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Journal articles on the topic 'Affinity-Based probe'

Author: Grafiati

Published: 4 June 2021

Last updated: 9 February 2022

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1

Lafreniere, Matthew A., Geneviève F. Desrochers, Kedous Mekbib, and John Paul Pezacki. "An affinity-based probe for methyltransferase enzymes based on sinefungin." Canadian Journal of Chemistry 95, no. 10 (2017): 1059–63. http://dx.doi.org/10.1139/cjc-2017-0168.

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Epigenetics control numerous cellular processes such as gene transcription, signal transduction, and protein stabilization. An understanding of epigenetic mechanisms can lead to the development of therapeutic agents for various diseases. Herein, we report the design and synthesis of a sinefungin affinity-probe (BpyneSF) that targets methyltranferase enzymes and proteins involved in recognition of methylation. This probe contains a bioorthogonal alkyne residue for conjugation using the copper-catalyzed azide–alkyne cycloaddition and a photoactivatable crosslinker group for covalent attachment of the probe to its proteomic targets. We investigate the efficiency and selectivity of the probe to inhibit and label methyltransferase enzymes, and we demonstrate, through in-gel fluorescence, on-bead digestion, and tandem mass spectrometry, that BpyneSF can label methyltransferase SETD2 and reader proteins in vitro. These results establish the utility of BpyneSF as a tool for affinity-based protein profiling in complex biological environments.

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2

Tano, Hanna, Maryam Oroujeni, Anzhelika Vorobyeva, et al. "Comparative Evaluation of Novel 177Lu-Labeled PNA Probes for Affibody-Mediated PNA-Based Pretargeting." Cancers 13, no. 3 (2021): 500. http://dx.doi.org/10.3390/cancers13030500.

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Affibody-mediated PNA-based pretargeting is a promising approach to radionuclide therapy of HER2-expressing tumors. In this study, we test the hypothesis that shortening the PNA pretargeting probes would increase the tumor-to-kidney dose ratio. The primary probe ZHER2:342-SR-HP15 and the complementary secondary probes HP16, HP17, and HP18, containing 9, 12, and 15 nucleobases, respectively, and carrying a 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelator were designed, synthesized, characterized in vitro, and labeled with 177Lu. In vitro pretargeting was studied in HER2-expressing SKOV3 and BT474 cell lines. The biodistribution of these novel probes was evaluated in immunodeficient mice bearing SKOV3 xenografts and compared to the previously studied [177Lu]Lu-HP2. Characterization confirmed the formation of high-affinity duplexes between HP15 and the secondary probes, with the affinity correlating with the length of the complementary PNA sequences. All the PNA-based probes were bound specifically to HER2-expressing cells in vitro. In vivo studies demonstrated HER2-specific uptake of all 177Lu-labeled probes in xenografts in a pretargeting setting. The ratio of cumulated radioactivity in the tumor to the radioactivity in kidneys was dependent on the secondary probe’s size and decreased with an increased number of nucleobases. The shortest PNA probe, [177Lu]Lu-HP16, showed the highest tumor-to-kidney ratio. [177Lu]Lu-HP16 is the most promising secondary probe for affibody-mediated tumor pretargeting.

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3

Yang, Xue, Thomas J. M. Michiels, Coen de Jong, et al. "An Affinity-Based Probe for the Human Adenosine A2A Receptor." Journal of Medicinal Chemistry 61, no. 17 (2018): 7892–901. http://dx.doi.org/10.1021/acs.jmedchem.8b00860.

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4

Schiedel, Matthias, Tobias Rumpf, Berin Karaman, et al. "Structure-Based Development of an Affinity Probe for Sirtuin 2." Angewandte Chemie International Edition 55, no. 6 (2016): 2252–56. http://dx.doi.org/10.1002/anie.201509843.

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5

Qiao, Chunhua, Daniel J. Wilson, Eric M. Bennett, and Courtney C. Aldrich. "A Mechanism-Based Aryl Carrier Protein/Thiolation Domain Affinity Probe." Journal of the American Chemical Society 129, no. 20 (2007): 6350–51. http://dx.doi.org/10.1021/ja069201e.

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6

Stubbs, Keith A., and David J. Vocadlo. "Affinity-Based Proteomics Probes; Tools for Studying Carbohydrate-Processing Enzymes." Australian Journal of Chemistry 62, no. 6 (2009): 521. http://dx.doi.org/10.1071/ch09140.

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As more information becomes available through the efforts of high-throughput screens, there is increasing pressure on the three main ‘omic’ fields, genomics, proteomics, and metabolomics, to organize this material into useful libraries that enable further understanding of biological systems. Proteomics especially is faced with two highly challenging tasks. The first is assigning the activity of thousands of putative proteins, the existence of which has been suggested by genomics studies. The second is to serve as a link between genomics and metabolomics by demonstrating which enzymes play roles in specific metabolic pathways. Underscoring these challenges in one area are the thousands of putative carbohydrate-processing enzymes that have been bioinformatically identified, mostly in prokaryotes, but that have unknown or unverified activities. Using two brief examples, we illustrate how biochemical pathways within bacteria that involve carbohydrate-processing enzymes present interesting potential antimicrobial targets, offering a clear motivation for gaining a functional understanding of biological proteomes. One method for studying proteomes that has been developed recently is to use synthetic compounds termed activity-based proteomics probes. Activity-based proteomic profiling using such probes facilitates rapid identification of enzyme activities within proteomes and assignment of function to putative enzymes. Here we discuss the general design principles for these probes with particular reference to carbohydrate-processing enzymes and give an example of using such a probe for the profiling of a bacterial proteome.

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7

Chattopadhaya, Souvik, Elaine W. S. Chan, and Shao Q. Yao. "An affinity-based probe for the proteomic profiling of aspartic proteases." Tetrahedron Letters 46, no. 23 (2005): 4053–56. http://dx.doi.org/10.1016/j.tetlet.2005.04.015.

