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Ishida Y, Murata T, Kakiuchi N, Ogawa S, Kabashima K. Emergence of multiple revertant keratinocyte clones in a patient with KID syndrome. J Eur Acad Dermatol Venereol 2024; 38:e285-e287. [PMID: 37907277 DOI: 10.1111/jdv.19595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023]
Affiliation(s)
- Y Ishida
- Department of Dermatology, Kyoto University, Kyoto, Japan
| | - T Murata
- Department of Dermatology, Hyogo Medical University, Hyogo, Japan
| | - N Kakiuchi
- The Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan
| | - S Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - K Kabashima
- Department of Dermatology, Kyoto University, Kyoto, Japan
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2
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Hoyer K, Hablesreiter R, Inoue Y, Yoshida K, Briest F, Christen F, Kakiuchi N, Yoshizato T, Shiozawa Y, Shiraishi Y, Striefler JK, Bischoff S, Lohneis P, Putter H, Blau O, Keilholz U, Bullinger L, Pelzer U, Hummel M, Riess H, Ogawa S, Sinn M, Damm F. A genetically defined signature of responsiveness to erlotinib in early-stage pancreatic cancer patients: Results from the CONKO-005 trial. EBioMedicine 2021; 66:103327. [PMID: 33862582 PMCID: PMC8054140 DOI: 10.1016/j.ebiom.2021.103327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 01/05/2021] [Revised: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 12/18/2022] Open
Abstract
Background high recurrence rates of up to 75% within 2 years in pancreatic ductal adenocarcinoma (PDAC) patients resected for cure indicate a high medical need for clinical prediction tools and patient specific treatment approaches. Addition of the EGFR inhibitor erlotinib to adjuvant chemotherapy failed to improve outcome but its efficacy in some patients warrants predictors of responsiveness. Patients and Methods we analysed tumour samples from 293 R0-resected patients from the randomized, multicentre phase III CONKO-005 trial (gemcitabine ± erlotinib) with targeted sequencing, copy number, and RNA expression analyses. Findings a total of 1086 mutations and 4157 copy-number aberrations (CNAs) with a mean of 17.9 /tumour were identified. Main pathways affected by genetic aberrations were the MAPK-pathway (99%), cell cycle control (92%), TGFβ signalling (77%), chromatin remodelling (71%), and the PI3K/AKT pathway (65%). Based on genetic signatures extracted with non-negative matrix factorization we could define five patient clusters, which differed in mutation patterns, gene expression profiles, and survival. In multivariable Cox regression analysis, SMAD4 aberrations were identified as a negative prognostic marker in the gemcitabine arm, an effect that was counteracted when treated with erlotinib (DFS: HR=1.59, p = 0.016, and OS: HR = 1.67, p = 0.014). Integration of differential gene expression analysis established SMAD4 alterations with low MAPK9 expression (n = 91) as a predictive biomarker for longer DFS (HR=0.49; test for interaction, p = 0.02) and OS (HR = 0.32; test for interaction, p = 0.001). Interpretation this study identified five biologically distinct patient clusters with different actionable lesions and unravelled a previously unappreciated association of SMAD4 alteration status with erlotinib effectiveness. Confirmatory studies and mechanistic experiments are warranted to challenge the hypothesis that SMAD4 status might guide addition of erlotinib treatment in early-stage PDAC patients.
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Affiliation(s)
- K Hoyer
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, Berlin 13353, Germany
| | - R Hablesreiter
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Y Inoue
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - K Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - F Briest
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, Berlin 13353, Germany
| | - F Christen
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, Berlin 13353, Germany
| | - N Kakiuchi
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - T Yoshizato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Y Shiozawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Y Shiraishi
- Laboratory of DNA information Analysis, Human Genome Centre, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - J K Striefler
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, Berlin 13353, Germany
| | - S Bischoff
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, Berlin 13353, Germany
| | - P Lohneis
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany; Institute of Pathology, University of Cologne, Cologne, Germany
| | - H Putter
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - O Blau
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, Berlin 13353, Germany
| | - U Keilholz
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - L Bullinger
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, Berlin 13353, Germany
| | - U Pelzer
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, Berlin 13353, Germany
| | - M Hummel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, Berlin, Germany
| | - H Riess
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, Berlin 13353, Germany
| | - S Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan; Department of Medicine, Centre for Haematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - M Sinn
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, Berlin 13353, Germany; Department of Oncology, Hematology and Bone Marrow Transplantation with Division of Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - F Damm
- Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, Berlin 13353, Germany; German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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3
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Nishimura T, Yoshida K, Kawata Y, Takeuchi Y, Kakiuchi N, Shiozawa Y, Aoki K, Hirata M, Kataoka TR, Sakurai T, Baba S, Shiraishi Y, Chiba K, Takeuchi K, Haga H, Miyano S, Toi M, Ogawa S. Abstract P3-06-04: Clonal evolution of non-malignant proliferative lesions into breast cancers. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p3-06-04] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
[Introduction] Non-malignant proliferative lesions in the breast have been implicated in the development of invasive breast cancer. Previous studies showed that adjacent atypical proliferative lesions and breast cancers shared common genetic alterations, suggesting that these evolved from the same ancestral cell. However, the clonal structure of atypical proliferative lesions and their clonal dynamics during progression to cancer are poorly understood. In this study, we compared genetic profiles (with and without pathogenic germline mutations) of normal mammary ducts, non-malignant proliferative lesions, and cancer tissues from the same patients to illustrate the clonal evolution of cancer from a non-malignant epithelial cell.
[Methods] Multiple samples were collected from different proliferative lesions within the cancer-borne breast, including invasive cancers, using micro-dissection from formalin-fixed, paraffin-embedded surgical specimens. Somatic mutations and copy number alterations (CNAs) were then evaluated by whole exome sequencing.
[Results] We analyzed a total of 34 samples from 5 premenopausal females carrying estrogen receptor-positive cancers, where the samples were obtained from normal ducts (N = 6), non-atypical (N = 1) and atypical (N = 8) proliferative lesions, and non-invasive (N = 16) and invasive (N = 3) cancers. The number of somatic mutations per sample ranged from 1 to 276 and increased with disease progression, regardless of the germline mutation status. Two cases with bilateral cancers had a pathogenic germline mutation of either BRCA2 or TP53, where no somatic mutations or CNAs were shared by individual proliferative lesions, suggesting multifocal independent cancerous evolutions. By contrast, in the remaining three unilateral cases, no pathogenic germline mutations were detected, but all proliferative lesions, which were separated by a distance of 7-25 mm, shared one or more driver alterations, such as an AKT1 mutation (UID: KU01), concurrent 1q gain and 16q loss (der(1;16)) (UID: KU02), and a GATA3 mutation and der(1;16) (UID: KU03), while harboring private mutations and/or CNAs of their own. The phylogenetic analysis based on the number of shared mutations predicted an early origin of these founder mutations, which frequently predated decades before the onset of cancer.
[Conclusions] Our results suggest that early breast cancer development is shaped by the evolution of multiple precancerous clones. These clones are originated from a common ancestor that acquired a founder mutation long before the onset of cancer, followed by branching evolution of multiple clones that acquired additional driver mutations of their own, from which an invasive cancer ultimately develops. In hereditary cases, this process is thought to be substantially promoted multi-focally from within the entire breasts by a germline mutation shared by all mammary cells, frequently resulting in bilateral and/or multifocal breast cancers. Our findings provide unique insight into the early development of breast cancer.
Citation Format: Nishimura T, Yoshida K, Kawata Y, Takeuchi Y, Kakiuchi N, Shiozawa Y, Aoki K, Hirata M, Kataoka TR, Sakurai T, Baba S, Shiraishi Y, Chiba K, Takeuchi K, Haga H, Miyano S, Toi M, Ogawa S. Clonal evolution of non-malignant proliferative lesions into breast cancers [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-04.
