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Nao SC, Huang LS, Shiu-Hin Chan D, Wang X, Li GD, Wu J, Wong CY, Wang W, Leung CH. Repurposing sodium stibogluconate as an uracil DNA glycosylase inhibitor against prostate cancer using a time-resolved oligonucleotide-based drug screening platform. Bioorg Chem 2024; 144:107176. [PMID: 38330721 DOI: 10.1016/j.bioorg.2024.107176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
Repurposing drugs can significantly reduce the time and costs associated with drug discovery and development. However, many drug compounds possess intrinsic fluorescence, resulting in aberrations such as auto-fluorescence, scattering and quenching, in fluorescent high-throughput screening assays. To overcome these drawbacks, time-resolved technologies have received increasing attention. In this study, we have developed a rapid and efficient screening platform based on time-resolved emission spectroscopy in order to screen for inhibitors of the DNA repair enzyme, uracil-DNA glycosylase (UDG). From a database of 1456 FDA/EMA-approved drugs, sodium stibogluconate was discovered as a potent UDG inhibitor. This compound showed synergistic cytotoxicity against 5-fluorouracil-resistant cancer cells. This work provides a promising future for time-resolved technologies for high-throughput screening (HTS), allowing for the swift identification of bioactive compounds from previously overlooked scaffolds due to their inherent fluorescence properties.
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Affiliation(s)
- Sang-Cuo Nao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Le-Sheng Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | | | - Xueliang Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China
| | - Guo-Dong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China
| | - Chun-Yuen Wong
- Department of Chemistry, City University of Hong Kong, Hong Kong, China.
| | - Wanhe Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi'an, Shaanxi 710072, China; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, 45 South Gaoxin Road, Shenzhen 518057, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau 999078, China; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau, China; Macao Centre for Research and Development in Chinese Medicine, University of Macau, Taipa, Macau, China; MoE Frontiers Science Centre for Precision Oncology, University of Macau, Taipa, Macau, China.
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2
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Liu L, Han C, Jiang M, Zhang T, Kang Q, Wang X, Wang P, Zhou F. Rapid and regenerable surface plasmon resonance determinations of biomarker concentration and biomolecular interaction based on tris-nitrilotriacetic acid chips. Anal Chim Acta 2021; 1170:338625. [PMID: 34090589 DOI: 10.1016/j.aca.2021.338625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 12/22/2022]
Abstract
The tris-nitrilotriacetic acid (tris-NTA) chip has been used for surface plasmon resonance (SPR) kinetic studies involving histidine (His)-tagged proteins. However, its full potential, especially for analyte quantification in complex biological media, has not been realized due to a lack of systematic studies on the factors governing ligand immobilization, surface regeneration, and data analysis. We demonstrate that the tris-NTA chip not only retains His-tagged proteins more strongly than its mono-NTA counterpart, but also orients them more uniformly than protein molecules coupled to carboxymethylated dextran films. We accurately and rapidly quantified immunoglobulin (IgG) molecules in sera by using the initial association phase of their conjugation with His-tagged protein G densely immobilized onto the tris-NTA chip, and established criteria for selecting the optimal time for constructing the calibration curve. The method is highly reproducible (less than 2% RSD) and three orders of magnitude more sensitive than immunoturbidimetry. In addition, we found that the amount of His-protein immobilized is highly dependent on the protein isoelectric point (pI). Reliable kinetic data in a multi-channel SPR instrument can also be rapidly obtained by using a low density of immobilized His-tagged protein. The experimental parameters and procedures outlined in this study help expand the range of SPR applications involving His-tagged proteins.
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Affiliation(s)
- Luyao Liu
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, 250022, PR China
| | - Chaowei Han
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, 250022, PR China
| | - Meng Jiang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, 250022, PR China
| | - Tiantian Zhang
- University Hospital, University of Jinan, Jinan, Shandong, 250022, PR China
| | - Qing Kang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, 250022, PR China
| | - Xiaoying Wang
- State Key Laboratory of Biobased Materials and Green Papermaking, Qilu University of Technology, Jinan, Shandong, 250353, PR China
| | - Pengcheng Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, 250022, PR China.
| | - Feimeng Zhou
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, 250022, PR China.
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3
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Perera S, Fernando A, Dallman J, Weeramange C, Lansakara A, Nguyen T, Rafferty RJ. Construction and Biological Evaluation of Small Libraries Based on the Intermediates within the Total Synthesis of Uvaretin. ChemMedChem 2021; 16:1631-1639. [PMID: 33491867 DOI: 10.1002/cmdc.202001010] [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: 12/30/2020] [Indexed: 11/12/2022]
Abstract
Discovering therapeutic agents: New bioactive agents, either as sole or combinational agents, have been constructed through the synthetic manipulation of the intermediates within the total synthesis of the uvaretin class of natural products. It was found that increasing the hydrophobic character of the phenolic core correlates to a decrease in sole agent cytotoxicity. The synthesis of new, small chemical screening libraries (CSL) constructed from the intermediates of our total synthesis route of the uvaretin class of natural products is demonstrated herein. Numerous chalcone-based CSLs with various substitution on the phenolic groups within the chalcone core were assembled. Through cytotoxicity investigations, it was found that the level of hydrophobicity of the phenolic core of the chalcones gives biases: less cytotoxicity with more hydrophobic cores. In addition, it was observed that the potentiation, evaluated with 6-thiopurine in the pancreatic cancer cell line MIA PaCa-2, is tunable by the inclusion of less-hydrophobic character on the phenolic core. The role of the o-hydroxybenzyl group, present within the uvaretin family, was revealed to be cytotoxic in character. Merging all of the structure-activity relationship studies performed on the CSLs constructed in this effort led to the construction of a new chalcone hybrid possessing both a cytotoxic enone group and a small-molecule-potentiating, reduced enone group.
