本文選題：宿主靶向抗病毒 + 藥物重定位��； 參考：《中國(guó)人民解放軍軍事醫(yī)學(xué)科學(xué)院》2015年博士論文

【摘要】：時(shí)至今日,病毒感染引發(fā)的疾病仍是人類(lèi)健康和公共衛(wèi)生的一大威脅,全球每年死于病毒感染性疾病的人數(shù)以百萬(wàn)計(jì)。面對(duì)慢性病毒感染性疾病的流行、急性新出現(xiàn)病毒疫情的爆發(fā)、一度消失或已被控制病毒的“死灰復(fù)燃”以及生化武器可能被恐怖襲擊利用這些威脅,迫切需要提出安全快捷有效的抗病毒策略。傳統(tǒng)的病毒靶向策略存在諸多問(wèn)題,主要包括靶標(biāo)選擇空間有限、病毒易產(chǎn)生耐藥性、以病毒為靶標(biāo)藥物的抗病毒譜較窄等。針對(duì)這些弊端提出的宿主靶向抗病毒策略,不僅具有靶標(biāo)選擇空間大、不易產(chǎn)生耐藥性、有望實(shí)現(xiàn)廣譜抗病毒的優(yōu)勢(shì),更為重要的是,為利用已知藥物抗病毒打開(kāi)了廣闊的空間。由于宿主靶向抗病毒策略一個(gè)突出的優(yōu)勢(shì)就在于存在大量靶向宿主蛋白的已知藥物,所以宿主靶向抗病毒藥物重定位策略應(yīng)運(yùn)而生。利用藥物重定位的方法可以充分利用已知藥物,縮短周期、節(jié)約成本、降低風(fēng)險(xiǎn),對(duì)于抗病毒藥物研發(fā)來(lái)說(shuō),不僅能夠滿(mǎn)足反恐和突發(fā)疫情控制的需要,為病毒性傳染病的防控提供應(yīng)急藥物解決方案,還能為通過(guò)模擬創(chuàng)新手段開(kāi)發(fā)新藥奠定基礎(chǔ)。另外,除了為人熟知的人工合成藥物,制藥產(chǎn)業(yè)也將目光轉(zhuǎn)向了天然藥物。由于天然藥物具有經(jīng)濟(jì)有效、安全性較高等優(yōu)勢(shì),同時(shí)順應(yīng)多向藥理學(xué)的思路,近年來(lái)制藥產(chǎn)業(yè)對(duì)天然藥物的研究蓬勃發(fā)展,天然藥物在當(dāng)前藥物研發(fā)領(lǐng)域表現(xiàn)出巨大的潛力。天然藥物對(duì)于新藥研發(fā)具有很大的價(jià)值和指導(dǎo)意義,在已有抗病毒藥物中來(lái)源于天然產(chǎn)物的化合物所占比例也很高,可見(jiàn)天然藥物用于抗病毒治療前景廣闊。本文綜合應(yīng)用關(guān)聯(lián)網(wǎng)絡(luò)的方法,收集整合了病毒感染過(guò)程中的病毒靶標(biāo)蛋白(Virus Targeting Proteins,VTPs)和關(guān)鍵宿主因子(Essential Host Factors,EHFs),結(jié)合藥物-靶標(biāo)關(guān)聯(lián)數(shù)據(jù)、天然藥物成分-靶標(biāo)關(guān)聯(lián)數(shù)據(jù)和蛋白質(zhì)相互作用數(shù)據(jù),以病毒、化合物共用靶標(biāo)為基礎(chǔ)關(guān)聯(lián)已知藥物化合物和病毒,評(píng)估已知化合物重定位于抗病毒應(yīng)用的可能性,并進(jìn)一步探索了它們用于廣譜抗病毒的潛力。本文首先收集整合了來(lái)源于文獻(xiàn)報(bào)道的病原體感染EHF,在此基礎(chǔ)上建立了EHFPI數(shù)據(jù)庫(kù)。其次將整合的病毒感染EHF數(shù)據(jù)集與來(lái)自Vir Host Net數(shù)據(jù)庫(kù)的VTP數(shù)據(jù)集進(jìn)行比較分析,闡述這兩種病毒感染宿主因子的聯(lián)系與區(qū)別。在此基礎(chǔ)上基于病毒與Drug Bank數(shù)據(jù)庫(kù)藥物的共用靶標(biāo)建立病毒-藥物關(guān)聯(lián)網(wǎng)絡(luò),系統(tǒng)分析已知藥物對(duì)于病毒感染進(jìn)行防治的可能性,并進(jìn)一步探討已知藥物應(yīng)用于廣譜抗病毒的潛力。此后我們還收集整理了來(lái)自HIT數(shù)據(jù)庫(kù)的天然藥物及其靶標(biāo)信息,與Drug Bank數(shù)據(jù)庫(kù)靶標(biāo)進(jìn)行對(duì)比,計(jì)算分析天然藥物靶標(biāo)的富集情況,預(yù)測(cè)天然藥物在治療人類(lèi)復(fù)雜疾病中的傾向與趨勢(shì)。最后以相同的思路基于共用靶標(biāo)探討了天然藥物重定位于抗病毒及廣譜抗病毒的可能性�；谙到y(tǒng)生物學(xué)和分子網(wǎng)絡(luò),以計(jì)算的方法理性預(yù)測(cè)已知藥物及天然藥物成分重定位于抗病毒的潛力,大規(guī)模系統(tǒng)地評(píng)估宿主靶向抗病毒已知化合物重定位的可能性可以為藥物的發(fā)現(xiàn)與設(shè)計(jì)提供新的方法和策略。本文第一章綜述了目前抗病毒藥物研究的背景、方法與現(xiàn)狀,提出了宿主靶向策略和藥物重定位運(yùn)用于抗病毒藥物研發(fā)的若干關(guān)鍵問(wèn)題,闡述了論文的主要研究?jī)?nèi)容、組織形式結(jié)構(gòu)和技術(shù)路線。高通量篩選與計(jì)算技術(shù)的飛速發(fā)展極大地促進(jìn)了微生物學(xué)發(fā)展水平,使微生物學(xué)家可以更為全面地解讀病原體-宿主相互作用關(guān)系。通過(guò)基因組規(guī)模的RNA干擾(RNA interference,RNAi)篩選實(shí)驗(yàn),可以得到病原體感染的EHF,敲除它們會(huì)嚴(yán)重影響病原體在宿主體內(nèi)的生存和復(fù)制。論文第二章展示了我們手動(dòng)收集整合的病原體感染宿主的EHF及其相關(guān)信息,在此基礎(chǔ)上我們建立了EHFPI生物信息學(xué)數(shù)據(jù)庫(kù)及相關(guān)分析資源。EHFPI數(shù)據(jù)庫(kù)包含了25種臨床上重要的病原體種類(lèi)的4634個(gè)EHF基因及其對(duì)應(yīng)的蛋白質(zhì),展示了相關(guān)論文、篩選實(shí)驗(yàn)、病原體和表型注釋等信息。另外,EHFPI數(shù)據(jù)庫(kù)還提供了6種有效的數(shù)據(jù)整合分析工具,以此促進(jìn)我們對(duì)EHF基因及其對(duì)應(yīng)產(chǎn)物生物學(xué)意義的理解,同時(shí)從多個(gè)角度闡釋蛋白質(zhì)相互作用網(wǎng)絡(luò)、藥物靶標(biāo)與疾病之間的關(guān)系。我們還進(jìn)一步選取了通過(guò)基因組規(guī)模RNAi篩選實(shí)驗(yàn)得到的病毒感染宿主的EHF。除此之外,還有一類(lèi)重要的宿主因子即VTP,它們與病毒直接相互作用以保障病毒在細(xì)胞內(nèi)的生存。然而,這兩種宿主因子之間的聯(lián)系卻很少被研究。