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Affiliation(s)
- T Nishimura
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - K Yoshida
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Y Kawata
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Y Takeuchi
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - N Kakiuchi
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Y Shiozawa
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - K Aoki
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - M Hirata
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - TR Kataoka
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - T Sakurai
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - S Baba
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Y Shiraishi
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - K Chiba
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - K Takeuchi
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - H Haga
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - S Miyano
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - M Toi
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - S Ogawa
- Graduate School of Medicine, Kyoto University, Kyoto, Japan; Kyoto University Hospital, Kyoto, Japan; Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan; Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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4
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Kitamura H, Terunuma N, Kurosaki S, Hata K, Ide R, Kuga H, Kakiuchi N, Masuda M, Totsuzaki T, Osato A, Uchino B, Kitahara K, Iwasaki A, Yoshizumi K, Morimoto Y, Kasai H, Murase T, Higashi T. Cross-sectional study on respiratory effect of toner-exposed work in manufacturing plants, Japan: pulmonary function, blood cells, and biochemical markers. Hum Exp Toxicol 2009; 28:331-8. [PMID: 19755444 DOI: 10.1177/0960327109105152] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The aim of the study is to examine the relationship between toner-exposed work and health indices related to respiratory disorders and to confirm the baseline of a cohort study to clarify the effect of toner exposure in manufacturing plants. Subjects were 1614 male workers (809 toner-exposed workers and 805 referents) who were engaged in toner manufacturing plants in Japan (Fuji Xerox Co., Ltd). The age of subjects was from 19 to 59 years, and the average age was 40.2 years(median 40 years, SD 7.67). We conducted a pulmonary function test (PEFR, VC, FVC, FEV(1.0)%, V25/Ht) and a blood cell test (RBC, Hb, Hct, Plt, WBC, cell contents of WBC) and measured biochemical indices in blood (ALT, AST, gamma-GTP, CRP, IgE) and 8-hydroxy-2'-deoxyguanosine (8-OHdG) in urine. Student t-test and logistic regression analysis were applied to compare between the toner-exposed workers and the referents and to analyze the relationship among indices of effects and independent factors. There was no significant difference between the two groups in blood cell count and biochemical indices. Inflammation- and allergy-related markers such as 8OHdG and IgE also showed no significant difference between toner-exposed workers and the referents. The influence of smoking on pulmonary function indices was observed, but there was no relationship between the pulmonary function and toner-exposed work. In this article, we report a preliminary cross-sectional analysis in the subjects of a cohort study. No difference in pulmonary function indices was observed between the toner-exposed workers and the referents, and there was no consistent relationship between the exposure status and examined indices; however, the prevalence of subjective respiratory symptoms was higher in the exposed workers as presented in another report. Further analysis is important in the ongoing cohort study to clarify the effect of toner exposure on respiratory systems.
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Affiliation(s)
- H Kitamura
- Institute of industrial and Ecological Sciences, University of occupational and Environmental Health, Japan, Kitakyusyu, Japan.
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5
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Hwang J, Fauzi H, Fukuda K, Sekiya S, Kakiuchi N, Taira K, Kusakabe I, Nishikawa S. Analysis of aptamer binding site for HCV-NS3 protease by alanine scanning mutagenesis. Nucleic Acids Symp Ser 2003:253-4. [PMID: 12903364 DOI: 10.1093/nass/44.1.253] [Citation(s) in RCA: 5] [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] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Nonstructural protein 3 (NS3) of Hepatitis C virus (HCV) is a multifunctional protein and possesses protease, nucleotide triphosphatase and helicase activities. The N-terminal domain of NS3 (amino acids 1027-1218; delta NS3) has a trypsin-like protease activity and is essential for processing of viral polyprotein. Accordingly it is a potential target for anti-HCV drugs and we isolated RNA aptamers (Kd = 10 nM, Ki = 100 nM) using in vitro selection strategy. To study the interaction between delta NS3 and its aptamer, we applied alanine scanning mutagenesis and constructed seven mutant proteins at positive amino acid residues on the surface of delta NS3. Binding and inhibitory activities of the NS3 aptamer against mutant proteins were kinetically analyzed. These results clarified that especially Arg161 and Arg130 are important for interaction with the NS3 aptamer.
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Affiliation(s)
- J Hwang
- National Institute of Bioscience and Human Technology, AIST, Institute of Applied Biochemistry, University of Tsukuba
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6
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Sekiya S, Fukuda K, Hwang J, Kakiuchi N, Taira K, Kusakabe I, Nishikawa S. Analysis of interaction between RNA aptamer and protein using nucleotide analogs. Nucleic Acids Symp Ser 2003:163-4. [PMID: 12903319 DOI: 10.1093/nass/44.1.163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Non-structural protein 3 (NS3) derived from Hepatitis C virus (HCV) is essential for viral proliferation and has two functional domains; trypsin-like serine protease and helicase. Recently we obtained three types of RNA aptamers (G9-I, -II and -III) bound to NS3 protease domain (delta NS3) by in vitro selection and confirmed their strong inhibition for protease activity. These aptamers have a common sequence, 5'-GA(A/U)UGGGAC-3', forming a loop structure by Mulfold secondary structure modeling. G9-I shows a three-way junction and G9-II and -III have four-way junction structures. To characterize the active structure of these aptamers, we applied modification interference analysis using nucleotide analogs and identified common important nucleotides in these three aptamers.
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Affiliation(s)
- S Sekiya
- National Institute of Bioscience and Human Technology, AIST, MITI, Institute of Applied Biochemistry, University of Tsukuba
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7
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Kakiuchi N, Fukuda K, Nishikawa F, Nishikawa S, Shimotohno K. Inhibition of hepatitis C virus serine protease in living cells by RNA aptamers detected using fluorescent protein substrates. Comb Chem High Throughput Screen 2003; 6:155-60. [PMID: 12678711 DOI: 10.2174/1386207033329788] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hepatitis C virus is one of the causative agents of non-A non-B hepatitis. Since one of viral proteins, NS3, has serine protease activity indispensable for virus maturation. NS3 serine protease is considered to be a suitable target for anti-HCV reagents. We report an assay of HCV NS3 protease in living cells. We designed peptide substrates bearing one of the sequences of HCV NS3 protease cleavage sites sandwiched with fluorescent proteins CFP and YFP. Substrates were expressed and cleaved efficiently in HeLa cells by cotransfection with HCV NS3 protease. The relationship between the progress of cleavage reaction and the change in fluorescence of the substrate emitted from living cells was confirmed. As a group of candidates for inhibitor of HCV NS3 protease, we chose RNA aptamers, nucleic acid ligands selected from a completely random RNA pool by in vitro selection. We found that 3 classes of aptamers, G9-I, II and III, bound NS3 protease specifically and inhibited cleavage in vitro. We studied the effect of RNA aptamers introduced into HeLa cells. The addition of G9-II RNA in the medium at a concentration of 2.5 micro g/ml reduced cleavage by one-third that of control.
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Affiliation(s)
- N Kakiuchi
- Institute of Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan.
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8
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Kakiuchi N, Maeda Y, Nishimura T, Uemura S. Pd(ii)-hydrotalcite-catalyzed oxidation of alcohols to aldehydes and ketones using atmospheric pressure of air. J Org Chem 2001; 66:6620-5. [PMID: 11578212 DOI: 10.1021/jo010338r] [Citation(s) in RCA: 193] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A heterogenized Pd catalyst, Pd(II)-hydrotalcite (palladium(II) acetate-pyridine complex supported by hydrotalcite) catalyzes the aerobic oxidation in toluene of a variety of primary and secondary alcohols into the corresponding aldehydes and ketones in high yields using atmospheric pressure of air as a sole oxidant under mild conditions. This catalyst is also effective for the oxidation of allylic alcohols, especially such as geraniol and nerol, without any isomerization of an alkenic part. The catalyst can be easily prepared from all commercially available reagents and reused several times.