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Affiliation(s)
- Shashika Perera
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Asantha Fernando
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Johnathan Dallman
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Chamitha Weeramange
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Ashabha Lansakara
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Thi Nguyen
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - Ryan J Rafferty
- Department of Chemistry, Kansas State University, 1212 Mid-Campus Drive North, Manhattan, KS 66506, USA
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4
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Howell LA, Beekman AM. In silico peptide-directed ligand design complements experimental peptide-directed binding for protein-protein interaction modulator discovery. RSC Chem Biol 2021; 2:215-219. [PMID: 34458784 PMCID: PMC8341744 DOI: 10.1039/d0cb00148a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/07/2020] [Indexed: 12/27/2022] Open
Abstract
Using the protein-protein interaction of Mcl-1/Noxa, two methods for efficient modulator discovery are directly compared. In silico peptide-directed ligand design is evaluated against experimental peptide-directed binding, allowing for the discovery of two new inhibitors of Mcl-1/Noxa with cellular activity. In silico peptide-directed ligand design demonstrates an in vitro hit rate of 80% (IC50 < 100 μM). The two rapid and efficient methods demonstrate complementary features for protein-protein interaction modulator discovery.
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Affiliation(s)
- Lesley Ann Howell
- School of Biological and Chemical Sciences, Queen Mary University of London Mile End Road London E1 4NS UK
| | - Andrew Michael Beekman
- School of Pharmacy, University of East Anglia, Norwich Research Park Norwich Norfolk NR47TJ UK
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5
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Amouzadeh Tabrizi M, Ferré-Borrull J, Marsal LF. Highly sensitive aptasensor based on interferometric reflectance spectroscopy for the determination of amyloid β as an Alzheimer's disease biomarkers using nanoporous anodic alumina. Biosens Bioelectron 2019; 137:279-286. [PMID: 31125817 DOI: 10.1016/j.bios.2019.04.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 02/06/2023]
Abstract
It is well known that Alzheimer's disease is one of the global challenges for the 21st century. Therefore, it is urgent to develop a reliable biosensor for the detection of this disease. Here in, we have developed for the first time, an aptasensor based on interferometric reflectance spectroscopy (IRS) for the determination of amyloid β (Aβ) oligomers that is an Alzheimer's disease biomarker. For this purpose, the nanoporous anodic alumina (NAA) was first fabricated. After that, the pore walls of the NAA were modified with (3-aminopropyl) trimethoxysilane (NAA-NH2). The amino-terminal aptamers probe were then attached to the pore walls of the NAA-NH2 by using glutaraldehyde (GA) as the cross-linking agent. Subsequently, methylene blue (MB) was immobilized into the aptamer as the photo-probe, generating the MB/G-quadruplex complex. Since MB has a high absorption coefficient, the intensity of the reflected white light to the charge-coupled device (CCD) detector decreased. In the presence of the Aβ oligomers that have high affinity to the immobilized aptamer, the MB/quadruplex complex broke and MB washed away from the aptasensor. Therefore, the intensity of the reflected white light to the CCD detector increased. The increased signal intensity of the aptasensor has a logarithmic relationship with the concentration of Aβ oligomers. The proposed aptasensor exhibited a good response to the concentration of Aβ oligomers in the range of 0.5-50.0 μg × mL-1. The experimental detection limit was of 0.02 μg × mL-1 (at 3σ/S). The proposed optical aptasensor exhibited good selectivity, linear range, and stability.
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Affiliation(s)
- Mahmoud Amouzadeh Tabrizi
- Departamento de Ingeniería Electrónica, Eléctrica y Automática, Universitat Rovira i Virgili, Avda. Països Catalans 26, 43007 Tarragona, Spain
| | - Josep Ferré-Borrull
- Departamento de Ingeniería Electrónica, Eléctrica y Automática, Universitat Rovira i Virgili, Avda. Països Catalans 26, 43007 Tarragona, Spain
| | - Lluis F Marsal
- Departamento de Ingeniería Electrónica, Eléctrica y Automática, Universitat Rovira i Virgili, Avda. Països Catalans 26, 43007 Tarragona, Spain.
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6
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Assessing molecular interactions with biophysical methods using the validation cross. Biochem Soc Trans 2018; 47:63-76. [DOI: 10.1042/bst20180271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/09/2018] [Accepted: 11/19/2018] [Indexed: 11/17/2022]
Abstract
Abstract
There are numerous methods for studying molecular interactions. However, each method gives rise to false negative- or false positive binding results, stemming from artifacts of the scientific equipment or from shortcomings of the experimental format. To validate an initial positive binding result, additional methods need to be applied to cover the shortcomings of the primary experiment. The aim of such a validation procedure is to exclude as many artifacts as possible to confirm that there is a true molecular interaction that meets the standards for publishing or is worth investing considerable resources for follow-up activities in a drug discovery project. To simplify this validation process, a graphical scheme — the validation cross — can be used. This simple graphic is a powerful tool for identifying blind spots of a binding hypothesis, for selecting the most informative combination of methods to reveal artifacts and, in general, for understanding more thoroughly the nature of a validation process. The concept of the validation cross was originally introduced for the validation of protein–ligand interactions by NMR in drug discovery. Here, an attempt is made to expand the concept to further biophysical methods and to generalize it for binary molecular interactions.
