potential for cyto-selectivity, which might be especially important in the development of safe and effective antivirals and anticancer compounds.
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Affiliation(s)
| | - Robert L. Nakamura
- Advanced Genetic Systems, San Francisco, California 94158, United States
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81
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Cheng KCC, Cao S, Raveh A, MacArthur R, Dranchak P, Chlipala G, Okoneski MT, Guha R, Eastman RT, Yuan J, Schultz PJ, Su XZ, Tamayo-Castillo G, Matainaho T, Clardy J, Sherman DH, Inglese J. Actinoramide A Identified as a Potent Antimalarial from Titration-Based Screening of Marine Natural Product Extracts. JOURNAL OF NATURAL PRODUCTS 2015; 78:2411-2422. [PMID: 26465675 PMCID: PMC4633019 DOI: 10.1021/acs.jnatprod.5b00489] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Methods to identify the bioactive diversity within natural product extracts (NPEs) continue to evolve. NPEs constitute complex mixtures of chemical substances varying in structure, composition, and abundance. NPEs can therefore be challenging to evaluate efficiently with high-throughput screening approaches designed to test pure substances. Here we facilitate the rapid identification and prioritization of antimalarial NPEs using a pharmacologically driven, quantitative high-throughput-screening (qHTS) paradigm. In qHTS each NPE is tested across a concentration range from which sigmoidal response, efficacy, and apparent EC50s can be used to rank order NPEs for subsequent organism reculture, extraction, and fractionation. Using an NPE library derived from diverse marine microorganisms we observed potent antimalarial activity from two Streptomyces sp. extracts identified from thousands tested using qHTS. Seven compounds were isolated from two phylogenetically related Streptomyces species: Streptomyces ballenaensis collected from Costa Rica and Streptomyces bangulaensis collected from Papua New Guinea. Among them we identified actinoramides A and B, belonging to the unusually elaborated nonproteinogenic amino-acid-containing tetrapeptide series of natural products. In addition, we characterized a series of new compounds, including an artifact, 25-epi-actinoramide A, and actinoramides D, E, and F, which are closely related biosynthetic congeners of the previously reported metabolites.
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Affiliation(s)
- Ken Chih-Chien Cheng
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Shugeng Cao
- Department of Pharmaceutical Sciences, Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI 96720, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, C-643, Boston, Massachusetts 021151, USA
| | - Avi Raveh
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Ryan MacArthur
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Patricia Dranchak
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - George Chlipala
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Matthew T. Okoneski
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
- Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Rajarshi Guha
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
| | - Richard T. Eastman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20852, USA
| | - Jing Yuan
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20852, USA
| | - Pamela J. Schultz
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - Xin-zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20852, USA
| | - Giselle Tamayo-Castillo
- Unidad Estrategica de Bioprospección, Instituto Nacional de Biodiversidad (INBio), Santo Domingo de Heredia, Costa Rica & CIPRONA-Escuela de Química, Universidad de Costa Rica, 2060 San Pedro, Costa Rica
| | - Teatulohi Matainaho
- School of Medicine and Health Sciences, University of Papua New Guinea, Boroko, Papua New Guinea
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, C-643, Boston, Massachusetts 021151, USA
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, USA
- Departments of Medicinal Chemistry, Chemistry, Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109-2216, USA
| | - James Inglese
- National Center of Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850
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82
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Herpoldt KL, Artzy-Schnirman A, Christofferson AJ, Makarucha AJ, de la Rica R, Yarovsky I, Stevens MM. Designing Fluorescent Peptide Sensors with Dual Specificity for the Detection of HIV-1 Protease. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2015; 27:7187-7195. [PMID: 28479671 PMCID: PMC5419500 DOI: 10.1021/acs.chemmater.5b03651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
HIV-1 protease is a key enzyme in the life cycle of HIV/AIDS, as it is responsible for the formation of the mature virus particle. We demonstrate here that phage-display peptides raised against this enzyme can be used as peptide sensors for the detection of HIV-1 protease in a simple, one-pot assay. The presence of the enzyme is detected through an energy transfer between two peptide sensors when simultaneously complexed with the target protein. The multivalent nature of this assay increases the specificity of the detection by requiring all molecules to be interacting in order for there to be a FRET signal. We also perform molecular dynamics simulations to explore the interaction between the protease and the peptides in order to guide the design of these peptide sensors and to understand the mechanisms which cause these simultaneous binding events. This approach aims to facilitate the development of new assays for enzymes that are not dependent on the cleavage of a substrate and do not require multiple washing steps.
