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Zhou C, Li X, Tang SW, Liu C, Lam MHW, Lam YW. A Dual-Enzyme Amplification Loop for the Sensitive Biosensing of Endopeptidases. ACS OMEGA 2023; 8:25592-25600. [PMID: 37483190 PMCID: PMC10357553 DOI: 10.1021/acsomega.3c03533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023]
Abstract
A rapid and sensitive approach for the detection of endopeptidases via a new analyte-triggered mutual emancipation of linker-immobilized enzymes (AMELIE) mechanism has been developed and demonstrated using a matrix metallopeptidase, a collagenase, as the model endopeptidase analyte. AMELIE involves an autocatalytic loop created by a pair of selected enzymes immobilized on solid substrates via linkers with specific sites that can be proteolyzed by one another. These bound enzymes are spatially separated so that they cannot act upon their corresponding substrates until the introduction of the target endopeptidase analyte that can also cleave one of the linkers. This triggers the self-sustained loop of enzymatic activities to emancipate all the immobilized enzymes. In this proof of concept, signal transduction was achieved by a colorimetric horseradish peroxidase-tetramethylbenzidine (HRP-TMB-H2O2) reaction with HRP that are also being immobilized by one of the linkers. The pair of immobilized enzymes were collagenase and alginate lyase, and they were immobilized by an alginate linker and a short peptide chain containing the amino acid sequence of Leu-Gly-Pro-Ala for collagenase. A detection limit of 2.5 pg collagenase mL-1 with a wide linear range up to 4 orders of magnitude was achieved. The AMELIE biosensor can detect extracellular collagenase in the supernatant of various bacteria cultures, with a sensitivity as low as 103 cfu mL-1 of E. coli. AMELIE can readily be adapted to provide the sensitive detection of other endopeptidases.
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Affiliation(s)
- Chuanwen Zhou
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Xiaomin Li
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Sze Wing Tang
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Chunxi Liu
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Michael H. W. Lam
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Yun Wah Lam
- Department
of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
- School
of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, U.K.
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2
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Filippova TA, Masamrekh RA, Shumyantseva VV, Latsis IA, Farafonova TE, Ilina IY, Kanashenko SL, Moshkovskii SA, Kuzikov AV. Electrochemical biosensor for trypsin activity assay based on cleavage of immobilized tyrosine-containing peptide. Talanta 2023; 257:124341. [PMID: 36821964 DOI: 10.1016/j.talanta.2023.124341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/13/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023]
Abstract
In this work, we proposed a biosensor for trypsin proteolytic activity assay using immobilization of model peptides on screen-printed electrodes (SPE) modified with gold nanoparticles (AuNPs) prepared by electrosynthetic method. Sensing of proteolytic activity was based on electrochemical oxidation of tyrosine residues of peptides. We designed peptides containing N-terminal cysteine residue for immobilization on an SPE, modified with gold nanoparticles, trypsin-specific cleavage site and tyrosine residue as a redox label. The peptides were immobilized on SPE by formation of chemical bonds between mercapto groups of the N-terminal cysteine residues and AuNPs. After the incubation with trypsin, time-dependent cleavage of the immobilized peptides was observed by decline in tyrosine electrochemical oxidation signal. The kinetic parameters of trypsin, such as the catalytic constant (kcat), the Michaelis constant (KM) and the catalytic efficiency (kcat/KM), toward the CGGGRYR peptide were determined as 0.33 ± 0.01 min-1, 198 ± 24 nM and 0.0016 min-1 nM-1, respectively. Using the developed biosensor, we demonstrated the possibility of analysis of trypsin specificity toward the peptides with amino acid residues disrupting proteolysis. Further, we designed the peptides with proline or glutamic acid residues after the cleavage site (CGGRPYR and CGGREYR), and trypsin had reduced activity toward both of them according to the existing knowledge of the enzyme specificity. The developed biosensor system allows one to perform a comparative analysis of the protease steady-state kinetic parameters and specificity toward model peptides with different amino acid sequences.
