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Morales-Luna L, Vázquez-Bautista M, Martínez-Rosas V, Rojas-Alarcón MA, Ortega-Cuellar D, González-Valdez A, Pérez de la Cruz V, Arreguin-Espinosa R, Rodríguez-Bustamante E, Rodríguez-Flores E, Hernández-Ochoa B, Gómez-Manzo S. Fused Enzyme Glucose-6-Phosphate Dehydrogenase::6-Phosphogluconolactonase (G6PD::6PGL) as a Potential Drug Target in Giardia lamblia, Trichomonas vaginalis, and Plasmodium falciparum. Microorganisms 2024; 12:112. [PMID: 38257939 PMCID: PMC10819308 DOI: 10.3390/microorganisms12010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/01/2024] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
Several microaerophilic parasites such as Giardia lamblia, Trichomonas vaginalis, and Plasmodium falciparum are major disease-causing organisms and are responsible for spreading infections worldwide. Despite significant progress made in understanding the metabolism and molecular biology of microaerophilic parasites, chemotherapeutic treatment to control it has seen limited progress. A current proposed strategy for drug discovery against parasitic diseases is the identification of essential key enzymes of metabolic pathways associated with the parasite's survival. In these organisms, glucose-6-phosphate dehydrogenase::6-phosphogluconolactonase (G6PD:: 6PGL), the first enzyme of the pentose phosphate pathway (PPP), is essential for its metabolism. Since G6PD:: 6PGL provides substrates for nucleotides synthesis and NADPH as a source of reducing equivalents, it could be considered an anti-parasite drug target. This review analyzes the anaerobic energy metabolism of G. lamblia, T. vaginalis, and P. falciparum, with a focus on glucose metabolism through the pentose phosphate pathway and the significance of the fused G6PD:: 6PGL enzyme as a therapeutic target in the search for new drugs.
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Affiliation(s)
- Laura Morales-Luna
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.M.-L.); (M.V.-B.); (V.M.-R.); (M.A.R.-A.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Montserrat Vázquez-Bautista
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.M.-L.); (M.V.-B.); (V.M.-R.); (M.A.R.-A.)
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Víctor Martínez-Rosas
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.M.-L.); (M.V.-B.); (V.M.-R.); (M.A.R.-A.)
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Miriam Abigail Rojas-Alarcón
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.M.-L.); (M.V.-B.); (V.M.-R.); (M.A.R.-A.)
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico
| | - Daniel Ortega-Cuellar
- Laboratorio de Nutrición Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico;
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Verónica Pérez de la Cruz
- Neurobiochemistry and Behavior Laboratory, National Institute of Neurology and Neurosurgery “Manuel Velasco Suárez”, Mexico City 14269, Mexico;
| | - Roberto Arreguin-Espinosa
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (R.A.-E.); (E.R.-B.); (E.R.-F.)
| | - Eduardo Rodríguez-Bustamante
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (R.A.-E.); (E.R.-B.); (E.R.-F.)
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey 64849, Mexico
| | - Eden Rodríguez-Flores
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; (R.A.-E.); (E.R.-B.); (E.R.-F.)
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Mexico City 06720, Mexico
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City 04530, Mexico; (L.M.-L.); (M.V.-B.); (V.M.-R.); (M.A.R.-A.)
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Nazli A, Qiu J, Tang Z, He Y. Recent Advances and Techniques for Identifying Novel Antibacterial Targets. Curr Med Chem 2024; 31:464-501. [PMID: 36734893 DOI: 10.2174/0929867330666230123143458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 11/11/2022] [Indexed: 02/04/2023]
Abstract
BACKGROUND With the emergence of drug-resistant bacteria, the development of new antibiotics is urgently required. Target-based drug discovery is the most frequently employed approach for the drug development process. However, traditional drug target identification techniques are costly and time-consuming. As research continues, innovative approaches for antibacterial target identification have been developed which enabled us to discover drug targets more easily and quickly. METHODS In this review, methods for finding drug targets from omics databases have been discussed in detail including principles, procedures, advantages, and potential limitations. The role of phage-driven and bacterial cytological profiling approaches is also discussed. Moreover, current article demonstrates the advancements being made in the establishment of computational tools, machine learning algorithms, and databases for antibacterial target identification. RESULTS Bacterial drug targets successfully identified by employing these aforementioned techniques are described as well. CONCLUSION The goal of this review is to attract the interest of synthetic chemists, biologists, and computational researchers to discuss and improve these methods for easier and quicker development of new drugs.
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Affiliation(s)
- Adila Nazli
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
| | - Jingyi Qiu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Ziyi Tang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, 266 Fangzheng Avenue, Chongqing, 400714, P. R. China
| | - Yun He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, P. R. China
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Morretta E, Ruggiero D, Belvedere R, Petrella A, Bruno I, Terracciano S, Monti MC. A multidisciplinary functional proteomics-aided strategy as a tool for the profiling of a novel cytotoxic thiadiazolopyrimidone. Bioorg Chem 2023; 138:106620. [PMID: 37229937 DOI: 10.1016/j.bioorg.2023.106620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 05/27/2023]
Abstract
In recent years, thiadiazolopyrimidine derivatives have been acknowledged for their striking poly-pharmacological framework, thus representing an interesting scaffold for the development of new therapeutic candidates. This paper examines the synthesis and the interactome characterization of a novel bioactive thiadiazolopyrimidone (compound 1), endowed with cytotoxic activity on HeLa cancer cells. In detail, starting from a small set of synthesized thiadiazolopyrimidones, a multi-disciplinary strategy has been carried out on the most bioactive one to disclose its potential biological targets by functional proteomics, using a label-free mass spectrometry based platform coupling Drug Affinity Responsive Target Stability and targeted Limited Proteolysis-Multiple Reaction Monitoring. The identification of Annexin A6 (ANXA6) as compound 1 most reliable cellular partner paved the way to deepen the protein-ligand interaction through bio-orthogonal approaches and to prove compound 1 action on migration and invasion processes governed by ANXA6 modulation. The identification of compund 1 as the first ANXA6 protein modulator represents a relevant tool to further explore the biological role of ANXA6 in cancer, as well as to develop novel anticancer candidates.
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Affiliation(s)
- Elva Morretta
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy.
| | - Dafne Ruggiero
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy.
| | - Raffaella Belvedere
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy.
| | - Antonello Petrella
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy.
| | - Ines Bruno
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy.
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy.
| | - Maria Chiara Monti
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy.
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Zhang Q, Cui Q. Target protein identification of andrographolide based on isomer approach. J Pharm Biomed Anal 2023; 222:115111. [PMID: 36279844 DOI: 10.1016/j.jpba.2022.115111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
The target identification of natural products is one of the most challenging issues in the standardized application of traditional Chinese medicine. It is widely recognized that magnetic nanoparticles (MNPs) could function as a tool that capture the target proteins of active molecule. However, the false positives caused by non-specific adsorption should not be ignored. Here, we reported a functionalized MNPs technique that could enrich the target proteins of andrographolide (AG) based on isomers approach. We designed and characterized MNPs and isomers of AG. The combination of the two could be used as an ideal coupling, which provides a feasible method for the target proteins enrichment of AG. In addition, the target proteins were identified by HPLC-MS/MS. Moreover, bioinformatics analysis and systematic computational dockings were performed to search for the interactions between target proteins and AG. Six inflammation-related proteins, including CD4, IKBKB, PKN1, PKN2, YWHAB and YWHAH were proved to be the anti-inflammatory targets of AG. All of the results indicated this integrated system could benefit target identification of bioactive natural products.
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Affiliation(s)
- Qi Zhang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Qingxin Cui
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China.
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Reddy MM, Jennings L, Thomas OP. Marine Biodiscovery in a Changing World. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2021; 116:1-36. [PMID: 34698944 DOI: 10.1007/978-3-030-80560-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The term "marine biodiscovery" has been recently been adopted to describe the area of marine natural products dedicated to the search of new drugs. Several maritime countries such as Australia, New Zealand, South Korea, and Japan as well as some European countries have invested significantly in this area of research over the last 50 years. In the late 2000s, research in this field has received significant interest and support in Ireland for exploring new marine bioresources from the nutrient-rich waters of the Northeastern Atlantic Ocean. Despite undeniable success exemplified by the marketing of new drugs, especially in oncology, the integration of new technical but also environmental aspects should be considered. Indeed, global change, particularly in our oceans, such as climate change, biodiversity loss, and the emergence of microbial pathogens, not only affects the environment but ultimately contributes to social inequalities. In this contribution, new avenues and best practices are proposed, such as the development of biorepositories and shared data for the future of marine biodiscovery research. The extension of this type of scientific work will allow humanity to finally make the optimum use of marine bioresources.
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Affiliation(s)
- Maggie M Reddy
- Marine Biodiscovery, School of Chemistry and Ryan Institute, NUI Galway, University Road, Galway, H91TK33, Ireland
| | - Laurence Jennings
- Marine Biodiscovery, School of Chemistry and Ryan Institute, NUI Galway, University Road, Galway, H91TK33, Ireland
| | - Olivier P Thomas
- Marine Biodiscovery, School of Chemistry and Ryan Institute, NUI Galway, University Road, Galway, H91TK33, Ireland.
