1
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Xie SC, Wang Y, Morton CJ, Metcalfe RD, Dogovski C, Pasaje CFA, Dunn E, Luth MR, Kumpornsin K, Istvan ES, Park JS, Fairhurst KJ, Ketprasit N, Yeo T, Yildirim O, Bhebhe MN, Klug DM, Rutledge PJ, Godoy LC, Dey S, De Souza ML, Siqueira-Neto JL, Du Y, Puhalovich T, Amini M, Shami G, Loesbanluechai D, Nie S, Williamson N, Jana GP, Maity BC, Thomson P, Foley T, Tan DS, Niles JC, Han BW, Goldberg DE, Burrows J, Fidock DA, Lee MCS, Winzeler EA, Griffin MDW, Todd MH, Tilley L. Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase. Nat Commun 2024; 15:937. [PMID: 38297033 PMCID: PMC10831071 DOI: 10.1038/s41467-024-45224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
Malaria poses an enormous threat to human health. With ever increasing resistance to currently deployed drugs, breakthrough compounds with novel mechanisms of action are urgently needed. Here, we explore pyrimidine-based sulfonamides as a new low molecular weight inhibitor class with drug-like physical parameters and a synthetically accessible scaffold. We show that the exemplar, OSM-S-106, has potent activity against parasite cultures, low mammalian cell toxicity and low propensity for resistance development. In vitro evolution of resistance using a slow ramp-up approach pointed to the Plasmodium falciparum cytoplasmic asparaginyl-tRNA synthetase (PfAsnRS) as the target, consistent with our finding that OSM-S-106 inhibits protein translation and activates the amino acid starvation response. Targeted mass spectrometry confirms that OSM-S-106 is a pro-inhibitor and that inhibition of PfAsnRS occurs via enzyme-mediated production of an Asn-OSM-S-106 adduct. Human AsnRS is much less susceptible to this reaction hijacking mechanism. X-ray crystallographic studies of human AsnRS in complex with inhibitor adducts and docking of pro-inhibitors into a model of Asn-tRNA-bound PfAsnRS provide insights into the structure-activity relationship and the selectivity mechanism.
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Affiliation(s)
- Stanley C Xie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Yinuo Wang
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Craig J Morton
- Biomedical Manufacturing Program, CSIRO, Clayton South, VIC, Australia
| | - Riley D Metcalfe
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Con Dogovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Elyse Dunn
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Krittikorn Kumpornsin
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Calibr, Division of the Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Eva S Istvan
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kate J Fairhurst
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Nutpakal Ketprasit
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tomas Yeo
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Okan Yildirim
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | | | - Dana M Klug
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Peter J Rutledge
- School of Chemistry, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Luiz C Godoy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jair L Siqueira-Neto
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yawei Du
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tanya Puhalovich
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Mona Amini
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gerry Shami
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | | | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gouranga P Jana
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Bikash C Maity
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Patrick Thomson
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Thomas Foley
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jeremy Burrows
- Medicines for Malaria Venture, 20, Route de Pré-Bois, 1215, Geneva 15, Switzerland
| | - David A Fidock
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Wellcome Centre for Anti-Infectives Research, Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 4HN, UK
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Matthew H Todd
- School of Pharmacy, University College London, London, WC1N 1AX, UK.
- Structural Genomics Consortium, University College London, London, WC1N 1AX, UK.
| | - Leann Tilley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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2
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Cerella C, Gajulapalli SR, Lorant A, Gerard D, Muller F, Lee Y, Kim KR, Han BW, Christov C, Récher C, Sarry JE, Dicato M, Diederich M. ATP1A1/BCL2L1 predicts the response of myelomonocytic and monocytic acute myeloid leukemia to cardiac glycosides. Leukemia 2024; 38:67-81. [PMID: 37904054 PMCID: PMC10776384 DOI: 10.1038/s41375-023-02076-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023]
Abstract
Myelomonocytic and monocytic acute myeloid leukemia (AML) subtypes are intrinsically resistant to venetoclax-based regimens. Identifying targetable vulnerabilities would limit resistance and relapse. We previously documented the synergism of venetoclax and cardiac glycoside (CG) combination in AML. Despite preclinical evidence, the repurposing of cardiac glycosides (CGs) in cancer therapy remained unsuccessful due to a lack of predictive biomarkers. We report that the ex vivo response of AML patient blasts and the in vitro sensitivity of established cell lines to the hemi-synthetic CG UNBS1450 correlates with the ATPase Na+/K+ transporting subunit alpha 1 (ATP1A1)/BCL2 like 1 (BCL2L1) expression ratio. Publicly available AML datasets identify myelomonocytic/monocytic differentiation as the most robust prognostic feature, along with core-binding factor subunit beta (CBFB), lysine methyltransferase 2A (KMT2A) rearrangements, and missense Fms-related receptor tyrosine kinase 3 (FLT3) mutations. Mechanistically, BCL2L1 protects from cell death commitment induced by the CG-mediated stepwise triggering of ionic perturbation, protein synthesis inhibition, and MCL1 downregulation. In vivo, CGs showed an overall tolerable profile while impacting tumor growth with an effect ranging from tumor growth inhibition to regression. These findings suggest a predictive marker for CG repurposing in specific AML subtypes.
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Affiliation(s)
- Claudia Cerella
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer (LBMCC), Fondation Recherche sur le Cancer et les Maladies du Sang, Pavillon 2, 6A rue Barblé, L-1210, Luxembourg, Luxembourg
| | - Sruthi Reddy Gajulapalli
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Anne Lorant
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer (LBMCC), Fondation Recherche sur le Cancer et les Maladies du Sang, Pavillon 2, 6A rue Barblé, L-1210, Luxembourg, Luxembourg
| | - Deborah Gerard
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer (LBMCC), Fondation Recherche sur le Cancer et les Maladies du Sang, Pavillon 2, 6A rue Barblé, L-1210, Luxembourg, Luxembourg
| | - Florian Muller
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer (LBMCC), Fondation Recherche sur le Cancer et les Maladies du Sang, Pavillon 2, 6A rue Barblé, L-1210, Luxembourg, Luxembourg
| | - Yejin Lee
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kyung Rok Kim
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Christo Christov
- University of Lorraine, Service Commun de Microscopie, Nancy, France
| | - Christian Récher
- Cancer Research Center of Toulouse, UMR 1037 INSERM/ Université Toulouse III-Paul Sabatier, 2 avenue Hubert Curien, Oncopôle, 31037, Toulouse, France
| | - Jean-Emmanuel Sarry
- Cancer Research Center of Toulouse, UMR 1037 INSERM/ Université Toulouse III-Paul Sabatier, 2 avenue Hubert Curien, Oncopôle, 31037, Toulouse, France
| | - Mario Dicato
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer (LBMCC), Fondation Recherche sur le Cancer et les Maladies du Sang, Pavillon 2, 6A rue Barblé, L-1210, Luxembourg, Luxembourg
| | - Marc Diederich
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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3
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Choi YJ, Yun SH, Yu J, Mun Y, Lee W, Park CJ, Han BW, Lee BH. Chaperone-mediated autophagy dysregulation during aging impairs hepatic fatty acid oxidation via accumulation of NCoR1. Mol Metab 2023; 76:101784. [PMID: 37524243 PMCID: PMC10448198 DOI: 10.1016/j.molmet.2023.101784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/21/2023] [Accepted: 07/27/2023] [Indexed: 08/02/2023] Open
Abstract
OBJECTIVE Alterations in lipid metabolism are associated with aging and age-related diseases. Chaperone-mediated autophagy (CMA) is a lysosome-dependent process involved in specific protein degradation. Heat shock cognate 71 kDa protein (Hsc70) recognizes cytosolic proteins with KFERQ motif and allows them to enter the lysosome via lysosome-associated membrane glycoprotein 2 isoform A (LAMP2A). CMA deficiency is associated with dysregulated lipid metabolism in the liver. In this study, we examined the effect of CMA on lipid metabolism in the aged liver. METHODS 12-week-old and 88-week-old mice were employed to assess the effect of aging on hepatic CMA activity. We generated CMA-deficient mouse primary hepatocytes using siRNA for Lamp2a and liver-specific LAMP2A knockdown mice via adeno-associated viruses expressing short hairpin RNAs to investigate the influence of CMA on lipid metabolism. RESULTS We noted aging-induced progression toward fatty liver and a decrease in LAMP2A levels in total protein and lysosomes. The expression of genes associated with fatty acid oxidation was markedly downregulated in the aged liver, as verified in CMA-deficient mouse primary hepatocytes. In addition, the aged liver accumulated nuclear receptor corepressor 1 (NCoR1), a negative regulator of peroxisome proliferator-activated receptor α (PPARα). We found that Hsc70 binds to NCoR1 via the KFERQ motif. Lamp2a siRNA treatment accumulated NCoR1 and decreased the fatty acid oxidation rate. Pharmacological activation of CMA by AR7 treatment increased LAMP2A expression, leading to NCoR1 degradation. A liver-specific LAMP2A knockdown via adeno-associated viruses expressing short hairpin RNAs caused NCoR1 accumulation, inactivated PPARα, downregulated the expression of fatty acid oxidation-related genes and significantly increased liver triglyceride levels. CONCLUSIONS Our results elucidated a novel PPARα regulatory mechanism involving CMA-mediated NCoR1 degradation during aging. These findings demonstrate that CMA dysregulation is crucial for the progression of aging-related fatty liver diseases.
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Affiliation(s)
- You-Jin Choi
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Ho Yun
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jihyeon Yu
- Division of Life Science, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Yewon Mun
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Wonseok Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Cheon Jun Park
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung Woo Han
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung-Hoon Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea.
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4
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Xie SC, Wang Y, Morton CJ, Metcalfe RD, Dogovski C, Pasaje CFA, Dunn E, Luth MR, Kumpornsin K, Istvan ES, Park JS, Fairhurst KJ, Ketprasit N, Yeo T, Yildirim O, Bhebhe MN, Klug DM, Rutledge PJ, Godoy LC, Dey S, De Souza ML, Siqueira-Neto JL, Du Y, Puhalovich T, Amini M, Shami G, Loesbanluechai D, Nie S, Williamson N, Jana GP, Maity BC, Thomson P, Foley T, Tan DS, Niles JC, Han BW, Goldberg DE, Burrows J, Fidock DA, Lee MC, Winzeler EA, Griffin MDW, Todd MH, Tilley L. Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase. Res Sq 2023:rs.3.rs-3198291. [PMID: 37546892 PMCID: PMC10402266 DOI: 10.21203/rs.3.rs-3198291/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Malaria poses an enormous threat to human health. With ever increasing resistance to currently deployed drugs, breakthrough compounds with novel mechanisms of action are urgently needed. Here, we explore pyrimidine-based sulfonamides as a new low molecular weight inhibitor class with drug-like physical parameters and a synthetically accessible scaffold. We show that the exemplar, OSM-S-106, has potent activity against parasite cultures, low mammalian cell toxicity and low propensity for resistance development. In vitro evolution of resistance using a slow ramp-up approach pointed to the Plasmodium falciparum cytoplasmic asparaginyl tRNA synthetase (PfAsnRS) as the target, consistent with our finding that OSM-S-106 inhibits protein translation and activates the amino acid starvation response. Targeted mass spectrometry confirms that OSM-S-106 is a pro-inhibitor and that inhibition of PfAsnRS occurs via enzyme-mediated production of an Asn-OSM-S-106 adduct. Human AsnRS is much less susceptible to this reaction hijacking mechanism. X-ray crystallographic studies of human AsnRS in complex with inhibitor adducts and docking of pro-inhibitors into a model of Asn-tRNA-bound PfAsnRS provide insights into the structure activity relationship and the selectivity mechanism.
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Affiliation(s)
- Stanley C. Xie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Yinuo Wang
- School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Craig J. Morton
- Biomedical Manufacturing Program, CSIRO, Clayton South, Australia
| | - Riley D. Metcalfe
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Con Dogovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Elyse Dunn
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Krittikorn Kumpornsin
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- Calibr, Division of the Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eva S Istvan
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, USA
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Kate J. Fairhurst
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Nutpakal Ketprasit
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tomas Yeo
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Okan Yildirim
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Dana M. Klug
- School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Peter J. Rutledge
- School of Chemistry, University of Sydney, Camperdown, NSW 2006, Australia
| | - Luiz C. Godoy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Jair L. Siqueira-Neto
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Yawei Du
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tanya Puhalovich
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mona Amini
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Gerry Shami
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Gouranga P. Jana
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Bikash C. Maity
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Patrick Thomson
- School of Chemistry, The University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Thomas Foley
- School of Chemistry, The University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Derek S. Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, USA
| | - Jeremy Burrows
- Medicines for Malaria Venture, 20, Route de Pré-Bois 1215, Geneva 15, Switzerland
| | - David A. Fidock
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Marcus C.S. Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- Wellcome Centre for Anti-Infectives Research, Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Elizabeth A. Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Michael D. W. Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Matthew H. Todd
- School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
- Structural Genomics Consortium, University College London, London WC1N 1AX, United Kingdom
| | - Leann Tilley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
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5
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Kwon EJ, Mashelkar KK, Seo J, Shin YZ, Sung K, Jang SC, Cheon SW, Lee H, Lee HW, Kim G, Han BW, Lee SK, Jeong LS, Cha HJ. In Silico Discovery of 5'-Modified 7-Deoxy-7-ethynyl-4'-thioadenosine as a HASPIN Inhibitor and Its Synergistic Anticancer Effect with the PLK1 Inhibitor. ACS Cent Sci 2023; 9:1140-1149. [PMID: 37396870 PMCID: PMC10311661 DOI: 10.1021/acscentsci.3c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Indexed: 07/04/2023]
Abstract
Despite genetic perturbations resulting in embryo lethality for most mitotic kinases, loss of the histone H3 mitotic kinase HASPIN reveals no adverse effect in mice models, establishing HASPIN as a promising target for anticancer therapy. However, developing a HASPIN inhibitor from conventional pharmacophores poses a technical challenge as this atypical kinase shares slight similarities with eukaryotic protein kinases. Chemically modifying a cytotoxic 4'-thioadenosine analogue through high genotoxicity yielded several novel nongenotoxic kinase inhibitors. In silico apporoaches utilizing transcriptomic and chemical similarities with known compounds and KINOMEscan profiles unveiled the HASPIN inhibitor LJ4827. LJ4827's specificity and potency as a HASPIN inhibitor were verified through in vitro kinase assay and X-ray crystallography. HASPIN inhibition by LJ4827 reduced histone H3 phosphorylation and impeded Aurora B recruitment in cancer cell centromeres but not in noncancer cells. Through transcriptome analysis of lung cancer patients, PLK1 was determined as a druggable synergistic partner to complement HASPIN inhibition. Chemical or genetic PLK1 perturbation with LJ4827 effectuated pronounced lung cancer cytotoxicity in vitro and in vivo. Therefore, LJ4827 is a novel anticancer therapeutic for selectively impeding cancer mitosis through potent HASPIN inhibition, and simultaneous HASPIN and PLK1 interference is a promising therapeutic strategy for lung cancer.