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Affiliation(s)
- N Kakiuchi
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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9
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Hwang J, Fauzi H, Fukuda K, Sekiya S, Kakiuchi N, Shimotohno K, Taira K, Kusakabe I, Nishikawa S. The RNA aptamer-binding site of hepatitis C virus NS3 protease. Biochem Biophys Res Commun 2000; 279:557-62. [PMID: 11118325 DOI: 10.1006/bbrc.2000.4007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Nonstructural protein 3 (NS3) of hepatitis C virus (HCV) is a trypsin-like protease and is essential for processing of viral polyprotein. Accordingly, it is a potential target for anti-HCV drugs. Recently we could isolate RNA aptamers (G9-I, II, and III) which bind and inhibit NS3 protease using in vitro selection strategy. In addition, G9-I aptamer showed noncompetitive inhibition. In order to elucidate the binding site of G9-I aptamer in NS3 protease domain (deltaNS3), we carried out alanine scanning mutagenesis at positive charged residues on the surface of deltaNS3. The result of binding analysis by surface plasmon resonance measurements and protease inhibition assay clarified that Arg161 as well as Arg130 of deltaNS3 are essential for interaction with G9-I aptamer. This region appears to be a potential targeting site for anti-HCV drugs.
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Affiliation(s)
- J Hwang
- National Institute of Bioscience & Human Technology, Tsukuba, Ibaraki, 305-8566, Japan
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10
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Abstract
One hundred fifty-two methanol and water extracts of different parts of 71 plants commonly used in Sudanese traditional medicine were screened for their inhibitory effects on hepatitis C virus (HCV) protease (PR) using in vitro assay methods. Thirty-four extracts showed significant inhibitory activity (>/=60% inhibition at 100 microg/mL). Of these, eight extracts, methanol extracts of Acacia nilotica, Boswellia carterii, Embelia schimperi, Quercus infectoria, Trachyspermum ammi and water extracts of Piper cubeba, Q. infectoria and Syzygium aromaticum, were the most active (>/=90% inhibition at 100 microg/mL). From the E. schimperi extract, two benzoquinones, embelin (I) and 5-O-methylembelin (II), were isolated and found as potent HCV-PR inhibitors with IC(50) values of 21 and 46 microM, respectively. Inhibitory activities of derivatives of I against HCV-PR as well as their effects on other serine proteases were also investigated.
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Affiliation(s)
- G Hussein
- Institute of Natural Medicine, Toyama Medical and Pharmaceutical University, 2630 Sugitani, Toyama 930-0194, Japan
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11
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Fukuda K, Vishnuvardhan D, Sekiya S, Hwang J, Kakiuchi N, Taira K, Shimotohno K, Kumar PK, Nishikawa S. Isolation and characterization of RNA aptamers specific for the hepatitis C virus nonstructural protein 3 protease. Eur J Biochem 2000; 267:3685-94. [PMID: 10848986 DOI: 10.1046/j.1432-1327.2000.01400.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nonstructural protein 3 (NS3) from hepatitis C virus (HCV) is a serine protease that provides an essential function in maturation of the virus by cleaving the nonstructural regions of the viral polyprotein. The goal of this work was to isolate RNA aptamers that bind specifically to the NS3 protease active site in the truncated polypeptide DeltaNS3. RNA aptamers were selected in vitro by systematic evolution of ligands by exponential enrichment (SELEX). The RNA pool for SELEX had a 30-nucleotide randomized core region. After nine selection cycles, a pool of DeltaNS3-specific RNA aptamers were obtained. This RNA pool included 45 clones that divided into three main classes (G9-I, II and III). These classes include the conserved sequence GA(A/U)UGGGAC. These aptamers bind to DeltaNS3 with a binding constant of about 10 nM and inhibit approximately 90% of the protease activity of DeltaNS3 and MBP-NS3 (full-length of NS3 fused with maltose binding protein). In addition, these aptamers inhibited approximately 70% of the MBP-NS3 protease activity in the presence of the NS4A peptide P41. G9-I aptamer appeared to be a noncompetitive inhibitor for DeltaNS3 with a Ki approximately 100 nM in the presence of P41. These results suggest that the pool of selected aptamers have potential as anti-HCV compounds. Mutational analysis of the G9-I aptamer demonstrated that the sequences required for protease inhibition are in stem I, stem III and loop III of the aptamer. These regions include the conserved sequence GA(A/U)UGGGAC.
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Affiliation(s)
- K Fukuda
- National Institute of Bioscience and Human Technology, AIST, MITI, Tsukuba Science City, Japan
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12
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Abstract
A simple assay was developed based on intramolecular fluorescence resonance energy transfer for detection of the activity of hepatitis C virus (HCV) serine proteinase. Two quenched-fluorogenic substrates, (7-methoxycoumarin-4-yl)acetyl (Mca) Asp-Asp-Ile-Val-Pro-Cys-Ser-Met-Ser-(2,4-dinitrophenyl, Dnp) Lys (Mca-Asp-Asp-Ile-Val-Pro-Cys-Ser-Met-Ser-Lys[Dnp], QF-1) and Mca-Asp-Asp-Ile-Val-Pro-Cys-Ser-Met-Lys(Dnp)-Arg-Arg (QF-2), which derived from the NS5A/5B junction of the HCV polyprotein, were designed. Kinetic studies revealed that QF-1 and QF-2 had high affinity for a recombinant enzyme which is a fusion protein of maltose binding protein and almost entire nonstructural protein (MBP-NS3), with Km values comparable to that of longer substrate based on the same cleavage site. QF-1 and QF-2 were cleaved by MBP-NS3 efficiently with kcat values of 7.5 and 4.2 min(-1), respectively. QF-2 was also found to be a good substrate of deltaNS3 which contained serine proteinase part of NS3 with kcat value of 4.3 min(-1). The cleavage reaction is detected continuously by the elevation of the fluorescence due to release from quenching. The fluorescence of the substrates increases in proportion to progress of the cleavage reaction under the standard conditions. This method was applied for screening of HCV serine protease inhibitors using a fluorescence multiwell plate reader. A group of natural occurring products, flavonoids, was subjected to be screened. Two flavonoids out of 25 were found to inhibit the enzyme moderately at a concentration of 100 microM. The data agreed with those obtained by high-performance liquid chromatography (HPLC). This method is suited to sensitive quantitation of the enzyme reaction as well as the high throughput analysis of the inhibitors.
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Affiliation(s)
- N Kakiuchi
- National Institute of Bioscience and Human Technology, AIST, MITI, Tsukuba, Japan.
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13
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Abstract
Forty-eight methanol and aqueous extracts from Sudanese plants were screened for their inhibitory activity on viral replication. Nineteen extracts showed inhibitory effects on HIV-induced cytopathic effects (CPE) on MT-4 cells. The extracts were further screened against HIV-1 protease (PR) using an HPLC assay method. Of the tested extracts, the methanol extracts of Acacia nilotica (bark and pods), Euphorbia granulata (leaves), Maytenus senegalensis (stem-bark) and aqueous extracts of A. nilotica (pods) and M. senegalensis (stem-bark) showed considerable inhibitory effects against HIV-1 PR. Inhibitory principles were isolated from M. senegalensis and their activities were also discussed.
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Affiliation(s)
- G Hussein
- Research Institute for Wakan-Yaku (Traditional Sino-Japanese Medicines), Toyama Medical and Pharmaceutical University, Japan
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14
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el-Mekkawy S, Meselhy MR, Nakamura N, Tezuka Y, Hattori M, Kakiuchi N, Shimotohno K, Kawahata T, Otake T. Anti-HIV-1 and anti-HIV-1-protease substances from Ganoderma lucidum. Phytochemistry 1998; 49:1651-7. [PMID: 9862140 DOI: 10.1016/s0031-9422(98)00254-4] [Citation(s) in RCA: 193] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
A new highly oxygenated triterpene named ganoderic acid alpha has been isolated from a methanol extract of the fruiting bodies of Ganoderma lucidum together with twelve known compounds. The structures of the isolated compounds were determined by spectroscopic means including 2D-NMR. Ganoderiol F and ganodermanontriol were found to be active as anti-HIV-1 agents with an inhibitory concentration of 7.8 micrograms ml-1 for both, and ganoderic acid B, ganoderiol B, ganoderic acid C1, 3 beta-5 alpha-dihydroxy-6 beta-methoxyergosta-7,22-diene, ganoderic acid alpha, ganoderic acid H and ganoderiol A were moderately active inhibitors against HIV-1 PR with a 50% inhibitory concentration of 0.17-0.23 mM.