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Kawatani M, Aono H, Hiranuma S, Shimizu T, Muroi M, Ogawa N, Ohishi T, Ohba SI, Kawada M, Nogawa T, Okano A, Hashizume D, Osada H. Identification of a Small-Molecule Glucose Transporter Inhibitor, Glutipyran, That Inhibits Cancer Cell Growth. ACS Chem Biol 2021; 16:1576-1586. [PMID: 34296611 DOI: 10.1021/acschembio.1c00480] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cancer cells reprogram their metabolism to survive and grow. Small-molecule inhibitors targeting cancer are useful for studying its metabolic pathways and functions and for developing anticancer drugs. Here, we discovered that glutipyran and its derivatives inhibit glycolytic activity and cell growth in human pancreatic cancer cells. According to proteomic profiling of glutipyran-treated cells using our ChemProteoBase, glutipyran was clustered within the group of endoplasmic reticulum (ER) stress inducers that included glycolysis inhibitors. Glutipyran inhibited glucose uptake and suppressed the growth of various cancer cells, including A431 cells that express glucose transporter class I (GLUT1) and DLD-1 GLUT1 knockout cells. When cotreated with the mitochondrial respiration inhibitor metformin, glutipyran exhibited a synergistic antiproliferative effect. Metabolome analysis revealed that glutipyran markedly decreased most metabolites of the glycolytic pathway and the pentose phosphate pathway. Glutipyran significantly suppressed tumor growth in a xenograft mouse model of pancreatic cancer. These results suggest that glutipyran acts as a broad-spectrum GLUT inhibitor and reduces cancer cell growth.
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Affiliation(s)
- Makoto Kawatani
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Harumi Aono
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Sayoko Hiranuma
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Takeshi Shimizu
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Makoto Muroi
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoko Ogawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tomokazu Ohishi
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, 18-24 Miyamoto, Numazu, Shizuoka 410-0301, Japan
| | - Shun-Ichi Ohba
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, 18-24 Miyamoto, Numazu, Shizuoka 410-0301, Japan
| | - Manabu Kawada
- Institute of Microbial Chemistry (BIKAKEN), Numazu, Microbial Chemistry Research Foundation, 18-24 Miyamoto, Numazu, Shizuoka 410-0301, Japan
| | - Toshihiko Nogawa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Akiko Okano
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Daisuke Hashizume
- Materials Characterization Support Team, RIKEN Center for Emergent Matter Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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van der Woude L, Piotrowski M, Klaasse G, Paulus JK, Krahn D, Ninck S, Kaschani F, Kaiser M, Novák O, Ljung K, Bulder S, van Verk M, Snoek BL, Fiers M, Martin NI, van der Hoorn RAL, Robert S, Smeekens S, van Zanten M. The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1523-1540. [PMID: 33768644 PMCID: PMC8360157 DOI: 10.1111/tpj.15250] [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: 01/06/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2-deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound 'Heatin', containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology.
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Affiliation(s)
- Lennard van der Woude
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Markus Piotrowski
- Department of Molecular Genetics and Physiology of PlantsFaculty of Biology and BiotechnologyUniversitätsstraße 150Bochum44801Germany
| | - Gruson Klaasse
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
| | - Judith K. Paulus
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Daniel Krahn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Sabrina Ninck
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Ondřej Novák
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
- Laboratory of Growth RegulatorsThe Czech Academy of Sciences & Faculty of ScienceInstitute of Experimental BotanyPalacký UniversityŠlechtitelů 27Olomouc78371Czech Republic
| | - Karin Ljung
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Suzanne Bulder
- Bejo Zaden B.V.Trambaan 1Warmenhuizen1749 CZthe Netherlands
| | - Marcel van Verk
- Plant‐Microbe InteractionsInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
- KeygeneAgro Business Park 90Wageningen6708 PWthe Netherlands
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Basten L. Snoek
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn Fiers
- BioscienceWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
- Biological Chemistry GroupSylvius LaboratoriesInstitute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEthe Netherlands
| | - Renier A. L. van der Hoorn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Stéphanie Robert
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Sjef Smeekens
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn van Zanten
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
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Panter F, Bader CD, Müller R. Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics. Chem Sci 2021; 12:5994-6010. [PMID: 33995996 PMCID: PMC8098685 DOI: 10.1039/d0sc06919a] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development based on natural products has faced a long lasting decline since the 1970s, while both the speed and the extent of antimicrobial resistance (AMR) development have been severely underestimated. The discovery of antimicrobial natural products of bacterial and fungal origin featuring new chemistry and previously unknown mode of actions is increasingly challenged by rediscovery issues. Natural products that are abundantly produced by the corresponding wild type organisms often featuring strong UV signals have been extensively characterized, especially the ones produced by extensively screened microbial genera such as streptomycetes. Purely synthetic chemistry approaches aiming to replace the declining supply from natural products as starting materials to develop novel antibiotics largely failed to provide significant numbers of antibiotic drug leads. To cope with this fundamental issue, microbial natural products science is being transformed from a 'grind-and-find' study to an integrated approach based on bacterial genomics and metabolomics. Novel technologies in instrumental analytics are increasingly employed to lower detection limits and expand the space of detectable substance classes, while broadening the scope of accessible and potentially bioactive natural products. Furthermore, the almost exponential increase in publicly available bacterial genome data has shown that the biosynthetic potential of the investigated strains by far exceeds the amount of detected metabolites. This can be judged by the discrepancy between the number of biosynthetic gene clusters (BGC) encoded in the genome of each microbial strain and the number of secondary metabolites actually detected, even when considering the increased sensitivity provided by novel analytical instrumentation. In silico annotation tools for biosynthetic gene cluster classification and analysis allow fast prioritization in BGC-to-compound workflows, which is highly important to be able to process the enormous underlying data volumes. BGC prioritization is currently accompanied by novel molecular biology-based approaches to access the so-called orphan BGCs not yet correlated with a secondary metabolite. Integration of metabolomics, in silico genomics and molecular biology approaches into the mainstream of natural product research will critically influence future success and impact the natural product field in pharmaceutical, nutritional and agrochemical applications and especially in anti-infective research.
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Affiliation(s)
- Fabian Panter
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
| | - Chantal D Bader
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Department of Pharmacy, Saarland University Campus E8 1 66123 Saarbrücken Germany
- German Centre for Infection Research (DZIF) Partner Site Hannover-Braunschweig Germany
- Helmholtz International Lab for Anti-infectives Campus E8 1 66123 Saarbrücken Germany
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Zhao M, Yao L, Zhang X, Wang L, Tu P, Zeng K. Global identification of the cellular targets for a multi-molecule system by a photochemically-induced coupling reaction. Chem Commun (Camb) 2021; 57:3449-3452. [PMID: 33870345 DOI: 10.1039/d1cc00392e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Current target identification strategies mainly focus on single compounds. However, no practical experimental methodologies have been developed for multi-molecule systems. Herein, we established a cellular target identification technology for a multi-molecule system by preparing 4,4'-dihydroxybenzophenone (DHBP)-bound Fe3O4 nanoparticles (NPs) with photochemically induced crosslinking capacity. DHBP-bound NPs reacted with the chemicals from the medicinal plant extract as a multi-molecule system under ultraviolet radiation by forming carbon-carbon bonds, thus generating extract-crosslinked NPs for capturing target proteins from cell lysates. The technology, which is named the Zhao-Yao (ZY) strategy, may promote the comprehensive interpretation of the pharmacological mechanism of multi-molecule systems via the global identification of cellular targets.
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Affiliation(s)
- Meimei Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.
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Wang X, Chen Y, Zhu J, Yang Z, Gong X, Hui R, Huang G, Jin J. A comprehensive screening method for investigating the potential binding targets of doxorubicin based on protein microarray. Eur J Pharmacol 2021; 896:173896. [PMID: 33508279 DOI: 10.1016/j.ejphar.2021.173896] [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: 10/08/2020] [Revised: 01/06/2021] [Accepted: 01/19/2021] [Indexed: 11/28/2022]
Abstract
With the development of precision therapy, pharmacological research pays more and more attention to seek and confirm the target of drugs in order to understand the mechanism of drug action and reduce side effects. Screening candidate proteins can be effectively used to predict potential drug targets and toxicity. Therefore, a high-throughput drug-binding protein screening method based on protein microarray which contains over 21,000 human proteins was introduced in this investigation. Doxorubicin, a classical chemotherapeutic agent widely used in clinical treatment, was taken as a drug example in our protein screening study. Through microarray and bioinformatics analysis, more potential targets were found with different binding affinity to doxorubicin, and HRAS stands out as a critical protein from candidate proteins. In addition, the results revealed that the formation of the HRAS-RAF complex is promoted by doxorubicin. It is our expectation that the outcomes could benefit to understand the various effect of the doxorubicin and push the protein microarray screening to apply in the comprehensive pharmacological and toxicological investigation of other drugs.
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Affiliation(s)
- Xu Wang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Yun Chen
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Jingyu Zhu
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Zhaoqi Yang
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Xiaohai Gong
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Renjie Hui
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
| | - Gang Huang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China.
| | - Jian Jin
- School of Pharmaceutical Sciences, Jiangnan University, Wuxi, 214122, PR China.