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Affiliation(s)
- Karla-Luise Herpoldt
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
| | - Arbel Artzy-Schnirman
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
| | | | - Adam J. Makarucha
- Health Innovations Research Institute, RMIT University, GPO Box 2476, Victoria 3001, Australia
| | - Roberto de la Rica
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
| | - Irene Yarovsky
- Health Innovations Research Institute, RMIT University, GPO Box 2476, Victoria 3001, Australia
| | - Molly M. Stevens
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
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83
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Viral Polymerase-Helicase Complexes Regulate Replication Fidelity To Overcome Intracellular Nucleotide Depletion. J Virol 2015; 89:11233-44. [PMID: 26311883 PMCID: PMC4645662 DOI: 10.1128/jvi.01553-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/20/2015] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED To date, the majority of work on RNA virus replication fidelity has focused on the viral RNA polymerase, while the potential role of other viral replicase proteins in this process is poorly understood. Previous studies used resistance to broad-spectrum RNA mutagens, such as ribavirin, to identify polymerases with increased fidelity that avoid misincorporation of such base analogues. We identified a novel variant in the alphavirus viral helicase/protease, nonstructural protein 2 (nsP2) that operates in concert with the viral polymerase nsP4 to further alter replication complex fidelity, a functional linkage that was conserved among the alphavirus genus. Purified chikungunya virus nsP2 presented delayed helicase activity of the high-fidelity enzyme, and yet purified replication complexes manifested stronger RNA polymerization kinetics. Because mutagenic nucleoside analogs such as ribavirin also affect intracellular nucleotide pools, we addressed the link between nucleotide depletion and replication fidelity by using purine and pyrimidine biosynthesis inhibitors. High-fidelity viruses were more resistant to these conditions, and viral growth could be rescued by the addition of exogenous nucleosides, suggesting that mutagenesis by base analogues requires nucleotide pool depletion. This study describes a novel function for nsP2, highlighting the role of other components of the replication complex in regulating viral replication fidelity, and suggests that viruses can alter their replication complex fidelity to overcome intracellular nucleotide-depleting conditions. IMPORTANCE Previous studies using the RNA mutagen ribavirin to select for drug-resistant variants have highlighted the essential role of the viral RNA-dependent RNA polymerase in regulating replication fidelity. However, the role of other viral replicase components in replication fidelity has not been studied in detail. We identified here an RNA mutagen-resistant variant of the nsP2 helicase/protease that conferred increased fidelity and yet could not operate in the same manner as high-fidelity polymerases. We show that the alphavirus helicase is a key component of the fidelity-regulating machinery. Our data show that the RNA mutagenic activity of compounds such as ribavirin is coupled to and potentiated by nucleotide depletion and that RNA viruses can fine-tune their replication fidelity when faced with an intracellular environment depleted of nucleotides.
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84
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Fluorogenic Assay for Inhibitors of HIV-1 Protease with Sub-picomolar Affinity. Sci Rep 2015; 5:11286. [PMID: 26261098 PMCID: PMC4531283 DOI: 10.1038/srep11286] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/14/2015] [Indexed: 11/17/2022] Open
Abstract
A fluorogenic substrate for HIV-1 protease was designed and used as the basis for a hypersensitive assay. The substrate exhibits a kcat of 7.4 s−1, KM of 15 μM, and an increase in fluorescence intensity of 104-fold upon cleavage, thus providing sensitivity that is unmatched in a continuous assay of HIV-1 protease. These properties enabled the enzyme concentration in an activity assay to be reduced to 25 pM, which is close to the Kd value of the protease dimer. By fitting inhibition data to Morrison’s equation, Ki values of amprenavir, darunavir, and tipranavir were determined to be 135, 10, and 82 pM, respectively. This assay, which is capable of measuring Ki values as low as 0.25 pM, is well-suited for characterizing the next generation of HIV-1 protease inhibitors.
