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Journal articles on the topic 'Affinity-Based protein profiling'

Author: Grafiati

Published: 8 June 2024

Last updated: 31 July 2025

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1

Wirsing, Lisette, Kai Naumann, and Thomas Vogt. "Arabidopsis methyltransferase fingerprints by affinity-based protein profiling." Analytical Biochemistry 408, no. 2 (2011): 220–25. http://dx.doi.org/10.1016/j.ab.2010.09.029.

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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 o

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3

Buneeva, Olga, Arthur Kopylov, Oksana Gnedenko, et al. "Proteomic Profiling of Mouse Brain Pyruvate Kinase Binding Proteins: A Hint for Moonlighting Functions of PKM1?" International Journal of Molecular Sciences 24, no. 8 (2023): 7634. http://dx.doi.org/10.3390/ijms24087634.

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Affinity-based proteomic profiling is widely used for the identification of proteins involved in the formation of various interactomes. Since protein–protein interactions (PPIs) reflect the role of particular proteins in the cell, identification of interaction partners for a protein of interest can reveal its function. The latter is especially important for the characterization of multifunctional proteins, which can play different roles in the cell. Pyruvate kinase (PK), a classical glycolytic enzyme catalyzing the last step of glycolysis, exists in four isoforms: PKM1, PKM2, PKL, and PKR. The

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4

Jung, Se-Hui, Kangseung Lee, Deok-Hoon Kong, Woo Jin Kim, Young-Myeong Kim, and Kwon-Soo Ha. "Integrative Proteomic Profiling of Protein Activity and Interactions Using Protein Arrays." Molecular & Cellular Proteomics 11, no. 11 (2012): 1167–76. http://dx.doi.org/10.1074/mcp.m112.016964.

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Proteomic studies based on abundance, activity, or interactions have been used to investigate protein functions in normal and pathological processes, but their combinatory approach has not been attempted. We present an integrative proteomic profiling method to measure protein activity and interaction using fluorescence-based protein arrays. We used an on-chip assay to simultaneously monitor the transamidating activity and binding affinity of transglutaminase 2 (TG2) for 16 TG2-related proteins. The results of this assay were compared with confidential scores provided by the STRING database to

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Ma, Nan, Zhi-Min Zhang, Jun-Seok Lee, et al. "Affinity-Based Protein Profiling Reveals Cellular Targets of Photoreactive Anticancer Inhibitors." ACS Chemical Biology 14, no. 12 (2019): 2546–52. http://dx.doi.org/10.1021/acschembio.9b00784.

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6

Chen, Xiong, Menglin Li, Manru Li, Dongmei Wang, and Jinlan Zhang. "Harnessing affinity-based protein profiling to reveal a novel target of nintedanib." Chemical Communications 57, no. 25 (2021): 3139–42. http://dx.doi.org/10.1039/d1cc00354b.

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We identified tripeptidyl-peptidase 1 (TPP1) as one of the direct targets of nintedanib (NDNB) employing clickable photoaffinity probes, which provides insights into the functional meaning of the well-known IPF therapeutic drug.

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Chou, Po-Hung, Shu-Hua Chen, Hsin-Kai Liao, et al. "Nanoprobe-Based Affinity Mass Spectrometry for Selected Protein Profiling in Human Plasma." Analytical Chemistry 77, no. 18 (2005): 5990–97. http://dx.doi.org/10.1021/ac050655o.

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Lyu, Peng, Shengrong Li, Ying Han, et al. "Affinity-based protein profiling-driven discovery of myricanol as a Nampt activator." Bioorganic Chemistry 133 (April 2023): 106435. http://dx.doi.org/10.1016/j.bioorg.2023.106435.

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9

Mezentsev, Yuri, Pavel Ershov, Evgeniy Yablokov, et al. "Protein Interactome Profiling of Stable Molecular Complexes in Biomaterial Lysate." International Journal of Molecular Sciences 23, no. 24 (2022): 15697. http://dx.doi.org/10.3390/ijms232415697.