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11
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Biswas S. High Content Analysis Across Signaling Modulation Treatments for Subcellular Target Identification Reveals Heterogeneity in Cellular Response. Front Cell Dev Biol 2021; 8:594750. [PMID: 33490062 PMCID: PMC7817946 DOI: 10.3389/fcell.2020.594750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/09/2020] [Indexed: 11/13/2022] Open
Abstract
Cellular phenotypes on bioactive compound treatment are a result of the downstream targets of the respective treatment. Here, a computational approach is taken for downstream subcellular target identification to understand the basis of the cellular response. This response is a readout of cellular phenotypes captured from cell-painting-based light microscopy images. The readouts are morphological profiles measured simultaneously from multiple cellular organelles. Cellular profiles generated from roughly 270 diverse treatments on bone cancer cell line form the high content screen used in this study. Phenotypic diversity across these treatments is demonstrated, depending on the image-based phenotypic profiles. Furthermore, the impact of the treatments on specific organelles and associated organelle sensitivities are determined. This revealed that endoplasmic reticulum has a higher likelihood of being targeted. Employing multivariate regression overall cellular response is predicted based on fewer organelle responses. This prediction model is validated against 1,000 new candidate compounds. Different compounds despite driving specific modulation outcomes elicit a varying effect on cellular integrity. Strikingly, this confirms that phenotypic responses are not conserved that enables quantification of signaling heterogeneity. Agonist-antagonist signaling pairs demonstrate switch of the targets in the cascades hinting toward evidence of signaling plasticity. Quantitative analysis of the screen has enabled the identification of these underlying signatures. Together, these image-based profiling approaches can be employed for target identification in drug and diseased states and understand the hallmark of cellular response.
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Affiliation(s)
- Sayan Biswas
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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12
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Microscale Thermophoresis (MST) to Detect the Interaction Between Purified Protein and Small Molecule. Methods Mol Biol 2021; 2213:187-193. [PMID: 33270204 DOI: 10.1007/978-1-0716-0954-5_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Microscale thermophoresis (MST) is a biophysical assay to quantify the interaction between molecules, such as proteins and small molecules. In recent years, the MST assay has been used to detect protein-protein and protein-drug interactions. The assay detects the interaction between molecules by quantifying the thermophoretic movement of fluorescent molecules in response to a temperature gradient. In practice, the fluorescent molecule is mixed with different concentrations of the nonfluorescent ligand, and the mixture of molecules in solution is loaded to capillaries. A temperature gradient is applied to samples in the capillaries, and the movement of the fluorescent molecule in the temperature gradient is detected and recorded. The effect of different concentrations of the nonfluorescent ligand on the movement of the fluorescent molecule is quantified to test for the interaction between molecules. If the fluorescent molecule interacts with the ligand, the molecular properties of the molecules, such as charge, size, and hydration shell, will influence the molecular motility. MST has the advantages of being quantitative and robust. In this chapter, we will use Endosidin2 and its target protein Arabidopsis thaliana EXO70A1 (AtEXO70A1), as an example to show the procedure of using MST to test the interaction between a GFP-tagged protein and a small molecule.
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13
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Chen F, Chen L, Liang W, Zhang Z, Li J, Zheng W, Zhu Z, Zhu J, Zhao Y. Identification and confirmation of 14-3-3 ζ as a novel target of ginsenosides in brain tissues. J Ginseng Res 2020; 45:465-472. [PMID: 34295206 PMCID: PMC8282492 DOI: 10.1016/j.jgr.2020.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 11/11/2020] [Accepted: 12/23/2020] [Indexed: 12/21/2022] Open
Abstract
Background Ginseng can help regulate brain excitability, promote learning and memory, and resist cerebral ischemia in the central nervous system. Ginsenosides are the major effective compounds of Ginseng, but their protein targets in the brain have not been determined. Methods We screened proteins that interact with the main components of ginseng (ginsenosides) by affinity chromatography and identified the 14-3-3 ζ protein as a potential target of ginsenosides in brain tissues. Results Biolayer interferometry (BLI) analysis showed that 20(S)-protopanaxadiol (PPD), a ginseng saponin metabolite, exhibited the highest direct interaction to the 14-3-3 ζ protein. Subsequently, BLI kinetics analysis and isothermal titration calorimetry (ITC) assay showed that PPD specifically bound to the 14-3-3 ζ protein. The cocrystal structure of the 14-3-3 ζ protein-PPD complex showed that the main interactions occurred between the residues R56, R127, and Y128 of the 14-3-3 ζ protein and a portion of PPD. Moreover, mutating any of the above residues resulted in a significant decrease of affinity between PPD and the 14-3-3 ζ protein. Conclusion Our results indicate the 14-3-3 ζ protein is the target of PPD, a ginsenoside metabolite. Crystallographic and mutagenesis studies suggest a direct interaction between PPD and the 14-3-3 ζ protein. This finding can help in the development of small-molecular compounds that bind to the 14-3-3 ζ protein on the basis of the structure of dammarane-type triterpenoid.
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Affiliation(s)
- Feiyan Chen
- Research and Innovation Center, College of Traditional Chinese Medicine Integrated Chinese and Western Medicine College, Nanjing University of Chinese Medicine, Nanjing, China.,Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Lin Chen
- Department of Physiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Weifeng Liang
- Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhengguang Zhang
- Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiao Li
- Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wan Zheng
- Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhu Zhu
- Department of Pharmacology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiapeng Zhu
- Department of Cell Biology and Medical Genetics, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yunan Zhao
- Department of Pathology and Pathophysiology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
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Jiang S, Dong F, Da L, Yang X, Wang X, Weng J, Feng L, Zhu L, Zhang Y, Zhang Z, Sun Y, Li J, Xu M. Ikarugamycin inhibits pancreatic cancer cell glycolysis by targeting hexokinase 2. FASEB J 2020; 34:3943-3955. [PMID: 31944405 DOI: 10.1096/fj.201901237r] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/09/2019] [Accepted: 12/27/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Shu‐Heng Jiang
- Key Laboratory of Systems Biomedicine (Ministry of Education) Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University Shanghai P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai P. R. China
| | - Fang‐Yuan Dong
- Department of Gastroenterology Shanghai Key Laboratory of Clinical Geriatric Medicine Huadong Hospital Fudan University Shanghai P. R. China
| | - Lin‐Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education) Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University Shanghai P. R. China
| | - Xiao‐Mei Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai P. R. China
| | - Xiao‐Xue Wang
- Instrumental Analysis Center Shanghai Jiao Tong University Shanghai P. R. China
| | - Jing‐Yi Weng
- Key Laboratory of Systems Biomedicine (Ministry of Education) Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University Shanghai P. R. China
| | - Lei Feng
- Instrumental Analysis Center Shanghai Jiao Tong University Shanghai P. R. China
| | - Li‐Li Zhu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai P. R. China
| | - Yan‐Li Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai P. R. China
| | - Zhi‐Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai P. R. China
| | - Yong‐Wei Sun
- Department of Biliary‐Pancreatic Surgery Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai P. R. China
| | - Jun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai P. R. China
| | - Min‐Juan Xu
- Key Laboratory of Systems Biomedicine (Ministry of Education) Shanghai Center for Systems Biomedicine Shanghai Jiao Tong University Shanghai P. R. China
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15
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Nozaka A, Nishiwaki A, Nagashima Y, Endo S, Kuroki M, Nakajima M, Narukawa M, Kamisuki S, Arazoe T, Taguchi H, Sugawara F, Kamakura T. Chloramphenicol inhibits eukaryotic Ser/Thr phosphatase and infection-specific cell differentiation in the rice blast fungus. Sci Rep 2019; 9:9283. [PMID: 31243315 PMCID: PMC6594944 DOI: 10.1038/s41598-019-41039-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/25/2019] [Indexed: 01/23/2023] Open
Abstract
Chloramphenicol (Cm) is a broad-spectrum classic antibiotic active against prokaryotic organisms. However, Cm has severe side effects in eukaryotes of which the cause remains unknown. The plant pathogenic fungus Magnaporthe oryzae, which causes rice blast, forms an appressorium to infect the host cell via single-cell differentiation. Chloramphenicol specifically inhibits appressorium formation, which indicates that Cm has a novel molecular target (or targets) in the rice blast fungus. Application of the T7 phage display method inferred that MoDullard, a Ser/Thr-protein phosphatase, may be a target of Cm. In animals Dullard functions in cell differentiation and protein synthesis, but in fungi its role is poorly understood. In vivo and in vitro analyses showed that MoDullard is required for appressorium formation, and that Cm can bind to and inhibit MoDullard function. Given that human phosphatase CTDSP1 complemented the MoDullard function during appressorium formation by M. oryzae, CTDSP1 may be a novel molecular target of Cm in eukaryotes.
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Affiliation(s)
- Akihito Nozaka
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Ayaka Nishiwaki
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Yuka Nagashima
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Shogo Endo
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Misa Kuroki
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Masahiro Nakajima
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Megumi Narukawa
- Osaka University, Research Institute for Microbial Diseases, Department of Molecular Microbiology, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shinji Kamisuki
- Azabu University, Department of Veterinary Science, Laboratory of Basic Education, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa, 252-5201, Japan
| | - Takayuki Arazoe
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Hayao Taguchi
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Fumio Sugawara
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Takashi Kamakura
- Tokyo University of Science, Department of Applied Biological Science, Faculty of Science and Technology, 2641, Yamazaki, Noda, Chiba, 278-8510, Japan.
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16
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Proteomic Profiling for Target Identification of Biologically Active Small Molecules Using 2D DIGE. Methods Mol Biol 2019; 1888:127-139. [PMID: 30519944 DOI: 10.1007/978-1-4939-8891-4_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent improvements in technologies such as omics analysis have enabled us to acquire a large amount of data regarding the biological changes in cells treated with bioactive small molecules. Using such data, a variety of profiling methods have been established for target identification of such bioactive compounds. In this chapter, we describe a proteomic profiling system, ChemProteoBase, based on proteome analysis using two-dimensional difference gel electrophoresis. This system compares the similarities in protein expression of 296 spots detected in the gel among the test compounds.