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7
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Carro L. Protein-protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics. Beilstein J Org Chem 2018; 14:2881-2896. [PMID: 30546472 PMCID: PMC6278769 DOI: 10.3762/bjoc.14.267] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/02/2018] [Indexed: 12/11/2022] Open
Abstract
Antibiotics are potent pharmacological weapons against bacterial infections; however, the growing antibiotic resistance of microorganisms is compromising the efficacy of the currently available pharmacotherapies. Even though antimicrobial resistance is not a new problem, antibiotic development has failed to match the growth of resistant pathogens and hence, it is highly critical to discover new anti-infective drugs with novel mechanisms of action which will help reducing the burden of multidrug-resistant microorganisms. Protein–protein interactions (PPIs) are involved in a myriad of vital cellular processes and have become an attractive target to treat diseases. Therefore, targeting PPI networks in bacteria may offer a new and unconventional point of intervention to develop novel anti-infective drugs which can combat the ever-increasing rate of multidrug-resistant bacteria. This review describes the progress achieved towards the discovery of molecules that disrupt PPI systems in bacteria for which inhibitors have been identified and whose targets could represent an alternative lead discovery strategy to obtain new anti-infective molecules.
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Affiliation(s)
- Laura Carro
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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8
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Choi JW, Jo BG, deMello AJ, Choo J, Kim HY. Streptavidin-triggered signal amplified fluorescence polarization for analysis of DNA-protein interactions. Analyst 2018; 141:6499-6502. [PMID: 27841380 DOI: 10.1039/c6an01671e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fluorescence polarization (FP) is a sensitive, robust, and homogeneous assay format, able to probe a diversity of biological molecules and their interactions. Herein, we describe a new FP strategy based on the use of streptavidin as a signal amplifier. Such signal amplified fluorescence polarization (SAFP) was used to monitor the binding affinity of human angiogenin and a single-stranded DNA aptamer. Streptavidin was bound to a biotinylated single-stranded DNA aptamer and the interaction between this complex and Alexa Fluor 488 labelled human angiogenin was measured. A dissociation constant of 135.3 ± 32.9 nM and a limit of detection of 6.3 nM were successfully extracted only when the FP signal was increased (without binding hindrance) via streptavidin. Moreover, the demonstrated approach was specific to target molecules without any non-specific binding. The streptavidin-triggered SAFP method unlike amplification strategies that utilize nanomaterials (such as graphene oxides, carbon nanotubes, and metal nanoparticles) is not compromised by fluorescence quenching, and it is able to operate within nanomolar concentration regimes. Furthermore, unlike the other FP signal amplification strategies that use dual binding DNA probes, the presented method is simple to implement with signal amplification only requiring the binding of streptavidin with biotinylated DNA. This method could be expanded to analyze molecular interactions and it may be a useful tool for FP measurement by reducing the concentration of rare and expensive protein samples.
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Affiliation(s)
- Jae-Won Choi
- Department of Biochemistry, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Byung-Gwan Jo
- Department of Biochemistry, Chungbuk National University, Cheongju 28644, Republic of Korea.
| | - Andrew J deMello
- Department of Chemistry & Applied Biosciences, ETH Zürich, Vladimir Prelog Weg 1, 8039 Zürich, Switzerland.
| | - Jaebum Choo
- Department of Bionano Technology, Hanyang University, Ansan 15588, Republic of Korea.
| | - Hak Yong Kim
- Department of Biochemistry, Chungbuk National University, Cheongju 28644, Republic of Korea.
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9
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Target Identification of Bioactive Covalently Acting Natural Products. Curr Top Microbiol Immunol 2018; 420:351-374. [PMID: 30105423 DOI: 10.1007/82_2018_121] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There are countless natural products that have been isolated from microbes, plants, and other living organisms that have been shown to possess therapeutic activities such as antimicrobial, anticancer, or anti-inflammatory effects. However, developing these bioactive natural products into drugs has remained challenging in part because of their difficulty in isolation, synthesis, mechanistic understanding, and off-target effects. Among the large pool of bioactive natural products lies classes of compounds that contain potential reactive electrophilic centers that can covalently react with nucleophilic amino acid hotspots on proteins and other biological molecules to modulate their biological action. Covalently acting natural products are more amenable to rapid target identification and mapping of specific druggable hotspots within proteins using activity-based protein profiling (ABPP)-based chemoproteomic strategies. In addition, the granular biochemical insights afforded by knowing specific sites of protein modifications of covalently acting natural products enable the pharmacological interrogation of these sites with more synthetically tractable covalently acting small molecules whose structures are more easily tuned. Both discovering binding pockets and targets hit by natural products and exploiting druggable modalities targeted by natural products with simpler molecules may overcome some of the challenges faced with translating natural products into drugs.
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10
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Peterson RD, Wilund KR, Cunningham BT, Andrade JE. Comparison of Methods Study between a Photonic Crystal Biosensor and Certified ELISA to Measure Biomarkers of Iron Deficiency in Chronic Kidney Disease Patients. SENSORS 2017; 17:s17102203. [PMID: 28946680 PMCID: PMC5677296 DOI: 10.3390/s17102203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 12/30/2022]
Abstract
The total analytical error of a photonic crystal (PC) biosensor in the determination of ferritin and soluble transferrin receptor (sTfR) as biomarkers of iron deficiency anemia in chronic kidney disease (CKD) patients was evaluated against certified ELISAs. Antigens were extracted from sera of CKD patients using functionalized iron-oxide nanoparticles (fAb-IONs) followed by magnetic separation. Immuno-complexes were recognized by complementary detection Ab affixed to the PC biosensor surface, and their signals were followed using the BIND instrument. Quantification was conducted against actual protein standards. Total calculated error (TEcalc) was estimated based on systematic (SE) and random error (RE) and compared against total allowed error (TEa) based on established quality specifications. Both detection platforms showed adequate linearity, specificity, and sensitivity for biomarkers. Means, SD, and CV were similar between biomarkers for both detection platforms. Compared to ELISA, inherent imprecision was higher on the PC biosensor for ferritin, but not for sTfR. High SE or RE in the PC biosensor when measuring either biomarker resulted in TEcalc higher than the TEa. This did not influence the diagnostic ability of the PC biosensor to discriminate CKD patients with low iron stores. The performance of the PC biosensor is similar to certified ELISAs; however, optimization is required to reduce TEcalc.