論文第三章以人類(lèi)免疫缺陷病毒1型(Human Immunodeficiency Virus-1,HIV-1)和流行性感冒A型病毒(influenza A virus,IAV)這兩種病毒的感染為模型,對(duì)其EHF和VTP集合進(jìn)行比對(duì)分析,發(fā)現(xiàn)兩種病毒EHF與VTP的重合程度非常小,二者都具有明顯的差異基因表達(dá),調(diào)控方向一致。EHF與VTP都傾向于占據(jù)人類(lèi)蛋白質(zhì)相互作用網(wǎng)絡(luò)上具有拓?fù)渲匾缘奈恢?兩者之間傾向于直接相互作用。我們還針對(duì)這兩種病毒識(shí)別出一些連接度比較大的EHF和VTP。進(jìn)一步研究發(fā)現(xiàn),對(duì)于EHF與VTP共通路的情形,多數(shù)EHF傾向于位于VTP上游起調(diào)節(jié)作用,以此強(qiáng)調(diào)了EHF在調(diào)節(jié)過(guò)程中的重要意義。由于當(dāng)前主流的病毒靶向策略存在一些困難,抗病毒藥物研發(fā)仍然充滿(mǎn)挑戰(zhàn)。宿主靶向抗病毒策略具有靶標(biāo)選擇空間大、不易產(chǎn)生耐藥性、容易實(shí)現(xiàn)廣譜抗病毒等優(yōu)勢(shì),同時(shí),有大量現(xiàn)成的藥物可以使用,避免了全新藥物開(kāi)發(fā)周期漫長(zhǎng)、耗資巨大、風(fēng)險(xiǎn)較高等弊端。因此,宿主靶向抗病毒藥物重定位策略已經(jīng)成為抗病毒藥物研發(fā)領(lǐng)域一個(gè)重要的方向。論文第四章基于對(duì)已有藥物-靶標(biāo)互聯(lián)關(guān)系和病毒-宿主相互作用關(guān)系知識(shí)的整合,力圖揭示哪些已經(jīng)驗(yàn)證的病毒生存依賴(lài)的宿主蛋白可能被現(xiàn)有藥物干擾,進(jìn)而通過(guò)整合病毒-宿主蛋白相互作用網(wǎng)絡(luò)和藥物-靶標(biāo)關(guān)系網(wǎng)絡(luò)構(gòu)建了藥物-病毒關(guān)系網(wǎng)絡(luò),系統(tǒng)梳理了可直接或間接作用于病毒依賴(lài)的宿主蛋白的已知藥物,給出了對(duì)現(xiàn)有藥物宿主靶向抗病毒潛力的系統(tǒng)評(píng)估,并進(jìn)一步討論了通過(guò)已知藥物進(jìn)行廣譜抗病毒的可能性。除了為人熟知的化學(xué)合成藥物,天然藥物或來(lái)源于天然產(chǎn)物的化合物在研究領(lǐng)域和制藥產(chǎn)業(yè)中也具有特別重要的意義。天然藥物已被人類(lèi)使用了很長(zhǎng)時(shí)間,由于其經(jīng)濟(jì)有效、安全性高、符合現(xiàn)代多向藥理學(xué)的理念,因而對(duì)現(xiàn)代藥物開(kāi)發(fā)也具有重要的價(jià)值,并且在現(xiàn)代藥物治療中取得了突出的成績(jī)。論文第五章主要以探索天然藥物在復(fù)雜疾病治療中的潛在應(yīng)用為目的,應(yīng)用大規(guī)模靶標(biāo)分析的方法,從靶標(biāo)蛋白相關(guān)通路和疾病分類(lèi)的角度將HIT數(shù)據(jù)庫(kù)提供的天然藥物靶標(biāo)與Drug Bank數(shù)據(jù)庫(kù)提供的合成藥物靶標(biāo)進(jìn)行對(duì)比,建立了天然藥物成分-直接靶標(biāo)關(guān)系二分網(wǎng)絡(luò)。我們從當(dāng)前藥物研發(fā)趨勢(shì)的視角討論了該網(wǎng)絡(luò)的關(guān)鍵特性和天然藥物及其靶標(biāo)之間的關(guān)聯(lián),發(fā)現(xiàn)天然藥物可能成為潛在的抗癌藥物。鑒于天然藥物具有許多獨(dú)特的優(yōu)勢(shì),又契合現(xiàn)代藥物研發(fā)領(lǐng)域多向藥理學(xué)的思路,探索天然藥物在宿主靶向抗病毒藥物重定位中的應(yīng)用可能帶來(lái)新的發(fā)現(xiàn)。論文第六章回顧整合了關(guān)于病毒、已知天然藥物成分及其靶標(biāo)蛋白的數(shù)據(jù)信息,基于共用靶標(biāo)探討天然藥物成分與病毒之間的二分關(guān)系進(jìn)而建立了天然藥物成分-病毒關(guān)系網(wǎng)絡(luò)。在此基礎(chǔ)上討論了天然藥物成分重定位于宿主靶向抗病毒的可能性,評(píng)估了它們用于廣譜抗病毒的潛力。大規(guī)模網(wǎng)絡(luò)分析表明,盡管總體上看,天然藥物成分重定位于廣譜抗病毒空間有限,但靶向被多種病毒共用靶標(biāo)蛋白的藥物成分更有可能成為潛在的廣譜抗病毒藥物。論文最后對(duì)全文所述工作進(jìn)行了簡(jiǎn)要總結(jié),并對(duì)下一步的工作計(jì)劃進(jìn)行了展望。
[Abstract]:Today, the disease caused by virus infection is still a major threat to human health and public health. Millions of people die of virus infection in the world every year. In the face of the epidemic of chronic viral infection, the outbreak of acute new virus epidemic, once disappeared or has been controlled by the "resurgence" and biochemical weapons. It is possible to use these threats by terrorist attacks, and it is urgent to propose a safe, efficient and effective antiviral strategy. There are many problems in the traditional virus targeting strategy, including the limited space of target selection, the susceptibility of the virus to drug resistance, the narrower antiviral spectrum of the virus as the target drug, and the host targeting against these disadvantages. Virus strategy not only has large target selection space, not easy to produce drug resistance, it is expected to realize the advantages of broad-spectrum antivirus. More importantly, it opens wide space for the use of known antiviral drugs. Because a prominent advantage of host targeting antiviral