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17
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Chen F, Zhu K, Chen L, Ouyang L, Chen C, Gu L, Jiang Y, Wang Z, Lin Z, Zhang Q, Shao X, Dai J, Zhao Y. Protein target identification of ginsenosides in skeletal muscle tissues: discovery of natural small-molecule activators of muscle-type creatine kinase. J Ginseng Res 2019; 44:461-474. [PMID: 32372868 PMCID: PMC7195589 DOI: 10.1016/j.jgr.2019.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/19/2019] [Accepted: 02/27/2019] [Indexed: 12/15/2022] Open
Abstract
Background Ginseng effectively reduces fatigue in both animal models and clinical trials. However, the mechanism of action is not completely understood, and its molecular targets remain largely unknown. Methods By screening for proteins that interact with the primary components of ginseng (ginsenosides) in an affinity chromatography assay, we have identified muscle-type creatine kinase (CK-MM) as a potential target in skeletal muscle tissues. Results Biolayer interferometry analysis showed that ginsenoside metabolites, instead of parent ginsenosides, had direct interaction with recombinant human CK-MM. Subsequently, 20(S)-protopanaxadiol (PPD), which is a ginsenoside metabolite and displayed the strongest interaction with CK-MM in the study, was selected as a representative to confirm direct binding and its biological importance. Biolayer interferometry kinetics analysis and isothermal titration calorimetry assay demonstrated that PPD specifically bound to human CK-MM. Moreover, the mutation of key amino acids predicted by molecular docking decreased the affinity between PPD and CK-MM. The direct binding activated CK-MM activity in vitro and in vivo, which increased the levels of tissue phosphocreatine and strengthened the function of the creatine kinase/phosphocreatine system in skeletal muscle, thus buffering cellular ATP, delaying exercise-induced lactate accumulation, and improving exercise performance in mice. Conclusion Our results suggest a cellular target and an initiating molecular event by which ginseng reduces fatigue. All these findings indicate PPD as a small molecular activator of CK-MM, which can help in further developing better CK-MM activators based on the dammarane-type triterpenoid structure.
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Affiliation(s)
- Feiyan Chen
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
- Research Center, Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Kexuan Zhu
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
- Hanlin College, Nanjing University of Chinese Medicine, Taizhou, China
| | - Lin Chen
- Department of Physiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Liufeng Ouyang
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
- Laboratory of Pathological Sciences, College of Medicine, Yan'an University, Yan'an, China
| | - Cuihua Chen
- Research Center, Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ling Gu
- Research Center, Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yucui Jiang
- Research Center, Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhongli Wang
- School of Nursing, Jiujiang University, Jiujiang, China
| | - Zixuan Lin
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qiang Zhang
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiao Shao
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jianguo Dai
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yunan Zhao
- Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
- Research Center, Basic Medical College, Nanjing University of Chinese Medicine, Nanjing, China
- Corresponding author. Department of Pathology and Pathophysiology, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, 210046, China.
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Luo Y, Zeng R, Guo Q, Xu J, Sun X, Wang L. Identifying a novel anticancer agent with microtubule-stabilizing effects through computational cell-based bioactivity prediction models and bioassays. Org Biomol Chem 2019; 17:1519-1530. [DOI: 10.1039/c8ob02193g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G03 is a novel anticancer agent with unusual microtubule-stabilizing effects.
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Affiliation(s)
- Yao Luo
- Joint International Research Laboratory of Synthetic Biology and Medicine
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals
- School of Biology and Biological Engineering
- South China University of Technology
- Guangzhou 510006
| | - Ranran Zeng
- Joint International Research Laboratory of Synthetic Biology and Medicine
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals
- School of Biology and Biological Engineering
- South China University of Technology
- Guangzhou 510006
| | - Qingqing Guo
- Joint International Research Laboratory of Synthetic Biology and Medicine
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals
- School of Biology and Biological Engineering
- South China University of Technology
- Guangzhou 510006
| | - Jianrong Xu
- Department of Pharmacology
- Institute of Medical Sciences
- Shanghai Jiao Tong University
- School of Medicine
- Shanghai 200025
| | - Xiaoou Sun
- Joint International Research Laboratory of Synthetic Biology and Medicine
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals
- School of Biology and Biological Engineering
- South China University of Technology
- Guangzhou 510006
| | - Ling Wang
- Joint International Research Laboratory of Synthetic Biology and Medicine
- Guangdong Provincial Engineering and Technology Research Center of Biopharmaceuticals
- School of Biology and Biological Engineering
- South China University of Technology
- Guangzhou 510006
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Chen GQ, Xu Y, Shen SM, Zhang J. Phenotype and target-based chemical biology investigations in cancers. Natl Sci Rev 2018; 6:1111-1127. [PMID: 34691990 PMCID: PMC8291603 DOI: 10.1093/nsr/nwy124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 12/14/2022] Open
Abstract
Chemical biology has been attracting a lot of attention because of the key roles of chemical methods and techniques in helping to decipher and manipulate biological systems. Although chemical biology encompasses a broad field, this review will focus on chemical biology aimed at using exogenous chemical probes to interrogate, modify and manipulate biological processes, at the cellular and organismal levels, in a highly controlled and dynamic manner. In this area, many advances have been achieved for cancer biology and therapeutics, from target identification and validation based on active anticancer compounds (forward approaches) to discoveries of anticancer molecules based on some important targets including protein-protein interaction (reverse approaches). Herein we attempt to summarize some recent progresses mainly from China through applying chemical biology approaches to explore molecular mechanisms of carcinogenesis. Additionally, we also outline several new strategies for chemistry to probe cellular activities such as proximity-dependent labeling methods for identifying protein-protein interactions, genetically encoded sensors, and light activating or repressing gene expression system.
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Affiliation(s)
- Guo-Qiang Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Ying Xu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Shao-Ming Shen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
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20
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Cui Q, Liu Y, Zhou M, Han Y, Yin C, Bai G. An Optimized MicroPET Imaging Method for the Distribution and Synergies of Natural Products. Front Pharmacol 2018; 9:948. [PMID: 30186178 PMCID: PMC6110851 DOI: 10.3389/fphar.2018.00948] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 08/02/2018] [Indexed: 12/03/2022] Open
Abstract
Purpose: Understanding the distribution and interaction of the Traditional Chinese Medicines (TCMs) is an integral source of herbal drug discovery. An optimized radio-labeled method was explored that could conduct in situ biodistribution studies in animals. We evaluated the feasibility of the method and applied glycyrrhetinic acid and platycodon (PG) polysaccharides as models. Procedures: [18F]-GA is a novel radiotracer which was performed positron emission tomography (PET) studies to assay the biodistribution of GA in mice. In addition, PG polysaccharide was used to intervene the biodistribution and dosimetry of GA. Scanning data were analyzed with professional software. Results: Record the time-activity curves for all organs then use the normalization method to calculate the area under the curve as a dosimetry for each organ. Moreover, the addition of PG polysaccharides can significantly improve the dosimetry of GA in the lungs, and its effect was related to the administration time. Conclusion: MicroPET imaging opens up a new avenue for the application of drug interactions between the TCMs.
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Affiliation(s)
- Qingxin Cui
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Yang Liu
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Mengge Zhou
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Yanqi Han
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Chengcheng Yin
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Gang Bai
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
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Target identification reveals protein arginine methyltransferase 1 is a potential target of phenyl vinyl sulfone and its derivatives. Biosci Rep 2018. [PMID: 29540535 PMCID: PMC5968187 DOI: 10.1042/bsr20171717] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Phenyl vinyl sulfone (PVS) and phenyl vinyl sulfonate (PVSN) inactivate protein tyrosine phosphatases (PTPs) by mimicking the phosphotyrosine structure and providing a Michael addition acceptor for the active-site cysteine residue of PTPs, thus forming covalent adducts between PVS (or PVSN) and PTPs. We developed a specific antiserum against PVS. This antiserum can be used in general antibody-based assays such as immunoblotting, immunofluorescence staining, and immunoprecipitation. Target identification through immunoprecipitation and mass spectrometry analysis reveals potential targets of PVS, mostly proteins with reactive cysteine residues or low-pKa cysteine residues that are prone to reversible redox modifications. Target identification of PVSN has been conducted because the anti-PVS antiserum can also recognize PVSN. Among the targets, protein arginine methyltransferase 1 (PRMT1), inosine-5'-monophosphate dehydrogenase 1, vimentin, and glutathione reductase (GR) were further confirmed by immunoprecipitation followed by immunoblotting. In addition, PVSN and Bay11-7082 inhibited GR activity, and PVS, PVSN, and Bay 11-7082 inhibited PRMT1 activity in in vitro assays. In addition, treatment of PVSN, Bay11-7082, or Bay 11-7085 in cultured HeLa cells can cause the quick decline in the levels of protein asymmetric dimethylarginine. These results indicate that the similar moiety among PVS, PVSN, Bay 11-7082, and Bay 11-7085 can be the key structure of lead compounds of PRMT1. Therefore, we expect to use this approach in the identification of potential targets of other covalent drugs.