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Affiliation(s)
- Ross D Peterson
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Kenneth R Wilund
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Brian T Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Juan E Andrade
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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11
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Choi S, Choi KY. Screening-based approaches to identify small molecules that inhibit protein–protein interactions. Expert Opin Drug Discov 2017; 12:293-303. [DOI: 10.1080/17460441.2017.1280456] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sehee Choi
- Translational Research Center for Protein Function Control, Yonsei University, Seoul, Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
| | - Kang-Yell Choi
- Translational Research Center for Protein Function Control, Yonsei University, Seoul, Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea
- CK Biotechnology Inc., 416 Advanced Science and Technology Center, 50 Yonsei-ro, Seoul, Korea
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12
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Kuang M, Wang J, Jiang L. Bio-inspired photonic crystals with superwettability. Chem Soc Rev 2016; 45:6833-6854. [DOI: 10.1039/c6cs00562d] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This review focus on the recent developments in the mechanism, fabrication and application of bio-inspired PCs with superwettability.
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Affiliation(s)
- Minxuan Kuang
- Laboratory of Bio-inspired Smart Interface Science
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Jingxia Wang
- Laboratory of Bio-inspired Smart Interface Science
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
| | - Lei Jiang
- Laboratory of Bio-inspired Smart Interface Science
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- P. R. China
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13
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Enhanced sandwich immunoassay using antibody-functionalized magnetic iron-oxide nanoparticles for extraction and detection of soluble transferrin receptor on a photonic crystal biosensor. Biosens Bioelectron 2015; 74:815-22. [DOI: 10.1016/j.bios.2015.07.050] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 07/20/2015] [Accepted: 07/22/2015] [Indexed: 11/17/2022]
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14
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Basiri-Esfahani S, Myers CR, Armin A, Combes J, Milburn GJ. Integrated quantum photonic sensor based on Hong-Ou-Mandel interference. OPTICS EXPRESS 2015; 23:16008-16023. [PMID: 26193575 DOI: 10.1364/oe.23.016008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Photonic-crystal-based integrated optical systems have been used for a broad range of sensing applications with great success. This has been motivated by several advantages such as high sensitivity, miniaturization, remote sensing, selectivity and stability. Many photonic crystal sensors have been proposed with various fabrication designs that result in improved optical properties. In parallel, integrated optical systems are being pursued as a platform for photonic quantum information processing using linear optics and Fock states. Here we propose a novel integrated Fock state optical sensor architecture that can be used for force, refractive index and possibly local temperature detection. In this scheme, two coupled cavities behave as an "effective beam splitter". The sensor works based on fourth order interference (the Hong-Ou-Mandel effect) and requires a sequence of single photon pulses and consequently has low pulse power. Changes in the parameter to be measured induce variations in the effective beam splitter reflectivity and result in changes to the visibility of interference. We demonstrate this generic scheme in coupled L3 photonic crystal cavities as an example and find that this system, which only relies on photon coincidence detection and does not need any spectral resolution, can estimate forces as small as 10(-7) Newtons and can measure one part per million change in refractive index using a very low input power of 10(-10)W. Thus linear optical quantum photonic architectures can achieve comparable sensor performance to semiclassical devices.
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15
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Blakskjaer P, Heitner T, Hansen NJV. Fidelity by design: Yoctoreactor and binder trap enrichment for small-molecule DNA-encoded libraries and drug discovery. Curr Opin Chem Biol 2015; 26:62-71. [PMID: 25732963 DOI: 10.1016/j.cbpa.2015.02.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/13/2015] [Accepted: 02/02/2015] [Indexed: 01/26/2023]
Abstract
DNA-encoded small-molecule library (DEL) technology allows vast drug-like small molecule libraries to be efficiently synthesized in a combinatorial fashion and screened in a single tube method for binding, with an assay readout empowered by advances in next generation sequencing technology. This approach has increasingly been applied as a viable technology for the identification of small-molecule modulators to protein targets and as precursors to drugs in the past decade. Several strategies for producing and for screening DELs have been devised by both academic and industrial institutions. This review highlights some of the most significant and recent strategies along with important results. A special focus on the production of high fidelity DEL technologies with the ability to eliminate screening noise and false positives is included: using a DNA junction called the Yoctoreactor, building blocks (BBs) are spatially confined at the center of the junction facilitating both the chemical reaction between BBs and encoding of the synthetic route. A screening method, known as binder trap enrichment, permits DELs to be screened robustly in a homogeneous manner delivering clean data sets and potent hits for even the most challenging targets.