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8

Bi, Xihe, Anton Schmitz, Alaa M Hayallah, Jin-Na Song, and Michael Famulok. "Affinity-Based Labeling of Cytohesins with a Bifunctional SecinH3 Photoaffinity Probe." Angewandte Chemie International Edition 47, no. 49 (2008): 9565–68. http://dx.doi.org/10.1002/anie.200803962.

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9

Chakraborty, Goutam, Alok K. Ray, Prabhat K. Singh, and Haridas Pal. "A styryl based fluorogenic probe with high affinity for a cyclodextrin derivative." Organic & Biomolecular Chemistry 17, no. 28 (2019): 6895–904. http://dx.doi.org/10.1039/c9ob01349k.

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A styryl-based fluorogenic near-IR probe registers a very high association constant with sulfobutylether substituted β-cyclodextrin host, having prospects as biological marker and improved pH and temperature sensor.

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10

Palstrøm, Nicolai Bjødstrup, Lars Melholt Rasmussen, and Hans Christian Beck. "Affinity Capture Enrichment versus Affinity Depletion: A Comparison of Strategies for Increasing Coverage of Low-Abundant Human Plasma Proteins." International Journal of Molecular Sciences 21, no. 16 (2020): 5903. http://dx.doi.org/10.3390/ijms21165903.

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In the present study, we evaluated four small molecule affinity-based probes based on agarose-immobilized benzamidine (ABA), O-Phospho-L-Tyrosine (pTYR), 8-Amino-hexyl-cAMP (cAMP), or 8-Amino-hexyl-ATP (ATP) for their ability to remove high-abundant proteins such as serum albumin from plasma samples thereby enabling the detection of medium-to-low abundant proteins in plasma samples by mass spectrometry-based proteomics. We compared their performance with the most commonly used immunodepletion method, the Multi Affinity Removal System Human 14 (MARS14) targeting the top 14 most abundant plasma proteins and also the ProteoMiner protein equalization method by label-free quantitative liquid chromatography tandem mass spectrometry (LC-MSMS) analysis. The affinity-based probes demonstrated a high reproducibility for low-abundant plasma proteins, down to picomol per mL levels, compared to the Multi Affinity Removal System (MARS) 14 and the Proteominer methods, and also demonstrated superior removal of the majority of the high-abundant plasma proteins. The ABA-based affinity probe and the Proteominer protein equalization method performed better compared to all other methods in terms of the number of analyzed proteins. All the tested methods were highly reproducible for both high-abundant plasma proteins and low-abundant proteins as measured by correlation analyses of six replicate experiments. In conclusion, our results demonstrated that small-molecule based affinity-based probes are excellent alternatives to the commonly used immune-depletion methods for proteomic biomarker discovery studies in plasma. Data are available via ProteomeXchange with identifier PXD020727.

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11

Zambaldo, Claudio, Kalyan K. Sadhu, Ganesan Karthikeyan, Sofia Barluenga, Jean-Pierre Daguer, and Nicolas Winssinger. "Selective affinity-based probe for oncogenic kinases suitable for live cell imaging." Chemical Science 4, no. 5 (2013): 2088. http://dx.doi.org/10.1039/c3sc21856b.

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12

Chen, Weizhi, Baozhong Shen, and Xilin Sun. "Analysis of Progress and Challenges of EGFR-Targeted Molecular Imaging in Cancer With a Focus on Affibody Molecules." Molecular Imaging 18 (January 1, 2019): 153601211882347. http://dx.doi.org/10.1177/1536012118823473.

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Epidermal growth factor receptor (EGFR)-targeted cancer therapy requires an accurate estimation of EGFR expression in tumors to identify responsive patients, monitor therapeutic effect, and estimate prognosis. The EGFR molecular imaging is an optimal method for evaluating EGFR expression in vivo accurately and noninvasively. In this review, we discuss the recent advances in EGFR-targeted molecular imaging in cancer, with a special focus on the development of imaging agents, including epidermal growth factor (EGF) ligand, monoclonal antibodies, antibody fragments, Affibody, and small molecules. Each substrate or probe, whether it is an endogenous ligand, antibody, peptide, or small molecule labeled with fluorochrome or radionuclide, has unique advantages and limitations. Antibody-based probes have high affinity but a long metabolic cycle and therefore offer poor imaging quality. Affibody molecules promise to surpass antibody-based probes due to their small size, stable chemical properties, and high affinity to the target. Small-molecule probes are safe, have favorable pharmacokinetics, and show high affinity and specificity, in addition to having an ideal size, but are inadequate for delayed imaging after injection due to their fast clearance.

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13

Tam, Eric K. W., Zhengqiu Li, Yi Ling Goh, et al. "Cell-Based Proteome Profiling Using an Affinity-Based Probe (AfBP) Derived from 3-Deazaneplanocin A ()." Chemistry - An Asian Journal 8, no. 8 (2013): 1818–28. http://dx.doi.org/10.1002/asia.201300303.

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14

La, Ming, Yuanqiang Hao, Zhaoyang Wang, Guo-Cheng Han, and Lingbo Qu. "Selective and Sensitive Detection of Cyanide Based on the Displacement Strategy Using a Water-Soluble Fluorescent Probe." Journal of Analytical Methods in Chemistry 2016 (2016): 1–6. http://dx.doi.org/10.1155/2016/1462013.

