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Qiu Z, Huang R, Wu Y, Li X, Sun C, Ma Y. Decoding the Structural Diversity: A New Horizon in Antimicrobial Prospecting and Mechanistic Investigation. Microb Drug Resist 2024; 30:254-272. [PMID: 38648550 DOI: 10.1089/mdr.2023.0232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024] Open
Abstract
The escalating crisis of antimicrobial resistance (AMR) underscores the urgent need for novel antimicrobials. One promising strategy is the exploration of structural diversity, as diverse structures can lead to diverse biological activities and mechanisms of action. This review delves into the role of structural diversity in antimicrobial discovery, highlighting its influence on factors such as target selectivity, binding affinity, pharmacokinetic properties, and the ability to overcome resistance mechanisms. We discuss various approaches for exploring structural diversity, including combinatorial chemistry, diversity-oriented synthesis, and natural product screening, and provide an overview of the common mechanisms of action of antimicrobials. We also describe techniques for investigating these mechanisms, such as genomics, proteomics, and structural biology. Despite significant progress, several challenges remain, including the synthesis of diverse compound libraries, the identification of active compounds, the elucidation of complex mechanisms of action, the emergence of AMR, and the translation of laboratory discoveries to clinical applications. However, emerging trends and technologies, such as artificial intelligence, high-throughput screening, next-generation sequencing, and open-source drug discovery, offer new avenues to overcome these challenges. Looking ahead, we envisage an exciting future for structural diversity-oriented antimicrobial discovery, with opportunities for expanding the chemical space, harnessing the power of nature, deepening our understanding of mechanisms of action, and moving toward personalized medicine and collaborative drug discovery. As we face the continued challenge of AMR, the exploration of structural diversity will be crucial in our search for new and effective antimicrobials.
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Affiliation(s)
- Ziying Qiu
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Rongkun Huang
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yuxuan Wu
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Xinghao Li
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Chunyu Sun
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yunqi Ma
- School of Pharmacy, Binzhou Medical University, Yantai, China
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2
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Peng C, Li J, Zhao A, Yu S, Zheng L, Deng ZY. Non-oxidized and oxidized flaxseed orbitides differently induce HepG2 cell apoptosis: involvement of cellular uptake and membrane death receptor DR4. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:4296-4308. [PMID: 38433335 DOI: 10.1002/jsfa.13315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/18/2023] [Accepted: 12/18/2023] [Indexed: 03/05/2024]
Abstract
BACKGROUND Flaxseed orbitides have health-promoting properties, particularly potent anti-cancer activity. However, flaxseed orbitides containing a methionine structure, such as [1-9-NαC]-linusorb B2 (CLB), are easily oxidized to sulfoxide ([1-9-NαC],[1-Rs,Ss-MetO]-linusorb-B2 (CLC)) and sulfone ([1-9-NαC], [1-MetO]-linusorb B2 (CLK)), with CLC having less anti-cancer ability than CLB. It is unclear why oxidized flaxseed orbitides are less effective against cancer than non-oxidized flaxseed orbitide. RESULTS Non-oxidized ([1-9-NαC]-linusorb-B3 (CLA) and CLB) and oxidized (CLC and CLK) flaxseed orbitides were found to significantly upregulate the levels of pro-apoptotic proteins, including Bax/Bcl-2, CytoC, caspase-3, and caspase-8, in a dose-dependent manner, with non-oxidized flaxseed orbitides being more effective than oxidized flaxseed orbitides. Mechanically, the cellular absorption of non-oxidized flaxseed orbitides was higher than that of oxidized flaxseed orbitides. Moreover, the significant fluorescence quenching of DR4 protein by flaxseed orbitides (especially non-oxidized orbitides) indicated the formation of a DR4-orbitide complex. Molecular docking demonstrated that non-oxidized orbitides could easily dock into the active cavity of DR4 protein. Further blocking DR4 significantly reduced the ability of non-oxidized flaxseed orbitides to stimulate caspase-3 expression, whereas oxidized flaxseed orbitides retained this ability. CONCLUSION Non-oxidized flaxseed orbitides are more effective against cancer than oxidized flaxseed orbitides due to higher cellular uptake and activation of the DR4-mediated death receptor signaling pathway. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Changmei Peng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Jing Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Aixiu Zhao
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Shaoqing Yu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Liufeng Zheng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Ze-Yuan Deng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, PR China
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3
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Pang Z, Cravatt BF, Ye L. Deciphering Drug Targets and Actions with Single-Cell and Spatial Resolution. Annu Rev Pharmacol Toxicol 2024; 64:507-526. [PMID: 37722721 DOI: 10.1146/annurev-pharmtox-033123-123610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
Recent advances in chemical, molecular, and genetic approaches have provided us with an unprecedented capacity to identify drug-target interactions across the whole proteome and genome. Meanwhile, rapid developments of single-cell and spatial omics technologies are revolutionizing our understanding of the molecular architecture of biological systems. However, a significant gap remains in how we align our understanding of drug actions, traditionally based on molecular affinities, with the in vivo cellular and spatial tissue heterogeneity revealed by these newer techniques. Here, we review state-of-the-art methods for profiling drug-target interactions and emerging multiomics tools to delineate the tissue heterogeneity at single-cell resolution. Highlighting the recent technical advances enabling high-resolution, multiplexable in situ small-molecule drug imaging (clearing-assisted tissue click chemistry, or CATCH), we foresee the integration of single-cell and spatial omics platforms, data, and concepts into the future framework of defining and understanding in vivo drug-target interactions and mechanisms of actions.
