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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 梁博煌(Po-Huang Liang) | |
dc.contributor.author | Kian-Pin Tan | en |
dc.contributor.author | 陳建儐 | zh_TW |
dc.date.accessioned | 2021-05-20T20:06:37Z | - |
dc.date.available | 2013-08-20 | |
dc.date.available | 2021-05-20T20:06:37Z | - |
dc.date.copyright | 2011-08-20 | |
dc.date.issued | 2011 | |
dc.date.submitted | 2011-08-16 | |
dc.identifier.citation | (April 2009). 'Influenza (Seasonal).' from http://www.who.int/mediacentre/factsheets/fs211/en/.
. 'International Programs.' from http://www.census.gov/population/international/. Ahlquist, P., A. O. Noueiry, et al. (2003). 'Host factors in positive-strand RNA virus genome replication.' J Virol 77(15): 8181-8186. Anand, K., J. Ziebuhr, et al. (2003). 'Coronavirus main proteinase (3CLpro) structure: basis for design of anti-SARS drugs.' Science 300(5626): 1763-1767. Atigadda, V. R., W. J. Brouillette, et al. (1999). 'Potent inhibition of influenza sialidase by a benzoic acid containing a 2-pyrrolidinone substituent.' J Med Chem 42(13): 2332-2343. Baboonian, C. and T. Treasure (1997). 'Meta-analysis of the association of enteroviruses with human heart disease.' Heart 78(6): 539-543. Babu, Y. S., P. Chand, et al. (2000). 'BCX-1812 (RWJ-270201): discovery of a novel, highly potent, orally active, and selective influenza neuraminidase inhibitor through structure-based drug design.' J Med Chem 43(19): 3482-3486. Bharatham, N., K. Bharatham, et al. (2007). 'Pharmacophore identification and virtual screening for methionyl-tRNA synthetase inhibitors.' J Mol Graph Model 25(6): 813-823. Binford, S. L., F. Maldonado, et al. (2005). 'Conservation of amino acids in human rhinovirus 3C protease correlates with broad-spectrum antiviral activity of rupintrivir, a novel human rhinovirus 3C protease inhibitor.' Antimicrob Agents Chemother 49(2): 619-626. Chand, P., Y. S. Babu, et al. (1997). 'Design and synthesis of benzoic acid derivatives as influenza neuraminidase inhibitors using structure-based drug design.' J Med Chem 40(25): 4030-4052. Chand, P., Y. S. Babu, et al. (2004). 'Syntheses and neuraminidase inhibitory activity of multisubstituted cyclopentane amide derivatives.' J Med Chem 47(8): 1919-1929. Chen, L., C. Gui, et al. (2005). 'Cinanserin is an inhibitor of the 3C-like proteinase of severe acute respiratory syndrome coronavirus and strongly reduces virus replication in vitro.' J Virol 79(11): 7095-7103. Cheng, P. K., T. W. Leung, et al. (2009). 'Oseltamivir- and amantadine-resistant influenza viruses A (H1N1).' Emerg Infect Dis 15(6): 966-968. Consortium., C. S. M. E. (2004). 'Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China.' Science 303(5664): 1666-1669. Debnath, A. K. (2002). 'Pharmacophore mapping of a series of 2,4-diamino-5-deazapteridine inhibitors of Mycobacterium avium complex dihydrofolate reductase.' J Med Chem 45(1): 41-53. Drosten, C., S. Gunther, et al. (2003). 'Identification of a novel coronavirus in patients with severe acute respiratory syndrome.' N Engl J Med 348(20): 1967-1976. Du, L. P., M. Y. Li, et al. (2005). 