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A water-soluble fluorescent probe (C-GGH) was used for the highly sensitive and selective detection of cyanide (CN−) in aqueous media based on the displacement strategy. Due to the presence of the recognition unit GGH (Gly-Gly-His), the probeC-GGH can coordinate with Cu2+and consequently display ON-OFF type fluorescence response. Furthermore, thein situformed nonfluorescentC-GGH-Cu2+complex can act as an effective OFF-ON type fluorescent probe for sensing CN−anion. Due to the strong binding affinity of CN−to Cu2+, CN−can extract Cu2+fromC-GGH-Cu2+complex, leading to the release ofC-GGH and the recovery of fluorescent emission of the system. The probeC-GGH-Cu2+allowed detection of CN−in aqueous solution with a LOD (limit of detection) of 0.017 μmol/L which is much lower than the maximum contaminant level (1.9 μmol/L) for CN−in drinking water set by the WHO (World Health Organization). The probe also displayed excellent specificity for CN−towards other anions, including F−, Cl−, Br−, I−, SCN−,PO43-,N3-,NO3-, AcO−,SO42-, andCO32-.

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15

Haes, Amanda J., Braden C. Giordano, and Greg E. Collins. "Aptamer-Based Detection and Quantitative Analysis of Ricin Using Affinity Probe Capillary Electrophoresis." Analytical Chemistry 78, no. 11 (2006): 3758–64. http://dx.doi.org/10.1021/ac060021x.

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16

Cheng, Xiamin, Lin Li, Mahesh Uttamchandani, and Shao Q. Yao. "A tuned affinity-based staurosporine probe for in situ profiling of protein kinases." Chemical Communications 50, no. 22 (2014): 2851. http://dx.doi.org/10.1039/c4cc00184b.

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17

Zhang, Song Bai, Bing Jun Zhang, Qian Liu, et al. "Electrochemical Aptasensor for Label-Free Detection of Protein Based on Gold Nanoparticle Involved Self-Assembly." Applied Mechanics and Materials 310 (February 2013): 177–82. http://dx.doi.org/10.4028/www.scientific.net/amm.310.177.

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A label-free electrochemical biosensing strategy based on gold nanoparticle involved layer-by-layer self assembly for the detection of protein is proposed using platelet derived growth factor-BB dimer (PDGF-BB) as the model analyte. Utilizing the strong sulfur-Au affinity, ethanthiol and capture probe modified gold nanoparticles are self-assembled onto the surface of gold electrode successively. The aptamer probe for target protein hybridizes with the capture probe and the biosensor is fabricated. By measuring ac current voltammetry, the target protein can be sensitively detected in a linear dynamic range from 1-1000 ng/mL with a low detection limit of 0.5 ng/mL. Making use of self-assembled gold nanoparticles layer, a large amount of capture probes can be modified onto the gold electrode, supporting the high sensitivity of the proposed strategy. In addition, good reproducibility, high selectivity and stability are achieved. In particular, the biosensor can be easily regenerated by melting in hot water, making it reusable.

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18

Zhang, Song Bai, Chun Jiao Tang, Liao Yong Luo, et al. "Reusable Electrochemical Biosensor for Sensitive Detection of Single Nucleotide Polymorphisms Based on Gold Nanoparticle Self-Assembly." Applied Mechanics and Materials 651-653 (September 2014): 293–96. http://dx.doi.org/10.4028/www.scientific.net/amm.651-653.293.

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A reusable electrochemical biosensing strategy based on gold nanoparticle involved layer-by-layer self-assembly for sensitive detection of single nucleotide polymorphisms is proposed in this study. Making use of the strong sulfur-Au affinity, ethanthiol and capture probe modified gold nanoparticles are self-assembled onto the surface of gold electrode successively. The target DNA hybridizes with the capture probe and ferrocene labeled signaling probe successively via sandwich hybridization reaction. By measuring ac current voltammetry, the target DNA can be sensitively detected in a linear dynamic range from 4.1-410 nM with a low detection limit of 2 nM. Making use of self-assembled gold nanoparticles layer, a large amount of capture probes can be modified onto the gold electrode, supporting the high sensitivity of the proposed strategy. In addition, good reproducibility, high selectivity and stability are achieved. In particular, the biosensor can be easily regenerated by melting in hot water, making it reusable.

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19

Wu, Jiang, Julia Shin, Cara M. M. Williams, et al. "Design and chemoproteomic functional characterization of a chemical probe targeted to bromodomains of BET family proteins." MedChemComm 5, no. 12 (2014): 1871–78. http://dx.doi.org/10.1039/c4md00259h.

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20

Wang, Penghui, Zhining Li, Lulu Jiang, Lu Zhou, and Deyong Ye. "Design and Synthesis of the Diazirine-based Clickable Photo-affinity Probe Targeting Sphingomyelin Synthase 2." Letters in Drug Design & Discovery 16, no. 6 (2019): 678–84. http://dx.doi.org/10.2174/1570180816666181106154601.

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Background:SMS family plays a very important role in sphingolipids metabolism and is involved in the membrane mobility and signaling transduction.Methods:SMS2 subtype was related to a variety of diseases and could be regarded as a promising potential drug target. However, the uncertainty of the binding sites and the molecular mechanism of action limited the development of SMS2 inhibitors. Herein, we discovered a photo-affinity probe PAL-1 targeting SMS2.Results:The enzyme inhibitory activity and the photo-affinity labeling experiments showed that PAL-1 could be mono-labeled on SMS2.Conclusion:In summary, starting from the N-arylbenzamides core structure and the minimalist terminal alkyne-containing diazirine photo-crosslinker, we designed and synthesized a photoaffinity probe PAL-1 targeting SMS2. The enzymatic inhibitory activity study showed that PAL-1 exhibited superior selectivities for SMS2 with an IC50 of 0.37 µM over SMS1.

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21

Tseng, Yen-Ta, Wan-Yun Li, Ya-Wen Yu, et al. "Fiber Optic Particle Plasmon Resonance Biosensor for Label-Free Detection of Nucleic Acids and Its Application to HLA-B27 mRNA Detection in Patients with Ankylosing Spondylitis." Sensors 20, no. 11 (2020): 3137. http://dx.doi.org/10.3390/s20113137.