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Affiliation(s)
- Zhengyuan Pang
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California, USA;
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA;
| | - Li Ye
- Department of Neuroscience, The Scripps Research Institute, La Jolla, California, USA;
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, USA
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4
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Kovačević T, Nujić K, Cindrić M, Dragojević S, Vinter A, Hozić A, Mesić M. Different chemical proteomic approaches to identify the targets of lapatinib. J Enzyme Inhib Med Chem 2023; 38:2183809. [PMID: 36856014 PMCID: PMC9980154 DOI: 10.1080/14756366.2023.2183809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The process of identifying the protein targets and off-targets of a biologically active compound is of great importance in modern drug discovery. Various chemical proteomics approaches have been established for this purpose. To compare the different approaches, and to understand which method would provide the best results, we have chosen the EGFR inhibitor lapatinib as an example molecule. Lapatinib derivatives were designed using linkers with motifs, including amino (amidation), alkyne (click chemistry) and the diazirine group (photo-affinity). These modified lapatinib analogues were validated for their ability to inhibit EGFR activity in vitro and were shown to pull down purified recombinant EGFR protein. In all of the approaches evaluated here, we identified EGFR as the main protein target from the lysate of immortalised cell line expressing EGFR, thus validating its potential use to identify unknown protein targets. Taken together, the results reported here give insight into the cellular activities of lapatinib.
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Affiliation(s)
| | | | | | | | | | | | - Milan Mesić
- Selvita Ltd., Zagreb, Croatia,CONTACT Milan Mesić Selvita Ltd., Zagreb, Croatia
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5
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Meem TM, Khan U, Mredul MBR, Awal MA, Rahman MH, Khan MS. A Comprehensive Bioinformatics Approach to Identify Molecular Signatures and Key Pathways for the Huntington Disease. Bioinform Biol Insights 2023; 17:11779322231210098. [PMID: 38033382 PMCID: PMC10683407 DOI: 10.1177/11779322231210098] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 10/07/2023] [Indexed: 12/02/2023] Open
Abstract
Huntington disease (HD) is a degenerative brain disease caused by the expansion of CAG (cytosine-adenine-guanine) repeats, which is inherited as a dominant trait and progressively worsens over time possessing threat. Although HD is monogenetic, the specific pathophysiology and biomarkers are yet unknown specifically, also, complex to diagnose at an early stage, and identification is restricted in accuracy and precision. This study combined bioinformatics analysis and network-based system biology approaches to discover the biomarker, pathways, and drug targets related to molecular mechanism of HD etiology. The gene expression profile data sets GSE64810 and GSE95343 were analyzed to predict the molecular markers in HD where 162 mutual differentially expressed genes (DEGs) were detected. Ten hub genes among them (DUSP1, NKX2-5, GLI1, KLF4, SCNN1B, NPHS1, SGK2, PITX2, S100A4, and MSX1) were identified from protein-protein interaction (PPI) network which were mostly expressed as down-regulated. Following that, transcription factors (TFs)-DEGs interactions (FOXC1, GATA2, etc), TF-microRNA (miRNA) interactions (hsa-miR-340, hsa-miR-34a, etc), protein-drug interactions, and disorders associated with DEGs were predicted. Furthermore, we used gene set enrichment analysis (GSEA) to emphasize relevant gene ontology terms (eg, TF activity, sequence-specific DNA binding) linked to DEGs in HD. Disease interactions revealed the diseases that are linked to HD, and the prospective small drug molecules like cytarabine and arsenite was predicted against HD. This study reveals molecular biomarkers at the RNA and protein levels that may be beneficial to improve the understanding of molecular mechanisms, early diagnosis, as well as prospective pharmacologic targets for designing beneficial HD treatment.
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Affiliation(s)
- Tahera Mahnaz Meem
- Statistics Discipline, Science, Engineering & Technology School, Khulna University, Khulna, Bangladesh
| | - Umama Khan
- Biotechnology & Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Md Bazlur Rahman Mredul
- Statistics Discipline, Science, Engineering & Technology School, Khulna University, Khulna, Bangladesh
| | - Md Abdul Awal
- Electronics and Communication Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia, Bangladesh
| | - Md Salauddin Khan
- Statistics Discipline, Science, Engineering & Technology School, Khulna University, Khulna, Bangladesh
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6
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Zhang J, Lin C, Jin S, Wang H, Wang Y, Du X, Hutchinson MR, Zhao H, Fang L, Wang X. The pharmacology and therapeutic role of cannabidiol in diabetes. EXPLORATION (BEIJING, CHINA) 2023; 3:20230047. [PMID: 37933286 PMCID: PMC10582612 DOI: 10.1002/exp.20230047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/31/2023] [Indexed: 11/08/2023]
Abstract
In recent years, cannabidiol (CBD), a non-psychotropic cannabinoid, has garnered substantial interest in drug development due to its broad pharmacological activity and multi-target effects. Diabetes is a chronic metabolic disease that can damage multiple organs in the body, leading to the development of complications such as abnormal kidney function, vision loss, neuropathy, and cardiovascular disease. CBD has demonstrated significant therapeutic potential in treating diabetes mellitus and its complications owing to its various pharmacological effects. This work summarizes the role of CBD in diabetes and its impact on complications such as cardiovascular dysfunction, nephropathy, retinopathy, and neuropathy. Strategies for discovering molecular targets for CBD in the treatment of diabetes and its complications are also proposed. Moreover, ways to optimize the structure of CBD based on known targets to generate new CBD analogues are explored.