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Affiliation(s)
- Eun-Ji Kwon
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | | | - Juhee Seo
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Yoon-Ze Shin
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Kisu Sung
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Chul Jang
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Natural Products
Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Won Cheon
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Haeseung Lee
- College
of Pharmacy, Pusan National University, Busan 46241, Republic of Korea
- Research
Institute for Drug Development, Pusan National
University, Busan 46241, Republic
of Korea
| | - Hyuk Woo Lee
- Future
Medicine Company, Limited, Seongnam, Gyeonggi-do 13449, Republic of Korea
| | - Gyudong Kim
- College
of Pharmacy, and Research Institute of Drug Development, Chonnam National University, Gwangju 61469, Republic of Korea
| | - Byung Woo Han
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Research
Institute of Pharmaceutical Sciences, Seoul
National University, Seoul 08826, Republic
of Korea
| | - Sang Kook Lee
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Natural Products
Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Lak Shin Jeong
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Research
Institute of Pharmaceutical Sciences, Seoul
National University, Seoul 08826, Republic
of Korea
- Future
Medicine Company, Limited, Seongnam, Gyeonggi-do 13449, Republic of Korea
| | - Hyuk-Jin Cha
- College
of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Research
Institute of Pharmaceutical Sciences, Seoul
National University, Seoul 08826, Republic
of Korea
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6
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Surh YJ, Lee JW, Diederich M, Han BW, Cha HJ, Kim KW. In Memoriam: Seung Ki Lee (1944-2022). Mol Cells 2023; 46:3. [PMID: 36697232 PMCID: PMC9880605 DOI: 10.14348/molcells.2023.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Affiliation(s)
- Young-Joon Surh
- College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Jung-Weon Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Marc Diederich
- College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Byung Woo Han
- College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Kyu-Won Kim
- College of Pharmacy, Seoul National University, Seoul 08826, Korea
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7
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Nguyen TQ, My Le LT, Kim DH, Ko KS, Lee HT, Kim Nguyen YT, Kim HS, Han BW, Kang W, Yang JK. Structural basis for the interaction between human Npl4 and Npl4-binding motif of human Ufd1. Structure 2022; 30:1530-1537.e3. [PMID: 36087575 DOI: 10.1016/j.str.2022.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 07/19/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022]
Abstract
The heterodimer of human ubiquitin fusion degradation 1 (hUfd1) and human nuclear protein localization 4 (hNpl4) is a major cofactor of human p97 adenosine triphosphatase (ATPase). The p97-Ufd1-Npl4 complex translocates the ubiquitin-conjugated proteins from the endoplasmic reticulum membrane to the cytoplasm. Ubiquitinated proteins are then degraded by the proteasome. The structures of Npl4 and Ufd1-Npl4 (UN) complex in Saccharomyces cerevisiae have been recently reported; however, the structures of hNpl4 and the human UN complex remain unknown. Here, we report the crystal structures of the human UN complex at a resolution of 2.7 Å and hNpl4 at a resolution of 3.0 Å. We also present atomic details and characterization of the human UN complex. Crystallographic studies and site-directed mutagenesis of the hUfd1 residues involved in the interaction with hNpl4 revealed the atomic details of the two proteins.
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Affiliation(s)
- Thang Quyet Nguyen
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Le Thi My Le
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Do Hyeon Kim
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Kyung Soo Ko
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Hee Taek Lee
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Yen Thi Kim Nguyen
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoun Sook Kim
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Byung Woo Han
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Wonchull Kang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea; Department of Physics and Integrative Institute of Basic Science, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea; Department of Green Chemistry and Material Engineering, Soongsil University, Seoul 06798, Republic of Korea.
| | - Jin Kuk Yang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea.
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8
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Jang DM, Oh EK, Hahn H, Kim HS, Han BW. Structural insights into apoptotic regulation of human Bfk as a novel Bcl-2 family member. Comput Struct Biotechnol J 2022; 20:745-756. [PMID: 35140891 PMCID: PMC8814693 DOI: 10.1016/j.csbj.2022.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/18/2022] [Accepted: 01/23/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Research Institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
| | - Eun Kyung Oh
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyunggu Hahn
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoun Sook Kim
- Research Institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
- Corresponding authors.
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Corresponding authors.
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9
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Kim DG, Baek I, Lee Y, Kim H, Kim JY, Bang G, Kim S, Yoon HJ, Han BW, Suh SW, Kim HS. Structural basis for SdgB- and SdgA-mediated glycosylation of staphylococcal adhesive proteins. Acta Crystallogr D Struct Biol 2021; 77:1460-1474. [PMID: 34726173 PMCID: PMC8561734 DOI: 10.1107/s2059798321010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/28/2021] [Indexed: 02/07/2023] Open
Abstract
The initiation of infection of host tissues by Staphylococcus aureus requires a family of staphylococcal adhesive proteins containing serine-aspartate repeat (SDR) domains, such as ClfA. The O-linked glycosylation of the long-chain SDR domain mediated by SdgB and SdgA is a key virulence factor that protects the adhesive SDR proteins against host proteolytic attack in order to promote successful tissue colonization, and has also been implicated in staphylococcal agglutination, which leads to sepsis and an immunodominant epitope for a strong antibody response. Despite the biological significance of these two glycosyltransferases involved in pathogenicity and avoidance of the host innate immune response, their structures and the molecular basis of their activity have not been investigated. This study reports the crystal structures of SdgB and SdgA from S. aureus as well as multiple structures of SdgB in complex with its substrates (for example UDP, N-acetylglucosamine or SDR peptides), products (glycosylated SDR peptides) or phosphate ions. Together with biophysical and biochemical analyses, this structural work uncovered the novel mechanism by which SdgB and SdgA carry out the glycosyl-transfer process to the long SDR region in SDR proteins. SdgB undergoes dynamic changes in its structure such as a transition from an open to a closed conformation upon ligand binding and takes diverse forms, both as a homodimer and as a heterodimer with SdgA. Overall, these findings not only elucidate the putative role of the three domains of SdgB in recognizing donor and acceptor substrates, but also provide new mechanistic insights into glycosylation of the SDR domain, which can serve as a starting point for the development of antibacterial drugs against staphylococcal infections.
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Affiliation(s)
- Dong-Gyun Kim
- Research Institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Inwha Baek
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yeon Lee
- Research Institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
| | - Hyerry Kim
- Research Institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
- R&D Center, Voronoi Inc., Incheon 21984, Republic of Korea
| | - Jin Young Kim
- Korea Basic Science Institute, Ochang, Chungbuk 28119, Republic of Korea
| | - Geul Bang
- Korea Basic Science Institute, Ochang, Chungbuk 28119, Republic of Korea
| | - Sunghwan Kim
- R&D Center, Voronoi Inc., Incheon 21984, Republic of Korea
| | - Hye Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoun Sook Kim
- Research Institute, National Cancer Center, Goyang, Gyeonggi 10408, Republic of Korea
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10
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Lee HN, Choi YS, Kim SH, Zhong X, Kim W, Park JS, Saeidi S, Han BW, Kim N, Lee HS, Choi YJ, Baek JH, Na HK, Surh YJ. Resolvin D1 suppresses inflammation-associated tumorigenesis in the colon by inhibiting IL-6-induced mitotic spindle abnormality. FASEB J 2021; 35:e21432. [PMID: 33794029 DOI: 10.1096/fj.202002392r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/15/2021] [Accepted: 01/25/2021] [Indexed: 01/07/2023]
Abstract
While failure in resolution of inflammation is considered to increase the risk of tumorigenesis, there is paucity of experimental as well as clinical evidence supporting this association. Resolvin D1 (RvD1) is a representative pro-resolving lipid mediator that is endogenously generated from docosahexaenoic acid for the resolution of inflammation. Here, we report a decreased level of RvD1 in the blood from colorectal cancer patients and mice having inflammation-induced colon cancer, suggesting plasma RvD1 as a potential biomarker for monitoring colorectal cancer. Administration of RvD1 attenuated dextran sodium sulfate (DSS)-induced colitis and azoxymethane (AOM) plus DSS-induced colorectal carcinogenesis by suppressing the production of interleukin-6 (IL-6) and IL-6-mediated chromosomal instability. The protective effect of RvD1 against chromosomal instability is associated with downregulation of IL-6-induced Cyclin D1 expression, which appears to be mediated by blocking the Janus kinase 2 (JAK2)-signal transducer and activator of transcription 3 (STAT3) axis. RvD1 inhibited the STAT3 signaling pathway by interfering with the binding of IL-6 to its receptor (IL-6R), suggesting the novel function of RvD1 as a putative IL-6R antagonist. Together, our findings suggest that RvD1-mediated blockade of IL-6 signal transmission may contribute to inhibition of chromosomal instability and tumorigenesis.
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Affiliation(s)
- Ha-Na Lee
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Yeon-Seo Choi
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Seong Hoon Kim
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Xiancai Zhong
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Wonki Kim
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Joon Sung Park
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Soma Saeidi
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea
| | - Byung Woo Han
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea
| | - Yoon Jin Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jeong-Heum Baek
- Division of Colon and Rectal Surgery, Department of Surgery, Gil Medical Center, Gachon University College of Medicine, Incheon, South Korea
| | - Hye-Kyung Na
- Department of Food and Nutrition, College of Human Ecology, Sungshin Women's University, Seoul, South Korea
| | - Young-Joon Surh
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea.,Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, South Korea.,Cancer Research Institute, Seoul National University, Seoul, South Korea
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11
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Hyun SY, Le HT, Min HY, Pei H, Lim Y, Song I, Nguyen YTK, Hong S, Han BW, Lee HY. Evodiamine inhibits both stem cell and non-stem-cell populations in human cancer cells by targeting heat shock protein 70. Theranostics 2021; 11:2932-2952. [PMID: 33456581 PMCID: PMC7806467 DOI: 10.7150/thno.49876] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Rationale: Cancer stem cells (CSCs) are known to cause tumor recurrence and drug resistance. The heat shock protein (HSP) system plays a major role in preserving expression and function of numerous oncoproteins, including those involved in the CSC activities. We explored novel anticancer drugs, especially those targeting HSP components required for the functional role of CSCs. Methods: Investigation of the role of the HSP system in CSCs and screening of a natural product chemical library were performed by utilizing cancer cell lines, primary cultures of patient-derived xenografts (PDXs), and their putative CSC subpopulations (i.e., those grown under sphere-forming conditions, stably transfected with reporter vectors carrying NANOG or POUSF1 promoters, or carrying high ALDH activity) in vitro and PDX and KrasG12D/+-driven tumor models in vivo. Regulation of the HSP system was investigated by immunoprecipitation, drug affinity responsive target stability assay, binding experiments using ATP-agarose beads and biotinylated drug, and docking analysis. Results: The HSP system was activated in CSCs via transcriptional upregulation of the HSP system components, especially HSP70. Evodiamine (Evo) was identified to induce apoptosis in both CSC and bulk non-CSC populations in human lung, colon, and breast cancer cells and their sublines with chemoresistance. Evo administration decreased the multiplicity, volume, and load of lung tumors in KrasG12D/+ transgenic mice and the growth of cancer cell line- and PDX-derived tumors without detectable toxicity. Mechanistically, Evo disrupted the HSP system by binding the N-terminal ATP-binding pocket of HSP70 and causing its ubiquitin-mediated degradation. Conclusions: Our findings illustrate HSP70 as a potential target for eliminating CSCs and Evo as an effective HSP70-targeting anticancer drug eradicating both CSCs and non-CSCs with a minimal toxicity.
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12
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Choi YJ, Ohn JH, Kim N, Kim W, Park K, Won S, Sael L, Shin CM, Lee SM, Lee S, An HJ, Jang DM, Han BW, Lee HS, Kang SJ, Kim JS, Lee DH. Family-based exome sequencing combined with linkage analyses identifies rare susceptibility variants of MUC4 for gastric cancer. PLoS One 2020; 15:e0236197. [PMID: 32701958 PMCID: PMC7377420 DOI: 10.1371/journal.pone.0236197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 06/30/2020] [Indexed: 12/24/2022] Open
Abstract
Genome-wide association studies of gastric cancer (GC) cases have revealed common gastric cancer susceptibility loci with low effect size. We investigated rare variants with high effect size via whole-exome sequencing (WES) of subjects with familial clustering of gastric cancer. WES of DNAs from the blood of 19 gastric cancer patients and 36 unaffected family members from 14 families with two or more gastric cancer patients were tested. Linkage analysis combined with association tests were performed using Pedigree Variant Annotation, Analysis, and Search Tool (pVAAST) software. Based on the logarithm of odds (LOD) and permutation-based composite likelihood ratio test (CLRT) from pVAAST, MUC4 was identified as a predisposing gene (LOD P-value = 1.9×10-5; permutation-based P-value of CLRT ≤ 9.9×10-9). In a larger cohort consisting of 597 GC patients and 9,759 healthy controls genotyped with SNP array, we discovered common variants in MUC4 regions (rs148735556, rs11717039, and rs547775645) significantly associated with GC supporting the association of MUC4 with gastric cancer. And the MUC4 variants were found in higher frequency in The Cancer Genome Atlas Study (TCGA) germline samples of patients with multiple cancer types. Immunohistochemistry indicated that MUC4 was downregulated in the noncancerous gastric mucosa of subjects with MUC4 germline missense variants, suggesting that loss of the protective function of MUC4 predisposes an individual to gastric cancer. Rare variants in MUC4 can be novel gastric cancer susceptibility loci in Koreans possessing the familial clustering of gastric cancer.