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Affiliation(s)
| | - Tara Heitner
- Vipergen ApS, Gammel Kongevej 23A, 1610 Copenhagen V, Denmark
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16
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Alonso N, Guillen R, Chambers JW, Leng F. A rapid and sensitive high-throughput screening method to identify compounds targeting protein-nucleic acids interactions. Nucleic Acids Res 2015; 43:e52. [PMID: 25653160 PMCID: PMC4417145 DOI: 10.1093/nar/gkv069] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 01/19/2015] [Indexed: 01/09/2023] Open
Abstract
DNA-binding and RNA-binding proteins are usually considered ‘undruggable’ partly due to the lack of an efficient method to identify inhibitors from existing small molecule repositories. Here we report a rapid and sensitive high-throughput screening approach to identify compounds targeting protein–nucleic acids interactions based on protein–DNA or protein–RNA interaction enzyme-linked immunosorbent assays (PDI-ELISA or PRI-ELISA). We validated the PDI-ELISA method using the mammalian high-mobility-group protein AT-hook 2 (HMGA2) as the protein of interest and netropsin as the inhibitor of HMGA2–DNA interactions. With this method we successfully identified several inhibitors and an activator for HMGA2–DNA interactions from a collection of 29 DNA-binding compounds. Guided by this screening excise, we showed that netropsin, the specific inhibitor of HMGA2–DNA interactions, strongly inhibited the differentiation of the mouse pre-adipocyte 3T3-L1 cells into adipocytes, most likely through a mechanism by which the inhibition is through preventing the binding of HMGA2 to the target DNA sequences. This method should be broadly applicable to identify compounds or proteins modulating many DNA-binding or RNA-binding proteins.
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Affiliation(s)
- Nicole Alonso
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, FL 33199, USA
| | - Roboan Guillen
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, FL 33199, USA
| | - Jeremy W Chambers
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Fenfei Leng
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA Department of Chemistry & Biochemistry, Florida International University, 11200 SW 8th Street, FL 33199, USA
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17
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Moon H, Lim HS. Synthesis and screening of small-molecule α-helix mimetic libraries targeting protein–protein interactions. Curr Opin Chem Biol 2015; 24:38-47. [DOI: 10.1016/j.cbpa.2014.10.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 12/11/2022]
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18
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Harvey AL, Edrada-Ebel R, Quinn RJ. The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 2015; 14:111-29. [PMID: 25614221 DOI: 10.1038/nrd4510] [Citation(s) in RCA: 1495] [Impact Index Per Article: 166.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein-protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.
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Affiliation(s)
- Alan L Harvey
- 1] Research and Innovation Support, Dublin City University, Dublin 9, Ireland. [2] Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Science, University of Strathclyde, Glasgow G4 0NR, UK
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Queensland 4111, Australia
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19
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Zhu H, Laveille P, Rosenfeld DC, Hedhili MN, Basset JM. A high-throughput reactor system for optimization of Mo–V–Nb mixed oxide catalyst composition in ethane ODH. Catal Sci Technol 2015. [DOI: 10.1039/c5cy00488h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
75 Mo–V–Nb mixed oxide catalysts with a broad range of compositions were tested using a high-throughput reactor in order to optimize the composition for the ethane oxidative dehydrogenation reaction.
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Affiliation(s)
- Haibo Zhu
- KAUST Catalysis Center
- King Abdullah University of Science and Technology
- Kingdom of Saudi Arabia
| | - Paco Laveille
- KAUST Catalysis Center
- King Abdullah University of Science and Technology
- Kingdom of Saudi Arabia
| | | | - Mohamed Nejib Hedhili
- KAUST Core Lab
- King Abdullah University of Science and Technology
- Kingdom of Saudi Arabia
| | - Jean-Marie Basset
- KAUST Catalysis Center
- King Abdullah University of Science and Technology
- Kingdom of Saudi Arabia
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20
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Potential pharmacological chaperones targeting cancer-associated MCL-1 and Parkinson disease-associated α-synuclein. Proc Natl Acad Sci U S A 2014; 111:11007-12. [PMID: 25024216 DOI: 10.1073/pnas.1320556111] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pharmacological chaperones are small molecules that bind to proteins and stabilize them against thermal denaturation or proteolytic degradation, as well as assist or prevent certain protein-protein assemblies. These activities are being exploited for the development of treatments for diseases caused by protein instability and/or aberrant protein-protein interactions, such as those found in certain forms of cancers and neurodegenerative diseases. However, designing or discovering pharmacological chaperones for specific targets is challenging because of the relatively featureless protein target surfaces, the lack of suitable chemical libraries, and the shortage of efficient high-throughput screening methods. In this study, we attempted to address all these challenges by synthesizing a diverse library of small molecules that mimic protein α-helical secondary structures commonly found in protein-protein interaction surfaces. This was accompanied by establishing a facile "on-bead" high-throughput screening method that allows for rapid and efficient discovery of potential pharmacological chaperones and for identifying novel chaperones/inhibitors against a cancer-associated protein, myeloid cell leukemia 1 (MCL-1), and a Parkinson disease-associated protein, α-synuclein. Our data suggest that the compounds and methods described here will be useful tools for the development of pharmaceuticals for complex-disease targets that are traditionally deemed "undruggable."
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21
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Dias AD, Kingsley DM, Corr DT. Recent advances in bioprinting and applications for biosensing. BIOSENSORS 2014; 4:111-36. [PMID: 25587413 PMCID: PMC4264374 DOI: 10.3390/bios4020111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 04/12/2014] [Accepted: 04/18/2014] [Indexed: 12/19/2022]
Abstract
Future biosensing applications will require high performance, including real-time monitoring of physiological events, incorporation of biosensors into feedback-based devices, detection of toxins, and advanced diagnostics. Such functionality will necessitate biosensors with increased sensitivity, specificity, and throughput, as well as the ability to simultaneously detect multiple analytes. While these demands have yet to be fully realized, recent advances in biofabrication may allow sensors to achieve the high spatial sensitivity required, and bring us closer to achieving devices with these capabilities. To this end, we review recent advances in biofabrication techniques that may enable cutting-edge biosensors. In particular, we focus on bioprinting techniques (e.g., microcontact printing, inkjet printing, and laser direct-write) that may prove pivotal to biosensor fabrication and scaling. Recent biosensors have employed these fabrication techniques with success, and further development may enable higher performance, including multiplexing multiple analytes or cell types within a single biosensor. We also review recent advances in 3D bioprinting, and explore their potential to create biosensors with live cells encapsulated in 3D microenvironments. Such advances in biofabrication will expand biosensor utility and availability, with impact realized in many interdisciplinary fields, as well as in the clinic.