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Affiliation(s)
- Jin Zhang
- Department of GeriatricsThe First Hospital of Jilin UniversityChangchunPeople's Republic of China
- State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijingPeople's Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
| | - Cong Lin
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
| | - Sha Jin
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiPeople's Republic of China
| | - Hongshuang Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
| | - Yibo Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
| | - Xiubo Du
- Shenzhen Key Laboratory of Marine Biotechnology and EcologyCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenPeople's Republic of China
| | - Mark R. Hutchinson
- Discipline of PhysiologyAdelaide Medical SchoolUniversity of AdelaideThe Commonwealth of AustraliaAdelaideAustralia
- ARC Centre for Nanoscale BioPhotonicsUniversity of AdelaideThe Commonwealth of AustraliaAdelaideAustralia
| | - Huiying Zhao
- Department of GeriatricsThe First Hospital of Jilin UniversityChangchunPeople's Republic of China
| | - Le Fang
- Department of NeurologyThe China‐Japan Union Hospital of Jilin UniversityChangchunPeople's Republic of China
| | - Xiaohui Wang
- State Key Laboratory of Natural and Biomimetic DrugsPeking UniversityBeijingPeople's Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunPeople's Republic of China
- School of Applied Chemistry and EngineeringUniversity of Science and Technology of ChinaHefeiPeople's Republic of China
- Beijing National Laboratory for Molecular SciencesBeijingPeople's Republic of China
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7
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Morretta E, Brullo C, Belvedere R, Petrella A, Spallarossa A, Monti MC. Targeting USP-7 by a Novel Fluorinated 5-Pyrazolyl-Urea Derivative. Int J Mol Sci 2023; 24:ijms24119200. [PMID: 37298148 DOI: 10.3390/ijms24119200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
The impact of innovative technologies on the target discovery has been employed here to characterize the interactome of STIRUR 41, a promising 3-fluoro-phenyl-5-pyrazolyl-urea derivative endowed with anti-cancer activity, on neuroblastoma-related cells. A drug affinity responsive target stability-based proteomic platform has been optimized to elucidate the molecular mechanism at the basis of STIRUR 41 action, together with immunoblotting analysis and in silico molecular docking. Ubiquitin Specific Protease 7 (USP-7), one of the deubiquitinating enzymes which protect substrate proteins from proteasomal degradation, has been identified as the most affine STIRUR 41 target. As further demonstrated by in vitro and in-cell assays, STIRUR 41 was able to inhibit both the enzymatic activity of USP-7 and its expression levels in neuroblastoma-related cells, thus laying an encouraging base for the blockade of USP-7 downstream signaling.
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Affiliation(s)
- Elva Morretta
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, Fisciano, 84084 Salerno, Italy
| | - Chiara Brullo
- Department of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Raffaella Belvedere
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, Fisciano, 84084 Salerno, Italy
| | - Antonello Petrella
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, Fisciano, 84084 Salerno, Italy
| | - Andrea Spallarossa
- Department of Pharmacy, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II, Fisciano, 84084 Salerno, Italy
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8
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Buneeva O, Kopylov A, Gnedenko O, Medvedeva M, Veselovsky A, Ivanov A, Zgoda V, Medvedev A. Proteomic Profiling of Mouse Brain Pyruvate Kinase Binding Proteins: A Hint for Moonlighting Functions of PKM1? Int J Mol Sci 2023; 24:ijms24087634. [PMID: 37108803 PMCID: PMC10143413 DOI: 10.3390/ijms24087634] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
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 enzyme isoform expressed in actively dividing cells, PKM2, exhibits many moonlighting (noncanonical) functions. In contrast to PKM2, PKM1, predominantly expressed in adult differentiated tissues, lacks well-documented moonlighting functions. However, certain evidence exists that it can also perform some functions unrelated to glycolysis. In order to evaluate protein partners, bound to PKM1, in this study we have combined affinity-based separation of mouse brain proteins with mass spectrometry identification. The highly purified PKM1 and a 32-mer synthetic peptide (PK peptide), sharing high sequence homology with the interface contact region of all PK isoforms, were used as the affinity ligands. This proteomic profiling resulted in the identification of specific and common proteins bound to both affinity ligands. Quantitative affinity binding to the affinity ligands of selected identified proteins was validated using a surface plasmon resonance (SPR) biosensor. Bioinformatic analysis has shown that the identified proteins, bound to both full-length PKM1 and the PK peptide, form a protein network (interactome). Some of these interactions are relevant for the moonlighting functions of PKM1. The proteomic dataset is available via ProteomeXchange with the identifier PXD041321.