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Affiliation(s)
- Yoon Jin Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Jung Hun Ohn
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
- * E-mail:
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Kyungtaek Park
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
| | - Sungho Won
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
- Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Lee Sael
- Department of Artificial Intelligence and Data Science, Ajou University, Seoul, South Korea
| | - Cheol Min Shin
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Sun Min Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Sejoon Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, South Korea
| | - Dong Man Jang
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Byung Woo Han
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Hye Seung Lee
- Department of Pathology, Seoul National University Bundang Hospital, Seongnam, South Korea
| | - Seung Joo Kang
- Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, South Korea
| | - Joo Sung Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Department of Internal Medicine and Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul, South Korea
| | - Dong Ho Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, South Korea
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, South Korea
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, South Korea
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13
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Losson H, Gajulapalli SR, Lernoux M, Lee JY, Mazumder A, Gérard D, Seidel C, Hahn H, Christov C, Dicato M, Kirsch G, Han BW, Schnekenburger M, Diederich M. The HDAC6 inhibitor 7b induces BCR-ABL ubiquitination and downregulation and synergizes with imatinib to trigger apoptosis in chronic myeloid leukemia. Pharmacol Res 2020; 160:105058. [PMID: 32619722 DOI: 10.1016/j.phrs.2020.105058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 06/24/2020] [Accepted: 06/28/2020] [Indexed: 12/12/2022]
Abstract
Despite the discovery of tyrosine kinase inhibitors (TKIs) for the treatment of breakpoint cluster region-Abelson (BCR-ABL)+ cancer types, patients with chronic myeloid leukemia (CML) treated with TKIs develop resistance and severe adverse effects. Combination treatment, especially with a histone deacetylase (HDAC) 6 inhibitor (HDAC6i), appears to be an attractive option to prevent TKI resistance, considering the potential capacity of an HDAC6i to diminish BCR-ABL expression. We first validated the in vivo anti-cancer potential of the compound 7b by significantly reducing the tumor burden of BALB/c mice xenografted with K-562 cells, without notable organ toxicity. Here, we hypothesize that the HDAC6i compound 7b can lead to BCR-ABL downregulation in CML cells and sensitize them to TKI treatment. The results showed that combination treatment with imatinib and 7b resulted in strong synergistic caspase-dependent apoptotic cell death and drastically reduced the proportion of leukemia stem cells, whereas this treatment only moderately affected healthy cells. Ultimately, the combination significantly decreased colony formation in a semisolid methylcellulose medium and tumor mass in xenografted zebrafish compared to each compound alone. Mechanistically, the combination induced BCR-ABL ubiquitination and downregulation followed by disturbance of key proteins in downstream pathways involved in CML proliferation and survival. Taken together, our results suggest that an HDAC6i potentiates the effect of imatinib and could overcome TKI resistance in CML cells.
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Affiliation(s)
- Hélène Losson
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg, Luxembourg
| | - Sruthi Reddy Gajulapalli
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Manon Lernoux
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg, Luxembourg
| | - Jin-Young Lee
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Aloran Mazumder
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Déborah Gérard
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg, Luxembourg
| | - Carole Seidel
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg, Luxembourg
| | - Hyunggu Hahn
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Christo Christov
- Service d'Histologie, Faculté de Médicine, Université de Lorraine, INSERM U1256 NGERE, 54000, Nancy, France
| | - Mario Dicato
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg, Luxembourg
| | - Gilbert Kirsch
- UMR CNRS 7053 LC2M, Université de Lorraine, 57070, Metz, France
| | - Byung Woo Han
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea
| | - Michael Schnekenburger
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg, Luxembourg
| | - Marc Diederich
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, South Korea.
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14
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Kim S, Kim W, Kim DH, Jang JH, Kim SJ, Park SA, Hahn H, Han BW, Na HK, Chun KS, Choi BY, Surh YJ. Resveratrol suppresses gastric cancer cell proliferation and survival through inhibition of PIM-1 kinase activity. Arch Biochem Biophys 2020; 689:108413. [PMID: 32473133 DOI: 10.1016/j.abb.2020.108413] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/01/2020] [Accepted: 05/17/2020] [Indexed: 02/06/2023]
Abstract
The proviral integration site for Moloney murine leukemia virus (PIM) family of serine/threonine-specific kinases consist of three isoforms, that regulate proliferation, apoptosis, metabolism, invasion, and metastasis of cancer cells. Among these, abnormally elevated kinase activity of PIM-1 contributes to the progression of gastric cancer and predicts poor prognosis and a low survival rate in gastric cancer patients. In the present study, we found that resveratrol, one of the representative chemopreventive and anticarcinogenic phytochemicals, directly binds to PIM-1 and thereby inhibits its catalytic activity in human gastric cancer SNU-601 cells. This resulted in suppression of phosphorylation of the proapoptotic Bad, a known substrate of PIM-1. Resveratrol, by inactivating PIM-1, also inhibited anchorage-independent growth and proliferation of SNU-601 cells. To understand the molecular interaction between resveratrol and PIM-1, we conducted docking simulation and found that resveratrol directly binds to the PIM-1 at the ATP-binding pocket. In conclusion, the proapototic and anti-proliferative effects of resveratrol in gastric cancer cells are likely to be mediated through suppression of PIM-1 kinase activity, which may represent a novel mechanism underlying its chemopreventive and anticarcinogenic actions.
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Affiliation(s)
- Sujin Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, South Korea; Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
| | - Wonki Kim
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
| | - Do-Hee Kim
- Department of Chemistry, College of Convergence and Integrated Science, Kyonggi University, Suwon, Gyeonggi-do 16227, South Korea
| | - Jeong-Hoon Jang
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
| | - Su-Jung Kim
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
| | - Sin-Aye Park
- Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan 31538, South Korea
| | - Hyunggu Hahn
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
| | - Byung Woo Han
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul 08826, South Korea
| | - Hye-Kyung Na
- Department of Food Science and Biotechnology, College of Knowledge-based Services Engineering, Sungshin Women's University, Seoul 01133, South Korea
| | - Kyung-Soo Chun
- Department of Pharmacy, College of Pharmacy, Keimyung University, Daegu 42601, South Korea
| | - Bu Young Choi
- Department of Pharmaceutical Science and Engineering, Seowon University, Cheongju, Chungbuk 28674, South Korea.
| | - Young-Joon Surh
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, South Korea; Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul 08826, South Korea; Cancer Research Institute, Seoul National University, Seoul 03080, South Korea.
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15
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Lernoux M, Schnekenburger M, Losson H, Vermeulen K, Hahn H, Gérard D, Lee JY, Mazumder A, Ahamed M, Christov C, Kim DW, Dicato M, Bormans G, Han BW, Diederich M. Novel HDAC inhibitor MAKV-8 and imatinib synergistically kill chronic myeloid leukemia cells via inhibition of BCR-ABL/MYC-signaling: effect on imatinib resistance and stem cells. Clin Epigenetics 2020; 12:69. [PMID: 32430012 PMCID: PMC7236970 DOI: 10.1186/s13148-020-00839-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Background Chronic myeloid leukemia (CML) pathogenesis is mainly driven by the oncogenic breakpoint cluster region-Abelson murine leukemia viral oncogene homolog 1 (BCR-ABL) fusion protein. Since BCR-ABL displays abnormal constitutive tyrosine kinase activity, therapies using tyrosine kinase inhibitors (TKis) such as imatinib represent a major breakthrough for the outcome of CML patients. Nevertheless, the development of TKi resistance and the persistence of leukemia stem cells (LSCs) remain barriers to cure the disease, justifying the development of novel therapeutic approaches. Since the activity of histone deacetylase (HDAC) is deregulated in numerous cancers including CML, pan-HDAC inhibitors may represent promising therapeutic regimens for the treatment of CML cells in combination with TKi. Results We assessed the anti-leukemic activity of a novel hydroxamate-based pan-HDAC inhibitor MAKV-8, which complied with the Lipinski’s “rule of five,” in various CML cells alone or in combination with imatinib. We validated the in vitro HDAC-inhibitory potential of MAKV-8 and demonstrated efficient binding to the ligand-binding pocket of HDAC isoenzymes. In cellulo, MAKV-8 significantly induced target protein acetylation, displayed cytostatic and cytotoxic properties, and triggered concomitant ER stress/protective autophagy leading to canonical caspase-dependent apoptosis. Considering the specific upregulation of selected HDACs in LSCs from CML patients, we investigated the differential toxicity of a co-treatment with MAKV-8 and imatinib in CML versus healthy cells. We also showed that beclin-1 knockdown prevented MAKV-8-imatinib combination-induced apoptosis. Moreover, MAKV-8 and imatinib co-treatment synergistically reduced BCR-ABL-related signaling pathways involved in CML cell growth and survival. Since our results showed that LSCs from CML patients overexpressed c-MYC, importantly MAKV-8-imatinib co-treatment reduced c-MYC levels and the LSC population. In vivo, tumor growth of xenografted K-562 cells in zebrafish was completely abrogated upon combined treatment with MAKV-8 and imatinib. Conclusions Collectively, the present findings show that combinations HDAC inhibitor-imatinib are likely to overcome drug resistance in CML pathology.
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Affiliation(s)
- Manon Lernoux
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg, Luxembourg
| | - Michael Schnekenburger
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg, Luxembourg
| | - Hélène Losson
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg, Luxembourg
| | - Koen Vermeulen
- Laboratory for Radiopharmaceutical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Hyunggu Hahn
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Déborah Gérard
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg, Luxembourg
| | - Jin-Young Lee
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Aloran Mazumder
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
| | - Muneer Ahamed
- Laboratory for Radiopharmaceutical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | | | - Dong-Wook Kim
- Seoul St. Mary's Hospital, Leukemia Research Institute, the Catholic University of Korea, Seoul, Korea
| | - Mario Dicato
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg, Luxembourg
| | - Guy Bormans
- Laboratory for Radiopharmaceutical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Byung Woo Han
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
| | - Marc Diederich
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea.
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16
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Ahn S, Jang DM, Park SC, An S, Shin J, Han BW, Noh M. Cyclin-Dependent Kinase 5 Inhibitor Butyrolactone I Elicits a Partial Agonist Activity of Peroxisome Proliferator-Activated Receptor γ. Biomolecules 2020; 10:biom10020275. [PMID: 32054125 PMCID: PMC7072624 DOI: 10.3390/biom10020275] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/07/2020] [Accepted: 02/07/2020] [Indexed: 12/15/2022] Open
Abstract
Adiponectin is an adipocyte-derived cytokine having an insulin-sensitizing activity. During the phenotypic screening of secondary metabolites derived from the marine fungus Aspergillus terreus, a poly cyclin-dependent kinase (CDK) inhibitor butyrolactone I affecting CDK1 and CDK5 was discovered as a potent adiponectin production-enhancing compound in the adipogenesis model of human bone marrow-derived mesenchymal stem cells (hBM-MSCs). CDK5 inhibitors exhibit insulin-sensitizing activities by suppressing the phosphorylation of peroxisome proliferator-activated receptor γ (PPARγ). However, the adiponectin production-enhancing activities of butyrolactone I have not been correlated with the potency of CDK5 inhibitor activities. In a target identification study, butyrolactone I was found to directly bind to PPARγ. In the crystal structure of the human PPARγ, the ligand-binding domain (LBD) in complex with butyrolactone I interacted with the amino acid residues located in the hydrophobic binding pockets of the PPARγ LBD, which is a typical binding mode of the PPARγ partial agonists. Therefore, the adiponectin production-enhancing effect of butyrolactone I was mediated by its polypharmacological dual modulator activities as both a CDK5 inhibitor and a PPARγ partial agonist.
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Affiliation(s)
- Sungjin Ahn
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (S.A.); (S.C.P.); (J.S.)
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea;
| | - Sung Chul Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (S.A.); (S.C.P.); (J.S.)
| | - Seungchan An
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (S.A.); (S.C.P.); (J.S.)
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (S.A.); (S.C.P.); (J.S.)
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea;
- Correspondence: (M.N); (B.W.H); Tel.: +82-2-880-7898 (B.W.H.); +82-2-880-2481 (M.N.)
| | - Minsoo Noh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (S.A.); (S.C.P.); (J.S.)
- Correspondence: (M.N); (B.W.H); Tel.: +82-2-880-7898 (B.W.H.); +82-2-880-2481 (M.N.)
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17
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Vo TTL, Park JH, Lee EJ, Nguyen YTK, Han BW, Nguyen HTT, Mun KC, Ha E, Kwon TK, Kim KW, Jeong CH, Seo JH. Characterization of Lysine Acetyltransferase Activity of Recombinant Human ARD1/NAA10. Molecules 2020; 25:molecules25030588. [PMID: 32013195 PMCID: PMC7036845 DOI: 10.3390/molecules25030588] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/23/2020] [Accepted: 01/27/2020] [Indexed: 02/04/2023] Open
Abstract
Arrest defective 1 (ARD1), also known as N(alpha)-acetyltransferase 10 (NAA10) was originally identified as an N-terminal acetyltransferase (NAT) that catalyzes the acetylation of N-termini of newly synthesized peptides. After that, mammalian ARD1/NAA10 expanded its' role to lysine acetyltransferase (KAT) that post-translationally acetylates internal lysine residues of proteins. ARD1/NAA10 is the only enzyme with both NAT and KAT activities. However, recent studies on the role of human ARD1/NAA10 (hARD1/NAA10) in lysine acetylation are contradictory, as crystal structure and in vitro acetylation assay results revealed the lack of KAT activity. Thus, the role of hARD1/NAA10 in lysine acetylation is still debating. Here, we found a clue that possibly explains these complicated and controversial results on KAT activity of hARD1/NAA10. Recombinant hARD1/NAA10 exhibited KAT activity, which disappeared soon in vitro. Size-exclusion analysis revealed that most recombinant hARD1/NAA10 formed oligomers over time, resulting in the loss of KAT activity. While oligomeric recombinant hARD1/NAA10 lost its ability for lysine acetylation, its monomeric form clearly exhibited lysine acetylation activity in vitro. We also characterized the KAT activity of hARD1/NAA10 that was influenced by several experimental conditions, including concentration of reactants and reaction time. Taken together, our study proves that recombinant hARD1/NAA10 exhibits KAT activity in vitro but only under accurate conditions, including reactant concentrations and reaction duration.
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Affiliation(s)
- Tam Thuy Lu Vo
- Department of Biochemistry, Keimyung University School of Medicine, Daegu 42601, Korea; (T.T.L.V.); (H.T.T.N.); (K.C.M.); (E.H.)
| | - Ji-Hyeon Park
- Departments of Radiology and Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; (J.-H.P.); (E.J.L.)
| | - Eun Ji Lee
- Departments of Radiology and Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA; (J.-H.P.); (E.J.L.)
| | - Yen Thi Kim Nguyen
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea; (Y.T.K.N.); (B.W.H.); (K.-W.K.)
| | - Byung Woo Han
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea; (Y.T.K.N.); (B.W.H.); (K.-W.K.)
| | - Hien Thi Thu Nguyen
- Department of Biochemistry, Keimyung University School of Medicine, Daegu 42601, Korea; (T.T.L.V.); (H.T.T.N.); (K.C.M.); (E.H.)
| | - Kyo Cheol Mun
- Department of Biochemistry, Keimyung University School of Medicine, Daegu 42601, Korea; (T.T.L.V.); (H.T.T.N.); (K.C.M.); (E.H.)
| | - Eunyoung Ha
- Department of Biochemistry, Keimyung University School of Medicine, Daegu 42601, Korea; (T.T.L.V.); (H.T.T.N.); (K.C.M.); (E.H.)
| | - Taeg Kyu Kwon
- Department of Immunology, Keimyung University School of Medicine, Daegu 42601, Korea;
| | - Kyu-Won Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul 08826, Korea; (Y.T.K.N.); (B.W.H.); (K.-W.K.)
| | - Chul-Ho Jeong
- College of Pharmacy, Keimyung University, Daegu 42601, Korea
- Correspondence: (C.-H.J.); (J.H.S.); Tel.: +82-53-580-6638 (C.-H.J.); +82-53-258-7436 (J.H.S.)
| | - Ji Hae Seo
- Department of Biochemistry, Keimyung University School of Medicine, Daegu 42601, Korea; (T.T.L.V.); (H.T.T.N.); (K.C.M.); (E.H.)