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Most proteins function as part of various complexes, forming via stable and dynamic protein–protein interactions (PPIs). The profiling of PPIs expands the fundamental knowledge about the structures, functions, and regulation patterns of protein complexes and intracellular molecular machineries. Protein interactomics aims at solving three main tasks: (1) identification of protein partners and parts of complex intracellular structures; (2) analysis of PPIs parameters (affinity, molecular-recognition specificity, kinetic rate constants, and thermodynamic-parameters determination); (3) the study o

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10

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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11

Battenberg, Oliver A., Matthew B. Nodwell та Stephan A. Sieber. "Evaluation of α-Pyrones and Pyrimidones as Photoaffinity Probes for Affinity-Based Protein Profiling". Journal of Organic Chemistry 76, № 15 (2011): 6075–87. http://dx.doi.org/10.1021/jo201281c.

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12

Palermo, Giulia, Wietse M. Schouten, Luis Lago Alonso, Chris Ulens, Jeroen Kool, and Julien Slagboom. "Acetylcholine-Binding Protein Affinity Profiling of Neurotoxins in Snake Venoms with Parallel Toxin Identification." International Journal of Molecular Sciences 24, no. 23 (2023): 16769. http://dx.doi.org/10.3390/ijms242316769.

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Snakebite is considered a concerning issue and a neglected tropical disease. Three-finger toxins (3FTxs) in snake venoms primarily cause neurotoxic effects since they have high affinity for nicotinic acetylcholine receptors (nAChRs). Their small molecular size makes 3FTxs weakly immunogenic and therefore not appropriately targeted by current antivenoms. This study aims at presenting and applying an analytical method for investigating the therapeutic potential of the acetylcholine-binding protein (AChBP), an efficient nAChR mimic that can capture 3FTxs, for alternative treatment of elapid snake

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13

Qiu, Wen-Wei, Jie Xu, Jing-Ya Li, Jia Li, and Fa-Jun Nan. "Activity-Based Protein Profiling for Type I Methionine Aminopeptidase by Using Photo-Affinity Trimodular Probes." ChemBioChem 8, no. 12 (2007): 1351–58. http://dx.doi.org/10.1002/cbic.200700148.

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Jones, Hannah B. L., Raphael Heilig, Simon Davis, Roman Fischer, Benedikt M. Kessler, and Adán Pinto-Fernández. "ABPP-HT*—Deep Meets Fast for Activity-Based Profiling of Deubiquitylating Enzymes Using Advanced DIA Mass Spectrometry Methods." International Journal of Molecular Sciences 23, no. 6 (2022): 3263. http://dx.doi.org/10.3390/ijms23063263.

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Activity-based protein profiling (ABPP) uses a combination of activity-based chemical probes with mass spectrometry (MS) to selectively characterise a particular enzyme or enzyme class. ABPP has proven invaluable for profiling enzymatic inhibitors in drug discovery. When applied to cell extracts and cells, challenging the ABP-enzyme complex formation with a small molecule can simultaneously inform on potency, selectivity, reversibility/binding affinity, permeability, and stability. ABPP can also be applied to pharmacodynamic studies to inform on cellular target engagement within specific organ

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15

Lopez, Mary F., Alvydas Mikulskis, Scott Kuzdzal, et al. "A Novel, High-Throughput Workflow for Discovery and Identification of Serum Carrier Protein-Bound Peptide Biomarker Candidates in Ovarian Cancer Samples." Clinical Chemistry 53, no. 6 (2007): 1067–74. http://dx.doi.org/10.1373/clinchem.2006.080721.

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Abstract Background: Most cases of ovarian cancer are detected at later stages when the 5-year survival is ∼15%, but 5-year survival approaches 90% when the cancer is detected early (stage I). To use mass spectrometry (MS) of serum proteins for early detection, a seamless workflow is needed that provides an opportunity for rapid profiling along with direct identification of the underpinning ions. Methods: We used carrier protein–bound affinity enrichment of serum samples directly coupled with MALDI orthagonal TOF MS profiling to rapidly search for potential ion signatures that contained discri

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Cheng, Bo, Qi Tang, Che Zhang, and Xing Chen. "Glycan Labeling and Analysis in Cells and In Vivo." Annual Review of Analytical Chemistry 14, no. 1 (2021): 363–87. http://dx.doi.org/10.1146/annurev-anchem-091620-091314.

