101
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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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102
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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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103
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Jang H, Lee J, Min DH. Graphene oxide for fluorescence-mediated enzymatic activity assays. J Mater Chem B 2014; 2:2452-2460. [DOI: 10.1039/c4tb00199k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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104
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Zhu L, Yuan Z, Simmons JT, Sreenath K. Zn(II)-coordination modulated ligand photophysical processes - the development of fluorescent indicators for imaging biological Zn(II) ions. RSC Adv 2014; 4:20398-20440. [PMID: 25071933 PMCID: PMC4111279 DOI: 10.1039/c4ra00354c] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Molecular photophysics and metal coordination chemistry are the two fundamental pillars that support the development of fluorescent cation indicators. In this article, we describe how Zn(II)-coordination alters various ligand-centered photophysical processes that are pertinent to developing Zn(II) indicators. The main aim is to show how small organic Zn(II) indicators work under the constraints of specific requirements, including Zn(II) detection range, photophysical requirements such as excitation energy and emission color, temporal and spatial resolutions in a heterogeneous intracellular environment, and fluorescence response selectivity between similar cations such as Zn(II) and Cd(II). In the last section, the biological questions that fluorescent Zn(II) indicators help to answer are described, which have been motivating and challenging this field of research.
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Affiliation(s)
- Lei Zhu
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, United States
| | - Zhao Yuan
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, United States
| | - J. Tyler Simmons
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, United States
| | - Kesavapillai Sreenath
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL 32306-4390, United States
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105
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Shen Y, Altman MD, Ali A, Nalam MNL, Cao H, Rana TM, Schiffer CA, Tidor B. Testing the substrate-envelope hypothesis with designed pairs of compounds. ACS Chem Biol 2013; 8:2433-41. [PMID: 23952265 PMCID: PMC3833293 DOI: 10.1021/cb400468c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
Acquired resistance to therapeutic
agents is a significant barrier to the development of clinically effective
treatments for diseases in which evolution occurs on clinical time
scales, frequently arising from target mutations. We previously reported
a general strategy to design effective inhibitors for rapidly mutating
enzyme targets, which we demonstrated for HIV-1 protease inhibition
[Altman et al. J. Am. Chem. Soc. 2008, 130, 6099–6113]. Specifically, we developed a computational inverse
design procedure with the added constraint that designed inhibitors
bind entirely inside the substrate envelope, a consensus volume occupied
by natural substrates. The rationale for the substrate-envelope constraint
is that it prevents designed inhibitors from making interactions beyond
those required by substrates and thus limits the availability of mutations
tolerated by substrates but not by designed inhibitors. The strategy
resulted in subnanomolar inhibitors that bind robustly across a clinically
derived panel of drug-resistant variants. To further test the substrate-envelope
hypothesis, here we have designed, synthesized, and assayed derivatives
of our original compounds that are larger and extend outside the substrate
envelope. Our designs resulted in pairs of compounds that are very
similar to one another, but one respects and one violates the substrate
envelope. The envelope-respecting inhibitor demonstrates robust binding
across a panel of drug-resistant protease variants, whereas the envelope-violating
one binds tightly to wild type but loses affinity to at least one
variant. This study provides strong support for the substrate-envelope
hypothesis as a design strategy for inhibitors that reduce susceptibility
to resistance mutations.
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Affiliation(s)
| | | | | | | | | | - Tariq M. Rana
- Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
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106
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Sloniec J, Resch-Genger U, Hennig A. Photophysics and Release Kinetics of Enzyme-Activatable Optical Probes Based on H-Dimerized Fluorophores on Self-Immolative Linkers. J Phys Chem B 2013; 117:14336-44. [DOI: 10.1021/jp409388b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jagoda Sloniec
- BAM Federal Institute for Materials Research and Testing, D-12489 Berlin, Germany
| | - Ute Resch-Genger
- BAM Federal Institute for Materials Research and Testing, D-12489 Berlin, Germany
| | - Andreas Hennig
- BAM Federal Institute for Materials Research and Testing, D-12489 Berlin, Germany
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107
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Mao P, Ning Y, Li W, Peng Z, Chen Y, Deng L. Novel strategy combining SYBR Green I with carbon nanotubes for highly sensitive detection of Salmonella typhimurium DNA. Enzyme Microb Technol 2013; 54:15-9. [PMID: 24267562 DOI: 10.1016/j.enzmictec.2013.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 11/30/2022]
Abstract
A simple, selective, sensitive and label-free fluorescent method for detecting trpS-harboring Salmonella typhimurium was developed in this study. This assay used the non-covalent interaction of single-stranded DNA (ssDNA) probes with SWNTs, since SWNTs can quench fluorescence. Fluorescence recovery (78% with 1.8 nM target DNA) was detected in the presence of target DNA as ssDNA probes detached from SWNTs hybridized with target DNA, and the resulting double-stranded DNA (dsDNA) intercalated with SYBR Green I (SG) dyes. The increasing fluorescence intensity reached 4.54-fold. In contrast, mismatched oligonucleotides (1- or 3-nt difference to the target DNA) did not contribute to significant fluorescent recovery, which demonstrated the specificity of the assay. The increasing fluorescence intensity increased 3.15-fold when purified PCR products containing complementary sequences of trpS gene were detected. These results confirmed the ability to use this assay for detecting real samples.