- Correspondence: (C.-H.J.); (J.H.S.); Tel.: +82-53-580-6638 (C.-H.J.); +82-53-258-7436 (J.H.S.)
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18
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Park JS, Lee JY, Nguyen YTK, Kang NW, Oh EK, Jang DM, Kim HJ, Kim DD, Han BW. Structural Analyses on the Deamidation of N-Terminal Asn in the Human N-Degron Pathway. Biomolecules 2020; 10:biom10010163. [PMID: 31968674 PMCID: PMC7022378 DOI: 10.3390/biom10010163] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/30/2019] [Accepted: 01/13/2020] [Indexed: 01/01/2023] Open
Abstract
The N-degron pathway is a proteolytic system in which a single N-terminal amino acid acts as a determinant of protein degradation. Especially, degradation signaling of N-terminal asparagine (Nt-Asn) in eukaryotes is initiated from its deamidation by N-terminal asparagine amidohydrolase 1 (NTAN1) into aspartate. Here, we have elucidated structural principles of deamidation by human NTAN1. NTAN1 adopts the characteristic scaffold of CNF1/YfiH-like cysteine hydrolases that features an α-β-β sandwich structure and a catalytic triad comprising Cys, His, and Ser. In vitro deamidation assays using model peptide substrates with varying lengths and sequences showed that NTAN1 prefers hydrophobic residues at the second-position. The structures of NTAN1-peptide complexes further revealed that the recognition of Nt-Asn is sufficiently organized to produce high specificity, and the side chain of the second-position residue is accommodated in a hydrophobic pocket adjacent to the active site of NTAN1. Collectively, our structural and biochemical analyses of the substrate specificity of NTAN1 contribute to understanding the structural basis of all three amidases in the eukaryotic N-degron pathway.
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Affiliation(s)
- Joon Sung Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Jae-Young Lee
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea;
| | - Yen Thi Kim Nguyen
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Nae-Won Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Eun Kyung Oh
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Korea;
| | - Dae-Duk Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.S.P.); (Y.T.K.N.); (N.-W.K.); (E.K.O.); (D.M.J.); (D.-D.K.)
- Correspondence: ; Tel.: +82-2-880-7899
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Hoang NX, Hoang VH, Luu TTT, Luu HN, Ngo T, Van Hieu D, Long NH, Anh LV, Ngo ST, Nguyen YTK, Han BW, Nguyen TX, Hai DTT, Hien TTT, Tran PT. Design, synthesis and bioevaluation of novel 6-substituted aminoindazole derivatives as anticancer agents. RSC Adv 2020; 10:45199-45206. [PMID: 35516257 PMCID: PMC9058813 DOI: 10.1039/d0ra09112j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 11/20/2020] [Indexed: 11/21/2022] Open
Abstract
In the present study, a series of 6-substituted aminoindazole derivatives were designed, synthesized, and evaluated for bio-activities. The compounds were initially designed as indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors based on the structural feature of five IDO1 inhibitors, which are currently on clinical trials, and the important anticancer activity of the indazole scaffold. One of them, compound N-(4-fluorobenzyl)-1,3-dimethyl-1H-indazol-6-amine (36), exhibited a potent anti-proliferative activity with an IC50 value of 0.4 ± 0.3 μM in human colorectal cancer cells (HCT116). This compound also remarkably suppressed the IDO1 protein expression. In the cell-cycle studies, the suppressive activity of compound 36 in HCT116 cells was related to the G2/M cell cycle arrest. Altogether, the current findings demonstrate that compound 36 would be promising for further development as a potential anticancer agent. In the present study, a series of 6-substituted aminoindazole derivatives were designed, synthesized, and evaluated for bio-activities.![]()
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Affiliation(s)
| | - Van-Hai Hoang
- Laboratory of Medicinal Chemistry
- Research Institute of Pharmaceutical Sciences
- College of Pharmacy
- Seoul National University
- Seoul 08826
| | - Thi-Thu-Trang Luu
- College of Pharmacy
- Natural Products Research Institute
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Hung N. Luu
- Division of Cancer Control and Population Sciences
- UPMC Hillman Cancer Center
- University of Pittsburgh
- Pittsburgh
- USA
| | - Thien Ngo
- Faculty of Pharmacy
- Thai Binh University of Medicine and Pharmacy
- Thai Binh City 410000
- Vietnam
| | | | | | - Le Viet Anh
- Hanoi University of Pharmacy
- Hanoi 100000
- Vietnam
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics
- Ton Duc Thang University
- Ho Chi Minh City 700000
- Vietnam
- Faculty of Applied Sciences
| | - Yen Thi Kim Nguyen
- College of Pharmacy
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Byung Woo Han
- College of Pharmacy
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Thanh Xuan Nguyen
- Department of Surgical Oncology
- Viet-Duc University Hospital
- Hanoi 100000
- Vietnam
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Nguyen YTK, Park JS, Jang JY, Kim KR, Vo TTL, Kim KW, Han BW. Structural and Functional Analyses of Human ChaC2 in Glutathione Metabolism. Biomolecules 2019; 10:biom10010031. [PMID: 31878259 PMCID: PMC7022552 DOI: 10.3390/biom10010031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 12/11/2019] [Accepted: 12/18/2019] [Indexed: 01/07/2023] Open
Abstract
Glutathione (GSH) degradation plays an essential role in GSH homeostasis, which regulates cell survival, especially in cancer cells. Among human GSH degradation enzymes, the ChaC2 enzyme acts on GSH to form 5-l-oxoproline and Cys-Gly specifically in the cytosol. Here, we report the crystal structures of ChaC2 in two different conformations and compare the structural features with other known γ-glutamylcyclotransferase enzymes. The unique flexible loop of ChaC2 seems to function as a gate to achieve specificity for GSH binding and regulate the constant GSH degradation rate. Structural and biochemical analyses of ChaC2 revealed that Glu74 and Glu83 play crucial roles in directing the conformation of the enzyme and in modulating the enzyme activity. Based on a docking study of GSH to ChaC2 and binding assays, we propose a substrate-binding mode and catalytic mechanism. We also found that overexpression of ChaC2, but not mutants that inhibit activity of ChaC2, significantly promoted breast cancer cell proliferation, suggesting that the GSH degradation by ChaC2 affects the growth of breast cancer cells. Our structural and functional analyses of ChaC2 will contribute to the development of inhibitors for the ChaC family, which could effectively regulate the progression of GSH degradation-related cancers.
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Affiliation(s)
- Yen T. K. Nguyen
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (Y.T.K.N.); (J.S.P.); (J.Y.J.); (K.R.K.); (K.-W.K.)
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (Y.T.K.N.); (J.S.P.); (J.Y.J.); (K.R.K.); (K.-W.K.)
| | - Jun Young Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (Y.T.K.N.); (J.S.P.); (J.Y.J.); (K.R.K.); (K.-W.K.)
| | - Kyung Rok Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (Y.T.K.N.); (J.S.P.); (J.Y.J.); (K.R.K.); (K.-W.K.)
| | - Tam T. L. Vo
- Department of Biochemistry, Keimyung University School of Medicine, Daegu 42601, Korea;
| | - Kyu-Won Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (Y.T.K.N.); (J.S.P.); (J.Y.J.); (K.R.K.); (K.-W.K.)
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; (Y.T.K.N.); (J.S.P.); (J.Y.J.); (K.R.K.); (K.-W.K.)
- Correspondence: ; Tel.: +82-2-8807898
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Jang JY, Kim H, Kim HJ, Suh SW, Park SB, Han BW. Publisher Correction: Structural basis for the inhibitory effects of a novel reversible covalent ligand on PPARγ phosphorylation. Sci Rep 2019; 9:15798. [PMID: 31659195 PMCID: PMC6817847 DOI: 10.1038/s41598-019-50831-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Jun Young Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyunsoo Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung Bum Park
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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Kim M, Park SH, Park JS, Kim HJ, Han BW. Crystal Structure of Human EOLA1 Implies Its Possibility of RNA Binding. Molecules 2019; 24:molecules24193529. [PMID: 31569543 PMCID: PMC6803910 DOI: 10.3390/molecules24193529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 01/07/2023]
Abstract
Human endothelial-overexpressed lipopolysaccharide-associated factor 1 (EOLA1) has been suggested to regulate inflammatory responses in endothelial cells by controlling expression of proteins, interleukin-6 and vascular cell adhesion molecule-1, and by preventing apoptosis. To elucidate the structural basis of the EOLA1 function, we determined its crystal structure at 1.71 Å resolution and found that EOLA1 is structurally similar to an activating signal cointegrator-1 homology (ASCH) domain with a characteristic β-barrel fold surrounded by α-helices. Despite its low sequence identity with other ASCH domains, EOLA1 retains a conserved 'GxKxxExR' motif in its cavity structure. The cavity harbors aromatic and polar residues, which are speculated to accommodate nucleotide molecules as do YT521-B homology (YTH) proteins. Additionally, EOLA1 exhibits a positively charged cleft, similar to those observed in YTH proteins and the ASCH protein from Zymomonas mobilis that exerts ribonuclease activity. This implies that the positively charged cleft in EOLA1 could stabilize the binding of RNA molecules. Taken together, we suggest that EOLA1 controls protein expression through RNA binding to play protective roles against endothelial cell injuries resulting from lipopolysaccharide (LPS)-induced inflammation responses.
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Affiliation(s)
- Minju Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Sang Ho Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Korea.
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
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23
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Hahn H, Park SH, Kim HJ, Kim S, Han BW. The DRS-AIMP2-EPRS subcomplex acts as a pivot in the multi-tRNA synthetase complex. IUCrJ 2019; 6:958-967. [PMID: 31576228 PMCID: PMC6760448 DOI: 10.1107/s2052252519010790] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/01/2019] [Indexed: 05/16/2023]
Abstract
Aminoacyl-tRNA synthetases (ARSs) play essential roles in protein biosynthesis as well as in other cellular processes, often using evolutionarily acquired domains. For possible cooperativity and synergistic effects, nine ARSs assemble into the multi-tRNA synthetase complex (MSC) with three scaffold proteins: aminoacyl-tRNA synthetase complex-interacting multifunctional proteins 1, 2 and 3 (AIMP1, AIMP2 and AIMP3). X-ray crystallographic methods were implemented in order to determine the structure of a ternary subcomplex of the MSC comprising aspartyl-tRNA synthetase (DRS) and two glutathione S-transferase (GST) domains from AIMP2 and glutamyl-prolyl-tRNA synthetase (AIMP2GST and EPRSGST, respectively). While AIMP2GST and EPRSGST interact via conventional GST heterodimerization, DRS strongly interacts with AIMP2GST via hydrogen bonds between the α7-β9 loop of DRS and the β2-α2 loop of AIMP2GST, where Ser156 of AIMP2GST is essential for the assembly. Structural analyses of DRS-AIMP2GST-EPRSGST reveal its pivotal architecture in the MSC and provide valuable insights into the overall assembly and conditionally required disassembly of the MSC.
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Affiliation(s)
- Hyunggu Hahn
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Ho Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
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24
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Jang JY, Kim H, Kim HJ, Suh SW, Park SB, Han BW. Structural basis for the inhibitory effects of a novel reversible covalent ligand on PPARγ phosphorylation. Sci Rep 2019; 9:11168. [PMID: 31371757 PMCID: PMC6671948 DOI: 10.1038/s41598-019-47672-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 07/22/2019] [Indexed: 12/13/2022] Open
Abstract
Peroxisome proliferator-activated receptor γ (PPARγ) is a major therapeutic target for the treatment of type 2 diabetes. However, the use of PPARγ-targeted drugs, such as rosiglitazone and pioglitazone, is limited owing to serious side effects caused by classical agonism. Using a rational drug discovery approach, we recently developed SB1495, a novel reversible covalent inhibitor of the cyclin-dependent kinase 5 (Cdk5)-mediated phosphorylation of PPARγ at Ser245, a key factor in the insulin-sensitizing effect of PPARγ-targeted drugs. In this study, we report the crystal structures of PPARγ in complex with SB1495 and its enantiomeric analogue SB1494, which rarely exhibits inhibitory activity, to visualize the mechanistic basis for their distinct activities. SB1495 occupies the Arm3 region near the Ω loop of the PPARγ ligand-binding domain, whereas its enantiomeric analogue SB1494 binds to the Arm2 region. In addition, the piperazine moiety of SB1495 directly pushes the helix H2′, resulting in the stabilization of the Ω loop just behind the helix H2′. Our results may contribute to the development of a new generation of antidiabetic drugs that selectively block PPARγ phosphorylation without classical agonism.
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Affiliation(s)
- Jun Young Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyunsoo Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung Bum Park
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea.
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25
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Ka D, Jang DM, Han BW, Bae E. Molecular organization of the type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. Nucleic Acids Res 2019; 46:9805-9815. [PMID: 30102386 PMCID: PMC6182153 DOI: 10.1093/nar/gky702] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/24/2018] [Indexed: 12/21/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against invading foreign nucleic acids. In type II-A CRISPR–Cas systems, the Cas1–Cas2 integrase complex and the subtype-specific Csn2 comprise the CRISPR adaptation module, which cooperates with the Cas9 nuclease effector for spacer selection. Here, we report the molecular organization of the Streptococcus pyogenes type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. We determined the crystal structure of S. pyogenes type II-A Cas2. Chromatographic and calorimetric analyses revealed the stoichiometry and topology of the type II-A adaptation module composed of Cas1, Cas2 and Csn2. We also demonstrated that Cas9 interacts with Csn2 in a direct and stoichiometric manner. Our results reveal a network of molecular interactions among type II-A Cas proteins and highlight the role of Csn2 in coordinating Cas components involved in the adaptation and interference stages of CRISPR-mediated immunity.
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Affiliation(s)
- Donghyun Ka
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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26
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Sliepen K, Han BW, Bontjer I, Mooij P, Garces F, Behrens AJ, Rantalainen K, Kumar S, Sarkar A, Brouwer PJM, Hua Y, Tolazzi M, Schermer E, Torres JL, Ozorowski G, van der Woude P, de la Peña AT, van Breemen MJ, Camacho-Sánchez JM, Burger JA, Medina-Ramírez M, González N, Alcami J, LaBranche C, Scarlatti G, van Gils MJ, Crispin M, Montefiori DC, Ward AB, Koopman G, Moore JP, Shattock RJ, Bogers WM, Wilson IA, Sanders RW. Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence. Nat Commun 2019; 10:2355. [PMID: 31142746 PMCID: PMC6541627 DOI: 10.1038/s41467-019-10262-5] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 04/26/2019] [Indexed: 02/06/2023] Open
Abstract
Stabilized HIV-1 envelope glycoproteins (Env) that resemble the native Env are utilized in vaccination strategies aimed at inducing broadly neutralizing antibodies (bNAbs). To limit the exposure of rare isolate-specific antigenic residues/determinants we generated a SOSIP trimer based on a consensus sequence of all HIV-1 group M isolates (ConM). The ConM trimer displays the epitopes of most known bNAbs and several germline bNAb precursors. The crystal structure of the ConM trimer at 3.9 Å resolution resembles that of the native Env trimer and its antigenic surface displays few rare residues. The ConM trimer elicits strong NAb responses against the autologous virus in rabbits and macaques that are significantly enhanced when it is presented on ferritin nanoparticles. The dominant NAb specificity is directed against an epitope at or close to the trimer apex. Immunogens based on consensus sequences might have utility in engineering vaccines against HIV-1 and other viruses.