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We developed a label-free, real-time, and highly sensitive nucleic acid biosensor based on fiber optic particle plasmon resonance (FOPPR). The biosensor employs a single-strand deoxyoligonucleotides (ssDNA) probe, conjugated to immobilized gold nanoparticles on the core surface of an optical fiber. We explore the steric effects on hybridization affinity and limit of detection (LOD), by using different ssDNA probe designs and surface chemistries, including diluent molecules of different lengths in mixed self-assembled monolayers, ssDNA probes of different oligonucleotide lengths, ssDNA probes in different orientations to accommodate target oligonucleotides with a hybridization region located unevenly in the strand. Based on the optimized ssDNA probe design and surface chemistry, we achieved LOD at sub-nM level, which makes detection of target oligonucleotides as low as 1 fmol possible in the 10-μL sensor chip. Additionally, the FOPPR biosensor shows a good correlation in determining HLA-B27 mRNA, in extracted blood samples from patients with ankylosing spondylitis (AS), with the clinically accepted real-time reverse transcription-polymerase chain reaction (RT-PCR) method. The results from this fundamental study should guide the design of ssDNA probe for anti-sense sensing. Further results through application to HLA-B27 mRNA detection illustrate the feasibility in detecting various nucleic acids of chemical and biological relevance.

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22

Park, Yong Dae, Jeum-Jong Kim, Sungbeom Lee, Chul-Hong Park, Hyoung-Woo Bai та Seung Sik Lee. "A Pyridazine-Based Fluorescent Probe Targeting AβPlaques in Alzheimer’s Disease". Journal of Analytical Methods in Chemistry 2018 (2018): 1–5. http://dx.doi.org/10.1155/2018/1651989.

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Accumulation ofβ-amyloid (Aβ) plaques comprising Aβ40 and Aβ42 in the brain is the most significant factor in the pathogenesis of Alzheimer’s disease (AD). Thus, the detection of Aβplaques has increasingly attracted interest in the context of AD diagnosis. In the present study, a fluorescent pyridazine-based dye that can detect and image Aβplaques was designed and synthesized, and its optical properties in the presence of Aβaggregates were evaluated. An approximately 34-fold increase in emission intensity was exhibited by the fluorescent probe after binding with Aβaggregates, for which it showed high affinity (KD = 0.35 µM). Moreover, the reasonable hydrophobic properties of the probe (logP = 2.94) allow it to penetrate the blood brain barrier (BBB). In addition, the pyridazine-based probe was used in the histological costaining of transgenic mouse (APP/PS1) brain sections to validate the selective binding of the probe to Aβplaques. The results suggest that the pyridazine-based compound has the potential to serve as a fluorescent probe for the diagnosis of AD.

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23

Ge, Xia, and Daniel S. Sem. "Affinity-based chemical proteomic probe for dehydrogenases: Fluorescence and visible binding assays in gels." Analytical Biochemistry 370, no. 2 (2007): 171–79. http://dx.doi.org/10.1016/j.ab.2007.08.010.

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24

OKADA, Hiroki, Masahiro MIMURA, Shunsuke TOMITA, and Ryoji KURITA. "Affinity Diversification of a Polymer Probe for Pattern-recognition-based Biosensing Using Chemical Additives." Analytical Sciences 37, no. 5 (2021): 713–19. http://dx.doi.org/10.2116/analsci.20scp23.

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25

Shanmugam, N. R., S. Muthukumar, and S. Prasad. "Surface modification of ZnO nanostructured electrodes with thiol and phosphonic acid moieties for biosensing applications." Analytical Methods 9, no. 37 (2017): 5525–33. http://dx.doi.org/10.1039/c7ay01625e.

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The analytical performance of affinity immunoassay based biosensor systems is determined by the efficiency of capture probe immobilization, which in turn depends on the stability of surface modification.

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26

Gee, Marvin H., Leah V. Sibener, Michael E. Birnbaum, et al. "Stress-testing the relationship between T cell receptor/peptide-MHC affinity and cross-reactivity using peptide velcro." Proceedings of the National Academy of Sciences 115, no. 31 (2018): E7369—E7378. http://dx.doi.org/10.1073/pnas.1802746115.

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T cell receptors (TCRs) bind to peptide-major histocompatibility complex (pMHC) with low affinity (Kd ∼ μM), which is generally assumed to facilitate cross-reactive TCR “scanning” of ligands. To understand the relationship between TCR/pMHC affinity and cross-reactivity, we sought to engineer an additional weak interaction, termed “velcro,” between the TCR and pMHC to probe the specificities of TCRs at relatively low and high affinities. This additional interaction was generated through an eight-amino acid peptide library covalently linked to the N terminus of the MHC-bound peptide. Velcro was selected through an affinity-based isolation and was subsequently shown to enhance the cognate TCR/pMHC affinity in a peptide-dependent manner by ∼10-fold. This was sufficient to convert a nonstimulatory ultra-low-affinity ligand into a stimulatory ligand. An X-ray crystallographic structure revealed how velcro interacts with the TCR. To probe TCR cross-reactivity, we screened TCRs against yeast-displayed pMHC libraries with and without velcro, and found that the peptide cross-reactivity profiles of low-affinity (Kd > 100 μM) and high-affinity (Kd ∼ μM) TCR/pMHC interactions are remarkably similar. The conservation of recognition of the TCR for pMHC across affinities reveals the nature of low-affinity ligands for which there are important biological functions and has implications for understanding the specificities of affinity-matured TCRs.

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27

Sha, Shuang, Fei Yang, Anle Wang, Honglin Jin, Zhihong Zhang, and Qiaoya Lin. "Fluorescent and quantitative mitochondrial redox imaging of tumor targeted by Octa-RGD probe." Journal of Innovative Optical Health Sciences 09, no. 04 (2016): 1642002. http://dx.doi.org/10.1142/s1793545816420025.