'Characterization of binding site of closed-state KCNQ1 potassium channel by homology modeling, molecular docking, and pharmacophore identification.' Biochem Biophys Res Commun 332(3): 677-687. Fan, K., P. Wei, et al. (2004). 'Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase.' J Biol Chem 279(3): 1637-1642. Fields, B. N. D. M. K., Robert M. Chanock, Joseph L. Melnick, Bernard Roizman, Robert E. Shope (1985). 'Fields Virology.' New York: Raven Press: 739-794. Guan, Y., B. J. Zheng, et al. (2003). 'Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China.' Science 302(5643): 276-278. Hayden, F. G., R. B. Belshe, et al. (1989). 'Emergence and apparent transmission of rimantadine-resistant influenza A virus in families.' N Engl J Med 321(25): 1696-1702. Huang, I. C., W. Li, et al. (2008). 'Influenza A virus neuraminidase limits viral superinfection.' J Virol 82(10): 4834-4843. Kim, C. U., W. Lew, et al. (1997). 'Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity.' J Am Chem Soc 119(4): 681-690. Kim, C. U., W. Lew, et al. (1998). 'Structure-activity relationship studies of novel carbocyclic influenza neuraminidase inhibitors.' J Med Chem 41(14): 2451-2460. Ksiazek, T. G., D. Erdman, et al. (2003). 'A novel coronavirus associated with severe acute respiratory syndrome.' N Engl J Med 348(20): 1953-1966. Kuo, C.-J. (2009). Characterization, Inhibition, and Engineering of 3C and 3C-Like Viral Proteases. Institute of Biochemical Science, National Taiwan University. Kuo, C. J., Y. H. Chi, et al. (2004). 'Characterization of SARS main protease and inhibitor assay using a fluorogenic substrate.' Biochem Biophys Res Commun 318(4): 862-867. Kuo, C. J., H. G. Liu, et al. (2009). 'Individual and common inhibitors of coronavirus and picornavirus main proteases.' FEBS Lett 583(3): 549-555. Kuo, C. J., J. J. Shie, et al. (2008). 'Design, synthesis, and evaluation of 3C protease inhibitors as anti-enterovirus 71 agents.' Bioorg Med Chem 16(15): 7388-7398. Lau, S. K., P. C. Woo, et al. (2005). 'Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats.' Proc Natl Acad Sci U S A 102(39): 14040-14045. Lee, C. C., C. J. Kuo, et al. (2009). 'Structural basis of inhibition specificities of 3C and 3C-like proteases by zinc-coordinating and peptidomimetic compounds.' J Biol Chem 284(12): 7646-7655. Lee, E. S., W. G. Lee, et al. (2007). 'Development of potent inhibitors of the coxsackievirus 3C protease.' Biochem Biophys Res Commun 358(1): 7-11. Lee, N., D. Hui, et al. (2003). 'A major outbreak of severe acute respiratory syndrome in Hong Kong.' N Engl J Med 348(20): 1986-1994. Lew, W., X. Chen, et al. (2000). 'Discovery and development of GS 4104 (oseltamivir): an orally active influenza neuraminidase inhibitor.' Curr Med Chem 7(6): 663-672. Lew, W., H. Wu, et al. (1998). 'A new series of C3-aza carbocyclic influenza neuraminidase inhibitors: synthesis and inhibitory activity.' Bioorg Med Chem Lett 8(23): 3321-3324. Li, W., Z. Shi, et al. (2005). 'Bats are natural reservoirs of SARS-like coronaviruses.' Science 310(5748): 676-679. Makoto Yamashita, T. T., Masayo Kakuta, Akane Tokumitsu, Hatsumi Nasu, and Shuku Kubo (2009). 