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Affiliation(s)
- Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Byung Woo Han
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA. .,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 08826, Korea.
| | - Ilja Bontjer
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Petra Mooij
- Department of Virology, Biomedical Primate Research Centre, 2280 GH, Rijswijk, The Netherlands
| | - Fernando Garces
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA.,Department of Therapeutics Discovery, Amgen Research, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Anna-Janina Behrens
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.,New England Biolabs Inc., 240 County Road, Ipswich, MA, 01938, USA
| | - Kimmo Rantalainen
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Sonu Kumar
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Anita Sarkar
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Philip J M Brouwer
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Yuanzi Hua
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Monica Tolazzi
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Edith Schermer
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Patricia van der Woude
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Alba Torrents de la Peña
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Mariëlle J van Breemen
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Juan Miguel Camacho-Sánchez
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Judith A Burger
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Max Medina-Ramírez
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Nuria González
- AIDS Immunopathology Unit, Instituto de Salud Carlos III, Madrid, 28220, Spain
| | - Jose Alcami
- AIDS Immunopathology Unit, Instituto de Salud Carlos III, Madrid, 28220, Spain
| | - Celia LaBranche
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Gabriella Scarlatti
- Viral Evolution and Transmission Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands
| | - Max Crispin
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.,Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - David C Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Gerrit Koopman
- Department of Virology, Biomedical Primate Research Centre, 2280 GH, Rijswijk, The Netherlands
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, 10021, USA
| | - Robin J Shattock
- Section of Virology, Division of Infectious Diseases, Department of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - Willy M Bogers
- Department of Virology, Biomedical Primate Research Centre, 2280 GH, Rijswijk, The Netherlands
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, Scripps CHAVI-ID, IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD), The Scripps Research Institute, La Jolla, CA, 92037, USA. .,The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam, 1105AZ, The Netherlands. .,Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, 10021, USA.
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27
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Florean C, Kim KR, Schnekenburger M, Kim HJ, Moriou C, Debitus C, Dicato M, Al-Mourabit A, Han BW, Diederich M. Synergistic AML Cell Death Induction by Marine Cytotoxin (+)-1( R), 6( S), 1'( R), 6'( S), 11( R), 17( S)-Fistularin-3 and Bcl-2 Inhibitor Venetoclax. Mar Drugs 2018; 16:md16120518. [PMID: 30572618 PMCID: PMC6316187 DOI: 10.3390/md16120518] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 11/23/2022] Open
Abstract
Treatment of acute myeloid leukemia (AML) patients is still hindered by resistance and relapse, resulting in an overall poor survival rate. Recently, combining specific B-cell lymphoma (Bcl)-2 inhibitors with compounds downregulating myeloid cell leukemia (Mcl)-1 has been proposed as a new effective strategy to eradicate resistant AML cells. We show here that 1(R), 6(S), 1’(R), 6’(S), 11(R), 17(S)-fistularin-3, a bromotyrosine compound of the fistularin family, isolated from the marine sponge Suberea clavata, synergizes with Bcl-2 inhibitor ABT-199 to efficiently kill Mcl-1/Bcl-2-positive AML cell lines, associated with Mcl-1 downregulation and endoplasmic reticulum stress induction. The absolute configuration of carbons 11 and 17 of the fistularin-3 stereoisomer was fully resolved in this study for the first time, showing that the fistularin we isolated from the marine sponge Subarea clavata is in fact the (+)-11(R), 17(S)-fistularin-3 stereoisomer keeping the known configuration 1(R), 6(S), 1’(R), and 6’(S) for the verongidoic acid part. Docking studies and in vitro assays confirm the potential of this family of molecules to inhibit DNA methyltransferase 1 activity.
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MESH Headings
- Animals
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/administration & dosage
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Cell Line, Tumor
- Cell Survival/drug effects
- Drug Screening Assays, Antitumor
- Drug Synergism
- Endoplasmic Reticulum Stress/drug effects
- HL-60 Cells
- Humans
- Isoxazoles/administration & dosage
- Isoxazoles/chemistry
- Isoxazoles/isolation & purification
- Isoxazoles/pharmacology
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Molecular Docking Simulation
- Porifera/chemistry
- Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Sulfonamides/administration & dosage
- Sulfonamides/pharmacology
- Tyrosine/administration & dosage
- Tyrosine/analogs & derivatives
- Tyrosine/chemistry
- Tyrosine/isolation & purification
- Tyrosine/pharmacology
- U937 Cells
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Affiliation(s)
- Cristina Florean
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg.
| | - Kyung Rok Kim
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Michael Schnekenburger
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg.
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 06974, Korea.
| | - Céline Moriou
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Univ. Paris-Sud, University of Paris-Saclay, 1, Avenue de la Terrasse, 91198 Gif-Sur-Yvette, France.
| | - Cécile Debitus
- LEMAR, IRD, UBO, CNRS, IFREMER, IUEM, 29280 Plouzané, France.
| | - Mario Dicato
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540 Luxembourg, Luxembourg.
| | - Ali Al-Mourabit
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Univ. Paris-Sud, University of Paris-Saclay, 1, Avenue de la Terrasse, 91198 Gif-Sur-Yvette, France.
| | - Byung Woo Han
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
| | - Marc Diederich
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
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28
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Lim HX, Jung HJ, Lee A, Park SH, Han BW, Cho D, Kim TS. Lysyl-Transfer RNA Synthetase Induces the Maturation of Dendritic Cells through MAPK and NF-κB Pathways, Strongly Contributing to Enhanced Th1 Cell Responses. J Immunol 2018; 201:2832-2841. [PMID: 30275047 DOI: 10.4049/jimmunol.1800386] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 08/28/2018] [Indexed: 01/26/2023]
Abstract
In addition to essential roles in protein synthesis, lysyl-tRNA synthetase (KRS) is secreted to trigger a proinflammatory function that induces macrophage activation and TNF-α secretion. KRS has been associated with autoimmune diseases such as polymyositis and dermatomyositis. In this study, we investigated the immunomodulatory effects of KRS on bone marrow-derived dendritic cells (DCs) of C57BL/6 mice and subsequent polarization of Th cells and analyzed the underlying mechanisms. KRS-treated DCs increased the expression of cell surface molecules and proinflammatory cytokines associated with DC maturation and activation. Especially, KRS treatment significantly increased production of IL-12, a Th1-polarizing cytokine, in DCs. KRS triggered the nuclear translocation of the NF-κB p65 subunit along with the degradation of IκB proteins and the phosphorylation of MAPKs in DCs. Additionally, JNK, p38, and ERK inhibitors markedly recovered the degradation of IκB proteins, suggesting the involvement of MAPKs as the upstream regulators of NF-κB in the KRS-induced DC maturation and activation. Importantly, KRS-treated DCs strongly increased the differentiation of Th1 cells when cocultured with CD4+ T cells. The addition of anti-IL-12-neutralizing Ab abolished the secretion of IFN-γ in the coculture, indicating that KRS induces Th1 cell response via DC-derived IL-12. Moreover, KRS enhanced the OVA-specific Th1 cell polarization in vivo following the adoptive transfer of OVA-pulsed DCs. Taken together, these results indicated that KRS effectively induced the maturation and activation of DCs through MAPKs/NF-κB-signaling pathways and favored DC-mediated Th1 cell response.
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Affiliation(s)
- Hui Xuan Lim
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Hak-Jun Jung
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Arim Lee
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Si Hoon Park
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Byung Woo Han
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea; and
| | - Daeho Cho
- Institute of Convergence Science, Korea University, Seoul 02841, Republic of Korea
| | - Tae Sung Kim
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea;
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29
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Park JS, Park MC, Lee KY, Goughnour PC, Jeong SJ, Kim HS, Kim HJ, Lee BJ, Kim S, Han BW. Unique N-terminal extension domain of human asparaginyl-tRNA synthetase elicits CCR3-mediated chemokine activity. Int J Biol Macromol 2018; 120:835-845. [PMID: 30171954 DOI: 10.1016/j.ijbiomac.2018.08.171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/24/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
Abstract
Asparaginyl-tRNA synthetase (NRS) is not only essential in protein translation but also associated with autoimmune diseases. Particularly, patients with antibodies that recognize NRS often develop interstitial lung disease (ILD). However, the underlying mechanism of how NRS is recognized by immune cells and provokes inflammatory responses is not well-understood. Here, we found that the crystal structure of the unique N-terminal extension domain of human NRS (named as UNE-N, where -N denotes NRS) resembles that of the chemotactic N-terminal domain of NRS from a filarial nematode, Brugia malayi, which recruits and activates specific immune cells by interacting with CXC chemokine receptor 1 and 2. UNE-N induced migration of CC chemokine receptor 3 (CCR3)-expressing cells. The chemokine activity of UNE-N was significantly reduced by suppressing CCR3 expression with CCR3-targeting siRNA, and the loop3 region of UNE-N was shown to interact mainly with the extracellular domains of CCR3 in nuclear magnetic resonance perturbation experiments. Based on these results, evolutionarily acquired UNE-N elicits chemokine activities that would promote NRS-CCR3-mediated proinflammatory signaling in ILD.
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Affiliation(s)
- Joon Sung Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Min Chul Park
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki-Young Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Peter C Goughnour
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Seung Jae Jeong
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoun Sook Kim
- Therapeutic Target Discovery Branch, Division of Precision Medicine and Cancer Informatics, Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408, Republic of Korea
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Bong-Jin Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 08826, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.
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30
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Kim Yen NT, Han BW. Structural characterization and functional studies of putative human glutathione-specific γ-glutamylcyclotransferase 2 (ChaC2 enzyme). Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s2053273318091763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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31
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Kim HS, Hahn H, Kim J, Jang DM, Lee JY, Back JM, Im HN, Kim H, Han BW, Suh SW. Structural basis for the substrate recognition of peptidoglycan pentapeptides by Enterococcus faecalis VanY B. Int J Biol Macromol 2018; 119:335-344. [PMID: 30016658 DOI: 10.1016/j.ijbiomac.2018.07.081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/15/2018] [Accepted: 07/12/2018] [Indexed: 11/19/2022]
Abstract
Vancomycin resistance in Enterococci and its transfer to methicillin-resistant Staphylococcus aureus are challenging problems in health care institutions worldwide. High-level vancomycin resistance is conferred by acquiring either transposable elements of the VanA or VanB type. Enterococcus faecalis VanYB in the VanB-type operon is a d,d-carboxypeptidase that recognizes the peptidyl-d-Ala4-d-Ala5 extremity of peptidoglycan and hydrolyses the terminal d-Ala on the extracellular side of the cell wall, thereby increasing the level of glycopeptide antibiotics resistance. However, at the molecular level, it remains unclear how VanYB manipulates peptidoglycan peptides for vancomycin resistance. In this study, we have determined the crystal structures of E. faecalis VanYB in the d-Ala-d-Ala-bound, d-Ala-bound, and -unbound states. The interactions between VanYB and d-Ala-d-Ala observed in the crystal provide the molecular basis for the recognition of peptidoglycan substrates by VanYB. Moreover, comparisons with the related VanX and VanXY enzymes reveal distinct structural features of E. faecalis VanYB around the active-site cleft, thus shedding light on its unique substrate specificity. Our results could serve as the foundation for unravelling the molecular mechanism of vancomycin resistance and for developing novel antibiotics against the vancomycin-resistant Enterococcus species.
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Affiliation(s)
- Hyoun Sook Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea; Therapeutic Target Discovery Branch, Division of Precision Medicine, National Cancer Center, Goyang, Gyeonggi, Republic of Korea; Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea.
| | - Hyunggu Hahn
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Jieun Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea
| | - Dong Man Jang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Ji Yeon Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Jang Mi Back
- Therapeutic Target Discovery Branch, Division of Precision Medicine, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Ha Na Im
- Therapeutic Target Discovery Branch, Division of Precision Medicine, National Cancer Center, Goyang, Gyeonggi, Republic of Korea
| | - Haelee Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea.
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Ji S, Lee JY, Schrör J, Mazumder A, Jang DM, Chateauvieux S, Schnekenburger M, Hong CR, Christov C, Kang HJ, Lee Y, Han BW, Kim KW, Shin HY, Dicato M, Cerella C, König GM, Orlikova B, Diederich M. The dialkyl resorcinol stemphol disrupts calcium homeostasis to trigger programmed immunogenic necrosis in cancer. Cancer Lett 2018; 416:109-123. [DOI: 10.1016/j.canlet.2017.12.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 12/06/2017] [Accepted: 12/07/2017] [Indexed: 01/18/2023]
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Schneider NFZ, Cerella C, Lee JY, Mazumder A, Kim KR, de Carvalho A, Munkert J, Pádua RM, Kreis W, Kim KW, Christov C, Dicato M, Kim HJ, Han BW, Braga FC, Simões CMO, Diederich M. Cardiac Glycoside Glucoevatromonoside Induces Cancer Type-Specific Cell Death. Front Pharmacol 2018; 9:70. [PMID: 29545747 PMCID: PMC5838923 DOI: 10.3389/fphar.2018.00070] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/19/2018] [Indexed: 11/25/2022] Open
Abstract
Cardiac glycosides (CGs) are natural compounds used traditionally to treat congestive heart diseases. Recent investigations repositioned CGs as potential anticancer agents. To discover novel cytotoxic CG scaffolds, we selected the cardenolide glucoevatromonoside (GEV) out of 46 CGs for its low nanomolar anti-lung cancer activity. GEV presented reduced toxicity toward non-cancerous cell types (lung MRC-5 and PBMC) and high-affinity binding to the Na+/K+-ATPase α subunit, assessed by computational docking. GEV-induced cell death was caspase-independent, as investigated by a multiparametric approach, and culminates in severe morphological alterations in A549 cells, monitored by transmission electron microscopy, live cell imaging and flow cytometry. This non-canonical cell death was not preceded or accompanied by exacerbation of autophagy. In the presence of GEV, markers of autophagic flux (e.g. LC3I-II conversion) were impacted, even in presence of bafilomycin A1. Cell death induction remained unaffected by calpain, cathepsin, parthanatos, or necroptosis inhibitors. Interestingly, GEV triggered caspase-dependent apoptosis in U937 acute myeloid leukemia cells, witnessing cancer-type specific cell death induction. Differential cell cycle modulation by this CG led to a G2/M arrest, cyclin B1 and p53 downregulation in A549, but not in U937 cells. We further extended the anti-cancer potential of GEV to 3D cell culture using clonogenic and spheroid formation assays and validated our findings in vivo by zebrafish xenografts. Altogether, GEV shows an interesting anticancer profile with the ability to exert cytotoxic effects via induction of different cell death modalities.