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Integrins, over-expressed in a broad range of cancer diseases, are widely utilized as a tumor biomarker. Metabolism investigation also plays important roles in tumor theranostics. Developing simple integrin-targetting probe and monitoring tumor metabolism will give opportunities to find ways for cancer treatment, however, the investigation of tumor metabolism with integrin receptor based probes has been rarely reported so far. Here, we developed an octavalent fluorescent probe Octa-RGD by convenient genetic method, based on one tetrameric far-red fluorescent protein (fRFP) linked with RGD peptides. We validated its intergin targeting by confocal imaging in vitro. Then we screened a variety of tumor cells, and differentiated their binding affinity based on the fluorescence of the probe via flow cytometry. Among these cells, CNE-2 cells had the highest uptake of the probe, while B16 cells had the lowest, corresponding with their intergin expression levels. Next, the fluorescent and metabolic imaging was performed in HT1080 (intergin postive) tumor, where nicotinamide adenine dinucleotide hydrogen (NADH), flavoprotein (Fp) and fRFP fluorescent signals were collected. The tumor from mice intravenously injected with Octa-RGD probe displayed obviously higher NADH redox ratio NADH/(Fp+NADH) and fRFP signal, than those with fRFP protein. It suggested that integrin targeting may have influence on the target cell metabolism, and further demonstrated Octa-RGD probe facilitated its uptake in the targeted tumor in vivo. This paper developed a useful probe, which can bind integrins specifically and efficiently in tumor cells, and together with tumor metabolic information, it may provide new insight for RGD targeting-based cancer therapeutics.

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Li, Ming, Sangeeta Ray Banerjee, Chao Zheng, Martin G. Pomper, and Ishan Barman. "Ultrahigh affinity Raman probe for targeted live cell imaging of prostate cancer." Chemical Science 7, no. 11 (2016): 6779–85. http://dx.doi.org/10.1039/c6sc01739h.

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Leveraging optimally engineered SERS tags and urea-based small-molecule inhibitor of PSMA, we report an ultrahigh binding affinity imaging nanoplex for castrate resistant prostate cancer and demonstrate live single cell vibrational spectroscopic imaging at ultralow concentrations.

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29

Yoo, Soyeon, and Min Su Han. "A fluorescent probe for butyrylcholinesterase activity in human serum based on a fluorophore with specific binding affinity for human serum albumin." Chemical Communications 55, no. 97 (2019): 14574–77. http://dx.doi.org/10.1039/c9cc07737e.

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30

Kumar, Nag S., Matthew P. Braun, Ashok G. Chaudhary, and Robert N. Young. "Synthesis of a tritium-labeled photo-affinity probe based on an atypical leukotriene biosynthesis inhibitor." Journal of Labelled Compounds and Radiopharmaceuticals 54, no. 1 (2011): 43–50. http://dx.doi.org/10.1002/jlcr.1804.

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31

Chen, Wei-Lin, Dong-Dong Li, Zhi-Hui Wang, et al. "Design, synthesis, and initial evaluation of affinity-based small molecular probe for detection of WDR5." Bioorganic Chemistry 76 (February 2018): 380–85. http://dx.doi.org/10.1016/j.bioorg.2017.11.018.

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32

Hirozane, Yoshihiko, Masashi Toyofuku, Takatoshi Yogo, et al. "Structure-based rational design of staurosporine-based fluorescent probe with broad-ranging kinase affinity for kinase panel application." Bioorganic & Medicinal Chemistry Letters 29, no. 21 (2019): 126641. http://dx.doi.org/10.1016/j.bmcl.2019.126641.

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33

Azim, Mohammad Anwar Ul, Takashi Kozaka, Izumi Uno, et al. "Syntheses and In-vitro Evaluation of Tetrahydroaminoacridine (THA) Based Analogues as High Affinity Choline Transporter (HAChT) Imaging Probe." Bangladesh Journal of Nuclear Medicine 17, no. 2 (2016): 97–102. http://dx.doi.org/10.3329/bjnm.v17i2.28192.

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Introduction: In cholinergic neurons, high affinity choline uptake (HACU) by the high affinity choline transporter (HAChT) is a rate-limiting and regulatory step for the synthesis of Acetylcholine (Ach).Thus, HAChT appear to be a relatively specific presynaptic marker for cholinergic neurons in Alzheimers disease.Objectives: The principle objective of the study is to check the affinity of tetrahydroaminoacridine (THA) derivatives for HAChT. Another objective of the research work is to clarify whether the hemicholinium-3 (ChT inhibitor) and HACU enhancer molecules share the same binding sites or not.Materials and Methods: The inhibition activities of tacrine, the 2,3-dimethylfuran derivative of tacrine (DMTA) and their corresponding 2-oxo-1-pyrrolidineacetyl derivatives, namely PTAA and MKC-231 were measured by displacement of a typical HAChT antagonist [3H]HC-3 in rat cerebral membrane. The percentage of inhibition against the binding of [3H]HC-3 to HAChT were calculated using GraphPad Prism v4 software.Results: Hemicholinium-3 showed affinity for HAChT (IC50 = 20 nM) in the in vitro binding assay. A very insignificant inhibition activity (IC50 = 1000 nM) of Tacrine was revealed. The newly synthesized tacrine derivatives, DMTA and PTAA did not show any affinity for HAChT. Although MKC-231 was reported to enhance cholinergic activity at synaptic terminals, it did not show any affinity for the HAChT in [3H]HC-3 binding assay.Conclusion: In vitro [3H]HC-3 binding assay revealed no affinity of MKC-231, tacrine and its corresponding2-oxo-1-pyrrolidineacetate derivative towards HAChT. So, it is worthy to develop radiolabeled HC-3 derivatives with high affinity for HAChT, which can diffuse the BBB, to enable the in vivo investigation of HACU system.Bangladesh J. Nuclear Med. 17(2): 97-102, July 2014

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Yilmaz, L. Safak, and Daniel R. Noguera. "Mechanistic Approach to the Problem of Hybridization Efficiency in Fluorescent In Situ Hybridization." Applied and Environmental Microbiology 70, no. 12 (2004): 7126–39. http://dx.doi.org/10.1128/aem.70.12.7126-7139.2004.