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Affiliation(s)
- Tatiana A Filippova
- Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow 117997, Russia; Institute of Biomedical Chemistry, 10, Pogodinskaya st., Moscow, 119121, Russia
| | - Rami A Masamrekh
- Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow 117997, Russia; Institute of Biomedical Chemistry, 10, Pogodinskaya st., Moscow, 119121, Russia
| | - Victoria V Shumyantseva
- Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow 117997, Russia; Institute of Biomedical Chemistry, 10, Pogodinskaya st., Moscow, 119121, Russia
| | - Ivan A Latsis
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a Malaya Pirogovskaya st., Moscow, 119435, Russia
| | | | - Irina Y Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine, 1a Malaya Pirogovskaya st., Moscow, 119435, Russia
| | - Sergey L Kanashenko
- Institute of Biomedical Chemistry, 10, Pogodinskaya st., Moscow, 119121, Russia
| | - Sergei A Moshkovskii
- Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow 117997, Russia; Federal Research and Clinical Center of Physical-Chemical Medicine, 1a Malaya Pirogovskaya st., Moscow, 119435, Russia.
| | - Alexey V Kuzikov
- Pirogov Russian National Research Medical University, 1 Ostrovityanova st., Moscow 117997, Russia; Institute of Biomedical Chemistry, 10, Pogodinskaya st., Moscow, 119121, Russia.
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3
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Hernández González JE, Alberca LN, Masforrol González Y, Reyes Acosta O, Talevi A, Salas-Sarduy E. Tetracycline Derivatives Inhibit Plasmodial Cysteine Protease Falcipain-2 through Binding to a Distal Allosteric Site. J Chem Inf Model 2021; 62:159-175. [PMID: 34962803 DOI: 10.1021/acs.jcim.1c01189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Allosteric inhibitors regulate enzyme activity from remote and usually specific pockets. As they promise an avenue for less toxic and safer drugs, the identification and characterization of allosteric inhibitors has gained great academic and biomedical interest in recent years. Research on falcipain-2 (FP-2), the major papain-like cysteine hemoglobinase of Plasmodium falciparum, might benefit from this strategy to overcome the low selectivity against human cathepsins shown by active site-directed inhibitors. Encouraged by our previous finding that methacycline inhibits FP-2 noncompetitively, here we assessed other five tetracycline derivatives against this target and characterized their inhibition mechanism. As previously shown for methacycline, tetracycline derivatives inhibited FP-2 in a noncompetitive fashion, with Ki values ranging from 121 to 190 μM. A possible binding to the S' side of the FP-2 active site, similar to that described by X-ray crystallography (PDB: 6SSZ) for the noncompetitive inhibitor E-chalcone 48 (EC48), was experimentally discarded by kinetic analysis using a large peptidyl substrate spanning the whole active site. By combining lengthy molecular dynamics (MD) simulations that allowed methacycline to diffuse from solution to different FP-2 surface regions and free energy calculations, we predicted the most likely binding mode of the ligand. Of note, the proposed binding pose explains the low differences in Ki values observed for the tested tetracycline derivatives and the calculated binding free energies match the experimental values. Overall, this study has implications for the design of novel allosteric inhibitors against FP-2 and sets the basis for further optimization of the tetracycline scaffold to produce more potent and selective inhibitors.