strategy lies in the existence of a large number of known drugs targeting the host protein, so the host has a large number of known drugs. The repositioning strategy of the main target to antiviral drugs came into being. The method of drug repositioning can make full use of the known drugs, shorten the cycle, save the cost and reduce the risk. For the research of antiviral drugs, it can not only meet the needs of anti-terrorism and outbreak control, but also provide an emergency drug solution for the prevention and control of viral infectious diseases. In addition, in addition to the known synthetic drugs, the pharmaceutical industry will also turn to natural drugs. The pharmaceutical industry has studied natural drugs in recent years because of its economic efficiency, high safety and multi direction pharmacology. Natural drugs have great potential in the field of drug research and development. Natural drugs have great value and guiding significance for the research and development of new drugs. The proportion of compounds derived from natural products in the existing antiviral drugs is also very high. It is obvious that natural drugs are widely used in antiviral treatment. This article is a comprehensive application. The combined network method collects and integrates virus target protein (Virus Targeting Proteins, VTPs) and key host factors (Essential Host Factors, EHFs) in the process of virus infection, combined with drug target related data, natural drug components - target related data and protein interaction data, based on virus and compound target as the basis. Associated with known drug compounds and viruses, the potential of known compounds relocated to antiviral applications was evaluated, and their potential for broad-spectrum antiviral treatment was further explored. First, a EHFPI database was established on the basis of an integrated pathogen infection EHF from the literature. Secondly, the integrated virus infection EHF was established. The data set and the VTP data set from the Vir Host Net database are compared and analyzed to explain the relationship and difference between the two virus infected host factors. Based on this, the virus drug association network is set up based on the common target of the virus and Drug Bank database drugs, and the possibility of prevention and control of the virus infection by known drugs is systematically analyzed. The potential of known drugs used in broad-spectrum antivirus was further explored. After that, we collected and collated the information of natural drugs and targets from the HIT database, compared with the target of Drug Bank database, calculated and analyzed the enrichment of natural drug targets, and predicted the tendency and trend of natural drugs in the treatment of human complex diseases. Finally, the possibility of relocating natural drugs to antiviral and broad-spectrum antiviral agents is discussed based on common targets. Based on systematic biology and molecular networks, the potential of the known drugs and natural drug components relocated to the antiviral potential is rationally predicted and a large systematic assessment