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22
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Yu CH, Chou CC, Tu HF, Huang WC, Ho YY, Khoo KH, Lee MS, Chang GD. Antibody-assisted target identification reveals afatinib, an EGFR covalent inhibitor, down-regulating ribonucleotide reductase. Oncotarget 2018; 9:21512-21529. [PMID: 29765556 PMCID: PMC5940374 DOI: 10.18632/oncotarget.25177] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 04/05/2018] [Indexed: 01/14/2023] Open
Abstract
Afatinib, used for the first-line treatment of non-small-cell lung carcinoma (NSCLC) patients with distinct epidermal growth factor receptor (EGFR) mutations, inactivates EGFR by mimicking ATP structure and forming a covalent adduct with EGFR. We developed a method to unravel potential targets of afatinib in NSCLC cells through immunoprecipitation of afatinib-labeling proteins with anti-afatinib antiserum and mass spectrometry analysis. Ribonucleotide reductase (RNR) is one of target proteins of afatinib revealed by this method. Treatment of afatinib at 10-100 nM potently inhibited intracellular RNR activity in an in vitro assay using permeabilized PC-9 cells (formerly known as PC-14). PC-9 cells treated with 10 μM afatinib displayed elevated markers of DNA damage. Long-term treatment of therapeutic concentrations of afatinib in PC-9 cells caused significant decrease in protein levels of RNR subunit M2 at 1-10 nM and RNR subunit M1 at 100 nM. EGFR-null Chinese hamster ovary (CHO) cells treated with afatinib also showed similar effects. Afatinib repressed the upregulation of RNR subunit M2 induced by gemcitabine. Covalent modification with afatinib resulting in inhibition and protein downregulation of RNR underscores the therapeutic and off-target effects of afatinib. Afatinib may serve as a lead compound of chemotherapeutic drugs targeting RNR. This method can be widely used in the identification of potential targets of other covalent drugs.
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Affiliation(s)
- Cheng-Han Yu
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chi-Chi Chou
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Hsin-Fang Tu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Wei-Chieh Huang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Ya-Yeh Ho
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Kay-Hooi Khoo
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ming-Shyue Lee
- Department of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Geen-Dong Chang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
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23
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Kapoor TM, Miller RM. Leveraging Chemotype-Specific Resistance for Drug Target Identification and Chemical Biology. Trends Pharmacol Sci 2017; 38:1100-1109. [PMID: 29037508 DOI: 10.1016/j.tips.2017.09.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 12/23/2022]
Abstract
Identifying the direct physiological targets of drugs and chemical probes remains challenging. Here we describe how resistance can be used to achieve 'gold-standard' validation of a chemical inhibitor's direct target in human cells. This involves demonstrating that a silent mutation in the target that suppresses inhibitor activity in cell-based assays can also reduce inhibitor potency in biochemical assays. Further, phenotypes due to target inhibition can be identified as those observed in the inhibitor-sensitive cells, across a range of inhibitor concentrations, but not in genetically matched cells with a silent resistance-conferring mutation in the target. We propose that chemotype-specific resistance, which is generally considered to be a limitation of molecularly targeted agents, can be leveraged to deconvolve the mechanism of action of drugs and to properly use chemical probes.
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Affiliation(s)
- Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, 1200 York Ave., New York, NY 10065, USA.
| | - Rand M Miller
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, 1200 York Ave., New York, NY 10065, USA
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24
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Yuan P, Mao X, Chong KC, Fu J, Pan S, Wu S, Yu C, Yao SQ. Simultaneous Imaging of Endogenous Survivin mRNA and On-Demand Drug Release in Live Cells by Using a Mesoporous Silica Nanoquencher. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1700569. [PMID: 28544466 DOI: 10.1002/smll.201700569] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/17/2017] [Indexed: 06/07/2023]
Abstract
The design of multifunctional drug delivery systems capable of simultaneous target detection, imaging, and therapeutics in live mammalian cells is critical for biomedical research. In this study, by using mesoporous silica nanoparticles (MSNs) chemically modified with a small-molecule dark quencher, followed by sequential drug encapsulation, MSN capping with a dye-labeled antisense oligonucleotide, and bioorthogonal surface modification with cell-penetrating poly(disulfide)s, the authors have successfully developed the first mesoporous silica nanoquencher (qMSN), characterized by high drug-loading and endocytosis-independent cell uptake, which is able to quantitatively image endogenous survivin mRNA and release the loaded drug in a manner that depends on the survivin expression level in tumor cells. The authors further show that this novel drug delivery system may be used to minimize potential cytotoxicity encountered by many existing small-molecule drugs in cancer therapy.
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Affiliation(s)
- Peiyan Yuan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore, Singapore
| | - Xin Mao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore, Singapore
| | - Kok Chan Chong
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore, Singapore
| | - Jiaqi Fu
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore, Singapore
| | - Sijun Pan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore, Singapore
| | - Shuizhu Wu
- College of Materials Science and Engineering, South China University of Technology, 510640, Guangzhou, China
| | - Changmin Yu
- College of Materials Science and Engineering, South China University of Technology, 510640, Guangzhou, China
| | - Shao Q Yao
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore, Singapore
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25
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Tsushima M, Sato S, Nakamura H. Selective purification and chemical labeling of a target protein on ruthenium photocatalyst-functionalized affinity beads. Chem Commun (Camb) 2017; 53:4838-4841. [PMID: 28418420 DOI: 10.1039/c7cc01595j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Selective purification and chemical labeling of a target protein in a protein mixture were simultaneously achieved on the surface of affinity beads functionalized with ligands, such as benzenesulfonamide and methotrexate (MTX), and a ruthenium complex containing 2,2'-bipyridine-4,4'-dicarboxylic acid (dcbpy). Chemical labeling of the target protein with a tyrosine radical trapper (TRT) proceeded on the surface of the beads when the target protein was in close proximity to the ruthenium photocatalyst. Both the protein purification and chemical labeling abilities of the affinity beads functionalized with ruthenium photocatalyst were not compromised after recycling several times. Dihydrofolate reductase (DHFR) endogenously expressed in HeLa cells was detected by chemical labeling with biotin-TRT on the affinity beads with high sensitivity compared to the conventional silver staining method.
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Affiliation(s)
- Michihiko Tsushima
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan.
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26
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Cui Q, Hou Y, Wang Y, Li X, Liu Y, Ma X, Wang Z, Wang W, Tao J, Wang Q, Jiang M, Chen D, Feng X, Bai G. Biodistribution of arctigenin-loaded nanoparticles designed for multimodal imaging. J Nanobiotechnology 2017; 15:27. [PMID: 28388905 PMCID: PMC5383946 DOI: 10.1186/s12951-017-0263-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/27/2017] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Tracking targets of natural products is one of the most challenging issues in fields ranging from pharmacognosy to biomedicine. It is widely recognized that the biocompatible nanoparticle (NP) could function as a "key" that opens the target "lock". RESULTS We report a functionalized poly-lysine NP technique that can monitor the target protein of arctigenin (ATG) in vivo non-invasively. The NPs were synthesized, and their morphologies and surface chemical properties were characterized by transmission electron microscopy (TEM), laser particle size analysis and atomic force microscopy (AFM). In addition, we studied the localization of ATG at the level of the cell and the whole animal (zebrafish and mice). We demonstrated that fluorescent NPs could be ideal carriers in the development of a feasible method for target identification. The distributions of the target proteins were found to be consistent with the pharmacological action of ATG at the cellular and whole-organism levels. CONCLUSIONS The results indicated that functionalized poly-lysine NPs could be valuable in the multimodal imaging of arctigenin.
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Affiliation(s)
- Qingxin Cui
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Yuanyuan Hou
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Yanan Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Science, Nankai University, Tianjin, 300071 China
| | - Xu Li
- Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Department of Physiology, School of Medicine, Nankai University, Tianjin, 300071 China
| | - Yang Liu
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Xiaoyao Ma
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Zengyong Wang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Weiya Wang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Jin Tao
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Qian Wang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Min Jiang
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 People’s Republic of China
| | - Dongyan Chen
- Tianjin Key Laboratory of Tumor Microenvironment and Neurovascular Regulation, Department of Physiology, School of Medicine, Nankai University, Tianjin, 300071 China
| | - Xizeng Feng
- State Key Laboratory of Medicinal Chemical Biology, College of Life Science, Nankai University, Tianjin, 300071 China
| | - Gang Bai
- College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071 People’s Republic of China
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27
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He B, Hoang TK, Wang T, Ferris M, Taylor CM, Tian X, Luo M, Tran DQ, Zhou J, Tatevian N, Luo F, Molina JG, Blackburn MR, Gomez TH, Roos S, Rhoads JM, Liu Y. Resetting microbiota by Lactobacillus reuteri inhibits T reg deficiency-induced autoimmunity via adenosine A2A receptors. J Exp Med 2016; 214:107-123. [PMID: 27994068 PMCID: PMC5206500 DOI: 10.1084/jem.20160961] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/17/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022] Open
Abstract
He et al. show that T reg deficiency markedly induces autoimmunity and shifts gut microbiota. Remodeling microbiota by Lactobacillus reuteri was found to inhibit autoimmunity via the metabolite inosine, which interacts with the adenosine A2A receptor. This finding establishes a link between the gut microbiota, A2A receptors, and autoimmunity induced by T reg cell deficiency. Regulatory T (T reg) cell deficiency causes lethal, CD4+ T cell–driven autoimmune diseases. Stem cell transplantation is used to treat these diseases, but this procedure is limited by the availability of a suitable donor. The intestinal microbiota drives host immune homeostasis by regulating the differentiation and expansion of T reg, Th1, and Th2 cells. It is currently unclear if T reg cell deficiency–mediated autoimmune disorders can be treated by targeting the enteric microbiota. Here, we demonstrate that Foxp3+ T reg cell deficiency results in gut microbial dysbiosis and autoimmunity over the lifespan of scurfy (SF) mouse. Remodeling microbiota with Lactobacillus reuteri prolonged survival and reduced multiorgan inflammation in SF mice. L. reuteri changed the metabolomic profile disrupted by T reg cell deficiency, and a major effect was to restore levels of the purine metabolite inosine. Feeding inosine itself prolonged life and inhibited multiorgan inflammation by reducing Th1/Th2 cells and their associated cytokines. Mechanistically, the inhibition of inosine on the differentiation of Th1 and Th2 cells in vitro depended on adenosine A2A receptors, which were also required for the efficacy of inosine and of L. reuteri in vivo. These results reveal that the microbiota–inosine–A2A receptor axis might represent a potential avenue for combatting autoimmune diseases mediated by T reg cell dysfunction.