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Affiliation(s)
- Jorge Enrique Hernández González
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista Júlio de Mesquita Filho, Rua Cristóvão Colombo, 2265, Jardim Nazareth, São José do Rio Preto, São Paulo CEP 15054-000, Brazil
| | - Lucas N Alberca
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata B1900ADU, Argentina
| | | | - Osvaldo Reyes Acosta
- Chemistry and Physics Department, Center for Genetic Engineering and Biotechnology, Havana 10600, Cuba
| | - Alan Talevi
- Laboratory of Bioactive Compounds Research and Development (LIDeB), Department of Biological Sciences, Exact Sciences College, Universidad Nacional de La Plata, La Plata B1900ADU, Argentina
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas "Dr. Rodolfo Ugalde"─Universidad Nacional de San Martín─CONICET, San Martín B1650HMP, Buenos Aires, Argentina
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4
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Sensing HIV Protease and Its Inhibitor Using "Helical Epitope"-Imprinted Polymers. SENSORS 2020; 20:s20123592. [PMID: 32630459 PMCID: PMC7348739 DOI: 10.3390/s20123592] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 12/15/2022]
Abstract
A helical epitope-peptide (lle85-Gly94) was selected from the α-helix structure of the HIV protease (PR) as the template, which represents an intricate interplay between structure conformation and dimerization. The peptide template was mixed with water, trifluoroethanol (TFE), and acetonitrile (ACN) at a certain ratio to enlarge the helical conformation in the solution for the fabrication of helical epitope-mediated molecularly imprinted polymers (HEMIPs) on a quartz crystal microbalance (QCM) chip. The template molecules were then removed under equilibrium batch rebinding conditions involving 5% acetic acid/water. The resulting HEMIPs chip exhibited a high affinity toward template peptide HIV PR85-94, His-tagged HIV PR, and HIV PR, with dissociation constants (Kd) as 160, 43.3, and 78.5 pM, respectively. The detection limit of the developed HIV PR85-94 QCM sensor is 0.1 ng/mL. The HEMIPs chip exhibited a high affinity and selectivity to bind HIV PR and subsequently to an inhibitor of HIV PR (nelfinavir). The HIV PR binding site was properly oriented on the HEMIPs-chip to develop a HIV PR/HEMIPs chip, which can effectively bind nelfinavir to establish a sandwich assay. The nelfinavir then attached to the HIV PR/HEMIPs chip, which can be easily removed involving 0.8% acetic acid/water. Therefore, HIV PR/HEMIPs chip can be useful to screen for other HIV PR inhibitors. This technique may improve drug targeting for HIV therapy and also strengthen investigations into other virus assays.
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5
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Zhang Y, Chen X, Roozbahani GM, Guan X. Graphene oxide-based biosensing platform for rapid and sensitive detection of HIV-1 protease. Anal Bioanal Chem 2018; 410:6177-6185. [PMID: 29968105 PMCID: PMC6159923 DOI: 10.1007/s00216-018-1224-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 05/28/2018] [Accepted: 06/22/2018] [Indexed: 12/26/2022]
Abstract
HIV-1 protease is essential for the life cycle of the human immunodeficiency virus (HIV), and is one of the most important clinical targets for antiretroviral therapies. In this work, we developed a graphene oxide (GO)-based fluorescence biosensing platform for the rapid, sensitive, and accurate detection of HIV-1 protease, in which fluorescent-labeled HIV-1 protease substrate peptide molecules were covalently linked to GO. In the absence of HIV-1 protease, fluorescein was effectively quenched by GO. In contrast, in the presence of HIV-1 protease, it would cleave the substrate peptide into short fragments, thus producing fluorescence. Based on this sensing strategy, HIV-1 protease could be detected at as low as 1.18 ng/mL. More importantly, the sensor could successfully detect HIV-1 protease in human serum. Such GO-based fluorescent sensors may find useful applications in many fields, including diagnosis of protease-related diseases, as well as sensitive and high-throughput screening of drug candidates. Graphical abstract ᅟ.
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Affiliation(s)
- Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA
| | - Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA
| | - Golbarg M Roozbahani
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 S Dearborn St, Chicago, IL, 60616, USA.
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6
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Wang Y, Zhang Z, Zhang Y, Yu C. A real-time fluorescence assay for protease activity and inhibitor screening based on the aggregation-caused quenching of a perylene probe. LUMINESCENCE 2018; 33:790-796. [PMID: 29607616 DOI: 10.1002/bio.3478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 02/04/2018] [Accepted: 02/10/2018] [Indexed: 01/01/2023]
Abstract
We have established a real-time and label-free fluorescence turn-on strategy for protease activity detection and inhibitor screening via peptide-induced aggregation-caused quenching of a perylene probe. Because of electrostatic interactions and high hydrophilicity, poly-l-glutamic acid sodium salt (PGA; a negatively charged peptide) could induce aggregation of a positively charged perylene probe (probe 1) and the monomer fluorescence of probe 1 was effectively quenched. After a protease was added, PGA was enzymatically hydrolyzed into small fragments and probe 1 disaggregated. The fluorescence recovery of probe 1 was found to be proportional to the concentration of protease in the range from 0 to 1 mU/ml. The detection limit was down to 0.1 mU/ml. In the presence of a protease inhibitor, protease activity was inhibited and fluorescence recovery reduced. Moreover, we demonstrated the potential application of our method in a complex mixture sample including 1% human serum. Our method is simple, fast and cost effective.