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Affiliation(s)
- Pingdao Mao
- The Co-construction Laboratory of Microbial Molecular Biology of Province and Ministry of Science and Technology, College of Life Science, Hunan Normal University, Changsha, Hunan, People's Republic of China
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108
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Hacker SM, Pagliarini D, Tischer T, Hardt N, Schneider D, Mex M, Mayer TU, Scheffner M, Marx A. Fluorogene ATP-Analoga zur Detektion von ATP-Verbrauch: Beobachtung der Aktivierung von Ubiquitin in Echtzeit. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201304723] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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109
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Hacker SM, Pagliarini D, Tischer T, Hardt N, Schneider D, Mex M, Mayer TU, Scheffner M, Marx A. Fluorogenic ATP analogues for online monitoring of ATP consumption: observing ubiquitin activation in real time. Angew Chem Int Ed Engl 2013; 52:11916-9. [PMID: 24105922 DOI: 10.1002/anie.201304723] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/19/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Stephan M Hacker
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany)
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110
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Holzmeister P, Acuna GP, Grohmann D, Tinnefeld P. Breaking the concentration limit of optical single-molecule detection. Chem Soc Rev 2013; 43:1014-28. [PMID: 24019005 DOI: 10.1039/c3cs60207a] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the last decade, single-molecule detection has been successfully utilized in the life sciences and materials science. Yet, single-molecule measurements only yield meaningful results when working in a suitable, narrow concentration range. On the one hand, diffraction limits the minimal size of the observation volume in optical single-molecule measurements and consequently a sample must be adequately diluted so that only one molecule resides within the observation volume. On the other hand, at ultra-low concentrations relevant for sensing, the detection volume has to be increased in order to detect molecules in a reasonable timespan. This in turn results in the loss of an optimal signal-to-noise ratio necessary for single-molecule detection. This review discusses the requirements for effective single-molecule fluorescence applications, reflects on the motivation for the extension of the dynamic concentration range of single-molecule measurements and reviews various approaches that have been introduced recently to solve these issues. For the high-concentration limit, we identify four promising strategies including molecular confinement, optical observation volume reduction, temporal separation of signals and well-conceived experimental designs that specifically circumvent the high concentration limit. The low concentration limit is addressed by increasing the measurement speed, parallelization, signal amplification and preconcentration. The further development of these ideas will expand our possibilities to interrogate research questions with the clarity and precision provided only by the single-molecule approach.
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Affiliation(s)
- Phil Holzmeister
- Braunschweig University of Technology, Institute for Physical & Theoretical Chemistry, Hans-Sommer-Str. 10, 38106 Braunschweig, Germany.
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111
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Morin Inhibits Sortase A and Subsequent Biofilm Formation in Streptococcus mutans. Curr Microbiol 2013; 68:47-52. [DOI: 10.1007/s00284-013-0439-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 07/09/2013] [Indexed: 11/29/2022]
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112
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Silver NW, King BM, Nalam MNL, Cao H, Ali A, Kiran Kumar Reddy GS, Rana TM, Schiffer CA, Tidor B. Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration. J Chem Theory Comput 2013; 9:5098-5115. [PMID: 24250277 PMCID: PMC3827837 DOI: 10.1021/ct400383v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Indexed: 01/02/2023]
Abstract
![]()
Here
we present a novel, end-point method using the dead-end-elimination
and A* algorithms to efficiently and accurately calculate the change
in free energy, enthalpy, and configurational entropy of binding for
ligand–receptor association reactions. We apply the new approach
to the binding of a series of human immunodeficiency virus (HIV-1)
protease inhibitors to examine the effect ensemble reranking has on
relative accuracy as well as to evaluate the role of the absolute
and relative ligand configurational entropy losses upon binding in
affinity differences for structurally related inhibitors. Our results
suggest that most thermodynamic parameters can be estimated using
only a small fraction of the full configurational space, and we see
significant improvement in relative accuracy when using an ensemble
versus single-conformer approach to ligand ranking. We also find that
using approximate metrics based on the single-conformation enthalpy
differences between the global minimum energy configuration in the
bound as well as unbound states also correlates well with experiment.
Using a novel, additive entropy expansion based on conditional mutual
information, we also analyze the source of ligand configurational
entropy loss upon binding in terms of both uncoupled per degree of
freedom losses as well as changes in coupling between inhibitor degrees
of freedom. We estimate entropic free energy losses of approximately
+24 kcal/mol, 12 kcal/mol of which stems from loss of translational
and rotational entropy. Coupling effects contribute only a small fraction
to the overall entropy change (1–2 kcal/mol) but suggest differences
in how inhibitor dihedral angles couple to each other in the bound
versus unbound states. The importance of accounting for flexibility
in drug optimization and design is also discussed.
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Affiliation(s)
- Nathaniel W Silver
- Department of Chemistry and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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113
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114
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Curcumin inhibits the Sortase A activity of the Streptococcus mutans UA159. Appl Biochem Biotechnol 2013; 171:396-402. [PMID: 23842671 DOI: 10.1007/s12010-013-0378-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Accepted: 07/01/2013] [Indexed: 02/08/2023]
Abstract
Streptococcus mutans (S. mutans) forms part of the commensal microflora and is deemed to be the major pathogen responsible for the generation of dental caries. The enzyme, sortase A enzyme, modulates the surface properties and cariogenicity of S. mutans. Curcumin has been reported to be an inhibitor of Staphylococcus aureus sortase A. In this study, inhibition of a purified S. mutans UA159 sortase A by curcumin was evaluated. Curcumin exerted strong inhibitory activity with a half maximal inhibitory concentration (IC50) of 10.2 ± 0.7 μM which was lower than the minimum inhibitory concentration of 175 μM and the minimum bactericidal concentration of 350 μM. These results indicated that curcumin is a S. mutans UA159 sortase A inhibitor and therefore represents as a promising anticaries agent.