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Affiliation(s)
- S el-Mekkawy
- Research Institute for Traditional Sino-Japanese Medicines, Toyama Medical and Pharmaceutical University, Japan
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15
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Fukuda K, Vishinuvardhan D, Sekiya S, Kakiuchi N, Shimotohno K, Kumar PK, Nishikawa S. Specific RNA aptamers to NS3 protease domain of hepatitis C virus. Nucleic Acids Symp Ser 1998:237-8. [PMID: 9586087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In order to isolate RNA aptamers that bind specifically to NS3 protease domain (delta NS3) of hepatitis C virus, we carried out in vitro selection procedure using RNA pool that had 30 N random core region. After repeating nine cycles of selections and amplifications, a pool of RNAs that bind specifically to the delta NS3 were selected. A comparative analysis of 45 clones that were isolated from 9th cycle revealed three main classes that contain the conserved loop sequences GANUGGGAC. Moreover, the predominant class of aptamer (class I and III) appear to inhibit the protease activity efficiently.
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Affiliation(s)
- K Fukuda
- Natioal Institute of Bioscience and Human Technology, Tsukuba Science City, Japan
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16
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Abstract
We screened a chemical library of 2000 compounds for inhibitors of hepatitis C virus (HCV) serine proteinase using an in vitro screening method measuring the hydrolysis of the peptide substrate. Three compounds were found to be the most potent inhibitors (IC50 < 10(-5) M). Two of them had a similar structure, that of halogenated benzanilide, and were not inhibitory for common serine proteinases. They inhibited the enzyme non-competitively with the substrate. Together with the result of the analogous compounds in the chemical library, the presumed structural requirements of the inhibition are pointed out.
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Affiliation(s)
- N Kakiuchi
- HQL Research Laboratories, Sumitomo Metal Industries, Kyoto, Japan.
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17
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Kumar PK, Machida K, Urvil PT, Kakiuchi N, Vishnuvardhan D, Shimotohno K, Taira K, Nishikawa S. Isolation of RNA aptamers specific to the NS3 protein of hepatitis C virus from a pool of completely random RNA. Virology 1997; 237:270-82. [PMID: 9356339 DOI: 10.1006/viro.1997.8773] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Hepatitis C virus (HCV) is a single-stranded RNA virus and its genome is translated into a single large polyprotein. The viral-encoded NS3 protein possesses protease, nucleoside triphosphatase, and helicase activities. Since these activities appear to be important for viral replication, efforts are being made to identify compounds that might inhibit the enzymatic activities of NS3 and serve as potential anti-HCV agents. We used a genetic selection strategy in vitro to isolate, from a pool of completely random RNA (120 random bases), those RNA aptamers that could bind to NS3. After six cycles of selection and amplification, 14% of the pooled RNAs could bind specifically to the NS3 protein. When the aptamers in the pool (cycle 6) were analyzed for binding and inhibition of the proteolytic activity of NS3 with the NS5A/NS5B peptide as substrate (S1), two aptamers, designated G6-16 and G6-19 RNA, were found to inhibit NS3 in vitro. Kinetic studies of the inhibition revealed that the aptamer G6-16 inhibited the NS3 protease with an inhibitory constant (Ki) of 3 microM. We also analyzed aptamers G6-16 and G6-19 for their action with a longer protein substrate (amino acid region 2203-2506) and found that these aptamers efficiently inhibited the proteolytic activity of NS3. In addition, both G6-16 and G6-19 aptamers were found to inhibit the helicase activity of NS3. Since these aptamers possesses dual inhibitory function for NS3, they could prove to be useful as anti-HCV drug leads.
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Affiliation(s)
- P K Kumar
- National Institute of Bioscience and Human Technology, MITI, AIST, 1-1 Higashi, Japan
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18
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Abstract
To study the character of the hepatitis C virus (HCV) encoding serine proteinase and to search for inhibitors, a practical in vitro assay system using the purified enzyme and synthetic peptide substrates was established. The enzyme used was expressed in Escherichia coli as a fusion form with protein tags and purified to apparent homogeneity by single-step affinity chromatography. The purified enzyme exhibited proteolytic activity with pH optima of around eight, and the addition of NS4A fragments increased the activity as well as the thermal stability of the enzyme. The activity was inhibited by EDTA and some divalent ions, i.e., copper and zinc, though calcium, magnesium, and manganese were stimulative both in the presence and absence of the NS4A fragment. None of the common protease inhibitors, including serine protease inhibitors, effectively inhibited the activity. Based on the kinetic parameters of the cleavage reaction of the synthetic 20 mer peptides corresponding to the three cleavage sites, NS4A/4B, NS4B/5A, and NS5A/5B, the peptide with the NS5A/5B junction was found to be the most efficient substrate. Analysis of the minimal peptide substrate of NS5A/5B indicated that 5 to 7 amino acids on both sides of the junction were required for efficient cleavage. These findings are expected to contribute to the search for a proteinase inhibitor.
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Affiliation(s)
- N Kakiuchi
- HQL Research Labs., Sumitomo Metal Industries Ltd., Kyoto.
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19
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Urvil PT, Kakiuchi N, Zhou DM, Shimotohno K, Kumar PK, Nishikawa S. Selection of RNA aptamers that bind specifically to the NS3 protease of hepatitis C virus. Eur J Biochem 1997; 248:130-8. [PMID: 9310370 DOI: 10.1111/j.1432-1033.1997.t01-1-00130.x] [Citation(s) in RCA: 47] [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] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The RNA genome of human hepatitis C virus (HCV) is translated into a large precursor polyprotein. The NS3 protease of HCV has a crucial role in the processing of the polyprotein into functional viral proteins. We have used an in vitro genetic-selection strategy to isolate high-affinity RNA aptamers that bind to the NS3 protein, especially to its protease domain. Starting from a RNA pool that had a random sequence core of 12-18 nucleotides, aptamers that bind specifically to the NS3 protein were selected after 10 rounds of selection and amplification. A single aptamer, 10G-1, was found predominantly (71%) in the selected pool. This aptamer could bind to the NS3 protein with a binding constant of 650 nM and inhibit the proteolytic activity in vitro. By phosphate-modification-interference analysis we showed that the phosphate residues that are critical for the binding of 10G-1 to NS3 lie within the selected regions of the aptamer and that binding involves electrostatic contacts with the phosphates of regions G28-U34 and A47-A55. The NS3-binding region in 10G-1 can serve as a basis for designing more potential inhibitors of the NS3 protein.
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Affiliation(s)
- P T Urvil
- National Institute of Bioscience and Human Technology, AIST, Tsukuba Science City, Ibaraki, Japan
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20
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Takeshita N, Kakiuchi N, Kanazawa T, Komoda Y, Nishizawa M, Tani T, Shimotohno K. An enzyme-linked immunosorbent assay for detecting proteolytic activity of hepatitis C virus proteinase. Anal Biochem 1997; 247:242-6. [PMID: 9177684 DOI: 10.1006/abio.1997.2063] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
An ELISA method for the quantitation in vitro of HCV serine proteinase activity was developed. A peptide substrate, Ac-Gly-Glu-Ala-Gly-Asp-Asp-Ile-Val-Pro-Cys-Ser-Met-Ser-Tyr-Thr-Trp-Thr-L ys (biotin) -OH (Sub-1), was hydrolyzed by a recombinant NS3 proteinase fused with maltose binding protein (MBP-NS3) into a product with a free amino moiety at the N-terminus. The product was immobilized, and the amino moiety was analyzed by digoxigenin labeling followed by immunological reaction with anti-digoxigenin-alkaline phosphatase conjugate and then the colorimeteric reaction. This method is suited for the high throughput screening of inhibitors, and the screening can be accelerated by automatic operation.