'CS-8958, a Prodrug of the New Neuraminidase Inhibitor R-125489, Shows Long-Acting Anti-Influenza Virus Activity.' Antimicrobial Agents and Chemotherapy 53: 7. Marra, M. A., S. J. Jones, et al. (2003). 'The Genome sequence of the SARS-associated coronavirus.' Science 300(5624): 1399-1404. Matthew A. Williams, W. L., Dirk B. Mendel, Chun Y. Tai, Paul A. Escarpe, W. Graeme Laver, Raymond C. Stevens and Choung U. Kim (1997). 'Structure-activity relationships of carbocyclic influenza neuraminidase inhibitors.' Bioorganic & Medicinal Chemistry Letters 7(14): 6. Maze, S. S. and R. J. Adolph (1990). 'Myocarditis: unresolved issues in diagnosis and treatment.' Clin Cardiol 13(2): 69-79. Memoli, M. J., R. J. Hrabal, et al. (2010). 'Rapid selection of oseltamivir- and peramivir-resistant pandemic H1N1 virus during therapy in 2 immunocompromised hosts.' Clin Infect Dis 50(9): 1252-1255. Niu, C., J. Yin, et al. (2008). 'Molecular docking identifies the binding of 3-chloropyridine moieties specifically to the S1 pocket of SARS-CoV Mpro.' Bioorg Med Chem 16(1): 293-302. Peiris, J. S., S. T. Lai, et al. (2003). 'Coronavirus as a possible cause of severe acute respiratory syndrome.' Lancet 361(9366): 1319-1325. Perola, E., W. P. Walters, et al. (2004). 'A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance.' Proteins 56(2): 235-249. Pinto, L. H. and R. A. Lamb (2006). 'The M2 proton channels of influenza A and B viruses.' J Biol Chem 281(14): 8997-9000. Ramajayam, R., K. P. Tan, et al. (2010). 'Synthesis and evaluation of pyrazolone compounds as SARS-coronavirus 3C-like protease inhibitors.' Bioorg Med Chem 18(22): 7849-7854. Ramajayam, R., K. P. Tan, et al. (2010). 'Synthesis, docking studies, and evaluation of pyrimidines as inhibitors of SARS-CoV 3CL protease.' Bioorg Med Chem Lett 20(12): 3569-3572. Rose, N. R. and S. L. Hill (1996). 'The pathogenesis of postinfectious myocarditis.' Clin Immunol Immunopathol 80(3 Pt 2): S92-99. Russell, R. J., L. F. Haire, et al. (2006). 'The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design.' Nature 443(7107): 45-49. Skehel, J. J. and D. C. Wiley (2000). 'Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin.' Annu Rev Biochem 69: 531-569. Snijder, E. J., P. J. Bredenbeek, et al. (2003). 'Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage.' J Mol Biol 331(5): 991-1004. von Itzstein, M., W. Y. Wu, et al. (1993). 'Rational design of potent sialidase-based inhibitors of influenza virus replication.' Nature 363(6428): 418-423. Wang, G. T., Y. Chen, et al. (2001). 'Design, synthesis, and structural analysis of influenza neuraminidase inhibitors containing pyrrolidine cores.' J Med Chem 44(8): 1192-1201. Watanabe, A., S. C. Chang, et al. (2010). 'Long-acting neuraminidase inhibitor laninamivir octanoate versus oseltamivir for treatment of influenza: A double-blind, randomized, noninferiority clinical trial.' Clin Infect Dis 51(10): 1167-1175. Yang, H., M. Yang, et al. (2003). 'The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor.' Proc Natl Acad Sci U S A 100(23): 13190-13195. Zhang, J., C. Huitema, et al. (2008). 