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As one of the major types of biomacromolecules in the cell, glycans play essential functional roles in various biological processes. Compared with proteins and nucleic acids, the analysis of glycans in situ has been more challenging. Herein we review recent advances in the development of methods and strategies for labeling, imaging, and profiling of glycans in cells and in vivo. Cellular glycans can be labeled by affinity-based probes, including lectin and antibody conjugates, direct chemical modification, metabolic glycan labeling, and chemoenzymatic labeling. These methods have been applied

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Ryu, Soyoung, Byron Gallis, Young Ah Goo, Scott A. Shaffer, Dragan Radulovic, and David R. Goodlett. "Comparison of a Label-Free Quantitative Proteomic Method Based on Peptide Ion Current Area to the Isotope Coded Affinity Tag Method." Cancer Informatics 6 (January 2008): CIN.S385. http://dx.doi.org/10.4137/cin.s385.

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Recently, several research groups have published methods for the determination of proteomic expression profiling by mass spectrometry without the use of exogenously added stable isotopes or stable isotope dilution theory. These so-called label-free, methods have the advantage of allowing data on each sample to be acquired independently from all other samples to which they can later be compared in silico for the purpose of measuring changes in protein expression between various biological states. We developed label free software based on direct measurement of peptide ion current area (PICA) and

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18

Ivanov, A. S., and A. E. Medvedev. "Optical surface plasmon resonance biosensors in molecular fishing." Biomeditsinskaya Khimiya 61, no. 2 (2015): 231–38. http://dx.doi.org/10.18097/pbmc20156102231.

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An optical biosensor employing surface plasmon resonance is a highly efficient instrument applicable for direct real time registration of molecular interactions without additional use of any labels or coupled processes. As an independent approach it is especially effective in analysis of various ligand receptor interactions. SPR-biosensors are used for validation of studies on intermolecular interactions in complex biological systems (affinity profiling of various groups of proteins, etc.). Recently, potential application of the SPR-biosensor for molecular fishing (direct affinity binding of t

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19

Won, Sang Joon, Joseph D. Eschweiler, Jaimeen D. Majmudar, et al. "Affinity-Based Selectivity Profiling of an In-Class Selective Competitive Inhibitor of Acyl Protein Thioesterase 2." ACS Medicinal Chemistry Letters 8, no. 2 (2016): 215–20. http://dx.doi.org/10.1021/acsmedchemlett.6b00441.

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20

Huang, Shuai, Fu-Jia Wang, Hao Lin, Tian Liu, Cheng-Xiao Zhao, and Lian-Guo Chen. "Affinity-based protein profiling to reveal targets of puerarin involved in its protective effect on cardiomyocytes." Biomedicine & Pharmacotherapy 134 (February 2021): 111160. http://dx.doi.org/10.1016/j.biopha.2020.111160.

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21

Timmer, John C., Mari Enoksson, Eric Wildfang, et al. "Profiling constitutive proteolytic events in vivo." Biochemical Journal 407, no. 1 (2007): 41–48. http://dx.doi.org/10.1042/bj20070775.

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Most known organisms encode proteases that are crucial for constitutive proteolytic events. In the present paper, we describe a method to define these events in proteomes from Escherichia coli to humans. The method takes advantage of specific N-terminal biotinylation of protein samples, followed by affinity enrichment and conventional LC (liquid chromatography)–MS/MS (tandem mass spectrometry) analysis. The method is simple, uses conventional and easily obtainable reagents, and is applicable to most proteomics facilities. As proof of principle, we demonstrate profiles of proteolytic events tha

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22

Azkargorta, Mikel, Ibon Iloro, Iraide Escobes, et al. "Human Serum Extracellular Vesicle Proteomic Profile Depends on the Enrichment Method Employed." International Journal of Molecular Sciences 22, no. 20 (2021): 11144. http://dx.doi.org/10.3390/ijms222011144.

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The proteomic profiling of serum samples supposes a challenge due to the large abundance of a few blood proteins in comparison with other circulating proteins coming from different tissues and cells. Although the sensitivity of protein detection has increased enormously in the last years, specific strategies are still required to enrich less abundant proteins and get rid of abundant proteins such as albumin, lipoproteins, and immunoglobulins. One of the alternatives that has become more promising is to characterize circulating extracellular vesicles from serum samples that have great interest

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23

Bennett, Kristen, Natalie C. Sadler, Aaron T. Wright, Chris Yeager, and Michael R. Hyman. "Activity-Based Protein Profiling of Ammonia Monooxygenase in Nitrosomonas europaea." Applied and Environmental Microbiology 82, no. 8 (2016): 2270–79. http://dx.doi.org/10.1128/aem.03556-15.