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Affiliation(s)
- Yan Wang
- School of Chemistry and Chemical Engineering, Yulin University, Shaanxi, Yulin, People's Republic of China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, People's Republic of China
| | - Zhifang Zhang
- School of Chemistry and Chemical Engineering, Yulin University, Shaanxi, Yulin, People's Republic of China
| | - Ya Zhang
- School of Chemistry and Chemical Engineering, Yulin University, Shaanxi, Yulin, People's Republic of China
| | - Cong Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, People's Republic of China
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7
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Matsunaga S, Masaoka T, Sawasaki T, Morishita R, Iwatani Y, Tatsumi M, Endo Y, Yamamoto N, Sugiura W, Ryo A. A cell-free enzymatic activity assay for the evaluation of HIV-1 drug resistance to protease inhibitors. Front Microbiol 2015; 6:1220. [PMID: 26583013 PMCID: PMC4628118 DOI: 10.3389/fmicb.2015.01220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 10/19/2015] [Indexed: 12/27/2022] Open
Abstract
Due to their high frequency of genomic mutations, human retroviruses often develop resistance to antiretroviral drugs. The emergence of drug-resistant human immunodeficiency virus type 1 (HIV-1) is a significant obstacle to the effective long-term treatment of HIV infection. The development of a rapid and versatile drug-susceptibility assay would enable acquisition of phenotypic information and facilitate determination of the appropriate choice of antiretroviral agents. In this study, we developed a novel in vitro method, termed the Cell-free drug susceptibility assay (CFDSA), for monitoring phenotypic information regarding the drug resistance of HIV-1 protease (PR). The CFDSA utilizes a wheat germ cell-free protein production system to synthesize enzymatically active HIV-1 PRs directly from PCR products amplified from HIV-1 molecular clones or clinical isolates in a rapid one-step procedure. Enzymatic activity of PRs can be readily measured by AlphaScreen (Amplified Luminescent Proximity Homogeneous Assay Screen) in the presence or absence of clinically used protease inhibitors (PIs). CFDSA measurement of drug resistance was based on the fold resistance to the half-maximal inhibitory concentration (IC50) of various PIs. The CFDSA could serve as a non-infectious, rapid, accessible, and reliable alternative to infectious cell-based phenotypic assays for evaluation of PI-resistant HIV-1.
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Affiliation(s)
- Satoko Matsunaga
- Department of Microbiology, School of Medicine, Yokohama City University Yokohama, Japan
| | - Takashi Masaoka
- Department of Infection and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan
| | | | - Ryo Morishita
- Department of Microbiology, School of Medicine, Yokohama City University Yokohama, Japan ; CellFree Sciences Co., Ltd. Matsuyama, Japan
| | - Yasumasa Iwatani
- Department of Infection and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan ; Department of AIDS Research, Nagoya University Graduate School of Medicine Nagoya, Japan
| | - Masashi Tatsumi
- Department of AIDS Research, AIDS Research Center, National Institute of Infectious Diseases Tokyo, Japan
| | - Yaeta Endo
- Proteo-Science Center, Ehime University Matsuyama, Japan
| | - Naoki Yamamoto
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore Singapore, Singapore
| | - Wataru Sugiura
- Department of Infection and Immunology, Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Japan ; Department of AIDS Research, Nagoya University Graduate School of Medicine Nagoya, Japan
| | - Akihide Ryo
- Department of Microbiology, School of Medicine, Yokohama City University Yokohama, Japan
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8
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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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9
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Seo S, Kim J, Jang G, Kim D, Lee TS. Aggregation-deaggregation-triggered, tunable fluorescence of an assay ensemble composed of anionic conjugated polymer and polypeptides by enzymatic catalysis of trypsin. ACS APPLIED MATERIALS & INTERFACES 2014; 6:918-924. [PMID: 24359429 DOI: 10.1021/am405120y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We prepared a water-soluble conjugated polymer composed of electron-donating units and electron-accepting groups in the backbone. The polymer exhibits a short wavelength (blue) emission in aqueous solution and long wavelength (red) emission in the solid state, because of intermolecular energy transfer. Considering this, we develop a new approach for the sensitive detection of trypsin, which is known to control pancreatic exocrine function, using an ensemble system composed of the anionically charged conjugated polymer and cationically charged polypeptides (such as polylysine and polyarginine). The blue-emitting, water-soluble conjugated polymer becomes aggregated upon exposure to the polypeptides, leading to a red-emitting assay ensemble. The red-emitting assay ensemble becomes dissociated in the conjugated polymer and polypeptide fragments by selective degradation of trypsin, which then exhibits recovery of blue emission. This emission-tuning assay ensemble allows for detection of trypsin at nanomolar concentrations, which enables naked-eye detection. Importantly, this strategy can be employed for label-free, continuous assay for trypsin.