'Aryl methylene ketones and fluorinated methylene ketones as reversible inhibitors for severe acute respiratory syndrome (SARS) 3C-like proteinase.' Bioorg Chem 36(5): 229-240. Zhang, J., H. I. Pettersson, et al. (2007). 'Design, synthesis, and evaluation of inhibitors for severe acute respiratory syndrome 3C-like protease based on phthalhydrazide ketones or heteroaromatic esters.' J Med Chem 50(8): 1850-1864. Zhang, J., K. Yu, et al. (2006). 'Neuraminidase pharmacophore model derived from diverse classes of inhibitors.' Bioorg Med Chem Lett 16(11): 3009-3014. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/9014 | - |
dc.description.abstract | 嚴重急性呼吸系統綜合症是一種具高度傳染性和致命性的呼吸系統疾病。它是由一種在嚴重急性呼吸系統綜合症爆發之前都沒有被發現過的新型冠狀病毒所造成的,即SARS冠狀病毒。這種疾病於2003年爆發,且有近10%的疾病患者因此死亡。雖然至今已經七年沒有確診病例,但是有研究顯示蝙蝠是SARS冠狀病毒的自然寄主,所以對於此疾病的再度爆發仍有疑慮。在開發對抗這種病毒的藥物的過程當中,科學家發現SARS 3CL蛋白酶在病毒的複製過程當中扮演了非常重要的角色,也因此SARS 3CL蛋白酶的抑制也成為了一個非常重要的藥物開發方向。根據先前的研究指出,吡啶化合物可以作為 SARS 3CL蛋白酶可逆抑製劑,一系列的嘧啶化合物也基於此基礎上被合成。此外,我們實驗室之前也應用高通量藥物篩選發現了一些吡唑啉酮化合物可以同時有效的抑制3C和3CL蛋白酶。作為實驗的延續,一系列的吡唑啉酮化合物也因此被合成。實驗結果表明,其中一個嘧啶化合物能夠有效的抑制SARS 3CL蛋白酶,且半抑制率為6.1μM。此外,其中一個吡唑啉酮化合物可以同時分別以8.4μM,及9.6μM的半抑制率有效地抑制SARS 3CL蛋白酶及柯薩奇B3 3C蛋白酶。
流感病毒是一種單股負鏈的RNA病毒,同時它也是造成的季節性流感和流感大流行的罪魁禍首。血凝素和神經氨酸酶在流感病毒的生活史中扮演了非常重要的角色。其中,神經氨酸酶催化唾液酸的水解協助成熟流感病毒脫離宿主細胞感染新的細胞,因此抑制流感神經氨酸酶一個非常重要的藥物開發方向。 我們的實驗室在之前的高通量藥物篩選中發現,VK84可以以16.6μM的半抑制率,有效的抑制H5N1的神經氨酸酶。之後我們也根據電腦模擬的結果為VK84做了改進,合成了一系列的衍生物。 VK84是一種吡唑啉酮化合物,它的衍生物之一VK94經實驗證明能以1.7μM證明能的半抑制率,有效的抑制H1N1神經氨酸酶。根據對接結果,我們發現VK94是一個非常有吸引力的和潛力可以進行改良的抑製劑,並且通過改良從而更有效的抑制神經氨酸酶。 此外,為了提高高通量藥物篩選準確度,並且從中節省資金和精力,我們應用了Catalyst 4.10這套軟體建構了一個3D-QSAR藥效團。經過一系列的驗證,Hypo1似乎是一個具預測能力並且可用來進行虛擬高通量藥物篩選的可靠模型。總體而言,一個從虛擬高通量藥物篩選到抑制劑檢定的完整實驗流程已經被完整建立,並且肯定將在未來的藥物開發過程中扮演一定的角色。 | zh_TW |
dc.description.abstract | Severe acute respiratory syndrome (SARS) is a highly contagious and fatal respiratory disease. It is caused by a novel coronavirus which never been discovered before the SARS, namely SARS-CoV. The outbreak of this deadly disease in 2003 had killed almost 10% of the infected patients. Although it has been 7 years since the last reported case of SARS, the evidences that bats are natural reservoirs of SARS-CoV have led to the concerns about the reemergence of the deadly disease. In search of the potential drugs against the deadly disease, SARS 3CLpro a protease which playing essential roles during the viral replication has been targeted for the drugs development. A series of pyrimidine compounds have been synthesized based on the findings that pyridine compounds could act as SARS 3CLpro reversible inhibitors. Furthermore, a series of pyrazolone compounds have also been synthesized as part of our laboratory’s continuation work of high throughput screenings. Some of the pyrazolone compounds have also been identified as common inhibitors for both 3C and 3CL protease, so that the Coxsackievirus B3 3Cpro have also been purified for further inhibition assay. The results show that one of the pyrimidine analogs could inhibit the SARS 3CLpro with an IC50 of 6.1μM. Meanwhile, a pyrazolone analog could inhibits SARS 3CLpro as well as inhibits CVB3 3Cpro with an IC50 of 8.4μM and 9.6μM respectively.