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ABSTRACTNitrosomonas europaeais an aerobic nitrifying bacterium that oxidizes ammonia (NH3) to nitrite (NO2−) through the sequential activities of ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase (HAO). Many alkynes are mechanism-based inactivators of AMO, and here we describe an activity-based protein profiling method for this enzyme using 1,7-octadiyne (17OD) as a probe. Inactivation of NH4+-dependent O2uptake byN. europaeaby 17OD was time- and concentration-dependent. The effects of 17OD were specific for ammonia-oxidizing activity, andde novoprotein synthesis was required to ree

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Buneeva, O. A., V. I. Fedchenko, O. V. Gnedenko, et al. "Interaction of rat kidney proteins with the renalase peptide RP220 and its potential proteolytic fragment RP224-232: a comparative proteomic analysis." Biomeditsinskaya Khimiya 71, no. 1 (2025): 65–70. https://doi.org/10.18097/pbmcr1559.

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Renalase (RNLS) is a protein playing different roles inside and outside cells. A 20-mer synthetic peptide corresponding to the human RNLS amino acid sequence 220–239 (RP220) exhibits a number of pharmacologically attractive activities in vitro and in vivo and can bind to many renal intracellular proteins. The RP220 sequence contains several cleavage sites for extracellular and circulating proteases. Here, we investigated the interaction of model proteins with the renalase peptide RP220 and a synthetic peptide corresponding to the amino acid sequence of RNLS 224–232, named RP224-232. We also pe

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25

Cheng, Ann-Joy, Li-Chiu Chen, Kun-Yi Chien, et al. "Oral Cancer Plasma Tumor Marker Identified with Bead-Based Affinity-Fractionated Proteomic Technology." Clinical Chemistry 51, no. 12 (2005): 2236–44. http://dx.doi.org/10.1373/clinchem.2005.052324.

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Abstract Background: There is no plasma marker for detecting oral cancer, one of the most frequent cancers worldwide. We developed a bead-based affinity-fractionated proteomic method to discover a novel plasma marker for oral cancer. Methods: Affinity purification of heparinized plasma with magnetic beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis were used to screen potential oral cancer markers. We compiled MS protein profiles for 57 patients with oral cancer and compared them with profiles from 29 healthy controls. The spectra we

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Hakaman, Harish, Felice Surya, Gizella Els Gerardine, Hanny Honggo, and Arli Aditya Parikesit. "In-Silico molecular docking analysis of monoclonal antibodies, approved inhibi-tors, and plant-based inhibitors targeting extracellular and intracellular HER2 receptor." Berkala Penelitian Hayati 31, no. 1 (2025): 33–48. https://doi.org/10.23869/bphjbr.31.1.20256.

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Human epidermal growth factor receptor or HER2 is a key player in breast, ovarian, and gastric cancers. Mutations that cause HER2 overexpression may alter their binding properties and sensitivity towards certain drugs. This study investigates the sequential amino acid interactions of extracellular HER2 receptor with antibody and intracellular HER2 receptor with chemical inhibitor ligands using Molecular Docking to obtain the best drug model with the greatest binding affinity to HER2 receptor. Additionally, analysis of the HER2 protein-protein interactions, degradation mechanism, and ADMET prof

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Jhansi, Laxmi C. H., B.V Suma, R. Jawale Nayana, and P. Hegde Shraddha. "Molecular Docking and ADMET Profiling of Stigmasterol for Evaluating Its Antimicrobial Potential." Journal of Research and Development in Pharmacological Practices 1, no. 1 (2025): 12–20. https://doi.org/10.5281/zenodo.15323191.

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<em>Due to development of resistance against antimicrobial agents, there arises a difficulty in treating microbial infections. </em><em>Stigmasterol, also referred to as stigmasterin, is an unsaturated plant sterol found in several medicinal plants and has been reported in literature to exhibit antimicrobial activity. This study aims to evaluate the binding affinity of stigmasterol with multiple target proteins of Staphylococcus aureus and to assess its ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties. Rigid molecular docking was employed to determine the bindin

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Song, Jayoung. "Applications of the Cellular Thermal Shift Assay to Drug Discovery in Natural Products: A Review." International Journal of Molecular Sciences 26, no. 9 (2025): 3940. https://doi.org/10.3390/ijms26093940.