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Affiliation(s)
- Seongwon Seo
- Organic and Optoelectronic Materials Laboratory, Department of Advanced Organic Materials and Textile System Engineering, Chungnam National University , Daejeon 305-764, Korea
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10
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Novel PCU cage diol peptides as potential targets against wild-type CSA HIV-1 protease: synthesis, biological screening and molecular modelling studies. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0350-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Pentacycloundecane derived hydroxy acid peptides: A new class of irreversible non-scissile ether bridged type isoster as potential HIV-1 wild type C-SA protease inhibitors. Bioorg Chem 2012; 40:19-29. [DOI: 10.1016/j.bioorg.2011.08.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 08/03/2011] [Accepted: 08/04/2011] [Indexed: 11/18/2022]
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12
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Li W, Chen J, Jiao H, Zhang Q, Zhou H, Yu C. A label-free real time fluorometric assay for protease and inhibitor screening with a released heme. Chem Commun (Camb) 2012; 48:10123-5. [DOI: 10.1039/c2cc35374a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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13
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Kukwikila M, Howorka S. Electrically sensing protease activity with nanopores. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:454103. [PMID: 21339591 DOI: 10.1088/0953-8984/22/45/454103] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The enzymatic activity of a protease was electrically detected using nanopore recordings. A peptide substrate was tethered to microscale beads, and cleavage by the enzyme trypsin released a soluble fragment that was electrophoretically driven through the α-hemolysin protein pore, leading to detectable blockades in the ionic current. Owing to its simplicity, this approach to sense enzymatic activity may be applied to other proteases.
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14
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Clé C, Martin C, Field RA, Kuzmič P, Bornemann S. Detection of enzyme-catalyzed polysaccharide synthesis on surfaces. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.3109/10242420903388744] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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15
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Selective and facile assay of human immunodeficiency virus protease activity by a novel fluorogenic reaction. Anal Biochem 2009; 397:197-201. [PMID: 19852926 PMCID: PMC7094380 DOI: 10.1016/j.ab.2009.10.030] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 10/07/2009] [Accepted: 10/16/2009] [Indexed: 02/06/2023]
Abstract
A highly selective and facile assay of human immunodeficiency virus protease (HIV-PR) has been required for the screening of medicinal inhibitors and also for classifying the subtypes of HIV in the therapeutic treatment of acquired immune deficiency syndrome (AIDS). This article describes a novel assay method of HIV-PR based on the selective fluorogenic reaction of peptides. A peptide fragment generated from a substrate by the enzymatic digestion with HIV-PR could be selectively quantified by the spectrofluorometric detection after the fluorogenic reaction with catechol in the presence of sodium periodate and sodium borate (pH 7.0). This assay system uses an N-terminal acetyl peptide as the substrate and crude extracts from Escherichia coli expressing recombinant HIV-PR. The activity obtained by the proposed assay correlated with that obtained by a conventional HIV-PR assay based on fluorescence resonance energy transfer detection.