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115
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Hu P, Huang P, Chen MW. Curcumin reduces Streptococcus mutans biofilm formation by inhibiting sortase A activity. Arch Oral Biol 2013; 58:1343-8. [PMID: 23778072 DOI: 10.1016/j.archoralbio.2013.05.004] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 05/18/2013] [Accepted: 05/21/2013] [Indexed: 11/18/2022]
Abstract
BACKGROUND Sortase A is an enzyme responsible for the covalent attachment of Pac proteins to the cell wall in Streptococcus mutans. It has been shown to play a role in modulating the surface properties and the biofilm formation and influence the cariogenicity of S. mutans. Curcumin, an active ingredient of turmeric, was reported to be an inhibitor for Staphylococcus aureus sortase A. The aim of this study was to investigate the inhibitory ability of curcumin against S. mutans sortase A and the effect of curcumin for biofilm formation. METHODS The antimicrobial activity of the curcumin to the S. mutans and inhibitory ability of the curcumin against the purified sortase A in vitro were detected. Western-blot and real-time PCR were used to analysis the sortase A mediated Pac protein changes when the S. mutans was cultured with curcumin. The curcumin on the S. mutans biofilm formation was determined by biofilm formation analysis. RESULTS Curcumin can inhibit purified S. mutans sortase A with a half-maximal inhibitory concentration (IC50) of (10.2±0.7)μmol/l, which is lower than minimum inhibitory concentration (MIC) of 175μmol/l. Curcumin (15μmol/l) was found to release the Pac protein to the supernatant and reduce S. mutans biofilm formation. CONCLUSIONS These results indicated that curcumin is an S. mutans sortase A inhibitor and has promising anti-caries characteristics through an anti-adhesion-mediated mechanism.
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Affiliation(s)
- Ping Hu
- Center of Stomatology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China.
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116
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Abstract
The 2A proteinase (2A(pro)) is an enterovirally encoded cysteine protease that plays essential roles in both the processing of viral precursor polyprotein and the hijacking of host cell translation and other processes in the virus life cycle. Crystallographic studies of 2A(pro) from enterovirus 71 (EV71) and its interaction with the substrate are reported here. EV71 2A(pro) was comprised of an N-terminal domain of a four-stranded antiparallel β sheet and a C-terminal domain of a six-stranded antiparallel β barrel with a tightly bound zinc atom. Unlike in other 2A(pro) structures, there is an open cleft across the surface of the protein in an open conformation. As demonstrated by the crystallographic studies and modeling of the complex structure, the open cleft could be fitted with the substrate. On comparison 2A(pro) of EV71 to those of the human rhinovirus 2 and coxsackievirus B4, the open conformation could be closed with a hinge motion in the bII2 and cII β strands. This was supported by molecular dynamic simulation. The structural variation among different 2A(pro) structures indicates a conformational flexibility in the substrate-binding cleft. The open structure provides an accessible framework for the design and development of therapeutics against the viral target.
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117
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Yi X, Hao Y, Ning X, Wang J, Quintero M, Li D, Zhou F. Sensitive and continuous screening of inhibitors of β-site amyloid precursor protein cleaving enzyme 1 (BACE1) at single SPR chips. Anal Chem 2013; 85:3660-6. [PMID: 23432118 PMCID: PMC3635668 DOI: 10.1021/ac303624z] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The development of new methods that meet the demand of high-throughput, high-fidelity screening of hit compounds is important to researching modalities of important diseases such as neurological disorders, HIV, and cancer. A surface plasmon resonance- (SPR-) based method capable of continuously screening enzyme inhibitors at a single chip with antibody-amplified signal enhancement has been developed. The proof of concept is demonstrated by monitoring the cleavage of chip-confined peptide substrates [a segment of the amyloid precursor protein (APP) with the Swiss mutation] by β-site APP-cleaving enzyme 1 (BACE1). In the presence of a noninhibitor, BACE1 clips the peptide substrate at the cleavage site, detaching a fragment that is homologous to the N-terminus of the amyloid beta (Aβ) peptide. Consequently, a subsequent injection of the Aβ antibody does not lead to any molecular recognition or SPR signal change at the chip. In contrast, suppression of the BACE1 activity by a strong inhibitor leaves the peptide substrate intact, and the subsequent antibody attachment produces an easily detectable SPR signal. Compared to the widely used FRET (fluorescence resonance energy transfer) assay, the method reported here is more cost-effective, as unlabeled peptide is used as the BACE1 substrate. Furthermore, the assay is faster (each screening cycle lasts for ca. 1.5 h) and can be continuously carried out at a single, regenerable SPR chip for more than 30 h. Consequently, excellent reproducibility (RSD < 5%) and throughput can be attained. Two inhibitors were screened, and their half-maximal inhibitory concentrations (IC50) determined by the SPR method were in excellent agreement with values deduced from ELISA and mass spectrometry.
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Affiliation(s)
- Xinyao Yi
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, P. R. China 410083
| | - Yuanqiang Hao
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, California 90032
| | - Xia Ning
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, California 90032
| | - Jianxiu Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, P. R. China 410083
| | - Monica Quintero
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, California 90032
| | - Ding Li
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, P. R. China 410083
| | - Feimeng Zhou
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, P. R. China 410083
- Department of Chemistry and Biochemistry, California State University, Los Angeles, Los Angeles, California 90032
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118
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Ko E, Raghuraman A, Perez LM, Ioerger TR, Burgess K. Exploring key orientations at protein-protein interfaces with small molecule probes. J Am Chem Soc 2013; 135:167-73. [PMID: 23270593 PMCID: PMC3551583 DOI: 10.1021/ja3067258] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecule probes that selectively perturb protein-protein interactions (PPIs) are pivotal to biomedical science, but their discovery is challenging. We hypothesized that conformational resemblance of semirigid scaffolds expressing amino acid side-chains to PPI-interface regions could guide this process. Consequently, a data mining algorithm was developed to sample huge numbers of PPIs to find ones that match preferred conformers of a selected semirigid scaffold. Conformations of one such chemotype (1aaa; all methyl side-chains) matched several biomedically significant PPIs, including the dimerization interface of HIV-1 protease. On the basis of these observations, four molecules 1 with side-chains corresponding to the matching HIV-1 dimerization interface regions were prepared; all four inhibited HIV-1 protease via perturbation of dimerization. These data indicate this approach may inspire design of small molecule interface probes to perturb PPIs.
