Think Twice: Understanding the High Potency of Bis(phenyl)methane Inhibitors of Thrombin

Successful design of potent and selective protein inhibitors, in terms of structure-based drug design, strongly relies on the correct understanding of the molecular features determining the ligand binding to the target protein. We present a case study of serine protease inhibitors with a bis(phenyl)methane moiety binding into the S3 pocket. These inhibitors bind with remarkable potency to the active site of thrombin, the blood coagulation factor IIa. A combination of X-ray crystallography and isothermal titration calorimetry provides conclusive insights into the driving forces responsible for the surprisingly high potency of these inhibitors. Analysis of six well-resolved crystal structures (resolution 1.58-2.25 Å) along with the thermodynamic data allows an explanation of the tight binding of the bis(phenyl)methane inhibitors. Interestingly, the two phenyl rings contribute to binding affinity for very different reasons — a fact that can only be elucidated by a structure-based approach. The first phenyl moiety occupies the hydrophobic S3 pocket, resulting in a mainly entropic advantage of binding. This observation is based on the displacement of structural water molecules from the S3 pocket that are observed in complexes with inhibitors that do not bind in the S3 pocket. The same classic hydrophobic effect cannot explain the enhanced binding affinity resulting from the attachment of the second, more solvent-exposed phenyl ring. For the bis(phenyl)methane inhibitors, an observed adaptive rotation of a glutamate residue adjacent to the S3 binding pocket attracted our attention. The rotation of this glutamate into salt-bridging distance with a lysine moiety correlates with an enhanced enthalpic contribution to binding for these highly potent thrombin binders. This explanation for the magnitude of the attractive force is confirmed by data retrieved by a Relibase search of several thrombin-inhibitor complexes deposited in the Protein Data Bank exhibiting similar molecular features.Special attention was attributed to putative changes in the protonation states of the interaction partners. For this purpose, two analogous inhibitors differing mainly in their potential to change the protonation state of a hydrogen-bond donor functionality were compared. Buffer dependencies of the binding enthalpy associated with complex formation could be traced by isothermal titration calorimetry, which revealed, along with analysis of the crystal structures (resolution 1.60 and 1.75 Å), that a virtually compensating proton interchange between enzyme, inhibitor and buffer is responsible for the observed buffer-independent thermodynamic signatures.     

慢性肝炎中乙型和丙型病毒混合感染的重症化研究

在慢性肝炎中,乙、丙型病毒性肝炎混合感染相当多见,可使肝炎慢性化、重症化,肝组织损伤加重,肝硬化(LC)和肝癌(HCC)发生率增加[1]。本文应用血清学和分子生物学方法对196例肝病患者的血清进行检测,初步探讨了乙型肝炎病毒(Hepatitis B virus,HBV)、丙型肝类病毒(Hepatitis C virus,HCV)的复制状况以及两者间的相互作用与预后的关系。1材料和方法1.1病例受检的196例病例均为2004年1月至2005年7月我院住院及门诊病人,男149例,女47例,年龄15~82岁,其中慢性肝炎(CH)患者139例,肝硬化(LC)患者42例,肝癌(HCC)患者15例。所有病例诊断符合…     

慢性肝炎中乙型和丙型病毒混合感染的重症化研究

在慢性肝炎中,乙、丙型病毒性肝炎混合感染相当多见,可使肝炎慢性化、重症化,肝组织损伤加重,肝硬化(LC)和肝癌(HCC)发生率增加[1].本文应用血清学和分子生物学方法对196例肝病患者的血清进行检测,初步探讨了乙型肝炎病毒(Hepatitis B virus,HBV)、丙型肝类病毒(Hepatitis C viruS,HCV)的复制状况以及两者间的相互作用与预后的关系.     

Evaluation and identification of hepatitis B virus entry inhibitors using HepG2 cells overexpressing a membrane transporter NTCP

Hepatitis B virus (HBV) entry has been analyzed using infection-susceptible cells, including primary human hepatocytes, primary tupaia hepatocytes, and HepaRG cells. Recently, the sodium taurocholate cotransporting polypeptide (NTCP) membrane transporter was reported as an HBV entry receptor. In this study, we established a strain of HepG2 cells engineered to overexpress the human NTCP gene (HepG2-hNTCP-C4 cells). HepG2-hNTCP-C4 cells were shown to be susceptible to infection by blood–borne and cell culture-derived HBV. HBV infection was facilitated by pretreating cells with 3% dimethyl sulfoxide permitting nearly 50% of the cells to be infected with HBV. Knockdown analysis suggested that HBV infection of HepG2-hNTCP-C4 cells was mediated by NTCP. HBV infection was blocked by an anti-HBV surface protein neutralizing antibody, by compounds known to inhibit NTCP transporter activity, and by cyclosporin A and its derivatives. The infection assay suggested that cyclosporin B was a more potent inhibitor of HBV entry than was cyclosporin A. Further chemical screening identified oxysterols, oxidized derivatives of cholesterol, as inhibitors of HBV infection. Thus, the HepG2-hNTCP-C4 cell line established in this study is a useful tool for the identification of inhibitors of HBV infection as well as for the analysis of the molecular mechanisms of HBV infection.     