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Affiliation(s)
- N Takeshita
- HQL Research Laboratories, Sumitomo Metal Industries Ltd., Kyoto, Japan
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21
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Vishnuvardhan D, Kakiuchi N, Urvil PT, Shimotohno K, Kumar PK, Nishikawa S. Expression of highly active recombinant NS3 protease domain of hepatitis C virus in E. coli. FEBS Lett 1997; 402:209-12. [PMID: 9037197 DOI: 10.1016/s0014-5793(96)01532-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The serine protease domain of HCV comprising amino acids 1027-1218 (deltaNS3) was expressed in E. coli with a His tag at its N-terminal end. The protease was purified to apparent homogeneity by a single step affinity chromatography resulting in high yields (approximately 3 mg/l of cultured cells). The deltaNS3 efficiently cleaves a 17-mer peptide corresponding to the NS5A-NS5B junction with kcat/Km = 160 x 10(-3) min(-1) microM(-1) in the presence of NS4A peptide. Our deltaNS3 represents the minimal domain possessing highly active protease of NS3 constructed so far. The deltaNS3 protein also efficiently processed a longer substrate corresponding to NS5A/5B junction (2203-2506 amino acids) that was synthesized by in vitro transcription and translation system.
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Affiliation(s)
- D Vishnuvardhan
- National Institute of Bioscience and Human Technology, AIST, Tsukuba, Ibaraki, Japan
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22
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Kakiuchi N, Hijikata M, Komoda Y, Tanji Y, Hirowatari Y, Shimotohno K. Bacterial expression and analysis of cleavage activity of HCV serine proteinase using recombinant and synthetic substrate. Biochem Biophys Res Commun 1995; 210:1059-65. [PMID: 7763234 DOI: 10.1006/bbrc.1995.1764] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
HCV encoding serine proteinase was expressed in E. coli as a fused form with maltose binding protein (MBP) and a six histidine tag. The enzyme was partially purified by using affinity chromatography for these fused peptides. Proteolytic cleavage activity of the partially purified enzyme was detected by means of an assay using both a recombinant protein and a synthetic peptide substrate which had an amino acid sequence corresponding to the most efficient cleavage site in vivo, the NS5A-NS5B junction. The cleavage occurred at the same site that was reported before.
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Affiliation(s)
- N Kakiuchi
- HQL Research Labs. Sumitomo Metal Industries Ltd., Kyoto, Japan
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23
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Hijikata M, Mizushima H, Akagi T, Mori S, Kakiuchi N, Kato N, Tanaka T, Kimura K, Shimotohno K. Two distinct proteinase activities required for the processing of a putative nonstructural precursor protein of hepatitis C virus. J Virol 1993; 67:4665-75. [PMID: 8392606 PMCID: PMC237852 DOI: 10.1128/jvi.67.8.4665-4675.1993] [Citation(s) in RCA: 375] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Gene products of hepatitis C virus (HCV), a possible major causative agent of posttransfusion non-A, non-B hepatitis, are considered to be produced from a precursor polyprotein via proteolytic processing mediated by either host cell or viral proteinases. The presence of HCV serine proteinase has been proposed from analyses of amino acid sequence homology. To examine the processing mechanism of the HCV precursor polyprotein, the amino-terminal region of the putative nonstructural protein region of the HCV genome, containing the serine proteinase motif, was expressed and analyzed by using an in vitro transcription/translation system and a transient expression system in cultured cells. Two distinct proteinase activities which function in the production of a 70-kDa protein (p70) from the precursor polyprotein were detected. One of these proteinase activities, which cleaved the carboxyl (C)-terminal side of p70, required the presence of the serine proteinase motif, which is located in the amino (N)-terminal region of p70. That suggested that the predicted HCV serine proteinase was functional. The other activity, which was responsible for the cleavage of the N-terminal side of p70, required the expression of the region upstream and downstream of that cleavage site, including the p70 serine proteinase domain. From the results of pulse-chase analysis, using proteinase inhibitors coupled with a point mutation analysis, the latter activity was proposed to be a novel zinc-dependent metalloproteinase.
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Affiliation(s)
- M Hijikata
- Virology Division, National Cancer Center Research Institute, Tokyo, Japan
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24
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Kusumoto IT, Shimada I, Kakiuchi N, Hattori M, Namba T, Supriyatna S. Inhibitory effects of indonesian plant extracts on reverse transcriptase of an RNA Tumour Virus (I). Phytother Res 1992. [DOI: 10.1002/ptr.2650060504] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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25
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Huang SL, Kakiuchi N, Hattori M, Namba T. A new monitoring system of cultured myocardial cell motion: effect of pilose antler extract and cardioactive agents on spontaneous beating of myocardial cell sheets. Chem Pharm Bull (Tokyo) 1991; 39:384-7. [PMID: 2054862 DOI: 10.1248/cpb.39.384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Effects of various cardioactive agents and a water extract of the pilose antler of Cervus nippon var. mantchuricus on periodic beating of cultured myocardial cell sheets were examined by using an image analyzing system. Norepinephrine increased the beating rate and the beating amplitude, whereas digoxin and forskolin enlarged only the beating amplitude. Verapamil and propranolol decreased both the beating rate and the beating amplitude. The water extract of the pilose antler showed no remarkable effects in a standard medium (2.1 mM Ca2+). However, it significantly increased the beating amplitude when the beating was suppressed by replacement with a low calcium medium (0.5 mM Ca2+). A similar effect was found for 70% ethanol-soluble and -insoluble fractions of the extract.
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Affiliation(s)
- S L Huang
- Research Institute for Wakan-yaku (Traditional Sino-Japanese Medicines), Toyama Medical and Pharmaceutical University
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26
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Namba T, Huang XL, Shu YZ, Huang SL, Hattori M, Kakiuchi N, Wang Q, Xu GJ. Chronotropic Effect of the Methanolic Extracts of the Plants of the Paris Species and Steroidal Glycosides Isolated from P. vietnamensis on Spontaneous Beating of Myocardial Cells1. Planta Med 1989; 55:501-5. [PMID: 17262471 DOI: 10.1055/s-2006-962080] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Rhizomes of five identified plants of the PARIS species, Liliaceae, and Rhizoma Paridis which are sold as a crude drug named "Zao Xiu", "Qiyeyizhihua" or other names in nine different markets in China were tested for their effects on cultured cardiomyocytes. In the standard medium, eight methanol extracts out of sixteen at a concentration of 0.2 mg/ml stopped the spontaneous beating of myocardial cell sheets, but these extracts significantly increased the beating rate when the concentration was reduced to one half. In the culture medium with a low calcium concentration, 0.5 mM, the beating rate of the cells decreased to about 60% of that of the control in the standard medium. The addition of five of the extracts to the low calcium medium at a concentration of 0.1 mg/ml caused a stop of cell beating, but the other extracts increased beating rate at least by 10%. Three steroidal glycosides isolated from the rhizomes of P. VIETNAMENSIS (Takht.) H. Li also stimulated cell beating. Among them, diosgenin-3- O-alpha- L-rhamnopyranosyl-(1-->2) - (alpha- L-arabinofuranosyl-(1-->4))- D-glucopranoside (compound 1) was the most effective stimulant for cell beating as well as calcium uptake by the myocardial cells.