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Affiliation(s)
- Andrew D Dias
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA; E-Mails: (A.D.D.); (D.M.K.)
| | - David M Kingsley
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA; E-Mails: (A.D.D.); (D.M.K.)
| | - David T Corr
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth St., Troy, NY 12180, USA; E-Mails: (A.D.D.); (D.M.K.)
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22
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Milroy LG, Grossmann TN, Hennig S, Brunsveld L, Ottmann C. Modulators of Protein–Protein Interactions. Chem Rev 2014; 114:4695-748. [DOI: 10.1021/cr400698c] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lech-Gustav Milroy
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Tom N. Grossmann
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Sven Hennig
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn Straße 15, 44227 Dortmund, Germany
| | - Luc Brunsveld
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology and Institute of Complex Molecular Systems, Department
of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech
2, 5612 AZ Eindhoven, The Netherlands
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23
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Nero TL, Morton CJ, Holien JK, Wielens J, Parker MW. Oncogenic protein interfaces: small molecules, big challenges. Nat Rev Cancer 2014; 14:248-62. [PMID: 24622521 DOI: 10.1038/nrc3690] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Historically, targeting protein-protein interactions with small molecules was not thought possible because the corresponding interfaces were considered mostly flat and featureless and therefore 'undruggable'. Instead, such interactions were targeted with larger molecules, such as peptides and antibodies. However, the past decade has seen encouraging breakthroughs through the refinement of existing techniques and the development of new ones, together with the identification and exploitation of unexpected aspects of protein-protein interaction surfaces. In this Review, we describe some of the latest techniques to discover modulators of protein-protein interactions and how current drug discovery approaches have been adapted to successfully target these interfaces.
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Affiliation(s)
- Tracy L Nero
- Australian Cancer Research Foundation Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Craig J Morton
- Australian Cancer Research Foundation Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Jessica K Holien
- Australian Cancer Research Foundation Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia
| | - Jerome Wielens
- 1] Australian Cancer Research Foundation Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia. [2] Department of Medicine, University of Melbourne, 41 Victoria Parade, Fitzroy, Victoria 3065, Australia
| | - Michael W Parker
- 1] Australian Cancer Research Foundation Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St. Vincent's Institute of Medical Research, 9 Princes Street, Fitzroy, Victoria 3065, Australia. [2] Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3052, Australia
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24
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Fenzl C, Hirsch T, Wolfbeis OS. Photonische Kristalle für die Chemo- und Biosensorik. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307828] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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25
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Fenzl C, Hirsch T, Wolfbeis OS. Photonic crystals for chemical sensing and biosensing. Angew Chem Int Ed Engl 2014; 53:3318-35. [PMID: 24473976 DOI: 10.1002/anie.201307828] [Citation(s) in RCA: 360] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Indexed: 01/03/2023]
Abstract
This Review covers photonic crystals (PhCs) and their use for sensing mainly chemical and biochemical parameters, with a particular focus on the materials applied. Specific sections are devoted to a) a lead-in into natural and synthetic photonic nanoarchitectures, b) the various kinds of structures of PhCs, c) reflection and diffraction in PhCs, d) aspects of sensing based on mechanical, thermal, optical, electrical, magnetic, and purely chemical stimuli, e) aspects of biosensing based on biomolecules incorporated into PhCs, and f) current trends and limitations of such sensors.
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Affiliation(s)
- Christoph Fenzl
- Institut für Analytische Chemie, Chemo- und Biosensorik, Universität Regensburg, 93040 Regensburg (Germany) http://www.wolfbeis.de
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26
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A photonic crystal biosensor assay for ferritin utilizing iron-oxide nanoparticles. Biosens Bioelectron 2014; 56:320-7. [PMID: 24530833 DOI: 10.1016/j.bios.2014.01.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/05/2014] [Accepted: 01/13/2014] [Indexed: 01/25/2023]
Abstract
Iron deficiency anemia afflicts 1 in 3 individuals, mostly women and children worldwide. A novel application using iron-oxide nanoparticles (IONPs) and a photonic crystal (PC) optical biosensor as an immunodiagnostic platform for detection of serum ferritin, a biomarker for iron deficiency, is presented. Human liver ferritin (450 kDa), clinical serum controls, and three commercially available ferritin ELISA tests were used to evaluate the PC biosensor assay in terms of inter- and intra-assay variability, spike-recovery (%), limit of detection (LOD), and matrix effects on binding. For the PC biosensor, signal response from label-free, sandwich with secondary antibody (pAb), and pAb functionalized with iron-oxide nanoparticles (FpAb) assays were detected using the Biomolecular Interaction Detection (BIND) system. Bland-Altman analysis was used to evaluate agreement between expected values for ferritin in control sera and each of the detection platforms. Inter- and intra-assay variability of the PC biosensor were both <10%. Percent mean recovery (±%RSD) of ferritin from two control sera samples were 94.3% (13.1%) and 96.9% (7.6%). Use of FpAb in PC biosensor resulted in two orders of magnitude increase in sensitivity compared to label-free assay; capable of measuring serum ferritin as low as 26 ng/mL. In comparison to ELISA tests, the PC biosensor assay had the lowest bias (-1.26; 95% CI [-3.0-5.5]) and narrower limit of agreement (-11.6-9.1 ng/mL) when determining ferritin concentrations from control sera. These proof-of-concept studies support the use of IONPs to enhance detection sensitivity of PC biosensors for determination of biomarkers of nutritional status.