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Affiliation(s)
- Eunhwa Ko
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
| | - Arjun Raghuraman
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
| | - Lisa M. Perez
- Laboratory for Molecular Simulation, Texas A & M University, Box 30012, College Station, TX 77842
| | - Thomas R. Ioerger
- Department of Computer Science, Texas A & M University, College Station, TX 77843-3112
| | - Kevin Burgess
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842
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119
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Suaifan GARY, Esseghaier C, Ng A, Zourob M. Ultra-rapid colorimetric assay for protease detection using magnetic nanoparticle-based biosensors. Analyst 2013; 138:3735-9. [DOI: 10.1039/c3an36881e] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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120
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4862F, a new inhibitor of HIV-1 protease, from the culture of Streptomyces I03A-04862. Molecules 2012; 18:236-43. [PMID: 23271463 PMCID: PMC6269790 DOI: 10.3390/molecules18010236] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 12/14/2012] [Accepted: 12/18/2012] [Indexed: 11/17/2022] Open
Abstract
We have isolated an extraordinary pentapeptide, called 4862F, from the culture broth of Streptomyces albosporus I03A-04862 by Diaion HP-20 macroporous adsorbent resin column, ODS-A and Sephadex LH-20 chromatography, followed by preparative HPLC. This peptide shows inhibitory activity against HIV-1 protease. The structure was elucidated by spectroscopic approaches, including ESI-MS and various NMR methods. Absolute configuration of the amino acid residues in 4862F was defined using Marfey’s method, and the structure was identified as N,N,N-(trimethylated)-Tyr-L-Leu-L-Val-L-Leu-(dehydrated)-His. The peptide 4862F displays inhibitory activity against HIV-1 protease, with IC50 values of 15.26 nM, using a fluorescence-based assay.
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121
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Hutter KJ, Miedl M, Kuhmann B, Nitzsche F, Bryce JH, Stewart GG. Detection of Proteinases inSaccharomyces cerevisiaeby Flow Cytometry. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2005.tb00645.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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122
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Regioselective fluorescent labeling of N,N,N-trimethyl chitosan via oxime formation. Carbohydr Polym 2012; 90:1273-80. [DOI: 10.1016/j.carbpol.2012.06.070] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 06/14/2012] [Accepted: 06/23/2012] [Indexed: 11/23/2022]
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123
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A drug discovery platform: a simplified immunoassay for analyzing HIV protease activity. J Virol Methods 2012; 186:21-9. [PMID: 22846787 DOI: 10.1016/j.jviromet.2012.07.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2011] [Revised: 07/17/2012] [Accepted: 07/18/2012] [Indexed: 01/09/2023]
Abstract
Although numerous methods for the determination of HIV protease (HIV-PR) activity have been described, new high-throughput assays are required for clinical and pharmaceutical applications due to the occurrence of resistant strains. In this study, a simple enzymatic immunoassay to identify HIV-PR activity was developed based on a Ni(2+)-immobilized His(6)-Matrix-Capsid substrate (H(6)MA-CA) is cleaved by HIV protease-His(6) (HIV-PRH(6)) which removes the CA domain and exposes the free C terminus of MA. Following this cleavage, two monoclonal antibodies specific for either the free C-terminal MA or CA epitope are used to quantify the proteolytic activity using a standard ELISA-based system. Specificity for detection of the HIV-PRH(6) activity was confirmed with addition of protease inhibitor (PI), lopinavir. In addition, the assay was able to detect an HIV-PR variant activity indicating that this assay is capable of assessing viral mutation affect HIV-PR activity. The efficacy of commercially available PIs and their 50% inhibitory concentration (IC(50)) were determined. This assay provides a high-throughput method for both validating the efficiency of new drugs in vitro and facilitating the discovery of new PIs. In addition, it could serve as a method for examining the influence of various mutations in HIV-PRs isolated from drug-resistant strains.
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Parai MK, Huggins DJ, Cao H, Nalam MNL, Ali A, Schiffer CA, Tidor B, Rana TM. Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance. J Med Chem 2012; 55:6328-41. [PMID: 22708897 PMCID: PMC3409094 DOI: 10.1021/jm300238h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of new HIV-1 protease inhibitors (PIs) were designed using a general strategy that combines computational structure-based design with substrate-envelope constraints. The PIs incorporate various alcohol-derived P2 carbamates with acyclic and cyclic heteroatomic functionalities into the (R)-hydroxyethylamine isostere. Most of the new PIs show potent binding affinities against wild-type HIV-1 protease and three multidrug resistant (MDR) variants. In particular, inhibitors containing the 2,2-dichloroacetamide, pyrrolidinone, imidazolidinone, and oxazolidinone moieties at P2 are the most potent with K(i) values in the picomolar range. Several new PIs exhibit nanomolar antiviral potencies against patient-derived wild-type viruses from HIV-1 clades A, B, and C and two MDR variants. Crystal structure analyses of four potent inhibitors revealed that carbonyl groups of the new P2 moieties promote extensive hydrogen bond interactions with the invariant Asp29 residue of the protease. These structure-activity relationship findings can be utilized to design new PIs with enhanced enzyme inhibitory and antiviral potencies.