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Natural products play a crucial role in drug discovery because of their structural diversity and biological activity. However, identifying their molecular targets remains a challenge. Traditional target identification approaches such as affinity-based protein profiling and activity-based protein profiling are limited by the need for chemical modification or reactive groups in natural products. The emergence of label-free techniques offers a powerful alternative for studying drug–target engagement in a physiological context. In particular, the cellular thermal shift assay (CETSA) exploits ligan

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Minamitani, Takeharu, Teruhito Yasui, Yijie Ma, et al. "Evasion of affinity-based selection in germinal centers by Epstein–Barr virus LMP2A." Proceedings of the National Academy of Sciences 112, no. 37 (2015): 11612–17. http://dx.doi.org/10.1073/pnas.1514484112.

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Epstein–Barr virus (EBV) infects germinal center (GC) B cells and establishes persistent infection in memory B cells. EBV-infected B cells can cause B-cell malignancies in humans with T- or natural killer-cell deficiency. We now find that EBV-encoded latent membrane protein 2A (LMP2A) mimics B-cell antigen receptor (BCR) signaling in murine GC B cells, causing altered humoral immune responses and autoimmune diseases. Investigation of the impact of LMP2A on B-cell differentiation in mice that conditionally express LMP2A in GC B cells or all B-lineage cells found LMP2A expression enhanced not on

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Le, Lyly, Kim Chi, Scott Tyldesley, et al. "Identification of Serum Amyloid A as a Biomarker to Distinguish Prostate Cancer Patients with Bone Lesions." Clinical Chemistry 51, no. 4 (2005): 695–707. http://dx.doi.org/10.1373/clinchem.2004.041087.

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Abstract Background: Prostate cancer has a propensity to metastasize to the bone. Currently, there are no curative treatments for this stage of the disease. Sensitive biomarkers that can be monitored in the blood to indicate the presence or development of bone metastases and/or response to therapies are lacking. Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) is an affinity-based approach that allows sensitive and high-throughput protein profiling and screening of biological samples. Methods: We used SELDI-TOF MS for protein profiling of sera from p

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Kim, Evelyn H., and David E. Misek. "Glycoproteomics-Based Identification of Cancer Biomarkers." International Journal of Proteomics 2011 (September 28, 2011): 1–10. http://dx.doi.org/10.1155/2011/601937.

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Protein glycosylation is one of the most common posttranslational modifications in mammalian cells. It is involved in many biological pathways and molecular functions and is well suited for proteomics-based disease investigations. Aberrant protein glycosylation may be associated with disease processes. Specific glycoforms of glycoproteins may serve as potential biomarkers for the early detection of disease or as biomarkers for the evaluation of therapeutic efficacy for treatment of cancer, diabetes, and other diseases. Recent technological developments, including lectin affinity chromatography

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Kempf, Karl, Oxana Kempf, Yoan Capello, et al. "Synthesis of Flavonol-Bearing Probes for Chemoproteomic and Bioinformatic Analyses of Asteraceae Petals in Search of Novel Flavonoid Enzymes." International Journal of Molecular Sciences 24, no. 11 (2023): 9724. http://dx.doi.org/10.3390/ijms24119724.

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This study aimed at searching for the enzymes that are responsible for the higher hydroxylation of flavonols serving as UV-honey guides for pollinating insects on the petals of Asteraceae flowers. To achieve this aim, an affinity-based chemical proteomic approach was developed by relying on the use of quercetin-bearing biotinylated probes, which were thus designed and synthesized to selectively and covalently capture relevant flavonoid enzymes. Proteomic and bioinformatic analyses of proteins captured from petal microsomes of two Asteraceae species (Rudbeckia hirta and Tagetes erecta) revealed

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Kang, Yoon‐Tae, Emma Purcell, Colin Palacios‐Rolston, et al. "Isolation and Profiling of Circulating Tumor‐Associated Exosomes Using Extracellular Vesicular Lipid–Protein Binding Affinity Based Microfluidic Device." Small 15, no. 47 (2019): 1903600. http://dx.doi.org/10.1002/smll.201903600.

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Rao, Abhinand, and Arun H. S. Kumar. "Computational Pharmacology Analysis of Lycopene to Identify Its Targets and Biological Effects in Humans." Applied Sciences 15, no. 14 (2025): 7815. https://doi.org/10.3390/app15147815.