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27
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Rafferty RJ, Hicklin RW, Maloof KA, Hergenrother PJ. Synthesis of complex and diverse compounds through ring distortion of abietic acid. Angew Chem Int Ed Engl 2013; 53:220-4. [PMID: 24273016 DOI: 10.1002/anie.201308743] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Indexed: 11/11/2022]
Abstract
Many compound screening collections are populated by members that possess a low degree of structural complexity. In an effort to generate compounds that are both complex and diverse, we have developed a strategy that uses natural products as a starting point for complex molecule synthesis. Herein we apply this complexity-to-diversity approach to abietic acid, an abundant natural product used commercially in paints, varnishes, and lacquers. From abietic acid we synthesize a collection of complex (as assessed by fraction of sp(3) -hybridized carbons and number of stereogenic centers) and diverse (as assessed by Tanimoto analysis) small molecules. The 84 compounds constructed herein, and those created through similar efforts, should find utility in a variety of biological screens.
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Affiliation(s)
- Ryan J Rafferty
- Department of Chemistry, University of Illinois at Urbana-Champaign, 261 RAL, Box 36-5, 600 S. Mathews, Urbana, IL 61801 (USA)
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28
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Rafferty RJ, Hicklin RW, Maloof KA, Hergenrother PJ. Synthesis of Complex and Diverse Compounds through Ring Distortion of Abietic Acid. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308743] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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29
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Fenzl C, Wilhelm S, Hirsch T, Wolfbeis OS. Optical sensing of the ionic strength using photonic crystals in a hydrogel matrix. ACS APPLIED MATERIALS & INTERFACES 2013; 5:173-178. [PMID: 23211147 DOI: 10.1021/am302355g] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Monodisperse, highly negatively charged, cross-linked polystyrene nanoparticles with diameters between 80 and 120 nm have been incorporated into a polyacrylamide hydrogel, where they display an iridescent color that conventionally is attributed to the so-called photonic crystal effect. The film is of red color if placed in plain water but turns to green in the presence of a 1 mM solution of an electrolyte such as sodium chloride and to purple in 100 mM solutions of electrolytes. Quantitative reflection spectroscopy was performed at various wavelengths and resulted in plots of reflected light wavelength versus ionic strength (IS) that are almost linear in the logarithmic concentration range from 5 × 10(-5) to 10(-2) mol·L(-1). We show that such films are capable of monitoring the IS of aqueous solutions in the pH range from 5 to 9. We also show that, in addition to visual and instrumental readout, the sensor films can be analyzed with a digital camera at fixed angle. The digital images were separated into their red, green, and blue channels and analyzed. The red channel was found to be best suited for determination of the IS and resulted in calibration plots that are comparable if not better than those obtained by reflectometry.
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Affiliation(s)
- Christoph Fenzl
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, 93040 Regensburg, Germany
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30
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Ponterini G. Fluorescence Observables and Enzyme Kinetics in the Investigation of PPI Modulation by Small Molecules: Detection, Mechanistic Insight, and Functional Consequences. DISRUPTION OF PROTEIN-PROTEIN INTERFACES 2013. [PMCID: PMC7123529 DOI: 10.1007/978-3-642-37999-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The potential of fluorescence-based methods and kinetic analysis in the screening and molecular-scale mechanistic investigation of PPI modulation by small molecules is discussed through several representative examples collected and commented. These experimental approaches take advantage of a variety of observables. Changes in the protein aggregation pattern have been monitored through fluorescence properties such as spectra, intensities (related to quantum yields), time-decays, and anisotropies of intrinsic protein fluorophores, of extrinsic fluorescent tags and, even, of the same small molecules added to modulate PPIs, as well as through bimolecular excited-state processes such as static and collisional quenching, including electron and excitation-energy transfer, or exciton interaction, whose efficiencies are crucially structure dependent. Besides allowing for qualitative and quantitative information on the small-molecule induced PPI modulation, these approaches can take advantage from the sensitivity of fluorescence observables on fine structural details to shed light on the molecular-scale mechanisms of action and their functional consequences. Direct investigation of the latter by kinetic inhibition analysis represents a useful change in perspective whenever PPI are relevant for enzyme activity. Dissociative inhibition, that is, the ability of some small molecules to inhibit enzymes by disrupting their active oligomeric assembly is shortly reviewed.
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31
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Martins SAM, Trabuco JRC, Monteiro GA, Chu V, Conde JP, Prazeres DMF. Towards the miniaturization of GPCR-based live-cell screening assays. Trends Biotechnol 2012; 30:566-74. [PMID: 22921755 DOI: 10.1016/j.tibtech.2012.07.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/23/2012] [Accepted: 07/24/2012] [Indexed: 01/13/2023]
Abstract
G protein-coupled receptors (GPCRs) play a key role in many physiological or disease-related processes and for this reason are favorite targets of the pharmaceutical industry. Although ~30% of marketed drugs target GPCRs, their potential remains largely untapped. The discovery of new leads calls for the screening of thousands of compounds with high-throughput cell-based assays. Although microtiter plate-based high-throughput screening platforms are well established, microarray and microfluidic technologies hold potential for miniaturization, automation, and biosensor integration that may well redefine the format of GPCR screening assays. This paper reviews the latest research efforts directed to bringing microarray and microfluidic technologies into the realm of GPCR-based, live-cell screening assays.