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Affiliation(s)
- Maloy Kumar Parai
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - David J. Huggins
- Department of Biological Engineering and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Hong Cao
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Akbar Ali
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Bruce Tidor
- Department of Biological Engineering and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Tariq M. Rana
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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125
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Marcotte PA, Davidsen SK. Characterization of matrix metalloproteinase inhibitors: enzymatic assays. ACTA ACUST UNITED AC 2012; Chapter 3:Unit3.7. [PMID: 21959756 DOI: 10.1002/0471141755.ph0307s13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The matrix metalloproteinases (MMPs) are a family of tightly regulated proteases that are involved in the catabolic aspect of remodeling and maintenance of normal tissue, and more than 20 human MMPs have been identified thus far. The MMPs collectively degrade a broad range of protein components of the extracellular matrix. While some substrate overlap exists, individual MMPs have been shown to process certain substrates more efficiently than others. These differences raise the critical issue of whether broad-spectrum inhibitors, active against all MMPs, or selective inhibitors, targeted to a subset of enzymes, represent the optimal therapeutic strategy for a given disease. This suggests the need to assess the inhibition potency of test compounds across a range of MMP family members. Described in this unit is a method for the in vitro characterization of MMP inhibitors. The is used to determine the potency of test compounds as inhibitors of 8 representative MMPs through the measurement of their inhibition of cleavage of a fluorogenic substrate. Since this substrate is efficiently hydrolyzed by all MMPs in the screening assays presented here, the method is convenient for assessing the selectivity of inhibitors against multiple enzymes. A describes the activation of MMP zymogens.
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126
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Alvizo O, Mittal S, Mayo SL, Schiffer CA. Structural, kinetic, and thermodynamic studies of specificity designed HIV-1 protease. Protein Sci 2012; 21:1029-41. [PMID: 22549928 DOI: 10.1002/pro.2086] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/23/2012] [Accepted: 04/10/2012] [Indexed: 02/02/2023]
Abstract
HIV-1 protease recognizes and cleaves more than 12 different substrates leading to viral maturation. While these substrates share no conserved motif, they are specifically selected for and cleaved by protease during viral life cycle. Drug resistant mutations evolve within the protease that compromise inhibitor binding but allow the continued recognition of all these substrates. While the substrate envelope defines a general shape for substrate recognition, successfully predicting the determinants of substrate binding specificity would provide additional insights into the mechanism of altered molecular recognition in resistant proteases. We designed a variant of HIV protease with altered specificity using positive computational design methods and validated the design using X-ray crystallography and enzyme biochemistry. The engineered variant, Pr3 (A28S/D30F/G48R), was designed to preferentially bind to one out of three of HIV protease's natural substrates; RT-RH over p2-NC and CA-p2. In kinetic assays, RT-RH binding specificity for Pr3 increased threefold compared to the wild-type (WT), which was further confirmed by isothermal titration calorimetry. Crystal structures of WT protease and the designed variant in complex with RT-RH, CA-p2, and p2-NC were determined. Structural analysis of the designed complexes revealed that one of the engineered substitutions (G48R) potentially stabilized heterogeneous flap conformations, thereby facilitating alternate modes of substrate binding. Our results demonstrate that while substrate specificity could be engineered in HIV protease, the structural pliability of protease restricted the propagation of interactions as predicted. These results offer new insights into the plasticity and structural determinants of substrate binding specificity of the HIV-1 protease.
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Affiliation(s)
- Oscar Alvizo
- Division of Biology, Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, California 91125, USA
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127
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Gravestock D, Rousseau AL, Lourens AC, Hoppe HC, Nkabinde LA, Bode ML. Novel branched isocyanides as useful building blocks in the Passerini-amine deprotection-acyl migration (PADAM) synthesis of potential HIV-1 protease inhibitors. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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128
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Lu S, Wang H, Sheng Y, Liu M, Chen P. Molecular binding of self-assembling peptide EAK16-II with anticancer agent EPT and its implication in cancer cell inhibition. J Control Release 2012; 160:33-40. [DOI: 10.1016/j.jconrel.2012.03.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 03/07/2012] [Accepted: 03/11/2012] [Indexed: 01/08/2023]
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129
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Kim CJ, Lee DI, Lee CH, Ahn IS. A dityrosine-based substrate for a protease assay: Application for the selective assessment of papain and chymopapain activity. Anal Chim Acta 2012; 723:101-7. [DOI: 10.1016/j.aca.2012.02.038] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 02/06/2012] [Accepted: 02/18/2012] [Indexed: 11/15/2022]
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130
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Matsuoka K, Arai H, Oka H, Koyama T, Hatano K. Synthetic Assembly of Bifluorescence-Labeled Glycopolymers as Substrates for Assaying α-Amylase by Resonance Energy Transfer. ACS Macro Lett 2012; 1:266-269. [PMID: 35578520 DOI: 10.1021/mz200135y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To meet the need for a convenient substrate for sensitive and continuous assay for α-amylase, we developed a fluorescence resonance energy transfer (FRET)-based polymer substrate. Radical copolymerization of FRET-component monomers in different ratios of fluorogenic donor and acceptor was utilized to prepare such polymers. A glycomonomer as a fluorogenic donor was derived from naphthylmethylated maltotetraose, and a dansyl derivative monomer was used as an acceptor. Their mixture and acryl amide were copolymerized in a typical radical polymerization to yield a bifluorescence-labeled polymer in good yield. All of the polymers showed effective FRET and were used for the continuous assay of human salivary α-amylase. The time course of α-amylase reactions led to the apparent kinetic parameters of Km = 4 μM and Vmax = 0.29 nmol/min. The results strongly suggested that FRET-sensitive polymers are conveniently accessible and applicable for the sensitive determination of biochemical events.