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16
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Gorris HH, Bade S, Röckendorf N, Albers E, Schmidt MA, Fránek M, Frey A. Rapid Profiling of Peptide Stability in Proteolytic Environments. Anal Chem 2009; 81:1580-6. [DOI: 10.1021/ac802324f] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hans H. Gorris
- Division of Mucosal Immunology, Research Center Borstel, Parkallee 22, 23845 Borstel, Germany, Institute of Infectiology, University of Münster, von-Esmarch-Strasse 56, 48149 Münster, Germany, and Department of Analytical Biotechnology, Veterinary Research Institute, Hudcova 70, 621 32 Brno, Czech Republic
| | - Steffen Bade
- Division of Mucosal Immunology, Research Center Borstel, Parkallee 22, 23845 Borstel, Germany, Institute of Infectiology, University of Münster, von-Esmarch-Strasse 56, 48149 Münster, Germany, and Department of Analytical Biotechnology, Veterinary Research Institute, Hudcova 70, 621 32 Brno, Czech Republic
| | - Niels Röckendorf
- Division of Mucosal Immunology, Research Center Borstel, Parkallee 22, 23845 Borstel, Germany, Institute of Infectiology, University of Münster, von-Esmarch-Strasse 56, 48149 Münster, Germany, and Department of Analytical Biotechnology, Veterinary Research Institute, Hudcova 70, 621 32 Brno, Czech Republic
| | - Eike Albers
- Division of Mucosal Immunology, Research Center Borstel, Parkallee 22, 23845 Borstel, Germany, Institute of Infectiology, University of Münster, von-Esmarch-Strasse 56, 48149 Münster, Germany, and Department of Analytical Biotechnology, Veterinary Research Institute, Hudcova 70, 621 32 Brno, Czech Republic
| | - M. Alexander Schmidt
- Division of Mucosal Immunology, Research Center Borstel, Parkallee 22, 23845 Borstel, Germany, Institute of Infectiology, University of Münster, von-Esmarch-Strasse 56, 48149 Münster, Germany, and Department of Analytical Biotechnology, Veterinary Research Institute, Hudcova 70, 621 32 Brno, Czech Republic
| | - Milan Fránek
- Division of Mucosal Immunology, Research Center Borstel, Parkallee 22, 23845 Borstel, Germany, Institute of Infectiology, University of Münster, von-Esmarch-Strasse 56, 48149 Münster, Germany, and Department of Analytical Biotechnology, Veterinary Research Institute, Hudcova 70, 621 32 Brno, Czech Republic
| | - Andreas Frey
- Division of Mucosal Immunology, Research Center Borstel, Parkallee 22, 23845 Borstel, Germany, Institute of Infectiology, University of Münster, von-Esmarch-Strasse 56, 48149 Münster, Germany, and Department of Analytical Biotechnology, Veterinary Research Institute, Hudcova 70, 621 32 Brno, Czech Republic
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17
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Foose LL, Blanch HW, Radke CJ. Kinetics of adsorption and proteolytic cleavage of a multilayer ovalbumin film by subtilisin Carlsberg. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:7388-7393. [PMID: 18564867 DOI: 10.1021/la8007014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Adsorption and proteolytic activity of the enzyme subtilisin Carlsberg have been studied on an immobilized, multilayer ovalbumin film. The cross-linked multilayer substrate permits protease adsorption to be examined unencumbered by the surface inhomogeneity typically observed in monolayer studies of protease surface kinetics. Decline of the protein film was measured over time using ellipsometry. Resulting kinetic data as a function of aqueous enzyme concentration and temperature were well fit by a Langmuir-Michaelis-Menten model for surface proteolysis. We observed that both the protein degradation kinetics and the in situ adsorption data were well described by the proposed model. The temperature dependence of the kinetic rate parameter yielded an activation energy of 12 kcal/mol. Further, the apparent Langmuir adsorption equilibrium constant of the enzyme at the protein/aqueous interface was 0.11 L/mg at 22 degrees C, 0.034 L/mg at 36 degrees C, and 0.011 L/mg at 50 degrees C. Although enzyme adsorption at a given aqueous enzyme concentration decreased at higher temperature, the enzyme cleaved the substrate more rapidly, leading to a net increase in the ovalbumin film degradation rate. We observed that the maximum enzyme coverage on the immobilized protein surface was approximately 40% of a close-packed monolayer at ambient temperature (22 degrees C).