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85
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Majerle A, Gaber R, Benčina M, Jerala R. Function-based mutation-resistant synthetic signaling device activated by HIV-1 proteolysis. ACS Synth Biol 2015; 4:667-72. [PMID: 25393958 PMCID: PMC4487218 DOI: 10.1021/sb5002483] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
![]()
The
high mutation rate of the human immunodeficiency virus type
1 (HIV-1) virus is a major problem since it evades the function of
antibodies and chemical inhibitors. Here, we demonstrate a viral detection
strategy based on synthetic biology principles to detect a specific
viral function rather than a particular viral protein. The resistance
caused by mutations can be circumvented since the mutations that cause
the loss of function also incapacitate the virus. Many pathogens encode
proteases that are essential for their replication and that have a
defined substrate specificity. A genetically encoded sensor composed
of a fused membrane anchor, viral protease target site, and an orthogonal
transcriptional activator was engineered into a human cell line. The
HIV-1 protease released the transcriptional activator from the membrane,
thereby inducing transcription of the selected genes. The device was
still strongly activated by clinically relevant protease mutants that
are resistant to protease inhibitors. In the future, a similar principle
could be applied to detect also other pathogens and functions.
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Affiliation(s)
- Andreja Majerle
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
| | - Rok Gaber
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
| | - Mojca Benčina
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
| | - Roman Jerala
- Laboratory
of Biotechnology, National Institute of Chemistry, Hajdrihova
19, 1000 Ljubljana, Slovenia
- EN-FIST Centre
of Excellence, Trg OF 13, 1000 Ljubljana, Slovenia
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86
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Plattner S, Gruber C, Stadlmann J, Widmann S, Gruber CW, Altmann F, Bohlmann H. Isolation and Characterization of a Thionin Proprotein-processing Enzyme from Barley. J Biol Chem 2015; 290:18056-18067. [PMID: 26013828 DOI: 10.1074/jbc.m115.647859] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Indexed: 01/17/2023] Open
Abstract
Thionins are plant-specific antimicrobial peptides that have been isolated from the endosperm and leaves of cereals, from the leaves of mistletoes, and from several other plant species. They are generally basic peptides with three or four disulfide bridges and a molecular mass of ~5 kDa. Thionins are produced as preproproteins consisting of a signal peptide, the thionin domain, and an acidic domain. Previously, only mature thionin peptides have been isolated from plants, and in addition to removal of the signal peptide, at least one cleavage processing step between the thionin and the acidic domain is necessary to release the mature thionin. In this work, we identified a thionin proprotein-processing enzyme (TPPE) from barley. Purification of the enzyme was guided by an assay that used a quenched fluorogenic peptide comprising the amino acid sequence between the thionin and the acidic domain of barley leaf-specific thionin. The barley TPPE was identified as a serine protease (BAJ93208) and expressed in Escherichia coli as a strep tag-labeled protein. The barley BTH6 thionin proprotein was produced in E. coli using the vector pETtrx1a and used as a substrate. We isolated and sequenced the BTH6 thionin from barley to confirm the N and C terminus of the peptide in planta. Using an in vitro enzymatic assay, the recombinant TPPE was able to process the quenched fluorogenic peptide and to cleave the acidic domain at least at six sites releasing the mature thionin from the proprotein. Moreover, it was found that the intrinsic three-dimensional structure of the BTH6 thionin domain prevents cleavage of the mature BTH6 thionin by the TPPE.
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Affiliation(s)
- Stephan Plattner
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, A-1190 Vienna
| | - Clemens Gruber
- Department of Chemistry, University of Natural Resources and Life Sciences, A-1190 Vienna
| | - Johannes Stadlmann
- Department of Chemistry, University of Natural Resources and Life Sciences, A-1190 Vienna
| | - Stefan Widmann
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, A-1190 Vienna
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, University of Natural Resources and Life Sciences, A-1190 Vienna
| | - Holger Bohlmann
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, A-1190 Vienna.
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87
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Hacker SM, Hintze C, Marx A, Drescher M. Monitoring enzymatic ATP hydrolysis by EPR spectroscopy. Chem Commun (Camb) 2015; 50:7262-4. [PMID: 24872080 DOI: 10.1039/c4cc02422b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An adenosine triphosphate (ATP) analogue modified with two nitroxide radicals is developed and employed to study its enzymatic hydrolysis by electron paramagnetic resonance spectroscopy. For this application, we demonstrate that EPR holds the potential to complement fluorogenic substrate analogues in monitoring enzymatic activity.