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Lycopene exhibits a broad spectrum of biological activities with potential therapeutic applications. Despite its established antioxidant and anti-inflammatory properties, the molecular basis for its pharmacological actions remains incompletely defined. Here we investigated the molecular targets, pharmacodynamic feasibility, and tissue-specific expression of lycopene targets using a computational pharmacology approach combined with affinity and protein–protein interaction (PPI) analyses. Lycopene-associated human protein targets were predicted using a Swiss target screening platform. Molecular

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Hamza, Ghaith M., Vladislav B. Bergo, Sergey Mamaev, et al. "Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics." International Journal of Molecular Sciences 21, no. 6 (2020): 2016. http://dx.doi.org/10.3390/ijms21062016.

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The ability to quantitatively probe diverse panels of proteins and their post-translational modifications (PTMs) across multiple samples would aid a broad spectrum of biological, biochemical and pharmacological studies. We report a novel, microarray analytical technology that combines immuno-affinity capture with Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS), which is capable of supporting highly multiplexed, targeted proteomic assays. Termed “Affinity-Bead Assisted Mass Spectrometry” (Affi-BAMS), this LC-free technology enables development of highly specific and cus

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Song, Jiabao, and Y. George Zheng. "Bioorthogonal Reporters for Detecting and Profiling Protein Acetylation and Acylation." SLAS DISCOVERY: Advancing the Science of Drug Discovery 25, no. 2 (2019): 148–62. http://dx.doi.org/10.1177/2472555219887144.

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Protein acylation, exemplified by lysine acetylation, is a type of indispensable and widespread protein posttranslational modification in eukaryotes. Functional annotation of various lysine acetyltransferases (KATs) is critical to understanding their regulatory roles in abundant biological processes. Traditional radiometric and immunosorbent assays have found broad use in KAT study but have intrinsic limitations. Designing acyl–coenzyme A (CoA) reporter molecules bearing chemoselective chemical warhead groups as surrogates of the native cofactor acetyl-CoA for bioorthogonal labeling of KAT sub

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Du, Hongyan, Dejun Jiang, Junbo Gao, et al. "Proteome-Wide Profiling of the Covalent-Druggable Cysteines with a Structure-Based Deep Graph Learning Network." Research 2022 (July 22, 2022): 1–15. http://dx.doi.org/10.34133/2022/9873564.

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Covalent ligands have attracted increasing attention due to their unique advantages, such as long residence time, high selectivity, and strong binding affinity. They also show promise for targets where previous efforts to identify noncovalent small molecule inhibitors have failed. However, our limited knowledge of covalent binding sites has hindered the discovery of novel ligands. Therefore, developing in silico methods to identify covalent binding sites is highly desirable. Here, we propose DeepCoSI, the first structure-based deep graph learning model to identify ligandable covalent sites in

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Kanderova, Veronika, Daniela Kuzilkova, Jan Stuchly, et al. "Novel Flow Cytometry-Based Method Of Affinity Proteomics Revealing Expression, Post-Translational Modification and Proteolysis In Primary Childhood Acute Leukemias." Blood 122, no. 21 (2013): 2553. http://dx.doi.org/10.1182/blood.v122.21.2553.2553.

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Abstract Leukemia is a complex disease pathologically manifested at the DNA, mRNA and protein level. Understanding leukemia pathogenesis is prevalently focused on mutations at the DNA (or mRNA) level, however the functional consequences of these changes on cellular machineries are not fully clarified. Since proteome analysis provides link between gene sequence and cellular physiology, proteomics can contribute to elucidate mechanism of disease and response to treatment. Moreover some alterations are manifested only at the protein level including subcellular localisation, post-translational mod

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Lu, Kuan-Yi, Sheng-Ce Tao, Tzu-Ching Yang, et al. "Profiling Lipid–protein Interactions Using Nonquenched Fluorescent Liposomal Nanovesicles and Proteome Microarrays." Molecular & Cellular Proteomics 11, no. 11 (2012): 1177–90. http://dx.doi.org/10.1074/mcp.m112.017426.

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Fluorescent liposomal nanovesicles (liposomes) are commonly used for lipid research and/or signal enhancement. However, the problem of self-quenching with conventional fluorescent liposomes limits their applications because these liposomes must be lysed to detect the fluorescent signals. Here, we developed a nonquenched fluorescent (NQF)1 liposome by optimizing the proportion of sulforhodamine B (SRB) encapsulant and lissamine rhodamine B-dipalmitoyl phosphatidylethanol (LRB-DPPE) on a liposomal surface for signal amplification. Our study showed that 0.3% of LRB-DPPE with 200 μm of SRB provide

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Wen, Jiachen, and M. Kyle Hadden. "Affinity-based protein profiling identifies vitamin D3 as a heat shock protein 70 antagonist that regulates hedgehog transduction in murine basal cell carcinoma." European Journal of Medicinal Chemistry 228 (January 2022): 114005. http://dx.doi.org/10.1016/j.ejmech.2021.114005.