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Affiliation(s)
- Olga Buneeva
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Arthur Kopylov
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Oksana Gnedenko
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Marina Medvedeva
- Department of Biochemistry, School of Biology, Moscow State University, Moscow 119991, Russia
| | - Alexander Veselovsky
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Alexis Ivanov
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Victor Zgoda
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
| | - Alexei Medvedev
- Institute of Biomedical Chemistry, 10 Pogodinskaya Street, Moscow 119121, Russia
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9
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Shang X, Wang Y, Hou Z, Wang X, Zhang H, Yang C, Li J, Huang X, Song S, Yao G. A natural PKM2 targeting agent as a potential drug for breast cancer treatment. Clin Transl Med 2022; 13:e1157. [PMID: 36579385 PMCID: PMC9798039 DOI: 10.1002/ctm2.1157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/30/2022] Open
Affiliation(s)
- Xin‐Yue Shang
- Key Laboratory of Computational Chemistry‐Based Natural Antitumor Drug Research & DevelopmentEngineering Research Center of Natural Medicine Active Molecule Research & DevelopmentShenyangChina,Key Laboratory of Natural Bioactive Compounds Discovery & ModificationShenyangLiaoningChina,Department of Natural Medicine Chemistry, School of Traditional Chinese Materia MedicaShenyang Pharmaceutical UniversityShenyangLiaoningChina,Department of PharmacologyShenyang Medical CollegeShenyangLiaoningChina
| | - Yu‐Jue Wang
- Key Laboratory of Computational Chemistry‐Based Natural Antitumor Drug Research & DevelopmentEngineering Research Center of Natural Medicine Active Molecule Research & DevelopmentShenyangChina,Key Laboratory of Natural Bioactive Compounds Discovery & ModificationShenyangLiaoningChina,Department of Natural Medicine Chemistry, School of Traditional Chinese Materia MedicaShenyang Pharmaceutical UniversityShenyangLiaoningChina
| | - Zi‐Lin Hou
- Key Laboratory of Computational Chemistry‐Based Natural Antitumor Drug Research & DevelopmentEngineering Research Center of Natural Medicine Active Molecule Research & DevelopmentShenyangChina,Key Laboratory of Natural Bioactive Compounds Discovery & ModificationShenyangLiaoningChina,Department of Natural Medicine Chemistry, School of Traditional Chinese Materia MedicaShenyang Pharmaceutical UniversityShenyangLiaoningChina
| | - Xin‐Ye Wang
- Key Laboratory of Computational Chemistry‐Based Natural Antitumor Drug Research & DevelopmentEngineering Research Center of Natural Medicine Active Molecule Research & DevelopmentShenyangChina,Key Laboratory of Natural Bioactive Compounds Discovery & ModificationShenyangLiaoningChina,Department of Natural Medicine Chemistry, School of Traditional Chinese Materia MedicaShenyang Pharmaceutical UniversityShenyangLiaoningChina
| | - Hao Zhang
- Key Laboratory of Computational Chemistry‐Based Natural Antitumor Drug Research & DevelopmentEngineering Research Center of Natural Medicine Active Molecule Research & DevelopmentShenyangChina,Key Laboratory of Natural Bioactive Compounds Discovery & ModificationShenyangLiaoningChina,Department of Natural Medicine Chemistry, School of Traditional Chinese Materia MedicaShenyang Pharmaceutical UniversityShenyangLiaoningChina
| | - Chen‐Yu Yang
- Key Laboratory of Computational Chemistry‐Based Natural Antitumor Drug Research & DevelopmentEngineering Research Center of Natural Medicine Active Molecule Research & DevelopmentShenyangChina,Key Laboratory of Natural Bioactive Compounds Discovery & ModificationShenyangLiaoningChina,Department of Natural Medicine Chemistry, School of Traditional Chinese Materia MedicaShenyang Pharmaceutical UniversityShenyangLiaoningChina
| | - Ji‐Chong Li
- Key Laboratory of Computational Chemistry‐Based Natural Antitumor Drug Research & DevelopmentEngineering Research Center of Natural Medicine Active Molecule Research & DevelopmentShenyangChina,Key Laboratory of Natural Bioactive Compounds Discovery & ModificationShenyangLiaoningChina,Department of Natural Medicine Chemistry, School of Traditional Chinese Materia MedicaShenyang Pharmaceutical UniversityShenyangLiaoningChina
| | - Xiao‐Xiao Huang
- Key Laboratory of Computational Chemistry‐Based Natural Antitumor Drug Research & DevelopmentEngineering Research Center of Natural Medicine Active Molecule Research & DevelopmentShenyangChina,Key Laboratory of Natural Bioactive Compounds Discovery & ModificationShenyangLiaoningChina,Department of Natural Medicine Chemistry, School of Traditional Chinese Materia MedicaShenyang Pharmaceutical UniversityShenyangLiaoningChina
| | - Shao‐Jiang Song
- Key Laboratory of Computational Chemistry‐Based Natural Antitumor Drug Research & DevelopmentEngineering Research Center of Natural Medicine Active Molecule Research & DevelopmentShenyangChina,Key Laboratory of Natural Bioactive Compounds Discovery & ModificationShenyangLiaoningChina,Department of Natural Medicine Chemistry, School of Traditional Chinese Materia MedicaShenyang Pharmaceutical UniversityShenyangLiaoningChina
| | - Guo‐Dong Yao
- Key Laboratory of Computational Chemistry‐Based Natural Antitumor Drug Research & DevelopmentEngineering Research Center of Natural Medicine Active Molecule Research & DevelopmentShenyangChina,Key Laboratory of Natural Bioactive Compounds Discovery & ModificationShenyangLiaoningChina,Department of Natural Medicine Chemistry, School of Traditional Chinese Materia MedicaShenyang Pharmaceutical UniversityShenyangLiaoningChina
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10