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Affiliation(s)
- Stephan M Hacker
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
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88
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Yang ZH, Bai XG, Zhou L, Wang JX, Liu HT, Wang YC. Synthesis and biological evaluation of novel HIV-1 protease inhibitors using tertiary amine as P2-ligands. Bioorg Med Chem Lett 2015; 25:1880-3. [PMID: 25838144 DOI: 10.1016/j.bmcl.2015.03.047] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 03/13/2015] [Accepted: 03/17/2015] [Indexed: 11/29/2022]
Abstract
A series of tertiary amine derivatives exhibiting potent HIV-1 protease inhibiting properties were identified. These novel inhibitors were designed based on the structure of Darunavir with modification on the P2 and P2' position. This effort led to discovery of 35e and 38e, which exhibited excellent HIV-1 protease inhibition with IC50 values of 15 nM and 64 nM, respectively.
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Affiliation(s)
- Zhi-Heng Yang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Xiao-Guang Bai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Lei Zhou
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Ju-Xian Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China
| | - Hong-Tao Liu
- Department of Pharmacy, Hebei General Hospital, Hebei, Shijiazhuang 050051, PR China
| | - Yu-Cheng Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, PR China.
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89
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Jensen JL, Jacobsen J, Moss ML, Rasmussen F, Qvist KB, Larsen S, van den Brink JM. The function of the milk-clotting enzymes bovine and camel chymosin studied by a fluorescence resonance energy transfer assay. J Dairy Sci 2015; 98:2853-60. [PMID: 25726113 DOI: 10.3168/jds.2014-8672] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 01/14/2015] [Indexed: 11/19/2022]
Abstract
Enzymatic coagulation of bovine milk can be divided in 2 steps: an enzymatic step, in which the Phe105-Met106 bond of the milk protein bovine κ-casein is cleaved, and an aggregation step. The aspartic peptidases bovine and camel chymosin (EC 3.4.23.4) are typically used to catalyze the enzymatic step. The most commonly used method to study chymosin activity is the relative milk-clotting activity test that measures the end point of the enzymatic and aggregation step. This method showed that camel chymosin has a 2-fold higher milk-clotting activity toward bovine milk than bovine chymosin. To enable a study of the enzymatic step independent of the aggregation step, a fluorescence resonance energy transfer assay has been developed using a peptide substrate derived from the 98-108 sequence of bovine κ-casein. This assay and Michaelis-Menten kinetics were employed to determine the enzymatic activity of camel and bovine chymosin under milk clotting-like conditions (pH 6.65, ionic strength 80 mM). The results obtained show that the catalytic efficiency of camel chymosin is 3-fold higher than bovine chymosin. The substrate affinity and catalytic activity of bovine and camel chymosin increase at lower pH (6.00 and 5.50). The glycosylation of bovine and camel chymosin did not affect binding of the fluorescence resonance energy transfer substrate, but doubly glycosylated camel chymosin seems to have slightly higher catalytic efficiency. In the characterization of the enzymes, the developed assay is easier and faster to use than the traditionally used relative milk-clotting activity test method.
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Affiliation(s)
- Jesper Langholm Jensen
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark; Chr. Hansen a/s, Bøge allé 10-12, DK-2970 Hørsholm, Denmark
| | - Jonas Jacobsen
- Chr. Hansen a/s, Bøge allé 10-12, DK-2970 Hørsholm, Denmark
| | | | | | | | - Sine Larsen
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark
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90
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Meng J, Lai MT, Munshi V, Grobler J, McCauley J, Zuck P, Johnson EN, Uebele VN, Hermes JD, Adam GC. Screening of HIV-1 Protease Using a Combination of an Ultra-High-Throughput Fluorescent-Based Assay and RapidFire Mass Spectrometry. ACTA ACUST UNITED AC 2015; 20:606-15. [PMID: 25681434 DOI: 10.1177/1087057115570838] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/12/2015] [Indexed: 12/19/2022]
Abstract
HIV-1 protease (PR) represents one of the primary targets for developing antiviral agents for the treatment of HIV-infected patients. To identify novel PR inhibitors, a label-free, high-throughput mass spectrometry (HTMS) assay was developed using the RapidFire platform and applied as an orthogonal assay to confirm hits identified in a fluorescence resonance energy transfer (FRET)-based primary screen of > 1 million compounds. For substrate selection, a panel of peptide substrates derived from natural processing sites for PR was evaluated on the RapidFire platform. As a result, KVSLNFPIL, a new substrate measured to have a ~ 20- and 60-fold improvement in k cat/K m over the frequently used sequences SQNYPIVQ and SQNYPIV, respectively, was identified for the HTMS screen. About 17% of hits from the FRET-based primary screen were confirmed in the HTMS confirmatory assay including all 304 known PR inhibitors in the set, demonstrating that the HTMS assay is effective at triaging false-positives while capturing true hits. Hence, with a sampling rate of ~7 s per well, the RapidFire HTMS assay enables the high-throughput evaluation of peptide substrates and functions as an efficient tool for hits triage in the discovery of novel PR inhibitors.