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Affiliation(s)
- Naira F Z Schneider
- Laboratorio de Virologia Applicada, Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Claudia Cerella
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, Luxembourg, Luxembourg.,Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Jin-Young Lee
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Aloran Mazumder
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Kyung Rok Kim
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Annelise de Carvalho
- Laboratorio de Virologia Applicada, Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Jennifer Munkert
- Department of Biology, Friedrich-Alexander Universität, Erlangen-Nürnberg, Erlangen, Germany
| | - Rodrigo M Pádua
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Wolfgang Kreis
- Department of Biology, Friedrich-Alexander Universität, Erlangen-Nürnberg, Erlangen, Germany
| | - Kyu-Won Kim
- SNU-Harvard Neurovascular Protection Center, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea
| | | | - Mario Dicato
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg, Luxembourg, Luxembourg
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul, South Korea
| | - Byung Woo Han
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Fernão C Braga
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Cláudia M O Simões
- Laboratorio de Virologia Applicada, Departamento de Ciências Farmacêuticas, Centro de Ciências da Saúde, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | - Marc Diederich
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, South Korea
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Lee JY, Talhi O, Jang D, Cerella C, Gaigneaux A, Kim KW, Lee JW, Dicato M, Bachari K, Han BW, Silva AMS, Orlikova B, Diederich M. Cytostatic hydroxycoumarin OT52 induces ER/Golgi stress and STAT3 inhibition triggering non-canonical cell death and synergy with BH3 mimetics in lung cancer. Cancer Lett 2017; 416:94-108. [PMID: 29247826 DOI: 10.1016/j.canlet.2017.12.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Accepted: 12/05/2017] [Indexed: 01/02/2023]
Abstract
Coumarins are natural compounds with antioxidant, anti-inflammatory and anti-cancer potential known to modulate inflammatory pathways. Here, non-toxic biscoumarin OT52 strongly inhibited proliferation of non-small cell lung cancer cells with KRAS mutations, inhibited stem-like characteristics by reducing aldehyde dehydrogenase expression and abrogated spheroid formation capacity. This cytostatic effect was characterized by cell cycle arrest and onset of senescence concomitant with endoplasmic reticulum and Golgi stress, leading to metabolic alterations. Mechanistically, this cellular response was associated with the novel capacity of biscoumarin OT52 to inhibit STAT3 transactivation and expression of its target genes linked to proliferation. These results were validated by computational docking of OT52 to the STAT3 DNA-binding domain. Combination treatments of OT52 with subtoxic concentrations of Bcl-xL and Mcl-1-targeting BH3 protein inhibitors triggered synergistic immunogenic cell death validated in colony formation assays as well as in vivo by zebrafish xenografts.
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Affiliation(s)
- Jin-Young Lee
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08626, Republic of Korea
| | - Oualid Talhi
- Department of Chemistry & QOPNA, University of Aveiro, 3810-193, Aveiro, Portugal; Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques - CRAPC, B. P. 384, Bou-Ismail, 42004 Tipaza, Algeria
| | - Dongman Jang
- Research Institute of Pharmaceutical Science, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08626, Republic of Korea
| | - Claudia Cerella
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08626, Republic of Korea; Laboratoire de Biologie Moléculaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg
| | - Anthoula Gaigneaux
- Laboratoire de Biologie Moléculaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg
| | - Kyu-Won Kim
- SNU-Harvard Neurovascular Protection Center, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Republic of Korea
| | - Jung Weon Lee
- Department of Pharmacy, Medicinal Bioconvergence Research Center, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Mario Dicato
- Laboratoire de Biologie Moléculaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg
| | - Khaldoun Bachari
- Centre de Recherche Scientifique et Technique en Analyses Physico-Chimiques - CRAPC, B. P. 384, Bou-Ismail, 42004 Tipaza, Algeria
| | - Byung Woo Han
- Research Institute of Pharmaceutical Science, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08626, Republic of Korea
| | - Artur M S Silva
- Department of Chemistry & QOPNA, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Barbora Orlikova
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08626, Republic of Korea; Laboratoire de Biologie Moléculaire du Cancer, Hôpital Kirchberg, 9, rue Edward Steichen, L-2540, Luxembourg
| | - Marc Diederich
- Department of Pharmacy, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08626, Republic of Korea.
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35
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Cha KJ, Kong SY, Lee JS, Kim HW, Shin JY, La M, Han BW, Kim DS, Kim HJ. Cell density-dependent differential proliferation of neural stem cells on omnidirectional nanopore-arrayed surface. Sci Rep 2017; 7:13077. [PMID: 29026125 PMCID: PMC5638797 DOI: 10.1038/s41598-017-13372-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 09/22/2017] [Indexed: 11/09/2022] Open
Abstract
Recently, the importance of surface nanotopography in the determination of stem cell fate and behavior has been revealed. In the current study, we generated polystyrene cell-culture dishes with an omnidirectional nanopore arrayed surface (ONAS) (diameter: 200 nm, depth: 500 nm, center-to-center distance: 500 nm) and investigated the effects of nanotopography on rat neural stem cells (NSCs). NSCs cultured on ONAS proliferated better than those on the flat surface when cell density was low and showed less spontaneous differentiation during proliferation in the presence of mitogens. Interestingly, NSCs cultured on ONAS at clonal density demonstrated a propensity to generate neurospheres, whereas those on the flat surface migrated out, proliferated as individuals, and spread out to attach to the surface. However, the differential patterns of proliferation were cell density-dependent since the distinct phenomena were lost when cell density was increased. ONAS modulated cytoskeletal reorganization and inhibited formation of focal adhesion, which is generally observed in NSCs grown on flat surfaces. ONAS appeared to reinforce NSC-NSC interaction, restricted individual cell migration and prohibited NSC attachment to the nanopore surface. These data demonstrate that ONAS maintains NSCs as undifferentiated while retaining multipotency and is a better topography for culturing low density NSCs.
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Affiliation(s)
- Kyoung Je Cha
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), San 31 Hyoja-dong Nam-gu, Pohang, 790-784, South Korea.,Ultimate Fabrication Technology Group, Korea Institute of Industrial Technology (KITECH), Techno sunhwan-ro Yuga-myeon Dalseong-gun, Deagu, 711-880, South Korea
| | - Sun-Young Kong
- Laboratory of Molecular and Stem Cell Pharmacology, College of Pharmacy, Chung-Ang University, 221 Heukseok-dong Dongjak-gu, Seoul, 156-756, South Korea
| | - Ji Soo Lee
- Laboratory of Molecular and Stem Cell Pharmacology, College of Pharmacy, Chung-Ang University, 221 Heukseok-dong Dongjak-gu, Seoul, 156-756, South Korea
| | - Hyung Woo Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), San 31 Hyoja-dong Nam-gu, Pohang, 790-784, South Korea
| | - Jae-Yeon Shin
- Laboratory of Molecular and Stem Cell Pharmacology, College of Pharmacy, Chung-Ang University, 221 Heukseok-dong Dongjak-gu, Seoul, 156-756, South Korea
| | - Moonwoo La
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), San 31 Hyoja-dong Nam-gu, Pohang, 790-784, South Korea.,Molds & Dies R&D Group, Korea Institute of Industrial Technology (KITECH), 156 Gaetbeol-ro, Yeonsu-gu, Incheon, 406-840, South Korea
| | - Byung Woo Han
- Department of Biochemistry, College of pharmacy, Seoul National University, San 56-1 Sillim-dong Gwanak-gu, Seoul, 151-742, South Korea
| | - Dong Sung Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology (POSTECH), San 31 Hyoja-dong Nam-gu, Pohang, 790-784, South Korea.
| | - Hyun-Jung Kim
- Laboratory of Molecular and Stem Cell Pharmacology, College of Pharmacy, Chung-Ang University, 221 Heukseok-dong Dongjak-gu, Seoul, 156-756, South Korea.
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Schnekenburger M, Goffin E, Lee JY, Jang JY, Mazumder A, Ji S, Rogister B, Bouider N, Lefranc F, Miklos W, Mathieu V, de Tullio P, Kim KW, Dicato M, Berger W, Han BW, Kiss R, Pirotte B, Diederich M. Discovery and Characterization of R/S-N-3-Cyanophenyl-N'-(6-tert-butoxycarbonylamino-3,4-dihydro-2,2-dimethyl-2H-1-benzopyran-4-yl)urea, a New Histone Deacetylase Class III Inhibitor Exerting Antiproliferative Activity against Cancer Cell Lines. J Med Chem 2017; 60:4714-4733. [PMID: 28475330 DOI: 10.1021/acs.jmedchem.7b00533] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A new series of N-aryl-N'-3,4-dihydro-2,2-dimethyl-2H-1-benzopyran-4-yl)ureas bearing an alkoxycarbonylamino group at the 6-position were synthesized and examined as putative anticancer agents targeting sirtuins in glioma cells. On the basis of computational docking combined to in vitro sirtuin 1/2 inhibition assays, we selected compound 18 [R/S-N-3-cyanophenyl-N'-(6-tert-butoxycarbonylamino-3,4-dihydro-2,2-dimethyl-2H-1-benzopyran-4-yl)urea] which displays a potent antiproliferative activity on various glioma cell types, assessed by quantitative videomicroscopy, eventually triggering senescence. The impact on normal glial cells was lower with a selectivity index of >10. Furthermore, human U373 and Hs683 glioblastoma cell lines served to demonstrate the inhibitory activity of 18 against histone deacetylase (HDAC) class III sirtuins 1 and 2 (SIRT1/2) by quantifying acetylation levels of histone and non-histone proteins. The translational potential of 18 was validated by an NCI-60 cell line screen and validation of growth inhibition of drug resistant cancer cell models. Eventually, the anticancer potential of 18 was validated in 3D glioblastoma spheroids and in vivo by zebrafish xenografts. In summary, compound 18 is the first representative of a new class of SIRT inhibitors opening new perspectives in the medicinal chemistry of HDAC inhibitors.
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Affiliation(s)
- Michael Schnekenburger
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg , 9, Rue Edward Steichen, L-2540 Luxembourg, Luxembourg
| | - Eric Goffin
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège , 4000 Liège, Belgium
| | - Jin-Young Lee
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
| | - Jun Young Jang
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
| | - Aloran Mazumder
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
| | - Seungwon Ji
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
| | - Bernard Rogister
- Nervous System Diseases and Treatment, GIGA-Neurosciences, University of Liège , 4000 Liège, Belgium
| | - Nafila Bouider
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège , 4000 Liège, Belgium
| | - Florence Lefranc
- Service de Neurochirurgie, Hôpital Erasme, Université Libre de Bruxelles, 1070 Brussels, Belgium
| | - Walter Miklos
- Department of Medicine I, Comprehensive Cancer Center and Institute of Cancer Research, Medical University of Vienna , 1090 Vienna, Austria
| | - Véronique Mathieu
- Laboratoire de Cancérologie et de Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles , 1050 Brussels, Belgium
| | - Pascal de Tullio
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège , 4000 Liège, Belgium
| | - Kyu-Won Kim
- SNU-Harvard Neurovascular Protection Center, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University , Seoul 151-742, Korea
| | - Mario Dicato
- Laboratoire de Biologie Moléculaire et Cellulaire du Cancer, Hôpital Kirchberg , 9, Rue Edward Steichen, L-2540 Luxembourg, Luxembourg
| | - Walter Berger
- Department of Medicine I, Comprehensive Cancer Center and Institute of Cancer Research, Medical University of Vienna , 1090 Vienna, Austria
| | - Byung Woo Han
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
| | - Robert Kiss
- Laboratoire de Cancérologie et de Toxicologie Expérimentale, Faculté de Pharmacie, Université Libre de Bruxelles , 1050 Brussels, Belgium
| | - Bernard Pirotte
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège , 4000 Liège, Belgium
| | - Marc Diederich
- Department of Pharmacy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University , 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea
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Chun SE, Thakkar N, Oh Y, Park JE, Han S, Ryoo G, Hahn H, Maeng SH, Lim YR, Han BW, Lee W. The N-terminal region of organic anion transporting polypeptide 1B3 (OATP1B3) plays an essential role in regulating its plasma membrane trafficking. Biochem Pharmacol 2017; 131:98-105. [PMID: 28216016 DOI: 10.1016/j.bcp.2017.02.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 02/14/2017] [Indexed: 10/20/2022]
Abstract
Organic anion transporting polypeptide 1B3 (OATP1B3) is a major influx transporter mediating the hepatic uptake of various endogenous substrates as well as clinically important drugs such as statins and anticancer drugs. However, molecular mechanisms controlling the membrane trafficking of OATP1B3 have been largely unknown. Several reports recently indicated the presence of a distinct, cancer-type OATP1B3 variant lacking the N-terminal 28 amino acids compared to OATP1B3 expressed in non-malignant hepatocytes. Interestingly, the cancer-type OATP1B3 variant is located predominantly in the cytoplasm, implicating the involvement of the N-terminal region of OATP1B3 in its membrane trafficking. In the current study, we set out to experimentally validate the importance of the N-terminal region of OATP1B3 and to identify responsible sequence motif(s) in that region. A number of truncation or point mutants of OATP1B3 were transiently expressed in HEK293T, HCT-8 or MDCK II cells and their expression in cytoplasmic and surface membrane fractions were analyzed by immunoblotting. Our results indicated that the N-terminal sequence of OATP1B3, in particular, at the amino acid positions between 12 and 28, may be indispensable in its membrane trafficking. Moreover, our results using a fusion construct indicated that the first 50 amino acids of OATP1B3 are sufficient for its membrane localization. The importance of the N-terminal region in membranous localization was shared among the other OATP1B subfamily members, OATP1B1 and rat Oatp1b2. Our efforts to identify the responsible amino acid(s) or structure motif(s) in the N-terminal region did not pinpoint individual amino acids or motifs with putative secondary structures. Our current findings however demonstrate that the N-terminal region is important for the membrane localization of the OATP1B subfamily members and should facilitate future investigations of the mechanisms involved in the regulation and membrane trafficking of these important transporter proteins.
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Affiliation(s)
- Se-Eun Chun
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul, Republic of Korea
| | - Nilay Thakkar
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY, USA
| | - Yunseok Oh
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul, Republic of Korea
| | - Ji Eun Park
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul, Republic of Korea
| | - Songhee Han
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul, Republic of Korea
| | - Gongmi Ryoo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul, Republic of Korea
| | - Hyunggu Hahn
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul, Republic of Korea
| | - Sang Hyun Maeng
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul, Republic of Korea
| | - Young-Ran Lim
- Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea
| | - Byung Woo Han
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul, Republic of Korea
| | - Wooin Lee
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-Gu, Seoul, Republic of Korea.