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Ogbeide, Uyi, Eunice Oriotor, and Henry Okeri. "Molecular docking assessment of the tocolytic potential of phytoconstituents of five medicinal plants used against preterm labour." Journal of Science and Practice of Pharmacy 10, no. 1 (2023): 522–32. http://dx.doi.org/10.47227/jsppharm.v10i1.5.

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Introduction: Preterm labour is currently being treated with a number of medications with untoward side effects, but many medicinal plants have also been found useful. This study aims to assess the tocolytic potentials of the phytoconstituents of Barteria fistulosa, Ficus capensis, Ficus exasperate, Newbouldia laevis and Zingiber officinale. Methods: Phytoconstituents present in these plants were obtained from literature sources, their 3D SDF structures were obtained from PubChem; the protein Beta-2 adrenergic receptor (7DHI) was processed using Chimera and molecular docking was done using PyR

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Rolland, Catherine, Rafael Gozalbes, Eric Nicolaï, et al. "G-Protein-Coupled Receptor Affinity Prediction Based on the Use of a Profiling Dataset: QSAR Design, Synthesis, and Experimental Validation." Journal of Medicinal Chemistry 48, no. 21 (2005): 6563–74. http://dx.doi.org/10.1021/jm0500673.

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Williamson, Yulanda M., Hercules Moura, Jennifer Whitmon, et al. "A Proteomic Characterization of Bordetella pertussis Clinical Isolates Associated with a California State Pertussis Outbreak." International Journal of Proteomics 2015 (May 24, 2015): 1–12. http://dx.doi.org/10.1155/2015/536537.

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Bordetella pertussis (Bp) is the etiologic agent of pertussis (whooping cough), a highly communicable infection. Although pertussis is vaccine preventable, in recent years there has been increased incidence, despite high vaccine coverage. Possible reasons for the rise in cases include the following: Bp strain adaptation, waning vaccine immunity, increased surveillance, and improved clinical diagnostics. A pertussis outbreak impacted California (USA) in 2010; children and preadolescents were the most affected but the burden of disease fell mainly on infants. To identify protein biomarkers assoc

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Ramatapa, Thabo, Anathi Msobo, Pfano W. Maphari, Efficient N. Ncube, Noluyolo Nogemane, and Msizi I. Mhlongo. "Identification of Plant-Derived Bioactive Compounds Using Affinity Mass Spectrometry and Molecular Networking." Metabolites 12, no. 9 (2022): 863. http://dx.doi.org/10.3390/metabo12090863.

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Affinity selection-mass spectrometry (AS-MS) is a label-free binding assay system that uses UHPLC-MS size-based separation methods to separate target-compound complexes from unbound compounds, identify bound compounds, classify compound binding sites, quantify the dissociation rate constant of compounds, and characterize affinity-extracted ligands. This label-free binding assay, in contrast to conventional biochemical (i.e., high-throughput screening (HTS)) approaches, is applicable to any drug target, and is also concise, accurate, and adaptable. Although AS-MS is an innovative approach for i

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Verkhivker, Gennady, Steve Agajanian, Ryan Kassab, and Keerthi Krishnan. "Integrating Conformational Dynamics and Perturbation-Based Network Modeling for Mutational Profiling of Binding and Allostery in the SARS-CoV-2 Spike Variant Complexes with Antibodies: Balancing Local and Global Determinants of Mutational Escape Mechanisms." Biomolecules 12, no. 7 (2022): 964. http://dx.doi.org/10.3390/biom12070964.

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In this study, we combined all-atom MD simulations, the ensemble-based mutational scanning of protein stability and binding, and perturbation-based network profiling of allosteric interactions in the SARS-CoV-2 spike complexes with a panel of cross-reactive and ultra-potent single antibodies (B1-182.1 and A23-58.1) as well as antibody combinations (A19-61.1/B1-182.1 and A19-46.1/B1-182.1). Using this approach, we quantify the local and global effects of mutations in the complexes, identify protein stability centers, characterize binding energy hotspots, and predict the allosteric control point

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Latosińska, Magdalena, and Jolanta Natalia Latosińska. "The Chameleon Strategy—A Recipe for Effective Ligand Screening for Viral Targets Based on Four Novel Structure–Binding Strength Indices." Viruses 16, no. 7 (2024): 1073. http://dx.doi.org/10.3390/v16071073.