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Affiliation(s)
- Baokun He
- Pediatrics Gastroenterology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030.,Pediatric Research Center, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
| | - Thomas K Hoang
- Pediatrics Gastroenterology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030.,Pediatric Research Center, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
| | - Ting Wang
- Pediatrics Gastroenterology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030.,Pediatric Research Center, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
| | - Michael Ferris
- Department of Microbiology, Immunology and Parasitology, Louisiana State University School of Medicine, New Orleans, LA 70118
| | - Christopher M Taylor
- Department of Microbiology, Immunology and Parasitology, Louisiana State University School of Medicine, New Orleans, LA 70118
| | - Xiangjun Tian
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030
| | - Meng Luo
- Department of Microbiology, Immunology and Parasitology, Louisiana State University School of Medicine, New Orleans, LA 70118
| | - Dat Q Tran
- Pediatric Research Center, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
| | - Jain Zhou
- Pathology and Laboratory Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
| | - Nina Tatevian
- Pathology and Laboratory Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
| | - Fayong Luo
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
| | - Jose G Molina
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
| | - Michael R Blackburn
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
| | - Thomas H Gomez
- Center for Laboratory Animal Medicine and Care, The University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Stefan Roos
- Department of Microbiology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden.,BioGaia AB, 103 64 Stockholm, Sweden
| | - J Marc Rhoads
- Pediatrics Gastroenterology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030 .,Pediatric Research Center, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
| | - Yuying Liu
- Pediatrics Gastroenterology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030 .,Pediatric Research Center, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030
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28
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Proteomic profiling reveals that collismycin A is an iron chelator. Sci Rep 2016; 6:38385. [PMID: 27922079 PMCID: PMC5138588 DOI: 10.1038/srep38385] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/09/2016] [Indexed: 12/13/2022] Open
Abstract
Collismycin A (CMA), a microbial product, has anti-proliferative activity against cancer cells, but the mechanism of its action remains unknown. Here, we report the identification of the molecular target of CMA by ChemProteoBase, a proteome-based approach for drug target identification. ChemProteoBase profiling showed that CMA is closely clustered with di-2-pyridylketone 4,4-dimethyl-3-thiosemicarbazone, an iron chelator. CMA bound to both Fe(II) and Fe(III) ions and formed a 2:1 chelator-iron complex with a redox-inactive center. CMA-induced cell growth inhibition was completely canceled by Fe(II) and Fe(III) ions, but not by other metal ions such as Zn(II) or Cu(II). Proteomic and transcriptomic analyses showed that CMA affects the glycolytic pathway due to the accumulation of HIF-1α. These results suggest that CMA acts as a specific iron chelator, leading to the inhibition of cancer cell growth.
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29
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Kim D, Hwang HY, Kim JY, Lee JY, Yoo JS, Marko-Varga G, Kwon HJ. FK506, an Immunosuppressive Drug, Induces Autophagy by Binding to the V-ATPase Catalytic Subunit A in Neuronal Cells. J Proteome Res 2016; 16:55-64. [PMID: 28056508 DOI: 10.1021/acs.jproteome.6b00638] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The drug FK506 (tacrolimus, fujimycin) exerts its immunosuppressive effects by regulating the nuclear factor of the activated T-cell (NFAT) family of transcription factors. However, FK506 also exhibits neuroprotective effects, but its direct target proteins that mediate these effects have not been determined. To identify the target proteins responsible for FK506's neuroprotective effects, the drug affinity responsive target stability (DARTS) method was performed using label-free FK506, and LC-MS/MS analysis of the FK506-treated proteome was also performed. Using DARTS and LC-MS/MS analyses in combination with reference studies, V-ATPase catalytic subunit A (ATP6V1A) was identified as a new target protein of FK506. The biological relevance of ATP6V1A in mediating the neuroprotective effects of FK506 was validated by analyzing FK506 activity with respect to autophagy via acridine orange staining and transcription factor EB (TFEB) translocation assay. These analyses demonstrated that the binding of FK506 with ATP6V1A induces autophagy by activating the translocation of TFEB from the cytosol into the nucleus. Because autophagy has been identified as a mechanism for treating neurodegenerative diseases and because we have demonstrated that FK506 induces autophagy, this study demonstrates that FK506 is a possible new therapy for treating neurodegenerative diseases.
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Affiliation(s)
- Dongyoung Kim
- Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University , Seoul 120-749, Korea
| | - Hui-Yun Hwang
- Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University , Seoul 120-749, Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute , Ochang, Chungbuk 28119, Korea
| | - Ju Yeon Lee
- Biomedical Omics Group, Korea Basic Science Institute , Ochang, Chungbuk 28119, Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute , Ochang, Chungbuk 28119, Korea
| | - György Marko-Varga
- Clinical Protein Science & Imaging, Biomedical Center, Department of Biomedical Engineering, Lund University , BMC D13, SE-221 84 Lund, Sweden
| | - Ho Jeong Kwon
- Global Research Laboratory, Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University , Seoul 120-749, Korea.,Department of Internal Medicine, College of Medicine, Yonsei University , Seoul 120-752, Korea
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30
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Chemical and biological studies of reveromycin A. J Antibiot (Tokyo) 2016; 69:723-730. [PMID: 27270304 DOI: 10.1038/ja.2016.57] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/12/2022]
Abstract
The research on antibiotics requires the integration of broad areas, such as microbiology, organic chemistry, biochemistry and pharmacology. It is similar to the field of chemical biology that is recently popular as an approach for drug discovery. When we isolate a new compound from a microorganism, we can pursue the interesting research on chemistry and biology. In this review, I would like to introduce our achievements in relation to reveromycin A.
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31
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Kapoor S, Waldmann H, Ziegler S. Novel approaches to map small molecule–target interactions. Bioorg Med Chem 2016; 24:3232-45. [DOI: 10.1016/j.bmc.2016.05.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/10/2016] [Accepted: 05/12/2016] [Indexed: 10/24/2022]
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32
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Lee B, Sun W, Lee H, Basavarajappa H, Sulaiman RS, Sishtla K, Fei X, Corson TW, Seo SY. Design, synthesis and biological evaluation of photoaffinity probes of antiangiogenic homoisoflavonoids. Bioorg Med Chem Lett 2016; 26:4277-81. [PMID: 27481561 DOI: 10.1016/j.bmcl.2016.07.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/16/2016] [Accepted: 07/20/2016] [Indexed: 12/26/2022]
Abstract
A naturally occurring homoisoflavonoid, cremastranone (1) inhibited angiogenesis in vitro and in vivo. We developed an analogue SH-11037 (2) which is more potent than cremastranone in human retinal microvascular endothelial cells (HRECs) and blocks neovascularization in animal models. Despite their efficacy, the mechanism of these compounds is not yet fully known. In the course of building on a strong foundation of SAR and creating a novel chemical tool for target identification of homoisoflavonoid-binding proteins, various types of photoaffinity probes were designed and synthesized in which benzophenone and biotin were attached to homoisoflavanonoids using PEG linkers on either the C-3' or C-7 position. Notably, the photoaffinity probes linking on the phenol group of the C-3' position retain excellent activity of inhibiting retinal endothelial cell proliferation with up to 72nM of GI50.
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Affiliation(s)
- Bit Lee
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, South Korea
| | - Wei Sun
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, South Korea
| | - Hyungjun Lee
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, South Korea
| | - Halesha Basavarajappa
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Rania S Sulaiman
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Kamakshi Sishtla
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Xiang Fei
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, South Korea
| | - Timothy W Corson
- Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Seung-Yong Seo
- College of Pharmacy and Gachon Institute of Pharmaceutical Sciences, Gachon University, Incheon 21936, South Korea.
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33
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Lee H, Lee JW. Target identification for biologically active small molecules using chemical biology approaches. Arch Pharm Res 2016; 39:1193-201. [DOI: 10.1007/s12272-016-0791-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/01/2016] [Indexed: 11/28/2022]
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34
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Modell AE, Blosser SL, Arora PS. Systematic Targeting of Protein-Protein Interactions. Trends Pharmacol Sci 2016; 37:702-713. [PMID: 27267699 DOI: 10.1016/j.tips.2016.05.008] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/14/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022]
Abstract
Over the past decade, protein-protein interactions (PPIs) have gone from being neglected as 'undruggable' to being considered attractive targets for the development of therapeutics. Recent advances in computational analysis, fragment-based screening, and molecular design have revealed promising strategies to address the basic molecular recognition challenge: how to target large protein surfaces with specificity. Several systematic and complementary workflows have been developed to yield successful inhibitors of PPIs. Here we review the major contemporary approaches utilized for the discovery of inhibitors and focus on a structure-based workflow, from the selection of a biological target to design.