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38
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Chun SE, Thakkar N, Park JE, Han S, Hahn H, Maeng SH, Lim YR, Han BW, Lee W. The N-terminal region of organic anion transporting polypeptide 1B3 (OATP1B3) plays an essential role in regulating its plasma membrane trafficking. Drug Metab Pharmacokinet 2017. [DOI: 10.1016/j.dmpk.2016.10.397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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39
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Ahn YH, Park S, Choi JJ, Park BK, Rhee KH, Kang E, Ahn S, Lee CH, Lee JS, Inn KS, Cho ML, Park SH, Park K, Park HJ, Lee JH, Park JW, Kwon NH, Shim H, Han BW, Kim P, Lee JY, Jeon Y, Huh JW, Jin M, Kim S. Secreted tryptophanyl-tRNA synthetase as a primary defence system against infection. Nat Microbiol 2016; 2:16191. [PMID: 27748732 DOI: 10.1038/nmicrobiol.2016.191] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/02/2016] [Indexed: 11/09/2022]
Abstract
The N-terminal truncated form of a protein synthesis enzyme, tryptophanyl-tRNA synthetase (mini-WRS), is secreted as an angiostatic ligand. However, the secretion and function of the full-length WRS (FL-WRS) remain unknown. Here, we report that the FL-WRS, but not mini-WRS, is rapidly secreted upon pathogen infection to prime innate immunity. Blood levels of FL-WRS were increased in sepsis patients, but not in those with sterile inflammation. FL-WRS was secreted from monocytes and directly bound to macrophages via a toll-like receptor 4 (TLR4)-myeloid differentiation factor 2 (MD2) complex to induce phagocytosis and chemokine production. Administration of FL-WRS into Salmonella typhimurium-infected mice reduced the levels of bacteria and improved mouse survival, whereas its titration with the specific antibody aggravated the infection. The N-terminal 154-amino-acid eukaryote-specific peptide of WRS was sufficient to recapitulate FL-WRS activity and its interaction mode with TLR4-MD2 is now suggested. Based on these results, secretion of FL-WRS appears to work as a primary defence system against infection, acting before full activation of innate immunity.
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Affiliation(s)
- Young Ha Ahn
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunyoung Park
- College of Korean Medicine, Daejeon University, Daejeon 34520, Republic of Korea
| | - Jeong June Choi
- College of Korean Medicine, Daejeon University, Daejeon 34520, Republic of Korea
| | - Bo-Kyung Park
- College of Korean Medicine, Daejeon University, Daejeon 34520, Republic of Korea
| | - Kyung Hee Rhee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Eunjoo Kang
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon 16229, Republic of Korea
| | - Soyeon Ahn
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jong Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Kyung-Soo Inn
- Department of Pharmaceutical Science, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Mi-La Cho
- Divison of Rheumatology, Department of Internal Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Sung-Hwan Park
- The Rheumatism Research Center, Catholic Research Institute of Medical Science, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Kyunghee Park
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Hye Jung Park
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jae-Hyun Lee
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Jung-Won Park
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Nam Hoon Kwon
- Medicinal Bioconvergence Research Center, Seoul National University, Suwon 16229, Republic of Korea
| | - Hyunbo Shim
- Departments of Bioinspired Science and Life Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Pilhan Kim
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Joo-Youn Lee
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.,Korea Chemical Bank, Korea Research Institute of Chemical Technology, Daejeon 34114, Republic of Korea
| | - Youngho Jeon
- College of Pharmacy, Korea University, Sejong 30019, Republic of Korea
| | - Jin Won Huh
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Mirim Jin
- College of Korean Medicine, Daejeon University, Daejeon 34520, Republic of Korea
| | - Sunghoon Kim
- College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea.,Medicinal Bioconvergence Research Center, Seoul National University, Suwon 16229, Republic of Korea
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40
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Han BW, Li ZH, Liu SF, Han HB, Dong SJ, Zou HJ, Sun RF, Jia J. A comprehensive review of microRNA-related polymorphisms in gastric cancer. Genet Mol Res 2016; 15:gmr8289. [PMID: 27421013 DOI: 10.4238/gmr.15028289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNA molecules of about 22 nucleotides in length. miRNAs are highly conserved in both plants and animals, and function as gene regulators by binding to the 3'-untranslated region of target mRNAs for cleavage and/or translational repression. miRNA biogenesis, stability, and regulation of expression are strongly sequence dependent. Sequence variants, such as single nucleotide polymorphisms (SNPs) in pri-miRNA, pre-miRNA, promoter regions, or miRNA-target sites, can influence miRNA function, thereby contributing to the pathological features of human disease. In this review, we focus on miRNA-related SNPs in gastric cancer and comprehensively analyze some commonly studied SNPs.
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Affiliation(s)
- B W Han
- Secondary Department of General Surgery, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - Z H Li
- Secondary Department of General Surgery, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - S F Liu
- Secondary Department of General Surgery, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - H B Han
- Secondary Department of General Surgery, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - S J Dong
- Secondary Department of General Surgery, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - H J Zou
- Central Laboratory, Yunnan University of Chinese Traditional Medicine, Kunming, Yunnan, China
| | - R F Sun
- Central Laboratory, Yunnan University of Chinese Traditional Medicine, Kunming, Yunnan, China
| | - J Jia
- Center for Molecular Medicine, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
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41
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Ha VT, Kien VT, Binh LH, Tien VD, My NTT, Nam NH, Baltas M, Hahn H, Han BW, Thao DT, Vu TK. Design, synthesis and biological evaluation of novel hydroxamic acids bearing artemisinin skeleton. Bioorg Chem 2016; 66:63-71. [DOI: 10.1016/j.bioorg.2016.03.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/16/2016] [Accepted: 03/16/2016] [Indexed: 11/29/2022]
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42
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Park SH, Kim HS, Park MS, Moon S, Song MK, Park HS, Hahn H, Kim SJ, Bae E, Kim HJ, Han BW. Structure and Stability of the Dimeric Triosephosphate Isomerase from the Thermophilic Archaeon Thermoplasma acidophilum. PLoS One 2015; 10:e0145331. [PMID: 26709515 PMCID: PMC4692482 DOI: 10.1371/journal.pone.0145331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/02/2015] [Indexed: 01/03/2023] Open
Abstract
Thermoplasma acidophilum is a thermophilic archaeon that uses both non-phosphorylative Entner-Doudoroff (ED) pathway and Embden-Meyerhof-Parnas (EMP) pathway for glucose degradation. While triosephosphate isomerase (TPI), a well-known glycolytic enzyme, is not involved in the ED pathway in T. acidophilum, it has been considered to play an important role in the EMP pathway. Here, we report crystal structures of apo- and glycerol-3-phosphate-bound TPI from T. acidophilum (TaTPI). TaTPI adopts the canonical TIM-barrel fold with eight α-helices and parallel eight β-strands. Although TaTPI shares ~30% sequence identity to other TPIs from thermophilic species that adopt tetrameric conformation for enzymatic activity in their harsh physiological environments, TaTPI exists as a dimer in solution. We confirmed the dimeric conformation of TaTPI by analytical ultracentrifugation and size-exclusion chromatography. Helix 5 as well as helix 4 of thermostable tetrameric TPIs have been known to play crucial roles in oligomerization, forming a hydrophobic interface. However, TaTPI contains unique charged-amino acid residues in the helix 5 and adopts dimer conformation. TaTPI exhibits the apparent Td value of 74.6°C and maintains its overall structure with some changes in the secondary structure contents at extremely acidic conditions (pH 1–2). Based on our structural and biophysical analyses of TaTPI, more compact structure of the protomer with reduced length of loops and certain patches on the surface could account for the robust nature of Thermoplasma acidophilum TPI.
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Affiliation(s)
- Sang Ho Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Hyoun Sook Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Mi Seul Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Sojin Moon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Mi Kyung Song
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Han Su Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Hyunggu Hahn
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Chonnam, Korea
| | - Euiyoung Bae
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
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Lee JH, Park KM, Han DJ, Bang NY, Kim DH, Na H, Lim S, Kim TB, Kim DG, Kim HJ, Chung Y, Sung SH, Surh YJ, Kim S, Han BW. PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine. PLoS One 2015; 10:e0142624. [PMID: 26555441 PMCID: PMC4640719 DOI: 10.1371/journal.pone.0142624] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 10/23/2015] [Indexed: 01/10/2023] Open
Abstract
Despite the growing attention given to Traditional Medicine (TM) worldwide, there is no well-known, publicly available, integrated bio-pharmacological Traditional Korean Medicine (TKM) database for researchers in drug discovery. In this study, we have constructed PharmDB-K, which offers comprehensive information relating to TKM-associated drugs (compound), disease indication, and protein relationships. To explore the underlying molecular interaction of TKM, we integrated fourteen different databases, six Pharmacopoeias, and literature, and established a massive bio-pharmacological network for TKM and experimentally validated some cases predicted from the PharmDB-K analyses. Currently, PharmDB-K contains information about 262 TKMs, 7,815 drugs, 3,721 diseases, 32,373 proteins, and 1,887 side effects. One of the unique sets of information in PharmDB-K includes 400 indicator compounds used for standardization of herbal medicine. Furthermore, we are operating PharmDB-K via phExplorer (a network visualization software) and BioMart (a data federation framework) for convenient search and analysis of the TKM network. Database URL: http://pharmdb-k.org, http://biomart.i-pharm.org.
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Affiliation(s)
- Ji-Hyun Lee
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 152–742, Republic of Korea
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151–742, Republic of Korea
- Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443–270, Republic of Korea
| | - Kyoung Mii Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151–742, Republic of Korea
- Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443–270, Republic of Korea
| | - Dong-Jin Han
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 152–742, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151–742, Republic of Korea
| | - Nam Young Bang
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 152–742, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151–742, Republic of Korea
| | - Do-Hee Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151–742, Republic of Korea
| | - Hyeongjin Na
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151–742, Republic of Korea
| | - Semi Lim
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 152–742, Republic of Korea
| | - Tae Bum Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151–742, Republic of Korea
| | - Dae Gyu Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 152–742, Republic of Korea
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul 156–756, Republic of Korea
| | - Yeonseok Chung
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151–742, Republic of Korea
| | - Sang Hyun Sung
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151–742, Republic of Korea
| | - Young-Joon Surh
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151–742, Republic of Korea
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, Seoul National University, Seoul 152–742, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151–742, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151–742, Republic of Korea
- Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443–270, Republic of Korea
- * E-mail:
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Kim HS, Im HN, An DR, Yoon JY, Jang JY, Mobashery S, Hesek D, Lee M, Yoo J, Cui M, Choi S, Kim C, Lee NK, Kim SJ, Kim JY, Bang G, Han BW, Lee BI, Yoon HJ, Suh SW. The Cell Shape-determining Csd6 Protein from Helicobacter pylori Constitutes a New Family of L,D-Carboxypeptidase. J Biol Chem 2015; 290:25103-17. [PMID: 26306031 PMCID: PMC4599014 DOI: 10.1074/jbc.m115.658781] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Indexed: 01/01/2023] Open
Abstract
Helicobacter pylori causes gastrointestinal diseases, including gastric cancer. Its high motility in the viscous gastric mucosa facilitates colonization of the human stomach and depends on the helical cell shape and the flagella. In H. pylori, Csd6 is one of the cell shape-determining proteins that play key roles in alteration of cross-linking or by trimming of peptidoglycan muropeptides. Csd6 is also involved in deglycosylation of the flagellar protein FlaA. To better understand its function, biochemical, biophysical, and structural characterizations were carried out. We show that Csd6 has a three-domain architecture and exists as a dimer in solution. The N-terminal domain plays a key role in dimerization. The middle catalytic domain resembles those of l,d-transpeptidases, but its pocket-shaped active site is uniquely defined by the four loops I to IV, among which loops I and III show the most distinct variations from the known l,d-transpeptidases. Mass analyses confirm that Csd6 functions only as an l,d-carboxypeptidase and not as an l,d-transpeptidase. The d-Ala-complexed structure suggests possible binding modes of both the substrate and product to the catalytic domain. The C-terminal nuclear transport factor 2-like domain possesses a deep pocket for possible binding of pseudaminic acid, and in silico docking supports its role in deglycosylation of flagellin. On the basis of these findings, it is proposed that H. pylori Csd6 and its homologs constitute a new family of l,d-carboxypeptidase. This work provides insights into the function of Csd6 in regulating the helical cell shape and motility of H. pylori.