Influenza viruses are negative sense, single-stranded, segmented RNA viruses. It is the viruses which cause the seasonal flu and even flu pandemics. Two glycoproteins, hemagglutinin and neuraminidase play very crucial roles during the influenza virus infection and replication. Neuraminidase facilitates the release of the replicate viruses from the infected cells by enzymatically cleavage of the sialic acid groups from host glycoproteins and hence it is a very good target for drugs development. VK84, an original hit that inhibits the H5N1 neuraminidase with an IC50 of 16.6 μM has been modified based on the computer modeling and a series of analogs were then been synthesized. VK84 is also a pyrazolone compound and one of its analogs, VK94, inhibits the H1N1 neuraminidase with an IC50 of 1.7μM. According to the docking results, VK94 shows some unexpected H-bonds and this made VK94 as an attractive and potential inhibitor for further modifications as pyrazolone compounds that have never been reported as neuraminidase inhibitors. Furthermore, in order to increase the accuracies and to save money and efforts for high throughput screening, Catalyst 4.10 was utilized to generate a reliable and predictive 3D-QSAR. The generated pharmacophore, Hypo1 has been validated and it seems that it is a reliable and predictive pharmacophore for virtual high throughput screening. In general, a complete procedure from the virtual high throughput screenings then to the inhibition assays has been developed. | en |
dc.description.provenance | Made available in DSpace on 2021-05-20T20:06:37Z (GMT). No. of bitstreams: 1 ntu-100-R98b46035-1.pdf: 2812042 bytes, checksum: 8009a0ee884d4221890f228ce2e943b5 (MD5) Previous issue date: 2011 | en |
dc.description.tableofcontents | CONTENTS
口試委員會審定書----------------------------------------------------------------------------------------i 誌謝------------------------------------------------------------------------------------------------------------ii 中文摘要----------------------------------------------------------------------------------------------------iii Abstract--------------------------------------------------------------------------------------------------------iv Chapter 1 INTRODUCTION 1.1 SARS-Coronavirus and SARS 3C-like Protease----------------------------------------1 1.2 Coxsackie Virus B3 and 3C Protease-----------------------------------------------------3 1.3 Influenza Virus and Neuraminidase------------------------------------------------------5 Chapter 2 MATERIALS AND METHODS 2.1 Inhibitors-------------------------------------------------------------------------------------8 2.2 Enzyme Expression and Purification 2.2.1 SARS-3CLpro-----------------------------------------------------------------------8 2.2.2 CVB3 3Cpro-------------------------------------------------------------------------9 2.2.3 H5N1 and H1N1 Viral Neuramidases------------------------------------------9 2.3 Enzyme Inhibition Assay and IC50 Determination 2.3.1 SARS 3CLpro and CVB3 3Cpro Inhibition Assay-----------------------------11 2.3.2 Influenza Viral Neuraminidase Inhibition Assay-----------------------------11 2.3.3 IC50 Determination ---------------------------------------------------------------12 2.4 Computer Modeling 2.4.1 Docking Studies of SARS 3CLpro and CVB3 3Cpro--------------------------12 2.4.2 Docking Studies of Viral Neuraminidase--------------------------------------13 2.5 3D-QSAR Pharmacophore Generation 2.5.1 Training Set------------------------------------------------------------------------13 2.5.2 Generation of Hypo1-------------------------------------------------------------14 2.5.3 Cost Analysis----------------------------------------------------------------------14 2.5.4 CatScramble-----------------------------------------------------------------------15 2.5.5 Test Set-----------------------------------------------------------------------------16 Chapter 3 RESULTS 3.1 Expression and Purification of SARS 3CLpro------------------------------------------17 3.2 Inhibition of Pyrimidine Compounds Against SARS 3CLpro and Their Binding Modes---------------------------------------------------------------------------------------------------------17 3.3 Inhibition of Pyrazolone Compounds Against SARS 3CLpro and Their binding modes---------------------------------------------------------------------------------------------------------18 3.4 Expression and Purification of CVB3 3Cpro-------------------------------------------20 3.5 Inhibition of Pyrazolone Compounds Against CVB3 3Cpro and Their Binding Modes---------------------------------------------------------------------------------------------------------20 3.6 Expression and