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Affiliation(s)
- T Namba
- Research Institute for Wakan-Yaku, Toyama Medical and Pharmaceutical University, 2630 Sugitani, Toyama, 930-01 Japan
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Hattori M, Miyachi K, Hada S, Kakiuchi N, Kiuchi F, Tsuda Y, Namba T. Effects of long-chain fatty acids and fatty alcohols on the growth of Streptococcus mutans. Chem Pharm Bull (Tokyo) 1987; 35:3507-10. [PMID: 3427727 DOI: 10.1248/cpb.35.3507] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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28
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Hattori M, Hada S, Watahiki A, Ihara H, Shu YZ, Kakiuchi N, Mizuno T, Namba T. Studies on dental caries prevention by traditional medicines. X. Antibacterial action of phenolic components from mace against Streptococcus mutans. Chem Pharm Bull (Tokyo) 1986; 34:3885-93. [PMID: 3815609 DOI: 10.1248/cpb.34.3885] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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29
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Kakiuchi N, Hattori M, Nishizawa M, Yamagishi T, Okuda T, Namba T. Studies on dental caries prevention by traditional medicines. VIII. Inhibitory effect of various tannins on glucan synthesis by glucosyltransferase from Streptococcus mutans. Chem Pharm Bull (Tokyo) 1986; 34:720-5. [PMID: 2939967 DOI: 10.1248/cpb.34.720] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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30
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Kakiuchi N, Hattori M, Namba T, Nishizawa M, Yamagishi T, Okuda T. Inhibitory effect of tannins on reverse transcriptase from RNA tumor virus. J Nat Prod 1985; 48:614-21. [PMID: 2413172 DOI: 10.1021/np50040a016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Twenty-four tannins and related compounds were examined for inhibition against reverse transcriptase from RNA tumor virus. Hydrolyzable tannins showed a potent inhibitory effect comparable to nitidine, in the presence of polyadenylic acid-oligothymidylic acid as a template-primer. A lesser inhibitory activity was observed for the monomeric ellagitannins, gallotannins, and nitidine using polycytidylic acid-oligodeoxyguanylic acid as a template-primer, whereas the inhibitory activity of dimeric ellagitannins was almost as potent as that observed for these compounds in the polyadenylic acid-oligothymidylic acid directed reaction. Inhibition by tannins was reversed by the addition of either template-primer or enzyme, suggesting that the inhibition is due to the interaction of tannins with both of them.
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31
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Aoyama H, Sarih-Cottin L, Tarrago-Litvak L, Kakiuchi N, Litvak S, Guschlbauer W. 2'-Fluoro-2'-deoxypolynucleotides as templates and inhibitors for RNA- and DNA-dependent DNA polymerases. Biochim Biophys Acta 1985; 824:225-32. [PMID: 2578820 DOI: 10.1016/0167-4781(85)90052-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Poly(2'-fluoro-2'-deoxyadenylic acid) (poly(dAfl)) and poly(2'-deoxycytidylic acid) (poly(dCfl)) were tested as templates in DNA synthesis reactions catalyzed by Xenopus laevis oocytes DNA polymerase alpha, mouse cell DNA polymerase gamma and avian myeloblastis virus (AMV) reverse transcriptase. Poly(dAfl).(dT)12 can fully substitute for poly(rA).(dT)12 as template with DNA polymerase gamma, to 50% with reverse transcriptase, but was poorly recognized by DNA polymerase alpha. DNA synthesis by reverse transcriptase with poly(dCfl).(dG)12 as template was 50% of that with poly(rC).(dG).(dG)12. The use of 2'-fluoropolymers as templates was more efficient at 37 degrees C than at 25 degrees C. No appreciable differences on the fidelity of DNA synthesis by reverse transcriptase were observed when dCMP misincorporation was measured with poly(dAfl).(dT)12 or poly(rA).(dT)12 as template primers. Poly(C) and poly-2'-O-methylcytidylic acid had no significant effect on the reaction catalyzed by DNA polymerase gamma and reverse transcriptase, independent of the synthetic polynucleotide complex utilized as template. On the other hand, poly(dCfl) was an inhibitor when poly(rA).(dT)12 or poly(dA).(dT)12 were used as templates, but not when poly(dAfl).(dT)12 was employed. Analogous results have been obtained with activated DNA and AMV 70 S RNA as templates in the reverse transcriptase reaction. The inhibition by poly(dCfl) was noncompetitive with regard to TTP, poly(dA) and poly(rA). Xenopus laevis oocytes DNA polymerase alpha was not inhibited by poly(dCfl).
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Hattori M, Sakamoto T, Endo Y, Kakiuchi N, Kobashi K, Mizuno T, Namba T. Metabolism of magnolol from magnoliae cortex. I. Application of liquid chromatography-mass spectrometry to the analysis of metabolites of magnolol in rats. Chem Pharm Bull (Tokyo) 1984; 32:5010-7. [PMID: 6534550 DOI: 10.1248/cpb.32.5010] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Marck C, Kakiuchi N, Guschlbauer W. Specific interaction of netropsin, distamycin-3 and analogs with LC duplexes: reversion towards the B form of the 2'-deoxy-.2'-deoxy-2'-fluoro-hybrid duplexes upon specific interaction with netropsin, distamycin-3 and analogs. Nucleic Acids Res 1982; 10:6147-61. [PMID: 6292869 PMCID: PMC320957 DOI: 10.1093/nar/10.19.6147] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Binding of the B-form specific ligands netropsin and distamycin-3, -4 and -5 has been used to monitor the presence and/or the inducibility of a B-type structure in various poly-inosinic.poly-cytidilic double stranded polymers with deoxyribose, ribose or 2'-deoxy-2'-fluororibose as sugar on either strand. The efficiency of binding was followed by circular dichroism and further evaluated by the increase in melting temperature of the complexes. The efficient binding of netropsin and distamycins to the hybrid polymer (dIfl)n. (dC)n demonstrated that the fluorine carrying strand may undergo a A to B-type transition reflecting a change of the 2'-deoxy-2'-fluororibose from the 3'-endo to the 1'-exo or 2'-endo pucker. The less efficient binding of the same ligands to the reverse hybrid (dI)n.(dCfl)n showed that the geometry of the pyrimidine strand is the most critical for the specific interaction. Taking into account the recent findings about the regular hydration in the minor groove of the B-type dodecamer dCGCGAATTCGCG in solid-state, the different binding modes observed between the different polymers and antibiotics are explained by differences in their possibilities of hydration. Binding of netropsin to a double stranded deoxypolymer is interpreted as a local replacement of water molecules by netropsin in the minor groove hydration network which is typical of the B-form.
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Fukui T, De Clerq E, Kakiuchi N, Ikehara M. Template activity of poly(2'-fluoro-2'-deoxyinosinic acid) for murine leukemia virus reverse transcriptase. Cancer Lett 1982; 16:129-35. [PMID: 6181866 DOI: 10.1016/0304-3835(82)90053-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The 2'-substituted analog of poly(inosinic acid) ((I)n), poly(2'-fluoro-2'-deoxyinosinic acid) ((dIfl)n) served as an effective template for the RNA-directed DNA polymerase (reverse transcriptase) from Moloney murine leukemia virus. When assayed under the same conditions, the parent compound (I)n showed little, if any, template activity. In the presence of other templates, i.e. poly (2-O-methylcytidylic acid), (dIfl)n could also assume the role of primer for the reverse transcriptase reaction, whereas, again, (I)n failed to do so.
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Abstract
Poly(2'-fluoro-2'-deoxyadenylic acid), poly(2'-chloro-2'-deoxyadenylic acid) and poly(2'-bromo-2'-deoxyadenylic acid) are used as messenger RNAs in protein synthesizing systems in vitro. All polynucleotides were active as messengers and [14 C]lysine was incorporated into polypeptides. The initial velocity of polylysine formation was greater using poly(2'-fluoro-2'-deoxyadenylic acid) as messenger than in the case of poly(rA), and all synthetic messengers lived longer in the protein synthetic system.
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Zimmer C, Kakiuchi N, Guschlbauer W. Differential stabilization by netropsin of inducible B-like conformations in deoxyribo-, ribo- and 2'-deoxy-2'-fluororibo-adenosine containing duplexes of (dA)n . (dT)n and (dA)n . (dU)na. Nucleic Acids Res 1982; 10:1721-32. [PMID: 6280155 PMCID: PMC320561 DOI: 10.1093/nar/10.5.1721] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Six polynucleotide duplexes containing polydeoxyadenylic acid, polyadenylic acid or poly-2'-deoxy-2'-fluoro-adenylic acid in one strand, and polydeoxyuridylic acid or polydeoxythymidylic acid in the other strand have been studied by circular dichroism, ionic strength dependence of melting temperatures and binding of the DNA specific antibiotic netropsin. Circular dichroism spectra of (dA)n . (dT)n and (dA)n . (dU)n indicated the presence of the B-form of DNA, while those of (dAfl)n . (dT)n and (rA)n . (dT)n (and the corresponding (dU)n hybrids) indicated the presence of the A-form. (dAfl)n . (dT)n and (dAfl)n . (dU)n bound netropsin only slightly less than the (dA)n containing duplexes, while replacement by (rA)n decreased netropsin binding to a large degree. Since netropsin requires B-DNA for binding, it is concluded that the A to B transition is facilitated in the case of fluorine substitution in the sugar moiety, while the 2'-OH group greatly limits this conformational change.