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Affiliation(s)
- Koji Matsuoka
- Area for Molecular Function,
Division of
Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
| | - Hirokatsu Arai
- Area for Molecular Function,
Division of
Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
| | - Hiroyuki Oka
- Area for Molecular Function,
Division of
Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
| | - Tetsuo Koyama
- Area for Molecular Function,
Division of
Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
| | - Ken Hatano
- Area for Molecular Function,
Division of
Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
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131
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Huang X, Swierczewska M, Choi KY, Zhu L, Bhirde A, Park J, Kim K, Xie J, Niu G, Lee KC, Lee S, Chen X. Multiplex imaging of an intracellular proteolytic cascade by using a broad-spectrum nanoquencher. Angew Chem Int Ed Engl 2012; 51:1625-30. [PMID: 22213412 PMCID: PMC3622558 DOI: 10.1002/anie.201107795] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2011] [Revised: 12/13/2011] [Indexed: 12/20/2022]
Affiliation(s)
- Xinglu Huang
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH, USA)
| | - Magdalena Swierczewska
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH, USA)
- Department of Biomedical Engineering, Stony Brook University (USA)
| | - Ki Young Choi
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH, USA)
| | - Lei Zhu
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH, USA)
| | - Ashwinkumar Bhirde
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH, USA)
| | | | - Kwangmeyung Kim
- Center for Theragnosis, Korea Institute of Science and Technology (KIST, Korea)
| | - Jin Xie
- Department of Chemistry and Bio-Imaging Research Center, University of Georgia (USA)
| | - Gang Niu
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH, USA)
| | | | - Seulki Lee
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH, USA)
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine (LOMIN), National Institute of Biomedical Imaging and Bioengineering (NIBIB), National Institutes of Health (NIH, USA)
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132
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Yan GW, Chen Y, Li Y, Chen HF. Revealing interaction mode between HIV-1 protease and mannitol analog inhibitor. Chem Biol Drug Des 2012; 79:916-25. [PMID: 22296911 DOI: 10.1111/j.1747-0285.2012.01348.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
HIV protease is a key enzyme to play a key role in the HIV-1 replication cycle and control the maturation from HIV viruses to an infectious virion. HIV-1 protease has become an important target for anti-HIV-1 drug development. Here, we used molecular dynamics simulation to study the binding mode between mannitol derivatives and HIV-1 protease. The results suggest that the most active compound (M35) has more stable hydrogen bonds and stable native contacts than the less active one (M17). These mannitol derivatives might have similar interaction mode with HIV-1 protease. Then, 3D-QSAR was used to construct quantitative structure-activity models. The cross-validated q(2) values are found as 0.728 and 0.611 for CoMFA and CoMSIA, respectively. And the non-cross-validated r(2) values are 0.973 and 0.950. Nine test set compounds validate the model. The results show that this model possesses better prediction ability than the previous work. This model can be used to design new chemical entities and make quantitative prediction of the bioactivities for HIV-1 protease inhibitors before resorting to in vitro and in vivo experiment.
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Affiliation(s)
- Guan-Wen Yan
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, China
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133
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Multiplex Imaging of an Intracellular Proteolytic Cascade by using a Broad-Spectrum Nanoquencher. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107795] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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134
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Zhang Y, Chen W, Feng D, Shi W, Li X, Ma H. A spectroscopic off-on probe for simple and sensitive detection ofcarboxylesterase activity and its application to cell imaging. Analyst 2012; 137:716-21. [DOI: 10.1039/c2an15952j] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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135
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Short peptides as biosensor transducers. Anal Bioanal Chem 2011; 402:3055-70. [DOI: 10.1007/s00216-011-5589-8] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/25/2011] [Accepted: 11/20/2011] [Indexed: 12/27/2022]
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136
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Crisalli P, Kool ET. Multi-path quenchers: efficient quenching of common fluorophores. Bioconjug Chem 2011; 22:2345-54. [PMID: 22034828 DOI: 10.1021/bc200424r] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Fluorescence quenching groups are widely employed in biological detection, sensing, and imaging. To date, a relatively small number of such groups are in common use. Perhaps the most commonly used quencher, dabcyl, has limited efficiency with a broad range of fluorophores. Here, we describe a molecular approach to improve the efficiency of quenchers by increasing their electronic complexity. Multi-Path Quenchers (MPQ) are designed to have multiple donor or acceptor groups in their structure, allowing for a multiplicity of conjugation pathways of varied length. This has the effect of broadening the absorption spectrum, which in turn can increase quenching efficiency and versatility. Six such MPQ derivatives are synthesized and tested for quenching efficiency in a DNA hybridization context. Duplexes placing quenchers and fluorophores within contact distance or beyond this distance are used to measure quenching via contact or FRET mechanisms. Results show that several of the quenchers are considerably more efficient than dabcyl at quenching a wider range of common fluorophores, and two quench fluorescein and TAMRA as well as or better than a Black Hole Quencher.
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Affiliation(s)
- Pete Crisalli
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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137
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Buzon MJ, Erkizia I, Pou C, Minuesa G, Puertas MC, Esteve A, Castello A, Santos JR, Prado JG, Izquierdo-Useros N, Pattery T, Van Houtte M, Carrasco L, Clotet B, Ruiz L, Martinez-Picado J. A non-infectious cell-based phenotypic assay for the assessment of HIV-1 susceptibility to protease inhibitors. J Antimicrob Chemother 2011; 67:32-8. [PMID: 21994909 DOI: 10.1093/jac/dkr433] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES HIV-1 genotyping is widely accepted as a diagnostic tool to optimize therapy changes in patients whose antiretroviral regimen is failing. Phenotyping can substantially complement the information obtained from genotyping, especially in the presence of complex mutational patterns. However, drug susceptibility tests are laborious and require biosafety facilities. We describe the molecular mechanism of a non-infectious HIV-1 protease phenotypic assay in eukaryotic cells and validate its applicability as a tool for monitoring drug resistance. METHODS A cloning vector containing the fusion protein green fluorescent protein-HIV-1 protease (GFP-PR) was modified to facilitate the insertion of HIV-1 protease from infected subjects. Real-time quantitative PCR and western blot analysis were used to establish the molecular mechanism of the new phenotypic assay. The method was validated by analysing HIV-1 protease from 46 clinical isolates. Statistical comparisons were made between values obtained using our assay and those reported from alternative standardized phenotypic assays. RESULTS The capacity of HIV-1 protease to cleave cellular translation factors, such as the eukaryotic translation initiation factor 4 (eIF4GI) and the poly(A)-binding protein (PABP), led to cyclical accumulation of GFP that varied with the dose of protease inhibitors. Validation and comparison revealed a significant correlation with the Virco TYPE HIV-1 test (P < 0.0001, Spearman's ρ = 0.60), the Antivirogram test (P = 0.0001, Spearman's ρ = 0.60) and the Stanford HIVdb (P < 0.0001, Spearman's ρ = 0.69). CONCLUSIONS This cell-based non-infectious phenotypic method with a well-understood molecular mechanism was highly reliable and comparable to other widely used assays. The method can be used for both phenotyping of HIV-1 viral isolates resistant to protease inhibitors and screening of new protease inhibitors.