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Affiliation(s)
- Juncai Meng
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Ming-Tain Lai
- Department of Infectious Disease, Merck Research Labs, West Point, PA, USA
| | - Vandna Munshi
- Department of Infectious Disease, Merck Research Labs, West Point, PA, USA
| | - Jay Grobler
- Department of Infectious Disease, Merck Research Labs, West Point, PA, USA
| | - John McCauley
- Medicinal Chemistry, Merck Research Labs, West Point, PA, USA
| | - Paul Zuck
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Eric N Johnson
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA Wuxi Apptech
| | - Victor N Uebele
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Jeffrey D Hermes
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
| | - Gregory C Adam
- Screening and Protein Sciences, Merck Research Labs, North Wales, PA, USA
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91
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Briciu-Burghina C, Heery B, Regan F. Continuous fluorometric method for measuring β-glucuronidase activity: comparative analysis of three fluorogenic substrates. Analyst 2015. [DOI: 10.1039/c5an01021g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A new continuous fluorometric method for measuring GUS activity shows a superior analytical performance to the established discontinuous method.
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Affiliation(s)
- Ciprian Briciu-Burghina
- Marine and Environmental Sensing Technology Hub (MESTECH)
- National Centre for Sensor Research (NCSR)
- School of Chemical Sciences
- Dublin City University
- Dublin
| | - Brendan Heery
- Marine and Environmental Sensing Technology Hub (MESTECH)
- National Centre for Sensor Research (NCSR)
- School of Chemical Sciences
- Dublin City University
- Dublin
| | - Fiona Regan
- Marine and Environmental Sensing Technology Hub (MESTECH)
- National Centre for Sensor Research (NCSR)
- School of Chemical Sciences
- Dublin City University
- Dublin
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92
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Zhang H, Yu D, Zhao Y, Fan A. Turn-on chemiluminescent sensing platform for label-free protease detection using streptavidin-modified magnetic beads. Biosens Bioelectron 2014; 61:45-50. [DOI: 10.1016/j.bios.2014.04.050] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/18/2014] [Accepted: 04/26/2014] [Indexed: 11/24/2022]
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93
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Sreenath K, Yi C, Knappenberger KL, Zhu L. Distinguishing Förster Resonance Energy Transfer and solvent-mediated charge-transfer relaxation dynamics in a zinc(II) indicator: a femtosecond time-resolved transient absorption spectroscopic study. Phys Chem Chem Phys 2014; 16:5088-92. [PMID: 24504046 DOI: 10.1039/c3cp55382e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A bifluorophoric molecule (1) capable of intramolecular Förster Resonance Energy Transfer (FRET) is reported. The emission intensity of the FRET acceptor in 1 depends on the molar absorptivity of the donor, which is a function of zinc(II) complexation. The FRET dynamics of [Zn(1)](ClO4)2 is characterized by femtosecond time-resolved transient absorption spectroscopy. The solvent-mediated relaxation of the charge-transfer (CT) state of the isolated donor and the FRET process of the donor–acceptor conjugate are on similar time scales (40–50 ps in CH3CN), but distinguishable by the opposite solvent polarity dependency. As the solvent polarity increases, the efficiency of Columbic-based FRET is reduced, whereas CT relaxation is accelerated. In addition to revealing a method to distinguish CT and FRET dynamics, this work provides a photophysical foundation for developing indicators based on the FRET strategy.
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Affiliation(s)
- Kesavapillai Sreenath
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, USA.