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ABSTRACT In fluorescent in situ hybridization (FISH), the efficiency of hybridization between the DNA probe and the rRNA has been related to the accessibility of the rRNA when ribosome content and cell permeability are not limiting. Published rRNA accessibility maps show that probe brightness is sensitive to the organism being hybridized and the exact location of the target site and, hence, it is highly unpredictable based on accessibility only. In this study, a model of FISH based on the thermodynamics of nucleic acid hybridization was developed. The model provides a mechanistic approach to calculate the affinity of the probe to the target site, which is defined as the overall Gibbs free energy change (ΔG°overall) for a reaction scheme involving the DNA-rRNA and intramolecular DNA and rRNA interactions that take place during FISH. Probe data sets for the published accessibility maps and experiments targeting localized regions in the 16S rRNA of Escherichia coli were used to demonstrate that ΔG°overall is a strong predictor of hybridization efficiency and superior to conventional estimates based on the dissociation temperature of the DNA/rRNA duplex. The use of the proposed model also allowed the development of mechanistic approaches to increase probe brightness, even in seemingly inaccessible regions of the 16S rRNA. Finally, a threshold ΔG°overall of −13.0 kcal/mol was proposed as a goal in the design of FISH probes to maximize hybridization efficiency without compromising specificity.

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Pallares, Roger M., Nguyen Thi Kim Thanh, and Xiaodi Su. "Quantifying the binding between proteins and open chromatin-like DNA sequences with gold nanorods." Chemical Communications 55, no. 100 (2019): 15041–44. http://dx.doi.org/10.1039/c9cc07511a.

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We developed a gold nanorod-based colorimetric assay for the binding of transcription factors to DNA in long open chromatin-like structures. After determining of the binding affinity and stoichiometry, we explored the effect of the probe length on the assay performance.

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Hamilton, Graham R. C., Simanpreet Kaur, Sukanta Kamila, Bridgeen Callan, and John F. Callan. "A low affinity nanoparticle based fluorescent ratiometric probe for the determination of Zn(ii) concentrations in living cells." New Journal of Chemistry 42, no. 18 (2018): 14986–93. http://dx.doi.org/10.1039/c7nj04520d.

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A ratiometric polymeric fluorescent probe for Zn(ii) was developed capable of measuring Zn(ii) concentrations in aqueous solution between 0 and 5 mM and was also capable of discriminating between resting and high Zn(ii) levels in living cells using confocal fluorescence microscopy.

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Mehta, Pramod Kumar, Eun-Taex Oh, Heon Joo Park, and Keun-Hyeung Lee. "Ratiometric fluorescent probe based on symmetric peptidyl receptor with picomolar affinity for Zn2+ in aqueous solution." Sensors and Actuators B: Chemical 245 (June 2017): 996–1003. http://dx.doi.org/10.1016/j.snb.2017.01.154.

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Yegorova, А. V., I. I. Leonenko, Yu V. Scrypynets, et al. "New luminescent probe based on a terbium(III) complex for studying DNA affinity of aminoalkoxy fluorenones." Journal of Applied Spectroscopy 80, no. 3 (2013): 429–36. http://dx.doi.org/10.1007/s10812-013-9784-6.

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Ahmed, A. R. H., G. W. J. Olivier, G. Adams, et al. "Isolation and partial purification of a melanocyte-stimulating hormone receptor from B16 murine melanoma cells. A novel approach using a cleavable biotinylated photoactivated ligand and streptavidin-coated magnetic beads." Biochemical Journal 286, no. 2 (1992): 377–82. http://dx.doi.org/10.1042/bj2860377.

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The alpha-melanocyte-stimulating hormone (alpha-MSH) receptor of B16 mouse melanoma cells was characterized by photoaffinity labelling using radiolabelled photoactive derivatives of alpha-MSH. A doublet band of 43-46 kDa representing a ligand-receptor complex was identified. A novel adaptation of the streptovadin/biotin-based affinity system was used to isolate the alpha-MSH receptor. A probe was synthesized which contained biotin connected to a photolabelled alpha-MSH analogue via a cleavable disulphide linker and which displayed high affinity for the alpha-MSH receptor. Streptavidin-coated magnetic beads were used as a solid support instead of an affinity column. Covalently linked probe-receptor complexes solubilized in Triton X-100 were equilibrated with the beads, and after magnetic separation and washing, specifically bound complexes were treated with dithiothreitol to cleave the disulphide bridge in the biotin-peptide spacer arm and so release the receptor-ligand complex. The identity of the isolated protein was established by SDS/PAGE analysis. Methods to achieve purification to homogeneity and to allow quantitative isolation of the receptor are discussed.

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Aryal, Gyan H., Kenneth W. Hunter, and Liming Huang. "A supramolecular red to near-infrared fluorescent probe for the detection of drugs in urine." Organic & Biomolecular Chemistry 16, no. 40 (2018): 7425–29. http://dx.doi.org/10.1039/c8ob02180e.

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A host–guest complex based on a newly designed and synthesized cationic perylene dye and cucurbit[8]uril exhibits red-NIR emission, high affinity and stability, and large Stokes shift. It can serve as a red-NIR fluorescent displacement probe for the detection of drugs in urine.

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Emaminejad, Sam, Mehdi Javanmard, Chaitanya Gupta, Shuai Chang, Ronald W. Davis, and Roger T. Howe. "Tunable control of antibody immobilization using electric field." Proceedings of the National Academy of Sciences 112, no. 7 (2015): 1995–99. http://dx.doi.org/10.1073/pnas.1424592112.