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Affiliation(s)
- Maria José Buzon
- Institut de Recerca de SIDA (IrsiCaixa), Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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138
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Terentyeva TG, Van Rossom W, Van der Auweraer M, Blank K, Hofkens J. Morpholinecarbonyl-Rhodamine 110 Based Substrates for the Determination of Protease Activity with Accurate Kinetic Parameters. Bioconjug Chem 2011; 22:1932-8. [DOI: 10.1021/bc2001038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tatyana G. Terentyeva
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Wim Van Rossom
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Mark Van der Auweraer
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
| | - Kerstin Blank
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
- Department of Molecular Materials, Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Johan Hofkens
- Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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139
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Makatini MM, Petzold K, Sriharsha SN, Ndlovu N, Soliman ME, Honarparvar B, Parboosing R, Naidoo A, Arvidsson PI, Sayed Y, Govender P, Maguire GE, Kruger HG, Govender T. Synthesis and structural studies of pentacycloundecane-based HIV-1 PR inhibitors: A hybrid 2D NMR and docking/QM/MM/MD approach. Eur J Med Chem 2011; 46:3976-85. [DOI: 10.1016/j.ejmech.2011.05.071] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/26/2011] [Accepted: 05/28/2011] [Indexed: 10/18/2022]
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140
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Abstract
The early detection of many human diseases is crucial if they are to be treated successfully. Therefore, the development of imaging techniques that can facilitate early detection of disease is of high importance. Changes in the levels of enzyme expression are known to occur in many diseases, making their accurate detection at low concentrations an area of considerable active research. Activatable fluorescent probes show immense promise in this area. If properly designed they should exhibit no signal until they interact with their target enzyme, reducing the level of background fluorescence and potentially endowing them with greater sensitivity. The mechanisms of fluorescence changes in activatable probes vary. This review aims to survey the field of activatable probes, focusing on their mechanisms of action as well as illustrating some of the in vitro and in vivo settings in which they have been employed.
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Affiliation(s)
- Christopher R Drake
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 185 Berry Street, Suite 350, Box 0946, San Francisco, CA, 94107, USA
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141
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Kasana RC, Salwan R, Yadav SK. Microbial proteases: Detection, production, and genetic improvement. Crit Rev Microbiol 2011; 37:262-76. [DOI: 10.3109/1040841x.2011.577029] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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142
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Jiang Y, Wong JH, Fu M, Ng TB, Liu ZK, Wang CR, Li N, Qiao WT, Wen TY, Liu F. Isolation of adenosine, iso-sinensetin and dimethylguanosine with antioxidant and HIV-1 protease inhibiting activities from fruiting bodies of Cordyceps militaris. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2011; 18:189-93. [PMID: 20576416 DOI: 10.1016/j.phymed.2010.04.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 12/17/2009] [Accepted: 04/27/2010] [Indexed: 05/21/2023]
Abstract
According to previous studies, a close relationship between oxidative stress and AIDS suggests that antioxidants might play an important role in the treatment of AIDS. Cordyceps militaris was selected from nine edible mushrooms by assay of inhibition of erythrocyte hemolysis. Macroporous adsorption resin and HPLC were used to purify three micromolecular compounds named L3a, L3b and L3c. L3a was identified to be adenosine with the molecular formula C(10)H(13)N(5)O(4); L3b was 6,7,2',4',5'-pentamethoxyflavone with the molecular formula C(20)H(20)O(7), and L3c was dimethylguanosine with the molecular formula C(12)H(17)N(5)O(5). The compound 6,7,2',4',5'-pentamethoxyflavone was first isolated from C. militaris. The assay of inhibition of HIV-1 protease (HIV-1 PR) was based on the fact that the expression of this enzyme can inhibit the growth of E. coli. This is a new screening system for HIV-1 PR inhibitors. Both L3a and L3b showed high inhibition to HIV-1 PR. These compounds could be new anti-HIV-1 PR drugs.
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Affiliation(s)
- Y Jiang
- Center for AIDS Research, Nankai University, Tianjin, China
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143
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Takahashi S, Ono H, Gotoh T, Yoshizawa-Kumagaye K, Sugiyama T. Novel internally quenched fluorogenic substrates for angiotensin I-converting enzyme and carboxypeptidase Y. Biomed Res 2011; 32:407-11. [DOI: 10.2220/biomedres.32.407] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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144
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Gabriel D, Zuluaga MF, Lange N. On the cutting edge: protease-sensitive prodrugs for the delivery of photoactive compounds. Photochem Photobiol Sci 2011; 10:689-703. [DOI: 10.1039/c0pp00341g] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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145
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Ali A, Kiran Kumar Reddy GS, Nalam MNL, Anjum SG, Cao H, Schiffer CA, Rana TM. Structure-based design, synthesis, and structure-activity relationship studies of HIV-1 protease inhibitors incorporating phenyloxazolidinones. J Med Chem 2010; 53:7699-708. [PMID: 20958050 PMCID: PMC2996262 DOI: 10.1021/jm1008743] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of new HIV-1 protease inhibitors with the hydroxyethylamine core and different phenyloxazolidinone P2 ligands were designed and synthesized. Variation of phenyl substitutions at the P2 and P2' moieties significantly affected the binding affinity and antiviral potency of the inhibitors. In general, compounds with 2- and 4-substituted phenyloxazolidinones at P2 exhibited lower binding affinities than 3-substituted analogues. Crystal structure analyses of ligand-enzyme complexes revealed different binding modes for 2- and 3-substituted P2 moieties in the protease S2 binding pocket, which may explain their different binding affinities. Several compounds with 3-substituted P2 moieties demonstrated picomolar binding affinity and low nanomolar antiviral potency against patient-derived viruses from HIV-1 clades A, B, and C, and most retained potency against drug-resistant viruses. Further optimization of these compounds using structure-based design may lead to the development of novel protease inhibitors with improved activity against drug-resistant strains of HIV-1.