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94
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Li J, Wang X, Liang X. Modification of Nucleic Acids by Azobenzene Derivatives and Their Applications in Biotechnology and Nanotechnology. Chem Asian J 2014; 9:3344-58. [DOI: 10.1002/asia.201402758] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 01/29/2023]
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95
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Donahue EH, Dawson LF, Valiente E, Firth-Clark S, Major MR, Littler E, Perrior TR, Wren BW. Clostridium difficile has a single sortase, SrtB, that can be inhibited by small-molecule inhibitors. BMC Microbiol 2014; 14:219. [PMID: 25183427 PMCID: PMC4155245 DOI: 10.1186/s12866-014-0219-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/12/2014] [Indexed: 01/05/2023] Open
Abstract
Background Bacterial sortases are transpeptidases that covalently anchor surface proteins to the peptidoglycan of the Gram-positive cell wall. Sortase protein anchoring is mediated by a conserved cell wall sorting signal on the anchored protein, comprising of a C-terminal recognition sequence containing an “LPXTG-like” motif, followed by a hydrophobic domain and a positively charged tail. Results We report that Clostridium difficile strain 630 encodes a single sortase (SrtB). A FRET-based assay was used to confirm that recombinant SrtB catalyzes the cleavage of fluorescently labelled peptides containing (S/P)PXTG motifs. Strain 630 encodes seven predicted cell wall proteins with the (S/P)PXTG sorting motif, four of which are conserved across all five C. difficile lineages and include potential adhesins and cell wall hydrolases. Replacement of the predicted catalytic cysteine residue at position 209 with alanine abolishes SrtB activity, as does addition of the cysteine protease inhibitor MTSET to the reaction. Mass spectrometry reveals the cleavage site to be between the threonine and glycine residues of the (S/P)PXTG peptide. Small-molecule inhibitors identified through an in silico screen inhibit SrtB enzymatic activity to a greater degree than MTSET. Conclusions These results demonstrate for the first time that C. difficile encodes a single sortase enzyme, which cleaves motifs containing (S/P)PXTG in-vitro. The activity of the sortase can be inhibited by mutation of a cysteine residue in the predicted active site and by small-molecule inhibitors. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0219-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Brendan W Wren
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.
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96
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Ung PMU, Dunbar JB, Gestwicki JE, Carlson HA. An allosteric modulator of HIV-1 protease shows equipotent inhibition of wild-type and drug-resistant proteases. J Med Chem 2014; 57:6468-78. [PMID: 25062388 PMCID: PMC4136727 DOI: 10.1021/jm5008352] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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NMR
and MD simulations have demonstrated that the flaps of HIV-1 protease
(HIV-1p) adopt a range of conformations that are coupled with its
enzymatic activity. Previously, a model was created for an allosteric
site located between the flap and the core of HIV-1p, called the Eye
site (Biopolymers2008, 89, 643−65218381626). Here, results from our first study were
combined with a ligand-based, lead-hopping method to identify a novel
compound (NIT). NIT inhibits HIV-1p, independent of the presence of
an active-site inhibitor such as pepstatin A. Assays showed that NIT
acts on an allosteric site other than the dimerization interface.
MD simulations of the ligand–protein complex show that NIT
stably binds in the Eye site and restricts the flaps. That bound state
of NIT is consistent with a crystal structure of similar fragments
bound in the Eye site (Chem.
Biol. Drug Des.2010, 75, 257−26820659109). Most importantly,
NIT is equally potent against wild-type and a multidrug-resistant
mutant of HIV-1p, which highlights the promise of allosteric inhibitors
circumventing existing clinical resistance.
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Affiliation(s)
- Peter M-U Ung
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan , 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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97
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Lin Y, Chapman R, Stevens MM. Label-free multimodal protease detection based on protein/perylene dye coassembly and enzyme-triggered disassembly. Anal Chem 2014; 86:6410-7. [PMID: 24914622 DOI: 10.1021/ac500777r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The development of novel assays for protease sensing plays an important role in clinical diagnostics and therapeutics. Herein, we report a supramolecular platform for label-free protease detection, based on protein/dye self-assembly and enzyme-triggered disassembly. In a typical case, coassembly of protamine sulfate and perylene dye via electrostatic attractions and π-π interactions caused significant colorimetric and fluorescent responses. Subsequent addition of trypsin was found to cleave the amide bonds of protein, triggering the dissociation of protein/dye aggregates and the release of perylene dyes. The enzyme-triggered disassembly was transduced into multiple readouts including absorption, fluorescence, and polarization, which were exploited for trypsin detection and inhibitor testing. This assay was also used for turn-on fluorescence detection of cathepsin B, an enzyme known to be overexpressed in mammalian cancer cells. The integration of supramolecular self-assembly into enzyme detection in this work has provided a novel label-free biosensing platform which is highly sensitive with multimodal readouts. The relative simplicity of the approach avoids the need for time-consuming substrate synthesis, and is also amenable to naked eye detection.