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Affiliation(s)
- Ladan L Foose
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
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18
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Saunders MJ, Kim H, Woods TA, Nolan JP, Sklar LA, Edwards BS, Graves SW. Microsphere-based protease assays and screening application for lethal factor and factor Xa. Cytometry A 2006; 69:342-52. [PMID: 16604538 DOI: 10.1002/cyto.a.20268] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Proteases regulate many biological pathways in humans and are components of several bacterial toxins. Protease studies and development of protease inhibitors do not follow a single established methodology and are mostly protease specific. METHODS We have created recombinant fusion proteins consisting of a biotinylated attachment sequence linked to a GFP via a protease cleavage site to develop a multiplexable microsphere-based protease assay system. Using the proteases lethal factor and factor Xa, we performed kinetic experiments to determine optimal conditions for inhibitor screens and detect known inhibitors using the HyperCyt flow cytometry system. RESULTS We have demonstrated specific cleavage of lethal factor and factor Xa substrates, optimized screening conditions for these substrates, shown specific inhibition of the proteases, and demonstrated high throughput detection of these inhibitors. CONCLUSIONS The assay developed here is adaptable to any site-specific protease, compatible with high throughput flow cytometry systems, and multiplexable. Coupled with flow cytometry, which provides continuous time resolution and intrinsic resolution of free vs. bound fluorophores, this assay will be useful for high throughput screening of protease inhibitors in general and could simplify assays designed to determine protease mechanism.
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Affiliation(s)
- Matthew J Saunders
- National Flow Cytometry Resource, Biosciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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19
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Halling PJ, Ulijn RV, Flitsch SL. Understanding enzyme action on immobilised substrates. Curr Opin Biotechnol 2005; 16:385-92. [PMID: 16005203 DOI: 10.1016/j.copbio.2005.06.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Revised: 06/10/2005] [Accepted: 06/24/2005] [Indexed: 11/22/2022]
Abstract
With increasing interest in automated synthesis and screening protocols, solid supported chemistry and biochemistry are attractive technologies. Studies with surface-immobilised substrates have been carried out to analyse enzyme accessibility, kinetics and thermodynamics. Several interesting new methods have been developed to monitor enzyme action on substrates attached to a solid phase such as polymer beads glass or gold surfaces. These include fluorescence measurements, MALDI-TOF mass spectrometry, and the use of quartz crystal microbalances to measure weight changes of immobilised molecules directly on the surface. Approaches that allow spatial resolution in single beads have also been reported. The ability of enzymes to reach the inside of beads is becoming better characterised and new supports have been developed that allow improved accessibility. The equilibrium position of reactions on the solid surface can be substantially shifted compared with reactions in solution, and this can be usefully exploited using hydrolases in reverse. Research is also starting to tackle the way in which kinetics are modified when the substrates are surface immobilised.
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Affiliation(s)
- Peter J Halling
- Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow G1 1XW, UK.
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20
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Gutiérrez OA, Chavez M, Lissi E. A theoretical approach to some analytical properties of heterogeneous enzymatic assays. Anal Chem 2005; 76:2664-8. [PMID: 15117213 DOI: 10.1021/ac049885d] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heterogeneous enzymatic assays (HEA), where an enzyme in solution acts upon an immobilized substrate, are been increasingly used. Given their high throughput and versatility they hold great potential for developing massive enzyme inhibitor screening. However, current HEA lack, in general, rigorous quantitative use. This is in part due to technical problems as a multiplicity of suboptimal substrate populations achieved with traditional immobilization techniques but, more importantly, is due to a poor understanding of the particular kinetic behavior of these systems. This paper addresses the kinetic features of HEA that arise from the very low amount of solid-phase substrate and the resulting inalterability of the free enzyme concentration during the assay, which classify HEA as enzyme quasi-saturable systems (EQSS). We assessed the optimal enzyme concentration working range and time of reaction. We also considered certain attributes of HEA for evaluating isosteric inhibitors. These studies were done on the basis of a simplified model for the kinetics of EQSS and a formal splitting of the functional factor of the analytical sensitivity of an enzymatic assay into [E(o)]/K(m)-dependent and temporal components.
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Affiliation(s)
- O A Gutiérrez
- Centro de Estudio de las Proteinas, Facultad de Biología, Universidad de la Habana, 25 # 455 entre J e I. CP 10 400, Vedado, Ciudad de la Habana, Cuba.