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Affiliation(s)
- Akbar Ali
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - G. S. Kiran Kumar Reddy
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Saima Ghafoor Anjum
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Hong Cao
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Tariq M. Rana
- Chemical Biology Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605
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146
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Urru SAM, Veglianese P, De Luigi A, Fumagalli E, Erba E, Gonella Diaza R, Carrà A, Davoli E, Borsello T, Forloni G, Pengo N, Monzani E, Cascio P, Cenci S, Sitia R, Salmona M. A new fluorogenic peptide determines proteasome activity in single cells. J Med Chem 2010; 53:7452-60. [PMID: 20883027 DOI: 10.1021/jm100362x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ubiquitin-proteasome system plays a critical role in many diseases, making it an attractive biomarker and therapeutic target. However, the impact of results obtained in vitro using purified proteasome particles or whole cell extracts is limited by the lack of efficient methods to assess proteasome activity in living cells. We have engineered an internally quenched fluorogenic peptide with a proteasome-specific cleavage motif fused to TAT and linked to the fluorophores DABCYL and EDANS. This peptide penetrates cell membranes and is rapidly cleaved by the proteasomal chymotrypsin-like activity, generating a quantitative fluorescent reporter of in vivo proteasome activity as assessed by time-lapse or flow cytometry fluorescence analysis. This reporter is an innovative tool for monitoring proteasomal proteolytic activities in physiological and pathological conditions.
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Affiliation(s)
- Silvana A M Urru
- Istituto di Ricerche Farmacologiche Mario Negri, Via La Masa 19, Milan 20156, Italy
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147
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Rhee HW, Lee SH, Shin IS, Choi SJ, Park HH, Han K, Park TH, Hong JI. Detection of kinase activity using versatile fluorescence quencher probes. Angew Chem Int Ed Engl 2010; 49:4919-23. [PMID: 20540130 DOI: 10.1002/anie.201000879] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hyun-Woo Rhee
- Department of Chemistry, School of Chemical & Biological Engineering, Seoul National University, Seoul 151-747, Korea
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148
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Lovell JF, Liu TWB, Chen J, Zheng G. Activatable photosensitizers for imaging and therapy. Chem Rev 2010; 110:2839-57. [PMID: 20104890 DOI: 10.1021/cr900236h] [Citation(s) in RCA: 1230] [Impact Index Per Article: 87.9] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jonathan F Lovell
- Institute of Biomaterials and Biomedical Engineering, Ontario Cancer Institute, University of Toronto, Ontario M5G 1L7, Canada
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149
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Small photoactivatable molecules for controlled fluorescence activation in living cells. Bioorg Med Chem 2010; 19:1023-9. [PMID: 20675143 DOI: 10.1016/j.bmc.2010.07.011] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 07/01/2010] [Accepted: 07/07/2010] [Indexed: 11/23/2022]
Abstract
The search for chemical probes which allow a controlled fluorescence activation in living cells represent a major challenge in chemical biology. To be useful, such probes have to be specifically targeted to cellular proteins allowing thereof the analysis of dynamic aspects of this protein in its cellular environment. The present paper describes different methods which have been developed to control cellular fluorescence activation emphasizing the photochemical activation methods known to be orthogonal to most cellular components and, in addition, allowing a spatio-temporal controlled triggering of the fluorescent signal.
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150
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Zhao X, Liu R, Chi Z, Teng Y, Qin P. New insights into the behavior of bovine serum albumin adsorbed onto carbon nanotubes: comprehensive spectroscopic studies. J Phys Chem B 2010; 114:5625-31. [PMID: 20373820 DOI: 10.1021/jp100903x] [Citation(s) in RCA: 361] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bovine serum albumin (BSA) nonspecifically binds to well-dispersed multiwalled carbon nanotubes (MWCNTs), forming a stable bioconjugate. After accounting for the inner filter effect, we found the fluorescence intensity of BSA was quenched by MWCNTs in static mode, which was authenticated by lifetime measurements and Stern-Volmer calculations. The thermodynamic parameters DeltaG(o), DeltaS(o), and DeltaH(o) were -9.67 x 10(3) + 2.48 x 10(3) ln lambda J x mol(-1), 41.0 - 0.828 ln lambda J x mol(-1) x K(-1), and 7.30 x 10(3) + 2.23 x 10(3) ln lambda J x mol(-1) (lambda < 1 x 10(-4)), respectively, which shows a spontaneous and electrostatic interaction. Scatchard analysis and UV-visible results provide statistical data concerning changes in the microenvironment of amide moieties in response to different doses of MWCNTs, revealing different behavior of the BSA molecules. The absorption spectra also show that the tertiary structure of the protein was partially destroyed. The content of secondary structure elements of BSA was changed by the tubes. This work elucidates the interaction mechanism of BSA and MWCNTs from a spectroscopic angle.
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Affiliation(s)
- Xingchen Zhao
- School of Environmental Science and Engineering, Shandong University, 27 Shanda South Road, Jinan 250100, PR China
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