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Ferraro G, Belvedere R, Petrella A, Tosco A, Stork B, Salamone S, Minassi A, Pollastro F, Morretta E, Monti MC. Drug affinity-responsive target stability unveils filamins as biological targets for artemetin, an anti-cancer flavonoid. Front Mol Biosci 2022; 9:964295. [PMID: 36090055 PMCID: PMC9452882 DOI: 10.3389/fmolb.2022.964295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Artemetin is a valuable 5-hydroxy-3,6,7,3′,4′-pentamethoxyflavone present in many different medicinal plants with very good oral bioavailability and drug-likeness values, owing to numerous bioactivities, such as anti-inflammatory and anti-cancer ones. Here, a multi-disciplinary plan has been settled and applied for identifying the artemetin target(s) to inspect its mechanism of action, based on drug affinity-responsive target stability and targeted limited proteolysis. Both approaches point to the disclosure of filamins A and B as direct artemetin targets in HeLa cell lysates, also giving detailed insights into the ligand/protein-binding sites. Interestingly, also 8-prenyl-artemetin, which is an artemetin more permeable semisynthetic analog, directly interacts with filamins A and B. Both compounds alter filamin conformation in living HeLa cells with an effect on cytoskeleton disassembly and on the disorganization of the F-actin filaments. Both the natural compound and its derivative are able to block cell migration, expectantly acting on tumor metastasis occurrence and development.
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Affiliation(s)
- Giusy Ferraro
- Department of Pharmacy, Università di Salerno, Fisciano, Italy
- PhD Program in Drug Discovery and Development, Department of Pharmacy, Università di Salerno, Fisciano, Italy
| | | | | | | | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Stefano Salamone
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Novara, Italy
- PlantaChem Srls, Novara, Italy
| | - Alberto Minassi
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Novara, Italy
- PlantaChem Srls, Novara, Italy
| | - Federica Pollastro
- Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Novara, Italy
- PlantaChem Srls, Novara, Italy
| | - Elva Morretta
- Department of Pharmacy, Università di Salerno, Fisciano, Italy
| | - Maria Chiara Monti
- Department of Pharmacy, Università di Salerno, Fisciano, Italy
- *Correspondence: Maria Chiara Monti,
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11
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Yang Y, Li B. Novel Peptide Motifs Containing Asp-Glu-Gly Target P 2Y 12 and Thromboxane A2 Receptors to Inhibit Platelet Aggregation and Thrombus Formation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:785-793. [PMID: 35016500 DOI: 10.1021/acs.jafc.1c06159] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Increasing evidence has shown that collagen peptides have multiple biological activities. Our previous study has separated and identified antiplatelet aggregation peptides Asp-Glu-Gly-Pro (DEGP) from Salmo salar skin. This study is to investigate the cellular target of DEGP on platelets and its underlying mechanism. DEGP inhibited platelet aggregation in a dose-dependent manner induced by 2MeS-ADP and U46619 and significantly attenuated tail thrombosis formation by 30% in mice at the dose of 50 mg/kg body weight. Mechanically, DEGP displayed apparent antagonism effects on TP and P2Y12 receptors by the drug affinity responsive target stability (DARTS) technique to regulate the phosphorylation of RhoAS188, PLCβ3S537, as well as VASPS157. The molecular docking results revealed a stronger binding energy with the target protein of modified peptides DEGI and DDEGL. Practically, DEGI exhibited the highest inhibition activity against 2MeS-ADP- and U46619-induced platelet aggregation in vitro with IC50 values of 0.88 ± 0.10 and 0.85 ± 0.10 mM, respectively, and comparable antithrombosis activity with aspirin at the dose of 25 mg/kg body weight in vivo. These results indicated the possibility that the peptide motifs containing Asp-Glu-Gly could potentially be developed as a novel therapeutic agent in the prevention and treatment of thrombotic diseases.
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Affiliation(s)
- Yijie Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Bo Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Functional Dairy, Ministry of Education, Beijing 100083, China
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12
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Ren YS, Li HL, Piao XH, Yang ZY, Wang SM, Ge YW. Drug affinity responsive target stability (DARTS) accelerated small molecules target discovery: Principles and application. Biochem Pharmacol 2021; 194:114798. [PMID: 34678227 DOI: 10.1016/j.bcp.2021.114798] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 12/19/2022]
Abstract
Drug affinity responsive target stability (DARTS) is a novel target discovery approach and is particularly adept at screening small molecule (SM) targets without requiring any structural modifications. The DARTS method is capable of revealing drug-target interactions from cells or tissues by tracking changes in the stability of proteins acting as receptors of bioactive SMs. Due to its simple operation and high efficiency, the DARTS method has been applied to uncover the drug-action mechanism. This review summarized analytical principles, protocols, validation approaches, applications, and challenges involved in the DARTS method. Due to the innate advantages of the DARTS method, it is expected to be a powerful tool to accelerate SM target discovery, especially for bioactive natural products with unknown mechanisms.