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21
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Pascual I, Gil-Parrado S, Cisneros M, Joseph-Bravo P, Díaz J, Possani LD, Charli JL, Chávez M. Purification of a specific inhibitor of pyroglutamyl aminopeptidase II from the marine annelide Hermodice carunculata. in vivo effects in rodent brain. Int J Biochem Cell Biol 2004; 36:138-52. [PMID: 14592539 DOI: 10.1016/s1357-2725(03)00175-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An inhibitor of the metallo-ectoenzyme, pyroglutamyl aminopeptidase II (PPII), a thyrotropin releasing hormone-specific peptidase, was identified by screening extracts from marine species of the Cuban coast-line belonging to the phylla Chordata, Echinodermata, Annelida, Mollusca, Cnidaria, Porifera, Chlorophyta and Magnoliophyta. Isolation of the inhibitor (HcPI), from the marine annelide Hermodice carunculata, was achieved by trichloroacetic acid treatment of the aqueous extract, followed by ion-exchange chromatography on DEAE Sephacel, gel filtration on Sephadex G-25 and reverse phase-HPLC. HcPI had a small apparent molecular weight (below 1000 Da) and was not a peptide. It inhibited rat PPII (a membrane preparation with 8.5mg protein/ml) with an apparent K(i) of 51 nM. HcPI did not inhibit serine (trypsin, chymotrypsin, elastase and dipeptidyl aminopeptidase IV), cysteine (papain, bromelain and pyroglutamyl aminopeptidase I), aspartic (pepsin and recombinant human immunodeficiency virus 1 protease (HIV1-PR)) nor other metallo proteinases (collagenase, gelatinase, angiotensin converting enzyme, aminopeptidase N and carboxypeptidase A). HcPI was non-toxic and active in vivo. Intraperitoneal injection of HcPI reduced mouse pituitary and brain PPII activity. Potency of the effect was higher in hypophysis and hypothalamus than in other brain regions. Intrathecal administration to male rats reduced PPII activity in the spinal cord. In conclusion we have identified a specific inhibitor of PPII that is the first M1 family zinc metallo-peptidase inhibitor isolated from marine invertebrates. It may be useful for elucidating the in vivo role of PPII in the pituitary and central nervous system.
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Affiliation(s)
- Isel Pascual
- Centro de Estudios de Proteínas, Facultad de Biología, Universidad de la Habana, Calle 25, Plaza de la Revolución, La Habana 10400, Cuba
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22
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Salas E, Ramírez A, Otero-Bilbao A, Vázquez R, Reyes O, Mendiola J, Duarte CA, Otero-González A, Gutiérrez OA, Chávez MA. A heterogeneous enzymatic assay for quantification of Plasmepsin II activity and the evaluation of its inhibitors. J Pharm Biomed Anal 2004; 34:833-40. [PMID: 15019062 DOI: 10.1016/s0731-7085(03)00566-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2003] [Indexed: 10/26/2022]
Abstract
The emergence and worldwide spreading of Plasmodium falciparum strains that shown to be resistant to traditional drugs is considered a very serious health problem, given the high mortality and morbidity rate of Malaria. In the search for new drugs against this parasite, Hb hydrolyzing enzymes, such as Plasmepsin II (Plm II), have been classified as very promising targets for therapeutic attacks. In this work, it is developed a cheap and high-throughput heterogeneous enzymatic assay for measuring Plasmepsin II activity in order to use it as a tool in the discovery of new inhibitors of this enzyme. In this assay, Plasmepsin II acts upon a solid-phase bound synthetic peptide (DU2) whose sequence comprises the cleavage site F(33)-L(34) present in Hb alpha-chain. The peptide surface density is quantified by means of a classical ELISA-based procedure. In order to estimate the kinetic constants of the system and to quantify both, enzymatic and inhibitory activity, it was used a model for the kinetics of enzyme quasi-saturable systems previously developed by our group, that fitted very well to the experimental data. It was used Pepstatin as a model inhibitor of Plasmepsin II and the resulting dose-response relation agreed with the expected behavior for the Pepstatin-Plasmepsin II pair under the employed experimental conditions.
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Affiliation(s)
- Emir Salas
- Centro de Estudio de Proteínas, Facultad de Biología, Universidad de la Habana, Calle 25 # 455 Entre J e I, Vedado, CP 10400, Havana City, Cuba.
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