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Affiliation(s)
- Ashley E Modell
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Sarah L Blosser
- Department of Chemistry, New York University, New York, NY 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, New York, NY 10003, USA
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35
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Chen S, Jiang H, Cao Y, Wang Y, Hu Z, Zhu Z, Chai Y. Drug target identification using network analysis: Taking active components in Sini decoction as an example. Sci Rep 2016; 6:24245. [PMID: 27095146 PMCID: PMC4837341 DOI: 10.1038/srep24245] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/21/2016] [Indexed: 12/13/2022] Open
Abstract
Identifying the molecular targets for the beneficial effects of active small-molecule compounds simultaneously is an important and currently unmet challenge. In this study, we firstly proposed network analysis by integrating data from network pharmacology and metabolomics to identify targets of active components in sini decoction (SND) simultaneously against heart failure. To begin with, 48 potential active components in SND against heart failure were predicted by serum pharmacochemistry, text mining and similarity match. Then, we employed network pharmacology including text mining and molecular docking to identify the potential targets of these components. The key enriched processes, pathways and related diseases of these target proteins were analyzed by STRING database. At last, network analysis was conducted to identify most possible targets of components in SND. Among the 25 targets predicted by network analysis, tumor necrosis factor α (TNF-α) was firstly experimentally validated in molecular and cellular level. Results indicated that hypaconitine, mesaconitine, higenamine and quercetin in SND can directly bind to TNF-α, reduce the TNF-α-mediated cytotoxicity on L929 cells and exert anti-myocardial cell apoptosis effects. We envisage that network analysis will also be useful in target identification of a bioactive compound.
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Affiliation(s)
- Si Chen
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Hailong Jiang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Yan Cao
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Yun Wang
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Ziheng Hu
- School of Pharmacy, University of Pittsburgh, 3501 Terrace Street, Pittsburgh, PA, 15261, USA
| | - Zhenyu Zhu
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
| | - Yifeng Chai
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai, 200433, China
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Kanoh N. Photo-cross-linked small-molecule affinity matrix as a tool for target identification of bioactive small molecules. Nat Prod Rep 2016; 33:709-18. [DOI: 10.1039/c5np00117j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review describes the status of the photo-cross-linked small-molecule affinity matrix while providing a useful tutorial for academic and industrial chemical biologists who are involved or interested in drug target identification.
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Affiliation(s)
- Naoki Kanoh
- Graduate School of Pharmaceutical Sciences
- Tohoku University
- Sendai 980-8578
- Japan
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37
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Muroi M, Futamura Y, Osada H. Integrated profiling methods for identifying the targets of bioactive compounds: MorphoBase and ChemProteoBase. Nat Prod Rep 2016; 33:621-5. [DOI: 10.1039/c5np00106d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Target identification of new bioactive compounds has been achieved by both our direct and indirect approaches. Here, we highlight the utility of the latter approaches, MorphoBase and ChemProteoBase.
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Affiliation(s)
- Makoto Muroi
- Chemical Biology Research Group
- RIKEN CSRS
- Saitama 351-0198
- Japan
| | - Yushi Futamura
- Chemical Biology Research Group
- RIKEN CSRS
- Saitama 351-0198
- Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group
- RIKEN CSRS
- Saitama 351-0198
- Japan
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38
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Chang J, Kim Y, Kwon HJ. Advances in identification and validation of protein targets of natural products without chemical modification. Nat Prod Rep 2016; 33:719-30. [DOI: 10.1039/c5np00107b] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This review focuses on and reports case studies of the latest advances in target protein identification methods for label-free natural products. The integration of newly developed technologies will provide new insights and highlight the value of natural products for use as biological probes and new drug candidates.
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Affiliation(s)
- J. Chang
- Department of Biotechnology
- Translational Research Center for Protein Function Control
- College of Life Science & Biotechnology
- Yonsei University
- Seoul 120-749
| | - Y. Kim
- Department of Biotechnology
- Translational Research Center for Protein Function Control
- College of Life Science & Biotechnology
- Yonsei University
- Seoul 120-749
| | - H. J. Kwon
- Department of Biotechnology
- Translational Research Center for Protein Function Control
- College of Life Science & Biotechnology
- Yonsei University
- Seoul 120-749
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Tang H, Duggan S, Richardson PL, Marin V, Warder SE, McLoughlin SM. Target Identification of Compounds from a Cell Viability Phenotypic Screen Using a Bead/Lysate-Based Affinity Capture Platform. ACTA ACUST UNITED AC 2015; 21:201-11. [DOI: 10.1177/1087057115622431] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 11/24/2015] [Indexed: 12/23/2022]
Abstract
The pharmaceutical industry has been continually challenged by dwindling target diversity. To obviate this trend, phenotypic screens have been adopted, complementing target-centric screening approaches. Phenotypic screens identify drug leads using clinically relevant and translatable mechanisms, remaining agnostic to targets. While target anonymity is advantageous early in the drug discovery process, it poses challenges to hit progression, including the development of backup series, retaining desired pharmacology during optimization, discovery of markers, and understanding mechanism-driven toxicity. Consequently, significant effort has been expended to elaborate the targets and mechanisms at work for promising screening hits. Affinity capture is commonly leveraged, where the compounds are linked to beads and targets are abstracted from cell homogenates. This technique has proven effective for identifying targets of kinase, PARP, and HDAC inhibitors, and examples of new targets have been reported. Herein, a three-pronged approach to target deconvolution by affinity capture is described, including the implementation of a uniqueness index that helps discriminate between bona fide targets and background. The effectiveness of this approach is demonstrated using characterized compounds that act on known and noncanonical target classes. The platform is subsequently applied to phenotypic screening hits, identifying candidate targets. The success rate of bead-based affinity capture is discussed.
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Affiliation(s)
- Hua Tang
- Target Enabling Science and Technologies, AbbVie, North Chicago, IL, USA
| | - Shannon Duggan
- Drug Metabolism & Pharmacokinetics, AbbVie, North Chicago, IL, USA
| | | | - Violeta Marin
- Discovery Chemistry and Technologies, AbbVie, North Chicago, IL, USA
| | - Scott E. Warder
- Target Enabling Science and Technologies, AbbVie, North Chicago, IL, USA
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Salvador-Reyes LA, Luesch H. Biological targets and mechanisms of action of natural products from marine cyanobacteria. Nat Prod Rep 2015; 32:478-503. [PMID: 25571978 DOI: 10.1039/c4np00104d] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Marine cyanobacteria are an ancient group of organisms and prolific producers of bioactive secondary metabolites. These compounds are presumably optimized by evolution over billions of years to exert high affinity for their intended biological target in the ecologically relevant organism but likely also possess activity in different biological contexts such as human cells. Screening of marine cyanobacterial extracts for bioactive natural products has largely focused on cancer cell viability; however, diversification of the screening platform led to the characterization of many new bioactive compounds. Targets of compounds have oftentimes been elusive if the compounds were discovered through phenotypic assays. Over the past few years, technology has advanced to determine mechanism of action (MOA) and targets through reverse chemical genetic and proteomic approaches, which has been applied to certain cyanobacterial compounds and will be discussed in this review. Some cyanobacterial molecules are the most-potent-in-class inhibitors and therefore may become valuable tools for chemical biology to probe protein function but also be templates for novel drugs, assuming in vitro potency translates into cellular and in vivo activity. Our review will focus on compounds for which the direct targets have been deciphered or which were found to target a novel pathway, and link them to disease states where target modulation may be beneficial.
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Affiliation(s)
- Lilibeth A Salvador-Reyes
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, Florida 32610, USA.
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41
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Zheng W, Li G, Li X. Affinity purification in target identification: the specificity challenge. Arch Pharm Res 2015; 38:1661-85. [DOI: 10.1007/s12272-015-0635-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/07/2015] [Indexed: 12/16/2022]
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Carson C, Raman P, Tullai J, Xu L, Henault M, Thomas E, Yeola S, Lao J, McPate M, Verkuyl JM, Marsh G, Sarber J, Amaral A, Bailey S, Lubicka D, Pham H, Miranda N, Ding J, Tang HM, Ju H, Tranter P, Ji N, Krastel P, Jain RK, Schumacher AM, Loureiro JJ, George E, Berellini G, Ross NT, Bushell SM, Erdemli G, Solomon JM. Englerin A Agonizes the TRPC4/C5 Cation Channels to Inhibit Tumor Cell Line Proliferation. PLoS One 2015; 10:e0127498. [PMID: 26098886 PMCID: PMC4476799 DOI: 10.1371/journal.pone.0127498] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/14/2015] [Indexed: 01/19/2023] Open
Abstract
Englerin A is a structurally unique natural product reported to selectively inhibit growth of renal cell carcinoma cell lines. A large scale phenotypic cell profiling experiment (CLiP) of englerin A on ¬over 500 well characterized cancer cell lines showed that englerin A inhibits growth of a subset of tumor cell lines from many lineages, not just renal cell carcinomas. Expression of the TRPC4 cation channel was the cell line feature that best correlated with sensitivity to englerin A, suggesting the hypothesis that TRPC4 is the efficacy target for englerin A. Genetic experiments demonstrate that TRPC4 expression is both necessary and sufficient for englerin A induced growth inhibition. Englerin A induces calcium influx and membrane depolarization in cells expressing high levels of TRPC4 or its close ortholog TRPC5. Electrophysiology experiments confirmed that englerin A is a TRPC4 agonist. Both the englerin A induced current and the englerin A induced growth inhibition can be blocked by the TRPC4/C5 inhibitor ML204. These experiments confirm that activation of TRPC4/C5 channels inhibits tumor cell line proliferation and confirms the TRPC4 target hypothesis generated by the cell line profiling. In selectivity assays englerin A weakly inhibits TRPA1, TRPV3/V4, and TRPM8 which suggests that englerin A may bind a common feature of TRP ion channels. In vivo experiments show that englerin A is lethal in rodents near doses needed to activate the TRPC4 channel. This toxicity suggests that englerin A itself is probably unsuitable for further drug development. However, since englerin A can be synthesized in the laboratory, it may be a useful chemical starting point to identify novel modulators of other TRP family channels.