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Affiliation(s)
- Ying-Shan Ren
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Hui-Lin Li
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Xiu-Hong Piao
- Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China; School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Zhi-You Yang
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Shu-Mei Wang
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Yue-Wei Ge
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Digital Quality Evaluation of Chinese Materia Medica of State Administration of TCM, Guangdong Pharmaceutical University, Guangzhou 510006, China; Engineering & Technology Research Center for Chinese Materia Medica Quality of the Universities of Guangdong Province, Guangdong Pharmaceutical University, Guangzhou 510006, China.
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13
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Sun J, Prabhu N, Tang J, Yang F, Jia L, Guo J, Xiao K, Tam WL, Nordlund P, Dai L. Recent advances in proteome-wide label-free target deconvolution for bioactive small molecules. Med Res Rev 2021; 41:2893-2926. [PMID: 33533067 DOI: 10.1002/med.21788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/04/2021] [Accepted: 01/20/2021] [Indexed: 01/01/2023]
Abstract
Small-molecule drugs modulate biological processes and disease states through engagement of target proteins in cells. Assessing drug-target engagement on a proteome-wide scale is of utmost importance in better understanding the molecular mechanisms of action of observed beneficial and adverse effects, as well as in developing next generation tool compounds and drugs with better efficacies and specificities. However, systematic assessment of drug-target engagement has been an arduous task. With the continuous development of mass spectrometry-based proteomics instruments and techniques, various chemical proteomics approaches for drug target deconvolution (i.e., the identification of molecular target for drugs) have emerged. Among these, the label-free target deconvolution approaches that do not involve the chemical modification of compounds of interest, have gained increased attention in the community. Here we provide an overview of the basic principles and recent biological applications of the most important label-free methods including the cellular thermal shift assay, pulse proteolysis, chemical denaturant and protein precipitation, stability of proteins from rates of oxidation, drug affinity responsive target stability, limited proteolysis, and solvent-induced protein precipitation. The state-of-the-art technical implications and future outlook for the label-free approaches are also discussed.
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Affiliation(s)
- Jichao Sun
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China.,Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Nayana Prabhu
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jun Tang
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong, China
| | - Fan Yang
- Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong, China
| | - Lin Jia
- College of Pharmacy, Shenzhen Technology University, Shenzhen, Guangdong, China
| | - Jinan Guo
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China
| | - Kefeng Xiao
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China
| | - Wai Leong Tam
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Pär Nordlund
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Lingyun Dai
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen, Guangdong, China.,Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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14
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Dousti M, Manzano-Román R, Rashidi S, Barzegar G, Ahmadpour NB, Mohammadi A, Hatam G. A proteomic glimpse into the effect of antimalarial drugs on Plasmodium falciparum proteome towards highlighting possible therapeutic targets. Pathog Dis 2021; 79:ftaa071. [PMID: 33202000 DOI: 10.1093/femspd/ftaa071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
There is no effective vaccine against malaria; therefore, chemotherapy is to date the only choice to fight against this infectious disease. However, there is growing evidences of drug-resistance mechanisms in malaria treatments. Therefore, the identification of new drug targets is an urgent need for the clinical management of the disease. Proteomic approaches offer the chance of determining the effects of antimalarial drugs on the proteome of Plasmodium parasites. Accordingly, we reviewed the effects of antimalarial drugs on the Plasmodium falciparum proteome pointing out the relevance of several proteins as possible drug targets in malaria treatment. In addition, some of the P. falciparum stage-specific altered proteins and parasite-host interactions might play important roles in pathogenicity, survival, invasion and metabolic pathways and thus serve as potential sources of drug targets. In this review, we have identified several proteins, including thioredoxin reductase, helicases, peptidyl-prolyl cis-trans isomerase, endoplasmic reticulum-resident calcium-binding protein, choline/ethanolamine phosphotransferase, purine nucleoside phosphorylase, apical membrane antigen 1, glutamate dehydrogenase, hypoxanthine guanine phosphoribosyl transferase, heat shock protein 70x, knob-associated histidine-rich protein and erythrocyte membrane protein 1, as promising antimalarial drugs targets. Overall, proteomic approaches are able to partially facilitate finding possible drug targets. However, the integration of other 'omics' and specific pharmaceutical techniques with proteomics may increase the therapeutic properties of the critical proteins identified in the P. falciparum proteome.