of the known host targeted antiviral activity is made in a large scale. The possibility of relocation of compounds can provide new methods and strategies for the discovery and design of drugs. In the first chapter, the background, methods and status of the research on antiviral drugs are reviewed. The key problems of host targeting strategy and drug relocation in the research and development of antiviral drugs are put forward, and the main research in this paper is expounded. The development of high throughput screening and computing technology has greatly promoted the level of Microbiology, enabling microbiologist to interpret the relationship between pathogen and host more comprehensively. The RNA interference (RNA interference, RNAi) screening experiments on the scale of the genome can obtain the sense of pathogen. The second chapter of the paper shows that we manually collect the EHF and related information of the infected host by manually collecting the integrated pathogens, and on this basis we have established the EHFPI bioinformatics database and the related analysis resource.EHFPI database containing 25 kinds of clinical weights. The 4634 EHF genes and their corresponding proteins of the pathogen species show relevant papers, screening experiments, pathogens and phenotypic annotations. In addition, the EHFPI database also provides 6 effective data integration tools to promote our understanding of the biological significance of the EHF gene and its products and from multiple angles. To explain the relationship between protein interaction network, drug target and disease, we have further selected the EHF. of the host virus infected by the genome scale RNAi screening experiment. In addition, there is a class of important host factors, VTP, which interact directly with the virus in order to ensure the survival of the virus in the cell. The relationship between the two host factors is rarely studied. The third chapter of the paper is the model of the two viruses, the Human Immunodeficiency Virus-1 (HIV-1) and the influenza A virus (influenza A virus, IAV), and the comparison and analysis of its EHF and VTP collection, and the discovery of the two virus EHF and the weight of the virus. The degree of coincidence is very small, and all of the two have distinct differentially expressed genes. The regulation direction.EHF and VTP tend to occupy the position of topological importance on the human protein interaction network, and they tend to interact directly with each other. We also identify some of the two kinds of viruses with larger EHF and VTP.. The step study shows that most EHF tends to adjust to the upstream of VTP in the case of EHF and VTP common path, which emphasizes the importance of EHF in the process of regulation. It is not easy to produce drug resistance and easy to achieve broad-spectrum antiviral and other advantages. At the same time, there are a large number of available drugs that can be used to avoid the long development cycle of new drugs, huge cost and high risk. Therefore, the repositioning strategy of host targeting antiviral drugs has become an important direction in