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Kakiuchi N, Marck C, Rousseau N, Leng M, De Clerq E, Guschlbauer W. Polynucleotide helix geometry and stability. Spectroscopic, antigenic and interferon-inducing properties of deoxyribose-, ribose-, or 2'-deoxy-2'-fluororibose-containing duplexes of poly(inosinic acid) . poly(cytidylic acid). J Biol Chem 1982; 257:1924-8. [PMID: 6173383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Circular dichroism, absorbance temperature profiles, antigenic properties, and interferon-inducing capacity of the nine double-stranded complexes between poly(inosinic acid) and poly(cytidylic acid) [(rI)n . (rC)n] and their deoxy- and 2'-deoxy-2'-fluoro-analogues were studied. The complexes containing only ribose or 2'-fluororibose chains showed similar CD spectra and thermal stabilities. Anti-(rI)n . (rC)n antibodies were well recognized by the duplexes containing 2'-fluororibose in either one strand. These two duplexes were also efficient interferon inducers. Presence of fluororibose in both strands decreased the affinity of anti-(rI)n . (rC)n antibodies slightly and abolished interferon-inducing activity. All polydeoxyriboside-containing complexes showed CD spectra significantly different from the previous group; they showed also 40- to 100-times lower affinity for the anti-(rI)n . (rC)n antibodies, and did not induce interferon. It is concluded that the structure of (rI)n . (rC)n, an A-type helix, is little perturbed by substitution of one or both strands by 2'-fluororibose. Substitution by deoxyribose in either strand considerably changes the structure of the helices. The hybrids containing poly(deoxycytidylic acid) retain at least some of the structural features of the B-type helix poly(deoxyinosinic acid) . poly(deoxycytidylic acid).
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Kakiuchi N, Marck C, Rousseau N, Leng M, De Clerq E, Guschlbauer W. Polynucleotide helix geometry and stability. Spectroscopic, antigenic and interferon-inducing properties of deoxyribose-, ribose-, or 2‘-deoxy-2‘-fluororibose-containing duplexes of poly(inosinic acid) . poly(cytidylic acid). J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)68127-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Kishima N, Wada E, Kakiuchi N. [Use of the stable isotopes in life science (I). Measurement of natural abundance of the stable isotopes by the mass spectrometer and its application in life science. (author's transl)]. Radioisotopes 1982; 31:58-67. [PMID: 7041201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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De Clercq E, Stollar BD, Hobbs J, Fukui T, Kakiuchi N, Ikehara M. Interferon induction by two 2'-modified double-helical RNAs, poly(2'-fluoro-2'-deoxyinosinic acid) x poly(cytidylic acid) and poly(2'-chloro-2'-deoxyinosinic acid) x poly(cytidylic acid). Eur J Biochem 1980; 107:279-88. [PMID: 6156830 DOI: 10.1111/j.1432-1033.1980.tb04648.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In addition to the 2'-azido analogue of (I)n x (C)n, (dIn3)n x (C)n, we have found two other (I)n x (C)n analogues, (dIfl)n x (C)n and (dIcl)n x (C)n, in which the 2'-hydroxyls of the (I)n strand are replaced by either fluorine or chlorine, to be highly effective in inducing interferon. This contrasted with the lack of interferon-inducing activity noted for various other 2'-halogeno analogues of (I)n x (C)n and (A)n x (U)n, i.e. (I)n x (dCcl)n, (dAfl)n x (U)n, (dAcl)n x (U)n, (A)n x (dUfl)n and (A)n x (dUcl)n. In most assay systems, viz. primary rabbit kidney cells, human diploid fibroblasts, HeLa cells, interferon-primed mouse L-929 cells, and intact rabbits, (dIfl)n x (C)n and (dIcl)n x (C)n induced interferon levels that were comparable to those induced by (I)n x (C)n. There was one particular system (L-929 cells treated with DEAE-dextran), however, in which (dIfl)n x (C)n and (dIcl)n x (C)n, unlike (I)n x (C)n, failed to stimulate interferon production. As monitored by both radiochemical and biological means, (dIfl)n x (C)n and, to a lesser extent, (dIcl)n x (C)n were more resistant to degradation by ribonuclease A, T1 and human serum nucleases than was (I)n x (C)n. In their reactivity towards antibodies to double-stranded RNA (dIfl)n x (C)n and (dIcl)n x (C)n conformed more closely to (I)n x (C)n than did other 2'-substituted (e.g. 2'-O-methyl or 2'-O-ethyl) analogues of (I)n x (C)n. The high interferon-inducing potency of (dIfl)n x (C)n and (dIcl)n x (C)n has both theoretical and practical implications. While our findings suggest that (dIfl)n x (C)n and (dIcl)n x (C)n should be further explored for their therapeutic potentials, they also strengthen the notion that the interferon-inducing capacity, and possibly other biological functions of double-stranded RNAs is dependent on the recognition of the overall conformation of the polynucleotide rather than on the binding of specific functional groups such as the 2'-hydroxyl group.
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Kakiuchi N, Fukui T, Ikehara M. Polynucleotides. LVII. Synthesis and properties of poly (2'-chloro-2'-deoxyinosinic acid). Nucleic Acids Res 1979; 6:2627-36. [PMID: 461198 PMCID: PMC327876 DOI: 10.1093/nar/6.7.2627] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Poly (2'-chloro-2'-deoxyinosinic acid) [poly(Icl)] was synthesized from Icl 5'-DP by polymerization with polynucleotide phosphorylase. UV absorption properties of poly(Icl) are very similar to those of poly(I). Poly(Icl) adopted a multi-stranded ordered form in the presence of 0.95M Na ion. The Tm value of this form was 36 degrees, which resembles that of poly(I) quadruple-stranded form at high salt. CD spectra also suggested presence of these two forms. Upon mixing with poly(C), poly-(Icl) forms a double-stranded 1 : 1 complex, which had very similar Tm-log[Na+] relationship to that of poly(I) . poly(C). Thus it was concluded that the chlorine substitution at 2'-position of the polynucleotide had the similar effect to OH on physical properties of polynucleotides.
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De Clercq E, Fukui T, Kakiuchi N, Ikehara M, Hattori M, Pfleiderer W. Influence of various 2- and 2'-substituted polyadenylic acids on murine leukemia virus reverse transcriptase. Cancer Lett 1979; 7:27-37. [PMID: 88259 DOI: 10.1016/s0304-3835(79)80073-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Several newly synthesized polyadenylic acid [(A)n] analogues, including poly(2-methyladenylic acid) [(m2A)n], poly(2-ethyladenylic acid) [(e2A)n], poly(2-isopropyladenylic acid) [(i-pro2A)n], poly(2-methylthioadenylic acid) [(ms2A)n], poly(2-ethylthioadenylic acid) [(e2A)n], poly(2'-fluoro-2'-deoxyadenylic acid) [(dAfl)n] and poly(2'-azido-2'-deoxyadenylic acid) [(dAz)n] have been evaluated for their effects on the RNA-directed DNA polymerase (reverse transcriptase) activity of Moloney murine leukemia virus; (m2A)n and (e2A)n did not markedly affect reverse transcriptase activity, (dAfl)n served as an efficient template for the reverse transcriptase reaction, and (i-pro2A)n, (ms2A)n, (es2A)n and (dAz)n strongly inhibited reverse transcriptase activity. (dAfl)n also served as an efficient template (Km : 0.025 micron) for the reverse transcriptase of avian myeloblastosis virus.