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The controlled immobilization of proteins on solid-state surfaces can play an important role in enhancing the sensitivity of both affinity-based biosensors and probe-free sensing platforms. Typical methods of controlling the orientation of probe proteins on a sensor surface involve surface chemistry-based techniques. Here, we present a method of tunably controlling the immobilization of proteins on a solid-state surface using electric field. We study the ability to orient molecules by immobilizing IgG molecules in microchannels while applying lateral fields. We use atomic force microscopy to both qualitatively and quantitatively study the orientation of antibodies on glass surfaces. We apply this ability for controlled orientation to enhance the performance of affinity-based assays. As a proof of concept, we use fluorescence detection to indirectly verify the modulation of the orientation of proteins bound to the surface. We studied the interaction of fluorescently tagged anti-IgG with surface immobilized IgG controlled by electric field. Our study demonstrates that the use of electric field can result in more than 100% enhancement in signal-to-noise ratio compared with normal physical adsorption.

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Chen, Xun, Steven Stout, Uwe Mueller, et al. "Label-Free, LC-MS-Based Assays to Quantitate Small-Molecule Antagonist Binding to the Mammalian BLT1 Receptor." SLAS DISCOVERY: Advancing the Science of Drug Discovery 22, no. 9 (2017): 1131–41. http://dx.doi.org/10.1177/2472555217719748.

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We have developed and validated label-free, liquid chromatography–mass spectrometry (LC-MS)-based equilibrium direct and competition binding assays to quantitate small-molecule antagonist binding to recombinant human and mouse BLT1 receptors expressed in HEK 293 cell membranes. Procedurally, these binding assays involve (1) equilibration of the BLT1 receptor and probe ligand, with or without a competitor; (2) vacuum filtration through cationic glass fiber filters to separate receptor-bound from free probe ligand; and (3) LC-MS analysis in selected reaction monitoring mode for bound probe ligand quantitation. Two novel, optimized probe ligands, compounds 1 and 2, were identified by screening 20 unlabeled BLT1 antagonists for direct binding. Saturation direct binding studies confirmed the high affinity, and dissociation studies established the rapid binding kinetics of probe ligands 1 and 2. Competition binding assays were established using both probe ligands, and the affinities of structurally diverse BLT1 antagonists were measured. Both binding assay formats can be executed with high specificity and sensitivity and moderate throughput (96-well plate format) using these approaches. This highly versatile, label-free method for studying ligand binding to membrane-associated receptors should find broad application as an alternative to traditional methods using labeled ligands.

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Gao, Yuefeng, Sai Xu, Zhijian Liu, Kezhen Yu, and Xinxiang Pan. "Dual-Emission Fluorescence Probe Based on CdTe Quantum Dots and Rhodamine B for Visual Detection of Mercury and Its Logic Gate Behavior." Micromachines 12, no. 6 (2021): 713. http://dx.doi.org/10.3390/mi12060713.

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It is urgent that a convenient and sensitive technique of detecting Hg2+ be developed because of its toxicity. Conventional fluorescence analysis works with a single fluorescence probe, and it often suffers from signal fluctuations which are influenced by external factors. In this research, a novel dual-emission probe assembled through utilizing CdTe quantum dots (QDs) and rhodamine B was designed to detect Hg2+ visually. Only the emission of CdTe QDs was quenched after adding Hg2+ in the dual-emission probe, which caused an intensity ratio change of the two different emission wavelengths and hence facilitated the visual detection of Hg2+. Compared to single emission QDs-based probe, a better linear relationship was shown between the variation of fluorescence intensity and the concentration of Hg2+, and the limit of detection (LOD) was found to be11.4 nM in the range of 0–2.6 μM. Interestingly, the intensity of the probe containing Hg2+ could be recovered in presence of glutathione (GSH) due to the stronger binding affinity of Hg2+ towards GSH than that towards CdTe QDs. Based on this phenomenon, an IMPLICATION logic gate using Hg2+/GSH as inputs and the fluorescence signal of QDs as an output was constructed.

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Yilmaz, L. Şafak, Hatice E. Ökten, and Daniel R. Noguera. "Making All Parts of the 16S rRNA of Escherichia coli Accessible In Situ to Single DNA Oligonucleotides." Applied and Environmental Microbiology 72, no. 1 (2006): 733–44. http://dx.doi.org/10.1128/aem.72.1.733-744.2006.

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ABSTRACT rRNA accessibility is a major sensitivity issue limiting the design of working probes for fluorescence in situ hybridization (FISH). Previous studies empirically highlighted the accessibility of target sites on rRNA maps by grouping probes into six classes according to their brightness levels. In this study, a recently proposed mechanistic model of FISH, based on the thermodynamics of secondary nucleic acid interactions, was used to evaluate the accessibility of the 16S rRNA of Escherichia coli to fluorescein-labeled oligonucleotides when thermodynamic and kinetic barriers were eliminated. To cover the entire 16S rRNA, 109 probes were designed with an average thermodynamic affinity (ΔG o overall) of −13.5 kcal/mol. Fluorescence intensity was measured by flow cytometry, and a brightness threshold between classes 3 and 4 was used as the requirement for proof of accessibility. While 46% of the probes were above this threshold with conventional 3-h hybridizations, extending the incubation period to 96 h dramatically increased the fraction of bright probes to 86%. Insufficient thermodynamic affinity and/or fluorophore quenching was demonstrated to cause the low fluorescence intensity of the remaining 14% of the probes. In the end, it was proven that every nucleotide in the 16S rRNA of E. coli could be targeted with a bright probe and, therefore, that there were no truly inaccessible target regions in the 16S rRNA. Based on our findings and mechanistic modeling, a rational design strategy involving ΔG o overall, hybridization kinetics, and fluorophore quenching is recommended for the development of bright probes.

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Chung, Sung-Wook, Andrew D. Presley, Selim Elhadj, et al. "Scanning Probe-based Fabrication of 3D Nanostructures via Affinity Templates, Functional RNA, and Meniscus-mediated Surface Remodeling." Scanning 30, no. 2 (2008): 159–71. http://dx.doi.org/10.1002/sca.20086.