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Affiliation(s)
- Majid Dousti
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Raúl Manzano-Román
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007, Salamanca, Spain
| | - Sajad Rashidi
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Barzegar
- Department of Parasitology and Mycology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Alireza Mohammadi
- Department of Disease Control, Komijan Treatment and Health Network, Arak University of Medical Science, Iran
| | - Gholamreza Hatam
- Basic Sciences in Infectious Diseases Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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15
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Drug Affinity Responsive Target Stability (DARTS ) Assay to Detect Interaction Between a Purified Protein and a Small Molecule. Methods Mol Biol 2021; 2213:175-182. [PMID: 33270202 DOI: 10.1007/978-1-0716-0954-5_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Drug affinity responsive target stability (DARTS) assay is used to detect the interaction between a ligand and a protein based on the observation that some ligands can protect the target protein from degradation by proteases when mixed in a solution. To set up the assay, a ligand is first mixed with a purified candidate target protein or a total cell lysate that contains a candidate target protein. Then, different amounts of protease are added to the mixture to allow the enzyme to digest the protein in the mixture. After protease digestion, the candidate target protein is detected by assays such as western blot, silver staining, or Coomassie blue staining. In theory, the candidate protein should be protected by the ligand from protease digestion, which is reflected by higher abundance of the candidate protein in mixtures containing the ligand compared with the control treatment. There are a few significant advantages of DARTS: (a) the ligand does not need to be modified so the native ligand could be used; (b) the candidate target protein could be either purified protein or protein that is present in the total cell lysate; and (c) the assay can be used together with proteomics analysis to identify an unknown target protein. The assay is especially valuable to test the interaction between the ligand and membrane proteins that are often challenging to purify. In this chapter, we use Endosidin2 (ES2) and its target protein Arabidopsis thaliana EXO70A1 (AtEXO70A1) as an example to show the step-by-step procedure of the DARTS assay.
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Kim TY, Ji ES, Lee JY, Kim JY, Yoo JS, Szasz AM, Dome B, Marko-Varga G, Kwon HJ. DNA Polymerase Alpha Subunit B Is a Binding Protein for Erlotinib Resistance in Non-Small Cell Lung Cancer. Cancers (Basel) 2020; 12:cancers12092613. [PMID: 32933200 PMCID: PMC7564424 DOI: 10.3390/cancers12092613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/05/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Non-small-cell lung carcinoma (NSCLC) covers for almost 85% of all lung cancers and a major contributor to the overall cancer death rate. Erlotinib is used to treat NSCLC via inhibition of epithelial growth factor receptor (EGFR) kinase activity. Despite its high efficacy, recurrence can occur in patients who become resistant to the drug. We performed DARTS LC-MS/MS with SWATH of DIA analysis and identified a novel binding protein of Erlotinib that may underlie NSCLC resistance. Our study indicated that Erlotinib binds POLA2 in addition to EGFR. This was confirmed by DARTS and CETSA results. Importantly, POLA2 expression levels in four NSCLC cell lines were positively correlated with anti-proliferative Erlotinib efficacy (Pearson correlation coefficient, R = 0.9886). These results suggest that POLA2 is a novel complementary target protein of Erlotinib, and could clinically provide validity as a surrogate marker for drug resistance in patients with NSCLC. Abstract Erlotinib inhibits epithelial growth factor receptor (EGFR) kinase activity and is used to treat non-small cell lung cancer (NSCLC). Despite its high efficacy, recurrence can occur in patients who become resistant to the drug. To address the underlying mechanism of Erlotinib resistance, we investigated additional mechanisms related to mode-of-drug-action, by multiple protein-binding interactions, besides EGFR by using drug affinity responsive target stability (DARTS) and liquid chromatography-mass spectrometry (LC-MS/MS) methods with non-labeled Erlotinib. DNA polymerase alpha subunit B (POLA2) was identified as a new Erlotinib binding protein that was validated by the DARTS platform, complemented with cellular thermal shift assays. Genetic knock-down of POLA2 promoted the anti-proliferative effect of the drug in the Erlotinib-resistant cell line H1299 with high POLA2 expression, whereas the overexpression of POLA2 restored anti-proliferative effects in the Erlotinib-sensitive cell line HCC827 with low POLA2 expression. Importantly, POLA2 expression levels in four NSCLC cell lines were positively correlated with anti-proliferative Erlotinib efficacy (Pearson correlation coefficient, R = 0.9886). These results suggest that POLA2 is a novel complementary target protein of Erlotinib, and could clinically provide validity as a surrogate marker for drug resistance in patients with NSCLC.
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Affiliation(s)
- Tae Young Kim
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Korea;
| | - Eun Sun Ji
- Korea Basic Science Institute, Ochang 28119, Korea; (E.S.J.); (J.Y.L.); (J.Y.K.); (J.S.Y.)
| | - Ju Yeon Lee
- Korea Basic Science Institute, Ochang 28119, Korea; (E.S.J.); (J.Y.L.); (J.Y.K.); (J.S.Y.)
| | - Jin Young Kim
- Korea Basic Science Institute, Ochang 28119, Korea; (E.S.J.); (J.Y.L.); (J.Y.K.); (J.S.Y.)
| | - Jong Shin Yoo
- Korea Basic Science Institute, Ochang 28119, Korea; (E.S.J.); (J.Y.L.); (J.Y.K.); (J.S.Y.)