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Affiliation(s)
- Yiyang Lin
- Department of Materials, Department of Bioengineering, and Institute for Biomedical Engineering, Imperial College London , Exhibition Road, London SW7 2AZ, United Kingdom
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98
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Thompson MP, Randolph LM, James CR, Davalos AN, Hahn ME, Gianneschi NC. Labelling Polymers and Micellar Nanoparticles via Initiation, Propagation and Termination with ROMP. Polym Chem 2014; 5:1954-1964. [PMID: 24855496 PMCID: PMC4023353 DOI: 10.1039/c3py01338c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this paper we compare and contrast three approaches for labelling polymers with functional groups via ring-opening metathesis polymerization (ROMP). We explored the incorporation of functionality via initiation, termination and propagation employing an array of novel initiators, termination agents and monomers. The goal was to allow the generation of selectively labelled and well-defined polymers that would in turn lead to the formation of labelled nanomaterials. Norbornene analogues, prepared as functionalized monomers for ROMP, included fluorescent dyes (rhodamine, fluorescein, EDANS, and coumarin), quenchers (DABCYL), conjugatable moieties (NHS esters, pentafluorophenyl esters), and protected amines. In addition, a set of symmetrical olefins for terminally labelling polymers, and for the generation of initiators in situ is described.
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Affiliation(s)
- Matthew P. Thompson
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, U.S.A.. Fax: XX XXXX XXXX; Tel: XX XXXX XXXX
| | - Lyndsay M. Randolph
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, U.S.A.. Fax: XX XXXX XXXX; Tel: XX XXXX XXXX
| | - Carrie R. James
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, U.S.A.. Fax: XX XXXX XXXX; Tel: XX XXXX XXXX
| | - Ashley N. Davalos
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, U.S.A.. Fax: XX XXXX XXXX; Tel: XX XXXX XXXX
| | - Michael E. Hahn
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, U.S.A.. Fax: XX XXXX XXXX; Tel: XX XXXX XXXX
| | - Nathan C. Gianneschi
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, CA, U.S.A.. Fax: XX XXXX XXXX; Tel: XX XXXX XXXX
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99
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Kaman WE, Hays JP, Endtz HP, Bikker FJ. Bacterial proteases: targets for diagnostics and therapy. Eur J Clin Microbiol Infect Dis 2014; 33:1081-7. [PMID: 24535571 DOI: 10.1007/s10096-014-2075-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/30/2014] [Indexed: 02/02/2023]
Abstract
Proteases are essential for the proliferation and growth of bacteria, and are also known to contribute to bacterial virulence. This makes them interesting candidates as diagnostic and therapeutic targets for infectious diseases. In this review, the authors discuss the most recent developments and potential applications for bacterial proteases in the diagnosis and treatment of bacterial infections. Current and future bacterial protease targets are described and their limitations outlined.
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Affiliation(s)
- W E Kaman
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, 's-Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands,
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100
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Speight LC, Samanta M, Petersson EJ. Minimalist Approaches to Protein Labelling: Getting the Most Fluorescent Bang for Your Steric Buck. Aust J Chem 2014. [DOI: 10.1071/ch13554] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescence methods allow one to monitor protein conformational changes, protein–protein associations, and proteolysis in real time, at the single molecule level and in living cells. The information gained in such experiments is a function of the spectroscopic techniques used and the strategic placement of fluorophore labels within the protein structure. There is often a trade-off between size and utility for fluorophores, whereby large size can be disruptive to the protein’s fold or function, but valuable characteristics, such as visible wavelength absorption and emission or brightness, require sizable chromophores. Three major types of fluorophore readouts are commonly used: (1) Förster resonance energy transfer (FRET); (2) photoinduced electron transfer (PET); and (3) environmental sensitivity. This review focuses on those probes small enough to be incorporated into proteins during ribosomal translation, which allows the probes to be placed on the interiors of proteins as they are folded during synthesis. The most broadly useful method for doing so is site-specific unnatural amino acid (UAA) mutagenesis. We discuss the use of UAA probes in applications relying on FRET, PET, and environmental sensitivity. We also briefly review other methods of protein labelling and compare their relative merits to UAA mutagenesis. Finally, we discuss small probes that have thus far been used only in synthetic peptides, but which have unusual value and may be candidates for incorporation using UAA methods.
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