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Cheng, Gong, Zhi-Gang Wang, Yan-Lin Liu, Ji-Lin Zhang, De-Hui Sun, and Jia-Zuan Ni. "A graphene-based multifunctional affinity probe for selective capture and sequential identification of different biomarkers from biosamples." Chemical Communications 48, no. 82 (2012): 10240. http://dx.doi.org/10.1039/c2cc35483g.

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Bian, Jinlei, Xiang Li, Lili Xu, et al. "Affinity-based small fluorescent probe for NAD(P)H:quinone oxidoreductase 1 (NQO1). Design, synthesis and pharmacological evaluation." European Journal of Medicinal Chemistry 127 (February 2017): 828–39. http://dx.doi.org/10.1016/j.ejmech.2016.10.062.

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Schlosser, Gitta, Petr Kačer, Marek Kuzma, et al. "Coupling Immunomagnetic Separation on Magnetic Beads with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Detection of Staphylococcal Enterotoxin B." Applied and Environmental Microbiology 73, no. 21 (2007): 6945–52. http://dx.doi.org/10.1128/aem.01136-07.

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ABSTRACT The growing importance of mass spectrometry for the identification and characterization of bacterial protein toxins is a consequence of the improved sensitivity and specificity of mass spectrometry-based techniques, especially when these techniques are combined with affinity methods. Here we describe a novel method based on the use of immunoaffinity capture and matrix-assisted laser desorption ionization-time of flight mass spectrometry for selective purification and detection of staphylococcal enterotoxin B (SEB). SEB is a potent bacterial protein toxin responsible for food poisoning, as well as a potential biological warfare agent. Unambiguous detection of SEB at low-nanogram levels in complex matrices is thus an important objective. In this work, an affinity molecular probe was prepared by immobilizing anti-SEB antibody on the surface of para-toluene-sulfonyl-functionalized monodisperse magnetic particles and used to selectively isolate SEB. Immobilization and affinity capture procedures were optimized to maximize the density of anti-SEB immunoglobulin G and the amount of captured SEB, respectively, on the surface of magnetic beads. SEB could be detected directly “on beads” by placing the molecular probe on the matrix-assisted laser desorption ionization target plate or, alternatively, “off beads” after its acidic elution. Application of this method to complex biological matrices was demonstrated by selective detection of SEB present in different matrices, such as cultivation media of Staphylococcus aureus strains and raw milk samples.

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Clément, David A., Clarisse Leseigneur, Muriel Gelin, et al. "New Chemical Probe Targeting Bacterial NAD Kinase." Molecules 25, no. 21 (2020): 4893. http://dx.doi.org/10.3390/molecules25214893.

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Nicotinamide adenine dinucleotide (NAD) kinases are essential and ubiquitous enzymes involved in the tight regulation of NAD/nicotinamide adenine dinucleotide phosphate (NADP) levels in many metabolic pathways. Consequently, they represent promising therapeutic targets in cancer and antibacterial treatments. We previously reported diadenosine derivatives as NAD kinase inhibitors with bactericidal activities on Staphylococcus aureus. Among them, one compound (namely NKI1) was found effective in vivo in a mouse infection model. With the aim to gain detailed knowledge about the selectivity and mechanism of action of this lead compound, we planned to develop a chemical probe that could be used in affinity-based chemoproteomic approaches. Here, we describe the first functionalized chemical probe targeting a bacterial NAD kinase. Aminoalkyl functional groups were introduced on NKI1 for further covalent coupling to an activated SepharoseTM matrix. Inhibitory properties of functionalized NKI1 derivatives together with X-ray characterization of their complexes with the NAD kinase led to identify candidate compounds that are amenable to covalent coupling to a matrix.

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Liu, Chao-Zong, Yi-Wen R. Wang, Ming-Ching Shen, and Tur-Fu Huang. "Analysis of Human Platelet Glycoprotein llb-llla by Fluorescein Isothiocyanate-Conjugated Disintegrins with Flow Cytometry." Thrombosis and Haemostasis 72, no. 06 (1994): 919–25. http://dx.doi.org/10.1055/s-0038-1648984.

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SummaryDisintegrins are a group of snake venom peptides which inhibit human platelet aggregation by acting as glycoprotein Ilb-IIIa (GPIIb-Ilia) antagonists. They are cysteine-rich, Arg-Gly-Asp (RGD)-containing peptides, and bind to GPIIb-Ilia complex on platelet membrane with a very high affinity (Kd, 10−7 ∼ 10−8 M). In this study, we analyzed GPIIb-Ilia complex on platelet membrane by flow cytometry using fluorescein isothiocyanate (FITC)-conjugated disintegrins as probes. Of these FITC-conjugated disintegrins, FITC-Rhodostomin is the most sensitive probe because Rhodostomin was conjugated with more FITC molecules than Trigramin and Halysin were. The binding fluorescence intensity of FITC-Trigramin (FITC-Tg), FITC-Halysin (FITC-Hy) and FITC-Rhodostomin (FITC-Rn) was measured in both resting and ADP-activated platelets of diluted human platelet-rich plasma. The binding fluorescence of FITC-disintegrins was abolished by EDTA and 7E3, a monoclonal antibody against GPIIb-Ilia. ADP markedly increased the fluorescence intensity of FITC-Tg and FITC-Hy bound on platelets especially when lower doses of these probes were used, whereas it had little effect on that of FITC-Rn. Therefore, FITC-Tg and FITC-Hy can be used for the detection of the activated platelets as noted by a higher ratio of fluorescence intensity (approx. 2-4) between ADP-activated and resting platelets as compared with that (approx. 1-1.3) in the case of FITC-Rn as the probe. The platelets from three patients with Glanzmann’s thrombasthenia were probed with FITC-disintegrins. As a result these three patients could be classified as type I thrombasthenia based on the extremely low level of GPIIb-Ilia detected by this method (<5% of normal value).

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