| | - A. Marcell Szasz
- Department of Tumor Biology, National Korányi Institute of Pulmonology, 1121 Budapest, Hungary;
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary
- Division Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, SE-221 84 Lund, Sweden;
| | - Balazs Dome
- Department of Thoracic Surgery, National Institute of Oncology and Semmelweis University, 1117 Budapest, Hungary;
- Division of Thoracic Surgery, Department of Surgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Gyorgy Marko-Varga
- Division Clinical Protein Science & Imaging, Department of Clinical Sciences (Lund) and Department of Biomedical Engineering, Lund University, SE-221 84 Lund, Sweden;
| | - Ho Jeong Kwon
- Chemical Genomics Global Research Lab, Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 120-749, Korea;
- Correspondence: ; Tel.: +82-2-2123-5883; Fax: +82-2-362-7265
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Zhao B, Liu N, Chen L, Geng S, Fan Z, Xing J. Direct label-free methods for identification of target proteins in agrochemicals. Int J Biol Macromol 2020; 164:1475-1483. [PMID: 32763403 DOI: 10.1016/j.ijbiomac.2020.07.237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 12/21/2022]
Abstract
Green agrochemicals are important guarantee for food production and security, and target protein identification is the most important basis for development of novel agrochemicals. Affinity chromatography methods for immobilization of agrochemicals have been widely used to identify and confirm new targets. However, this method often requires modification of the active molecules which can affect or damage its biological activity, and biomacromolecules, particularly most natural products, are hard to be modified either. In order to overcome the shortcomings of molecular modification, label-free technology has been developed based on evaluating responses to thermal or proteolytic treatments. Combined with the chemical biology technology and molecular biology technology, it has been used in the development of drugs and agrochemicals. Herein, common methods of label-free technology for identification of direct target of agrochemicals are reviewed, including the principle, advantages, limitations and applications in the research of agrochemicals in the last decade. And the methods for validation of candidate targets obtained by the label-free methods are also reviewed, which are important to obtain the accurate and reliable targets. Combined application of these methods will greatly reduce the experimental costs and shorten the period for the new target identification and validation by improving its accuracy, which will provide a systematic solution for new ecological agrochemicals research and development.
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Affiliation(s)
- Bin Zhao
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China; State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, PR China
| | - Ning Liu
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding 071001, PR China
| | - Lai Chen
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China; State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, PR China
| | - Shuo Geng
- College of Plant Protection, Hebei Agricultural University, Baoding 071001, PR China
| | - Zhijin Fan
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, PR China.
| | - Jihong Xing
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding 071001, PR China.
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Yang L, Bui L, Hanjaya-Putra D, Bruening ML. Membrane-Based Affinity Purification to Identify Target Proteins of a Small-Molecule Drug. Anal Chem 2020; 92:11912-11920. [DOI: 10.1021/acs.analchem.0c02316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Ceccacci S, Deitersen J, Mozzicafreddo M, Morretta E, Proksch P, Wesselborg S, Stork B, Monti MC. Carbamoyl-Phosphate Synthase 1 as a Novel Target of Phomoxanthone A, a Bioactive Fungal Metabolite. Biomolecules 2020; 10:biom10060846. [PMID: 32498414 PMCID: PMC7356042 DOI: 10.3390/biom10060846] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
Phomoxanthone A, a bioactive xanthone dimer isolated from the endophytic fungus Phomopsis sp., is a mitochondrial toxin weakening cellular respiration and electron transport chain activity by a fast breakup of the mitochondrial assembly. Here, a multi-disciplinary strategy has been developed and applied for identifying phomoxanthone A target(s) to fully address its mechanism of action, based on drug affinity response target stability and targeted limited proteolysis. Both approaches point to the identification of carbamoyl-phosphate synthase 1 as a major phomoxanthone A target in mitochondria cell lysates, giving also detailed insights into the ligand/target interaction sites by molecular docking and assessing an interesting phomoxanthone A stimulating activity on carbamoyl-phosphate synthase 1. Thus, phomoxanthone A can be regarded as an inspiring molecule for the development of new leads in counteracting hyperammonemia states.
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Affiliation(s)
- Sara Ceccacci
- Department of Pharmacy, Università di Salerno, Via Giovanni Paolo II 132, Fisciano, 84084 Salerno, Italy; (S.C.); (E.M.)
- PhD Program in Drug Discovery and Development, Department of Pharmacy, Università di Salerno, Via Giovanni Paolo II 132, Fisciano, 84084 Salerno, Italy
| | - Jana Deitersen
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany; (J.D.); (S.W.); (B.S.)
| | - Matteo Mozzicafreddo
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032 Camerino, Italy;
| | - Elva Morretta
- Department of Pharmacy, Università di Salerno, Via Giovanni Paolo II 132, Fisciano, 84084 Salerno, Italy; (S.C.); (E.M.)
| | - Peter Proksch
- Institute of Pharmaceutical Biology and Biotechnology, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany;
| | - Sebastian Wesselborg
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany; (J.D.); (S.W.); (B.S.)
| | - Björn Stork
- Institute of Molecular Medicine I, Medical Faculty, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany; (J.D.); (S.W.); (B.S.)
| | - Maria Chiara Monti
- Department of Pharmacy, Università di Salerno, Via Giovanni Paolo II 132, Fisciano, 84084 Salerno, Italy; (S.C.); (E.M.)
- Correspondence:
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