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Affiliation(s)
- Cheryl Carson
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Pichai Raman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Jennifer Tullai
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Lei Xu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Martin Henault
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Emily Thomas
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Sarita Yeola
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Jianmin Lao
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Mark McPate
- Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - J. Martin Verkuyl
- Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - George Marsh
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Jason Sarber
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Adam Amaral
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Scott Bailey
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Danuta Lubicka
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Helen Pham
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Nicolette Miranda
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Jian Ding
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Hai-Ming Tang
- Novartis Institutes for Biomedical Research, East Hanover, New Jersey, United States of America
| | - Haisong Ju
- Novartis Institutes for Biomedical Research, East Hanover, New Jersey, United States of America
| | - Pamela Tranter
- Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Nan Ji
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Philipp Krastel
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Rishi K. Jain
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Andrew M. Schumacher
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Joseph J. Loureiro
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Elizabeth George
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Giuliano Berellini
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Nathan T. Ross
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Simon M. Bushell
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Gül Erdemli
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Jonathan M. Solomon
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
- * E-mail:
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Ursu A, Waldmann H. Hide and seek: Identification and confirmation of small molecule protein targets. Bioorg Med Chem Lett 2015; 25:3079-86. [PMID: 26115575 DOI: 10.1016/j.bmcl.2015.06.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 12/14/2022]
Abstract
Target identification and confirmation for small molecules is often the rate limiting step in drug discovery. A robust method to identify proteins addressed by small molecules is affinity chromatography using chemical probes. These usually consist of the compound of interest equipped with a linker molecule and a proper tag. Recently, methods emerged that allow the identification of protein targets without prior functionalization of the small molecule of interest. The digest offers an update on the newest developments in the area of target identification with special focus on confirmation techniques.
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Affiliation(s)
- Andrei Ursu
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Chemical Biology, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Chemical Biology, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany.
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44
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Gebre AA, Okada H, Kim C, Kubo K, Ohnuki S, Ohya Y. Profiling of the effects of antifungal agents on yeast cells based on morphometric analysis. FEMS Yeast Res 2015; 15:fov040. [DOI: 10.1093/femsyr/fov040] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2015] [Indexed: 12/14/2022] Open
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45
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Target deconvolution of bioactive small molecules: the heart of chemical biology and drug discovery. Arch Pharm Res 2015; 38:1627-41. [DOI: 10.1007/s12272-015-0618-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 05/19/2015] [Indexed: 01/01/2023]
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46
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Lo YC, Senese S, Li CM, Hu Q, Huang Y, Damoiseaux R, Torres JZ. Large-scale chemical similarity networks for target profiling of compounds identified in cell-based chemical screens. PLoS Comput Biol 2015; 11:e1004153. [PMID: 25826798 PMCID: PMC4380459 DOI: 10.1371/journal.pcbi.1004153] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/26/2015] [Indexed: 01/17/2023] Open
Abstract
Target identification is one of the most critical steps following cell-based phenotypic chemical screens aimed at identifying compounds with potential uses in cell biology and for developing novel disease therapies. Current in silico target identification methods, including chemical similarity database searches, are limited to single or sequential ligand analysis that have limited capabilities for accurate deconvolution of a large number of compounds with diverse chemical structures. Here, we present CSNAP (Chemical Similarity Network Analysis Pulldown), a new computational target identification method that utilizes chemical similarity networks for large-scale chemotype (consensus chemical pattern) recognition and drug target profiling. Our benchmark study showed that CSNAP can achieve an overall higher accuracy (>80%) of target prediction with respect to representative chemotypes in large (>200) compound sets, in comparison to the SEA approach (60–70%). Additionally, CSNAP is capable of integrating with biological knowledge-based databases (Uniprot, GO) and high-throughput biology platforms (proteomic, genetic, etc) for system-wise drug target validation. To demonstrate the utility of the CSNAP approach, we combined CSNAP's target prediction with experimental ligand evaluation to identify the major mitotic targets of hit compounds from a cell-based chemical screen and we highlight novel compounds targeting microtubules, an important cancer therapeutic target. The CSNAP method is freely available and can be accessed from the CSNAP web server (http://services.mbi.ucla.edu/CSNAP/). Determining the targets of compounds identified in cell-based high-throughput chemical screens is a critical step for downstream drug development and understanding of compound mechanism of action. However, current computational target prediction approaches like chemical similarity database searches are limited to single or sequential ligand analyses, which limits their ability to accurately deconvolve a large number of compounds that often have chemically diverse structures. Here, we have developed a new computational drug target prediction method, called CSNAP that is based on chemical similarity networks. By clustering diverse chemical structures into distinct sub-networks corresponding to chemotypes, we show that CSNAP improves target prediction accuracy and consistency over a board range of drug classes. We further coupled CSNAP to a mitotic database and successfully determined the major mitotic drug targets of a diverse compound set identified in a cell-based chemical screen. We demonstrate that CSNAP can easily integrate with diverse knowledge-based databases for on/off target prediction and post-target validation, thus broadening its applicability for identifying the targets of bioactive compounds from a wide range of chemical screens.
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Affiliation(s)
- Yu-Chen Lo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, United States of America
- Program in Bioengineering, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Silvia Senese
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Chien-Ming Li
- Drug Studies Unit, Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Qiyang Hu
- Institute for Digital Research and Education, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Yong Huang
- Drug Studies Unit, Department of Bioengineering & Therapeutic Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Robert Damoiseaux
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Jorge Z. Torres
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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47
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Drug affinity responsive target stability (DARTS) for small-molecule target identification. Methods Mol Biol 2015; 1263:287-98. [PMID: 25618353 DOI: 10.1007/978-1-4939-2269-7_22] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Drug affinity responsive target stability (DARTS) is a relatively quick and straightforward approach to identify potential protein targets for small molecules. It relies on the protection against proteolysis conferred on the target protein by interaction with a small molecule. The greatest advantage of this method is being able to use the native small molecule without having to immobilize or modify it (e.g., by incorporation of biotin, fluorescent, radioisotope, or photoaffinity labels). Here we describe in detail the protocol for performing unbiased DARTS with complex protein lysates to identify binding targets of small molecules and for using DARTS-Western blotting to test, screen, or validate potential small-molecule targets. Although the ideas have mainly been developed from studying molecules in areas of biology that are currently of interest to us and our collaborators, the general principles should be applicable to the analysis of all molecules in nature.
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48
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The Chemistry-Biology-Medicine Continuum and the Drug Discovery and Development Process in Academia. ACTA ACUST UNITED AC 2014; 21:1039-45. [DOI: 10.1016/j.chembiol.2014.07.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 06/30/2014] [Accepted: 07/21/2014] [Indexed: 12/21/2022]
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49
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Nakajima A, Ohizumi Y, Yamada K. Anti-dementia Activity of Nobiletin, a Citrus Flavonoid: A Review of Animal Studies. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE 2014; 12:75-82. [PMID: 25191498 PMCID: PMC4153867 DOI: 10.9758/cpn.2014.12.2.75] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 02/23/2014] [Accepted: 03/31/2014] [Indexed: 12/24/2022]
Abstract
Alzheimer's disease (AD), the most common form of dementia among the elderly, is characterized by the progressive decline of cognitive function and has a detrimental impact worldwide. Despite intensive laboratory and clinical research over the last three decades, pharmacological options for the prevention and effective long-term treatment of AD are not currently available. Consequently, successful therapeutic and preventive treatments for AD are needed. When researching materials from natural resources having anti-dementia drug activity, we identified nobiletin, a polymethoxylated flavone from the peel of Citrus depressa. Nobiletin exhibited memory-improving effects in various animal models of dementia and exerted a wide range of beneficial effects against pathological features of AD including amyloid-β (Aβ) pathology, tau hyperphosphorylation, oxidative stress, cholinergic neurodegeneration and dysfunction of synaptic plasticity-related signaling, suggesting this natural compound could become a novel drug for the treatment and prevention of AD.
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Affiliation(s)
- Akira Nakajima
- Department of Neuropsychopharmacology and Hospital Pharmacy, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Yasushi Ohizumi
- Department of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan. ; Department of Anti-Dementia Functional Food Development, Research Center of Supercritical Fluid Technology, Graduate School of Engineering, Tohoku University, Sendai, Japan. ; Laboratory of Kampo Medicines, Yokohama College of Pharmacy, Yokohama, Japan. ; Kansei Fukushi Research Institute, Tohoku Fukushi University, Sendai, Japan
| | - Kiyofumi Yamada
- Department of Neuropsychopharmacology and Hospital Pharmacy, Graduate School of Medicine, Nagoya University, Nagoya, Japan
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50
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Tang J, Szwajda A, Shakyawar S, Xu T, Hintsanen P, Wennerberg K, Aittokallio T. Making Sense of Large-Scale Kinase Inhibitor Bioactivity Data Sets: A Comparative and Integrative Analysis. J Chem Inf Model 2014; 54:735-43. [DOI: 10.1021/ci400709d] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jing Tang
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Agnieszka Szwajda
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Sushil Shakyawar
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Tao Xu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Petteri Hintsanen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, FI-00290, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, FI-00290, Helsinki, Finland
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