Purification of H1N1 and H5N1 Neuraminidase------------------21 3.7 Inhibition of Pyrazolone Compounds Against the H1N1 and H5N1 NA---------22 3.8 Generation of the Catalyst Hypotheses-------------------------------------------------24 3.9 Validation of the Hypo ------------------------------------------------------------------24 Chapter 4 DISCUSSIONS 4.1 SARS-CoV 3CLpro and its Inhibitors----------------------------------------------------26 4.2 Neuraminidase and its Inhibitors --------------------------------------------------------26 4.3 Hypo1 and its Modification --------------------------------------------------------------27 FIGURES Figure 1-------------------------------------------------------------------------------------------------------29 Figure 2a & 2b-----------------------------------------------------------------------------------------------30 Figure 3a & 3b-----------------------------------------------------------------------------------------------31 Figure 4a & 4b-----------------------------------------------------------------------------------------------32 Figure 5a & 5b-----------------------------------------------------------------------------------------------33 Figure 6a & 6b-----------------------------------------------------------------------------------------------34 Figure 7a & 7b-----------------------------------------------------------------------------------------------35 Figure 7c------------------------------------------------------------------------------------------------------36 Figure 8a------------------------------------------------------------------------------------------------------37 Figure 8b------------------------------------------------------------------------------------------------------38 Figure 9 -------------------------------------------------------------------------------------------------------39 TABLES Table 1--------------------------------------------------------------------------------------------------------40 Table 2--------------------------------------------------------------------------------------------------------41 Table 3--------------------------------------------------------------------------------------------------------42 Table 4--------------------------------------------------------------------------------------------------------43 Table 5--------------------------------------------------------------------------------------------------------44 Table 6--------------------------------------------------------------------------------------------------------45 GRAPHS Graph 1--------------------------------------------------------------------------------------------------------46 Graph 2--------------------------------------------------------------------------------------------------------47 SUPPLEMENTARY Supplementary figure 1 -------------------------------------------------------------------------------------48 Supplementary figure 2 -------------------------------------------------------------------------------------49 Supplementary table 1---------------------------------------------------------------------------------------55 Supplementary table 2---------------------------------------------------------------------------------------56 Supplementary table 3---------------------------------------------------------------------------------------59 APPENDIXES Appendix 1----------------------------------------------------------------------------------------------------60 Appendix 2----------------------------------------------------------------------------------------------------61 Appendix 3----------------------------------------------------------------------------------------------------62 REFERENCES ---------------------------------------------------------------------------------------------63 | |
dc.language.iso | en | |
dc.title | 探索致命病毒的潛力藥物:病毒3C及3CL蛋白酶與流感病毒之神經氨酸酶的抑制 | zh_TW |
dc.title | Exploring the potent drugs for life-threatening viruses: Inhibition of 3C & 3C-Like Viral Proteases and Influenza Neuraminidase | en |
dc.type | Thesis | |
dc.date.schoolyear | 99-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 蔡蔭和(Inn-Ho Tsai),陳昭岑(Chao-Tsen Chen) | |
dc.subject.keyword | 嚴重急性呼吸系統綜合症,3C 蛋白酶,3CL蛋白酶,流感病毒,神經胺酸酶,嘧啶化合物,吡,唑啉,酮化合物,3D-構效關係藥效團, | zh_TW |
dc.subject.keyword | Severe acute respiratory syndrome,3C protease,3CL protease,Influenza virus,Neuraminidase,Pyrimidine,Pyrazolone,3D-QSAR pharmacophore, | en |
dc.relation.page | 69 | |
dc.rights.note | 同意授權(全球公開) | |
dc.date.accepted | 2011-08-16 | |
dc.contributor.author-college | 生命科學院 | zh_TW |
dc.contributor.author-dept | 生化科學研究所 | zh_TW |
顯示於系所單位: | 生化科學研究所 |
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