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Fukui T, Kakiuchi N, Ikehara M. Polynucleotides. XLIV. Synthesis and properties of poly (2-azaadenylic acid) and poly(2-azainosinic acid). Biochim Biophys Acta 1978; 520:441-51. [PMID: 361091 DOI: 10.1016/0005-2787(78)90241-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chemically synthesized 2-azaadenosine 5'-diphosphate (n2ADP) and 2-azainosine 5'-diphosphate (n2IDP) were polymerized to yield poly(2-azaadenylic acid), poly(n2A), and poly(2-azainosinic acid), poly(n2I), using Escherichia coli polynucleotide phosphorylase. In neutral solution, poly(n2A) and poly(n2I) had hypochromicities of 32 and 5.5%, respectively. Poly(n2A) formed an ordered structure, which had a melting temperature (Rm) of 20 degrees C at 0.15 M salt concentration. Upon mixing with poly(U), poly(n2A) formed a 1 : 2 complex with Tm of 41 degrees C at 0.15 M salt concentration. Poly(n2A) and poly(n2I) formed three-stranded complexes with poly(I), and poly(A), respectively. Poly(n2A) . 2poly(I), poly(A) . 2poly(n2I), and poly(n2A) . 2poly(n2I) complexes had Tm values of 23, 48, and 31 degrees C at 0.15 M salt concentration, respectively. Poly(n2I) formed a double-stranded complex with poly(C), but its Tm was very low.
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Abstract
Poly (2'-deoxy-2'-fluoroinosinic acid) [ poly(If)] was synthesized by polymerization of 2'-deoxy-2'-fluoroinosine 5'-diphosphate catalyzed by Escherichia coli polynucleotide phosphorylase. Although the UV absorption properties of poly(If) closely resembled those of poly(I), thermal melting curves at Na+ concentrations of 0.15M and 0.75M suggested two ordered structures for poly(If) neutral form. CD psectra taken at 0.15M Na+ concentration showed rather larger amplitudes in both a peak at 273 nm and a trough at 246 nm, suggesting rather strong vertical stacking of bases. When complexed with poly(C), poly(If) forms a double-stranded complex, poly(If).poly(C) which has Tm's higher by 10-20 degrees than those of poly(If).poly(C) measured under the same conditions. The CD spectrum of this complex resembled that of poly(I).poly(C). The effect of the fluorine atom at the 2'-position on thermal stability of polynucleotides is discussed.
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de Clercq E, Torrence PF, Stollar BD, Hobbs J, Fukui T, Kakiuchi N, Ikehara M. Interferon induction by a 2'-modified double-helical RNA, poly(2'-azido-2'-deoxyinosinic acid) . polycytidylic acid. Eur J Biochem 1978; 88:341-9. [PMID: 80316 DOI: 10.1111/j.1432-1033.1978.tb12455.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Abstract
2'-Deoxy-2'-fluoroadenosine was chemically transformed to its 5'-diphosphate and polymerized with polynucleotide phosphorylase to give poly(2'-deoxy-2'-fluoroadenylic acid) [poly(Af)]. Polymerization proceeded smoothly as in the case of poly(A) and the yield of the polymerization was 55%. The UV absorption spectra of poly(Af) closely resembled those of poly(A) and the hypochromicity was 32% at pH 7.0. The CD profile at 25 degrees and neutrality showed similar pattern to that of other poly(2'-deoxy-2'-halogenoadenylic acids) with somewhat larger [theta] values both in the positive and negative maxima. Acid titration of poly(Af) showed a transition point at pH 5.2 and the Tm of the acid form was 37 degrees which was significantly lower than that of poly(A), but similar to that of poly(2'-azido-2'-deoxyadenylic acid). Poly(Af) formed 1:1 and 1:2 complexes with poly-(U) having Tm of 49 degrees and 62 degrees at 0.04M and 0.15M Na(+) concentration, respectively. Poly(Af) also formed a 1:2 complex with poly(I) and its Tm was 36 degrees at 0.05M Na(+) concentration. These data showed that poly(Af) has rather similar properties to those of poly(A), but not to poly(dA).
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Ikehara M, Fukui T, Kakiuchi N. Polynucleotides. L. Synthesis and properties of poly (2'-chloro-2'-deoxyadenylic acid) and poly (2'-bromo-2'-deoxyadenylic acid). Nucleic Acids Res 1977; 4:4249-60. [PMID: 341084 PMCID: PMC343238 DOI: 10.1093/nar/4.12.4249] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Poly (2'-chloro-2'-deoxyadenylic acid) and poly (2'-bromo-2'-deoxyadenylic acid) were synthesized from the corresponding diphosphates with the aid of polynucleotide phosphorylase from E. coli. UV, CD, acid titration and mixing with poly (U) were investigated. Comparing these properties with those of poly (A) and poly (2'-azido-2'-deoxyadenylic acid), it was found that 2''substituents exert significant effects on the thermal stability of these polynucleotides, though the overall conformational structure was not greatly changed.
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De Clercq E, Huang GF, Torrence PF, Fukui T, Kakiuchi N, Ikehara M. Biologic activities of poly (2-azaadenylic acid) and poly (2-azainosinic acid). Nucleic Acids Res 1977; 4:3643-53. [PMID: 73166 PMCID: PMC342679 DOI: 10.1093/nar/4.10.3643] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Poly (2-azaadenylic acid) [(aza2A)n] and poly(2-azainosinic acid [(aza2I)n], two newly synthesized analogues of (A)n and (I)n, in which CH-2 of the purine ring is replaced by a nitrogen atom, have been evaluated in various biological assay systems. (Aza2A) n formed a complex with (U)n and (br5U)n, and (aza2I)n formed a complex with (C)n and (br5C)n, but these complexes were markedly destabilized relative to the corresponding (A)n or (I)n complexes. The (aza2A)n-and (aza2I)n-derived complexes failed to stimulate the production of interferon in primary rabbit kidney cells and human diploid fibroblasts, under conditions (A)n. (U)n, (I)n. (C)n and (I)n. (br5C)n induced high amounts of interferon. both (aza2A)n and (aza2I)n exerted a marked inhibitory effect on the endogenous RNA directed DNA polymerase (reverse transcriptase) activity associated with murine leukemia virus. They caused a relatively mild inhibition of complement activity in an hemolytic assay system.
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Abstract
Poly (2'-azido-2'-deoxyinosinic acid), [poly (Iz)], was synthesized from 2'-azido-2'-deoxyinosine diphosphate by the action of polynucleotide phosphorylase. Poly (Iz) has UV absorption properties similar to poly (I) and hypochromicity of 11% at 0.15M Na+ and neutrality. In solutions of high Na+ ion concentration, poly (Iz) forms a multi-stranded complex and its Tm at 1.0M Na+ ion concentration was 43 degrees. Upon mixing with poly (C), poly (Iz) forms a 1:1 complex having a Tm lower than that of poly (I)-poly (C) complex in the same conditions. The effect of substitution at the 2'-position of the poly (I) strand was discussed in relation to the interferon-inducing activity.
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Ikehara M, Fukui T, Kakiuchi N. Polynucleotides. XLVI. 1 Synthesis and properties of poly (2'-amino-2'-deoxyadenylic acid). Nucleic Acids Res 1977; 4:989-1000. [PMID: 17102 PMCID: PMC342499 DOI: 10.1093/nar/4.4.989] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Poly (2'-amino-2'-deoxyadenylic acid) [poly (Aa)] was prepared from chemically synthesized 2'-amino-2'-deoxy-ADP by the catalysis of polynucleotide phosphorylase. Poly (Aa) showed a similar UV absorption spectra to poly (A), but quite different CD spectra at pH 7.0 and 5.7. At the former pH it showed a single negative Cotton band and at the latter a curve with a large splitting of bands. Acid titration of poly (Aa) suggested protonated form below pH 7.0. Temperature absorption profiles and their dependency on sodium ion concentration suggested an ordered structure for poly (Aa) which is stabilized by stacking of bases and intrastrand interaction between 2'-amino and internucleotidic phosphate groups. Poly (Aa) forms a 1:2 complex with poly (U) at neutrality and its Tm was 45 degrees in the presence of 0.15M sodium ion.
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