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The RNA viruses SARS-CoV, SARS-CoV-2 and MERS-CoV encode the non-structural Nsp16 (2′-O-methyltransferase) that catalyzes the transfer of a methyl group from S-adenosylmethionine (SAM) to the first ribonucleotide in mRNA. Recently, it has been found that breaking the bond between Nsp16 and SAM substrate results in the cessation of mRNA virus replication. To date, only a limited number of such inhibitors have been identified, which can be attributed to a lack of an effective “recipe”. The aim of our study was to propose and verify a rapid and effective screening protocol dedicated to such purpo

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Stenke, Leif, Lukas Orre, Sumeer Dhar, Rolf Larsson, Rolf Lewensohn, and Janne Lehtiö. "Detection of Proteins Related to Therapeutic Outcome, Including Drug Resistance, in Acute Myeloid Leukemia Using Mass Spectrometry and Gel Based Proteomic Profiling." Blood 106, no. 11 (2005): 2367. http://dx.doi.org/10.1182/blood.v106.11.2367.2367.

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Abstract To further improve and individualize curative treatment approaches for patients with AML, novel proteins and protein functions need to be discovered. In particular, the mechanisms responsible for chemotherapy resistance appear essential to unravel. Clinical proteomics may help to provide such information. We have used a chip-based technique, surface enhanced laser desorption/ionization mass spectrometry (SELDI-MS), to compare protein expression profiles in AML. With this technique proteins in the molecular weight area of 2–40 kDa can be spotted. For selected samples, a two-dimensional

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Limaye, Akanksha, Jajoriya Sweta, Maddala Madhavi, et al. "In Silico Insights on GD2 : A Potential Target for Pediatric Neuroblastoma." Current Topics in Medicinal Chemistry 19, no. 30 (2020): 2766–81. http://dx.doi.org/10.2174/1568026619666191112115333.

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Background: Originating from the abnormal growth of neuroblasts, pediatric neuroblastoma affects the age group below 15 years. It is an aggressive heterogenous cancer with a high morbidity rate. Biological marker GD2 synthesised by the GD2 gene acts as a powerful predictor of neuroblastoma cells. GD2 gangliosides are sialic acid-containing glycosphingolipids. Differential expression during brain development governs the function of the GD2. The present study explains the interaction of the GD2 with its established inhibitors and discovers the compound having a high binding affinity against the

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Lupitha, Santhik Subhasingh, Pramod Darvin, Aneesh Chandrasekharan, et al. "A rapid bead-based assay for screening of SARS-CoV-2 neutralizing antibodies." Antibody Therapeutics 5, no. 2 (2022): 100–110. http://dx.doi.org/10.1093/abt/tbac007.

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Abstract Quantitative determination of neutralizing antibodies against Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) is paramount in immunodiagnostics, vaccine efficacy testing, and immune response profiling among the vaccinated population. Cost-effective, rapid, easy-to-perform assays are essential to support the vaccine development process and immunosurveillance studies. We describe a bead-based screening assay for S1-neutralization using recombinant fluorescent proteins of hACE2 and SARS-CoV2-S1, immobilized on solid beads employing nanobodies/metal-affinity tags. Nanobody-m

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Fazilat, Ahmad, Nadia Rashid, Aruna Nigam, Shadab Anjum, Nimisha Gupta, and Saima Wajid. "Differential Expression of MARK4 Protein and Related Perturbations in Females with Ovulatory PCOS." Endocrine, Metabolic & Immune Disorders - Drug Targets 19, no. 7 (2019): 1064–74. http://dx.doi.org/10.2174/1871530319666190719145823.

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Background: Ovulatory PCOS (OPCOS) is the mildest form of the polycystic ovarian syndrome among all four determined phenotypes. Though the females with OPCOS are ovulating, hyperandrogenism and polycystic ovarian morphology increase the susceptibility of cardiovascular diseases, insulin resistance, hyperlipidemia and metabolic syndrome in these females. Objectives: The aim of the study was to identify the significance associated with OPCOS phenotype through serum proteomic profiling of OPCOS females and normal age-matched healthy ovulating females. Methods: One and two-dimensional gel-based pr

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