the field of antiviral drugs research and development. The fourth chapter, based on the integration of the existing drug target interconnections and the knowledge of virus host interaction, tries to reveal which host proteins that have been verified to be dependent on the survival of the virus may be interfered by the existing drugs, and then construct a drug disease by integrating the virus host protein interaction network and the drug target relationship network. The drug relationship network, which systematically combs known drugs that can directly or indirectly acts on virus dependent host proteins, gives a systematic assessment of the potential of the current drug host targeting antiviral potential, and further discusses the possibility of broad-spectrum antiviral use of known drugs. Compounds derived from natural products are also of particular importance in the field of research and the pharmaceutical industry. Natural drugs have been used for a long time by human beings. Because of their economic efficiency, high safety, and modern multidirectional pharmacology, it is also of great value to modern drug development and is taken in modern drug treatment. The fifth chapter of the paper aims at exploring the potential application of natural drugs in the treatment of complex diseases. By using the method of large-scale target analysis, the synthetic drug targets provided by the natural drug target of the HIT database and the Drug Bank database provided by the target protein related pathway and the disease classification are carried out. In contrast, a natural drug component direct target relationship is established in the two sub network. From the perspective of current drug development trends, we discuss the key characteristics of the network and the association between natural drugs and their targets, and find that natural drugs may become potential anticancer drugs. The application of natural drugs in the relocation of host targets to antiviral drugs may bring new discoveries. The sixth chapter of the paper reviewed and integrated the data information about the virus, the known components of natural drugs and their target proteins, and explored the relationship between the natural drug components and the virus based on the common target. The two sub relationship then established the natural drug component virus relationship network. On this basis, the possibility of relocating the natural drug components at the host target was discussed, and the potential of their application to the broad-spectrum antivirus was evaluated. Large-scale network analysis showed that, in general, the drug components were relocated in the broad-spectrum antiviral space. It is limited, but the drug components that target the target protein of various viruses are more likely to be potential broad-spectrum antiviral drugs. Finally, the paper briefly summarizes the work described in the full text, and looks forward to the next work plan.
【學(xué)位授予單位】：中國(guó)人民解放軍軍事醫(yī)學(xué)科學(xué)院
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2015
【分類(lèi)號(hào)】：R978.7

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