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Affiliation(s)
- Hyoun Sook Kim
- From the Departments of Chemistry and Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ha Na Im
- Biophysics and Chemical Biology, College of Natural Sciences, and
| | - Doo Ri An
- Biophysics and Chemical Biology, College of Natural Sciences, and
| | - Ji Young Yoon
- Biophysics and Chemical Biology, College of Natural Sciences, and
| | | | - Shahriar Mobashery
- the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Dusan Hesek
- the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Mijoon Lee
- the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Jakyung Yoo
- the National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Minghua Cui
- the National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Sun Choi
- the National Leading Research Laboratory of Molecular Modeling and Drug Design, College of Pharmacy, Graduate School of Pharmaceutical Sciences, and Global Top 5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Cheolhee Kim
- the Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Nam Ki Lee
- the Department of Physics, POSTECH, Pohang 790-784, Republic of Korea
| | - Soon-Jong Kim
- the Department of Chemistry, Mokpo National University, Chonnam 534-729, Republic of Korea
| | - Jin Young Kim
- the Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea, and
| | - Geul Bang
- the Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea, and
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Byung Il Lee
- the Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Gyeonggi 410-769, Republic of Korea
| | | | - Se Won Suh
- From the Departments of Chemistry and Biophysics and Chemical Biology, College of Natural Sciences, and
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Kim HS, Han BW, Suh SW. The cell-shape determining Csd6 protein from Helicobacter pyloriconstitutes a new family of L, D-carboxypeptidase. Acta Crystallogr A Found Adv 2015. [DOI: 10.1107/s2053273315096953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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46
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Kim DJ, Bitto E, Bingman CA, Kim HJ, Han BW, Phillips GN. Crystal structure of the protein At3g01520, a eukaryotic universal stress protein-like protein from Arabidopsis thaliana in complex with AMP. Proteins 2015; 83:1368-73. [PMID: 25921306 PMCID: PMC4624624 DOI: 10.1002/prot.24821] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/20/2015] [Accepted: 04/24/2015] [Indexed: 11/11/2022]
Abstract
Members of the universal stress protein (USP) family are conserved in a phylogenetically diverse range of prokaryotes, fungi, protists, and plants and confer abilities to respond to a wide range of environmental stresses. Arabidopsis thaliana contains 44 USP domain‐containing proteins, and USP domain is found either in a small protein with unknown physiological function or in an N‐terminal portion of a multi‐domain protein, usually a protein kinase. Here, we report the first crystal structure of a eukaryotic USP‐like protein encoded from the gene At3g01520. The crystal structure of the protein At3g01520 was determined by the single‐wavelength anomalous dispersion method and refined to an R factor of 21.8% (Rfree = 26.1%) at 2.5 Å resolution. The crystal structure includes three At3g01520 protein dimers with one AMP molecule bound to each protomer, comprising a Rossmann‐like α/β overall fold. The bound AMP and conservation of residues in the ATP‐binding loop suggest that the protein At3g01520 also belongs to the ATP‐binding USP subfamily members. Proteins 2015; 83:1368–1373. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Do Jin Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 151-742, Korea
| | - Eduard Bitto
- Department of Chemistry and Biochemistry, Georgian Court University, Lakewood, New Jersey, 08701
| | - Craig A Bingman
- Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Hyun-Jung Kim
- Laboratory of Stem Cell and Molecular Pharmacology, College of Pharmacy, Chung-Ang University, Seoul, 156-756, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, 151-742, Korea
| | - George N Phillips
- Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison, Wisconsin, 53706.,BioSciences at Rice and Department of Chemistry, Rice University, Houston, Texas, 77251
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47
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Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G, Bardou P, Beck T, Blake A, Bonierbale M, Brookes AJ, Bucci G, Buetti I, Burge S, Cabau C, Carlson JW, Chelala C, Chrysostomou C, Cittaro D, Collin O, Cordova R, Cutts RJ, Dassi E, Di Genova A, Djari A, Esposito A, Estrella H, Eyras E, Fernandez-Banet J, Forbes S, Free RC, Fujisawa T, Gadaleta E, Garcia-Manteiga JM, Goodstein D, Gray K, Guerra-Assunção JA, Haggarty B, Han DJ, Han BW, Harris T, Harshbarger J, Hastings RK, Hayes RD, Hoede C, Hu S, Hu ZL, Hutchins L, Kan Z, Kawaji H, Keliet A, Kerhornou A, Kim S, Kinsella R, Klopp C, Kong L, Lawson D, Lazarevic D, Lee JH, Letellier T, Li CY, Lio P, Liu CJ, Luo J, Maass A, Mariette J, Maurel T, Merella S, Mohamed AM, Moreews F, Nabihoudine I, Ndegwa N, Noirot C, Perez-Llamas C, Primig M, Quattrone A, Quesneville H, Rambaldi D, Reecy J, Riba M, Rosanoff S, Saddiq AA, Salas E, Sallou O, Shepherd R, Simon R, Sperling L, Spooner W, Staines DM, Steinbach D, Stone K, Stupka E, Teague JW, Dayem Ullah AZ, Wang J, Ware D, Wong-Erasmus M, Youens-Clark K, Zadissa A, Zhang SJ, Kasprzyk A. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res 2015; 43:W589-98. [PMID: 25897122 PMCID: PMC4489294 DOI: 10.1093/nar/gkv350] [Citation(s) in RCA: 491] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 04/02/2015] [Indexed: 01/17/2023] Open
Abstract
The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.
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Affiliation(s)
- Damian Smedley
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Syed Haider
- The Weatherall Institute Of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Steffen Durinck
- Genentech, Inc. 1 DNA Way South San Francisco, CA 94080, USA
| | - Luca Pandini
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Paolo Provero
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Dept of Molecular Biotechnology and Health Sciences University of Turin, Italy
| | - James Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Olivier Arnaiz
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - Mohammad Hamza Awedh
- Department of Electrical and Computer Engineering, Faculty of Engineering, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Richard Baldock
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Giulia Barbiera
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | | | - Tim Beck
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Andrew Blake
- MRC Harwell, Harwell Science and Innovation Campus, Oxfordshire, OX11 0RD, UK
| | | | - Anthony J Brookes
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Gabriele Bucci
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Iwan Buetti
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Sarah Burge
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | | | | | - Claude Chelala
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | | | - Davide Cittaro
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | | | - Raul Cordova
- International Potato Center (CIP), Lima, 1558, Peru
| | - Rosalind J Cutts
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Erik Dassi
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Alex Di Genova
- Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Beauchef 851, 7th floor, Chile
| | - Anis Djari
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | | | | | - Eduardo Eyras
- Catalan Institute for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, E-08010 Barcelona, Spain Universitat Pompeu Fabra, Dr Aiguader 88 E-08003 Barcelona, Spain
| | | | - Simon Forbes
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Robert C Free
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | | | - Emanuela Gadaleta
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jose M Garcia-Manteiga
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - David Goodstein
- Department of Energy, Joint Genome Institute, Walnut Creek, USA
| | - Kristian Gray
- HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - José Afonso Guerra-Assunção
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Bernard Haggarty
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Dong-Jin Han
- Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443-270, Republic of Korea
| | - Todd Harris
- Ontario Institute for Cancer Research, Toronto, M5G 0A3, Canada
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan
| | - Robert K Hastings
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Richard D Hayes
- Department of Energy, Joint Genome Institute, Walnut Creek, USA
| | - Claire Hoede
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Shen Hu
- School of Dentistry and Dental Research Institute, University of California Los Angeles (UCLA), Los Angeles, CA 90095-1668, USA
| | | | - Lucie Hutchins
- Mouse Genomic Informatics Group, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Zhengyan Kan
- Oncology Computational Biology, Pfizer, La Jolla, USA
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies (CLST), Division of Genomic Technologies (DGT), Kanagawa, 230-0045, Japan RIKEN Preventive Medicine and Diagnosis Innovation Program, Saitama 351-0198, Japan
| | - Aminah Keliet
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Arnaud Kerhornou
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Sunghoon Kim
- Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Department of Molecular Medicine and Biopharmaceutical Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Rhoda Kinsella
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Christophe Klopp
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Lei Kong
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China
| | - Daniel Lawson
- VectorBase, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Dejan Lazarevic
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Ji-Hyun Lee
- Medicinal Bioconvergence Research Center, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea Information Center for Bio-pharmacological Network, Seoul National University, Suwon 443-270, Republic of Korea
| | - Thomas Letellier
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Chuan-Yun Li
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Pietro Lio
- Computer Laboratory, University of Cambridge, Cambridge, CB3 0FD, UK
| | - Chu-Jun Liu
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jie Luo
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alejandro Maass
- Center for Mathematical Modeling and Center for Genome Regulation, University of Chile, Beauchef 851, 7th floor, Chile Department of Mathematical Engineering, University of Chile, Av. Beauchef 851, 5th floor, Santiago, Chile
| | - Jerome Mariette
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Thomas Maurel
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stefania Merella
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Azza Mostafa Mohamed
- Departament of Biochemistry, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Ibounyamine Nabihoudine
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | - Nelson Ndegwa
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, PO Box 281, 17177 Stockholm, Sweden
| | - Céline Noirot
- Plate-forme bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRA, Castanet-Tolosan, France
| | | | - Michael Primig
- Inserm U1085 IRSET, University of Rennes 1, 35042 Rennes, France
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Hadi Quesneville
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Davide Rambaldi
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | | | - Michela Riba
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Steven Rosanoff
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Amna Ali Saddiq
- Department of Biological Sciences, Faculty of Science for Girls, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Elisa Salas
- International Potato Center (CIP), Lima, 1558, Peru
| | | | - Rebecca Shepherd
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | | | - Linda Sperling
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris Sud, 1 avenue de la terrasse, 91198 Gif sur Yvette, France
| | - William Spooner
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA Eagle Genomics Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Daniel M Staines
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Delphine Steinbach
- INRA URGI Centre de Versailles, bâtiment 18 Route de Saint Cyr 78026 Versailles, France
| | - Kevin Stone
- Mouse Genomic Informatics Group, The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Elia Stupka
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Jon W Teague
- Wellcome Trust Sanger Institute, Welcome Trust Genome Campus, Hinxton, CB10 1SD, UK
| | - Abu Z Dayem Ullah
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jun Wang
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, 100871, P.R. China
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Marie Wong-Erasmus
- Human Longevity, Inc. 10835 Road to the Cure 140 San Diego, CA 92121, USA
| | - Ken Youens-Clark
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Amonida Zadissa
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Shi-Jian Zhang
- Institute of Molecular Medicine, Peking University, Beijing, China
| | - Arek Kasprzyk
- Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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Park MS, Bitto E, Kim KR, Bingman CA, Miller MD, Kim HJ, Han BW, Phillips GN. Crystal structure of human protein N-terminal glutamine amidohydrolase, an initial component of the N-end rule pathway. PLoS One 2014; 9:e111142. [PMID: 25356641 PMCID: PMC4214742 DOI: 10.1371/journal.pone.0111142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 09/28/2014] [Indexed: 11/22/2022] Open
Abstract
The N-end rule states that half-life of protein is determined by their N-terminal amino acid residue. N-terminal glutamine amidohydrolase (Ntaq) converts N-terminal glutamine to glutamate by eliminating the amine group and plays an essential role in the N-end rule pathway for protein degradation. Here, we report the crystal structure of human Ntaq1 bound with the N-terminus of a symmetry-related Ntaq1 molecule at 1.5 Å resolution. The structure reveals a monomeric globular protein with alpha-beta-alpha three-layer sandwich architecture. The catalytic triad located in the active site, Cys-His-Asp, is highly conserved among Ntaq family and transglutaminases from diverse organisms. The N-terminus of a symmetry-related Ntaq1 molecule bound in the substrate binding cleft and the active site suggest possible substrate binding mode of hNtaq1. Based on our crystal structure of hNtaq1 and docking study with all the tripeptides with N-terminal glutamine, we propose how the peptide backbone recognition patch of hNtaq1 forms nonspecific interactions with N-terminal peptides of substrate proteins. Upon binding of a substrate with N-terminal glutamine, active site catalytic triad mediates the deamination of the N-terminal residue to glutamate by a mechanism analogous to that of cysteine proteases.
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Affiliation(s)
- Mi Seul Park
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Eduard Bitto
- Department of Chemistry and Biochemistry, Georgian Court University, Lakewood, New Jersey, United States of America
| | - Kyung Rok Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Craig A. Bingman
- Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
| | - Mitchell D. Miller
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
| | - Hyun-Jung Kim
- College of Pharmacy, Chung-Ang University, Seoul, Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Korea
- * E-mail: (BWH); (GNP)
| | - George N. Phillips
- Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin Madison, Madison, Wisconsin, United States of America
- Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America
- * E-mail: (BWH); (GNP)
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Kim HS, Kim J, Im HN, An DR, Lee M, Hesek D, Mobashery S, Kim JY, Cho K, Yoon HJ, Han BW, Lee BI, Suh SW. Structural basis for the recognition of muramyltripeptide by Helicobacter pylori Csd4, a D,L-carboxypeptidase controlling the helical cell shape. ACTA ACUST UNITED AC 2014; 70:2800-12. [PMID: 25372672 PMCID: PMC4220969 DOI: 10.1107/s1399004714018732] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 08/18/2014] [Indexed: 01/01/2023]
Abstract
H. pylori Csd4 (HP1075), together with other peptidoglycan hydrolases, plays an important role in determining the helical cell shape. Its crystal structure has been determined in three different forms. Helicobacter pylori infection causes a variety of gastrointestinal diseases, including peptic ulcers and gastric cancer. Its colonization of the gastric mucosa of the human stomach is a prerequisite for survival in the stomach. Colonization depends on its motility, which is facilitated by the helical shape of the bacterium. In H. pylori, cross-linking relaxation or trimming of peptidoglycan muropeptides affects the helical cell shape. Csd4 has been identified as one of the cell shape-determining peptidoglycan hydrolases in H. pylori. It is a Zn2+-dependent d,l-carboxypeptidase that cleaves the bond between the γ-d-Glu and the mDAP of the non-cross-linked muramyltripeptide (muramyl-l-Ala-γ-d-Glu-mDAP) of the peptidoglycan to produce the muramyldipeptide (muramyl-l-Ala-γ-d-Glu) and mDAP. Here, the crystal structure of H. pylori Csd4 (HP1075 in strain 26695) is reported in three different states: the ligand-unbound form, the substrate-bound form and the product-bound form. H. pylori Csd4 consists of three domains: an N-terminal d,l-carboxypeptidase domain with a typical carboxypeptidase fold, a central β-barrel domain with a novel fold and a C-terminal immunoglobulin-like domain. The d,l-carboxypeptidase domain recognizes the substrate by interacting primarily with the terminal mDAP moiety of the muramyltripeptide. It undergoes a significant structural change upon binding either mDAP or the mDAP-containing muramyltripeptide. It it also shown that Csd5, another cell-shape determinant in H. pylori, is capable of interacting not only with H. pylori Csd4 but also with the dipeptide product of the reaction catalyzed by Csd4.
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Affiliation(s)
- Hyoun Sook Kim
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Jieun Kim
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ha Na Im
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Doo Ri An
- Department of Biophysics and Chemical Biology, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jin Young Kim
- Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea
| | - Kun Cho
- Division of Mass Spectrometry, Korea Basic Science Institute, Chungbuk 363-883, Republic of Korea
| | - Hye Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 151-742, Republic of Korea
| | - Byung Il Lee
- Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Gyeonggi 410-769, Republic of Korea
| | - Se Won Suh
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742, Republic of Korea
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50
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Lee J, Jung J, Tak MH, Wee J, Lee B, Jang Y, Chun H, Yang DJ, Yang YD, Park SH, Han BW, Hyun S, Yu J, Cho H, Hartzell HC, Oh U. Two helices in the third intracellular loop determine anoctamin 1 (TMEM16A) activation by calcium. Pflugers Arch 2014; 467:1677-87. [PMID: 25231974 PMCID: PMC4502317 DOI: 10.1007/s00424-014-1603-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 08/28/2014] [Accepted: 08/29/2014] [Indexed: 11/24/2022]
Abstract
Anoctamin 1 (ANO1)/TMEM16A is a Cl− channel activated by intracellular Ca2+ mediating numerous physiological functions. However, little is known of the ANO1 activation mechanism by Ca2+. Here, we demonstrate that two helices, “reference” and “Ca2+ sensor” helices in the third intracellular loop face each other with opposite charges. The two helices interact directly in a Ca2+-dependent manner. Positively and negatively charged residues in the two helices are essential for Ca2+-dependent activation because neutralization of these charges change the Ca2+ sensitivity. We now predict that the Ca2+ sensor helix attaches to the reference helix in the resting state, and as intracellular Ca2+ rises, Ca2+ acts on the sensor helix, which repels it from the reference helix. This Ca2+-dependent push-pull conformational change would be a key electromechanical movement for gating the ANO1 channel. Because chemical activation of ANO1 is viewed as an alternative means of rescuing cystic fibrosis, understanding its gating mechanism would be useful in developing novel treatments for cystic fibrosis.
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Affiliation(s)
- Jesun Lee
- Sensory Research Center, Creative Research Initiatives, College of Pharmacy, Seoul National University, Seoul, South Korea
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