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Affiliation(s)
- Sofia A M Martins
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Department of Bioengineering, Instituto Superior Técnico, Technical University of Lisbon, 1049-001 Lisbon, Portugal
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32
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Fang Y. Ligand-receptor interaction platforms and their applications for drug discovery. Expert Opin Drug Discov 2012; 7:969-88. [PMID: 22860803 DOI: 10.1517/17460441.2012.715631] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
INTRODUCTION The study of drug-target interactions is essential for the understanding of biological processes and for the efforts to develop new therapeutic molecules. Increased ligand-binding assays have coincided with the advances in reagents, detection and instrumentation technologies, the expansion in therapeutic targets of interest, and the increasingly recognized importance of biochemical aspects of drug-target interactions in determining the clinical performance of drug molecules. Nowadays, ligand-binding assays can determine every aspect of many drug-target interactions. AREAS COVERED Given that ligand-target interactions are very diverse, the author has decided to focus on the binding of small molecules to protein targets. This article first reviews the key biochemical aspects of drug-target interactions, and then discusses the detection principles of various ligand-binding techniques in the context of their primary applications for drug discovery and development. EXPERT OPINION Equilibrium-binding affinity should not be used as a solo indicator for the in vivo pharmacology of drugs. The clinical relevance of drug-binding kinetics demands high throughput kinetics early in drug discovery. The dependence of ligand binding and function on the conformation of targets necessitates solution-based and whole cell-based ligand-binding assays. The increasing need to examine ligand binding at the proteome level, driven by the clinical importance of the polypharmacology of ligands, has started to make the structure-based in silico binding screen an indispensable technique for drug discovery and development. Integration of different ligand-binding assays is important to improve the efficiency of the drug discovery and development process.
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Affiliation(s)
- Ye Fang
- Biochemical Technologies, Science and Technology Division, Corning, Inc., Corning, NY 14831, USA.
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33
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Jeong YC, Jung B, Park JH, Park JK. A Fresnel zone plate biosensor for signal amplification with enhanced signal-to-noise ratio. Chem Commun (Camb) 2012; 48:6378. [PMID: 22617843 DOI: 10.1039/c2cc32008h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
We describe a signal amplified biosensor based on self-assembled optical diffraction grating of a Fresnel zone plate structure. Diffracted light rays passed through gratings are interfered constructively at the focal point, resulting in the enhanced signal amplification without sacrificing signal-to-noise ratio (SNR).
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Affiliation(s)
- Yong-Cheol Jeong
- Department of Chemical and Biomolecular Engineering, KAIST, 373-1, Daejeon, 305-701, Republic of Korea.
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34
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Developing peptide-based multivalent antagonists of proliferating cell nuclear antigen and a fluorescence-based PCNA binding assay. Anal Biochem 2012; 427:69-78. [PMID: 22522186 DOI: 10.1016/j.ab.2012.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 03/30/2012] [Accepted: 04/11/2012] [Indexed: 02/06/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) is a critical player in cell proliferation. It interacts with a myriad of cellular proteins in genomic DNA replication and cell cycle control. This makes PCNA an attractive target for developing antiproliferative therapeutics. Indeed, the binding of a human tumor suppressor protein, p21, to PCNA contributes to its antiproliferative effect in cells. In this work, we report a fluorescence polarization-based binding assay for determining the affinity between the p21 peptide and human PCNA. To improve the potency of the p21-based PCNA antagonist, we exploited the homotrimeric structure of PCNA and developed multivalent peptide-based PCNA antagonists. The di- and trivalent p21-based antagonists bind to PCNA with low nanomolar dissociation constant. Moreover, we show that the multivalent PCNA antagonists inhibited PCNA-dependent DNA synthesis in a human cell extract with improved avidity when compared with the monovalent p21 peptide. The fluorescence polarization assay holds promise for the discovery of potent small-molecule PCNA inhibitors given its ready adaptability to a high-throughput screening format.
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35
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O' Connor CJ, Beckmann HSG, Spring DR. Diversity-oriented synthesis: producing chemical tools for dissecting biology. Chem Soc Rev 2012; 41:4444-56. [DOI: 10.1039/c2cs35023h] [Citation(s) in RCA: 348] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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36
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Hieb AR, D'Arcy S, Kramer MA, White AE, Luger K. Fluorescence strategies for high-throughput quantification of protein interactions. Nucleic Acids Res 2011; 40:e33. [PMID: 22121211 PMCID: PMC3299996 DOI: 10.1093/nar/gkr1045] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Advances in high-throughput characterization of protein networks in vivo have resulted in large databases of unexplored protein interactions that occur during normal cell function. Their further characterization requires quantitative experimental strategies that are easy to implement in laboratories without specialized equipment. We have overcome many of the previous limitations to thermodynamic quantification of protein interactions, by developing a series of in-solution fluorescence-based strategies. These methods have high sensitivity, a broad dynamic range, and can be performed in a high-throughput manner. In three case studies we demonstrate how fluorescence (de)quenching and fluorescence resonance energy transfer can be used to quantitatively probe various high-affinity protein–DNA and protein–protein interactions. We applied these methods to describe the preference of linker histone H1 for nucleosomes over DNA, the ionic dependence of the DNA repair enzyme PARP1 in DNA binding, and the interaction between the histone chaperone Nap1 and the histone H2A–H2B heterodimer.
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Affiliation(s)
- Aaron R Hieb
- Howard Hughes Medical Institute and Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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