黑龙江省乙型肝炎血清流行病学调查分析

为了掌握黑龙江省乙型肝炎(乙肝)病毒(HBV)流行现状和人群免疫水平,评价我省儿童乙肝疫苗预防接种效果,为制订乙肝预防控制策略提供依据。采用横断面调查方法,选择全省7个国家级疾病监测点,在每个监测点随机抽取2个乡级单位,1～59岁作为目标人群共调查3337名人群。黑龙江省1～59岁人群乙肝病毒表面抗原(HBsAg)阳性率、乙肝病毒表面抗体(抗-HBs)阳性率和乙肝病毒核心抗体(抗-HBc)阳性率经标化后为5.65%、55.45%、30.50%,1～3岁人群乙肝表面抗原阳性率明显低于15～59岁人群。1～3岁、4～10岁和11～14岁人群乙肝疫苗全程接种率为99.43%、89.40%和64.81%;首针及时接种率分别为86.64%、75.57%和49.87。城市和农村HbsAg阳性率分别为3.26%和5.04%。医院出生儿童乙肝疫苗首针及时接种率高于在家出生儿童。结果显示接种乙肝疫苗可明显提高抗-HBs阳性率,提高人群对HBV的免疫保护能力,降低HBsAg携带率。     

应用RNAi文库筛选HBV复制相关基因

深入研究HBV复制机理,筛选参与HBV复制的基因,可能为开发抗乙肝病毒新药提供新 的靶点．本文拟建立一种筛选HBV复制相关基因的方法: RNAi文库感染HepG2.2.15细胞后,利用免疫磁珠收集HBsAg表达降低的细胞,提取DNA,PCR扩增siRNA编码序列,将PCR产物克隆入T-easy载体,随机挑选克隆测序,发现DDB1基因可能参与HBV复制．本试验建立了一种筛选HBV复制相关基因的方法,为大规模全基因组筛选参与HBV复制的基因奠定了基础．     

乙肝治疗性疫苗的研制与临床应用

尽管乙肝预防性疫苗非常有效,我国仍有约9300万乙肝病毒(HBV)携带者。抗病毒治疗疗效有限,患者长期使用容易产生耐药性。因此,研制乙肝治疗性疫苗可补充甚至替代目前的抗病毒治疗。T细胞免疫对于乙肝病毒的控制和清除至关重要,目前已经设计出蛋白疫苗、表位多肽疫苗以及DNA或病毒载体疫苗通过临床试验检验其疗效。将就研制乙肝治疗性疫苗这一日益活跃的领域加以概述,着重评价疫苗的细胞免疫应答和临床疗效。     

Recent advances in research on hepadnaviral infection in the woodchuck model

The woodchuck model is an excellent animal model to study hepadnaviral infection. The new progresses in this model made possible to examine the T-cell mediated immune responses in acute and chronic hepadnaviral infection. Recently, a new assay for cytotoxic T-cells based on detection of CD107 was established for the woodchuck model. In addition, new immunotherapeutic approaches based on combination of potent antiviral treatment and DNA-protein vaccines were proven to be useful for treatment of chronic hepatitis B.     

Recent Advances in Research on Hepadnaviral Infection in the Woodchuck Model

The woodchuck model is an excellent animal model to study hepadnaviral infection. The new progresses in this model made possible to examine the T-cell mediated immune responses in acute and chronic hepadnaviral infection. Recently, a new assay for cytotoxic T-cells based on detection of CD107 was established for the woodchuck model. In addition, new immunotherapeutic approaches based on combination of potent antiviral treatment and DNA-protein vaccines were proven to be useful for treatment of chronic hepatitis B.     

湖北咸宁地区乙型肝炎病毒基因型的调查

乙型肝炎病毒(Hepatitis B virus,HBV)是引起急性和慢性肝炎的最主要的病原[1]。目前根据HBsAg的共同抗原决定簇“α”和两对相互排斥的抗原决定簇将HBV分为ayw1, ayw2, ayw3, ayw4,ayr, adw2, adw2, adw4, adrq 和adrq-9种不同的血清学亚型,1988年Okamoto[2]等根据HBV基因组核苷酸的差异又提出了HBV基因型的概念,并以全基因组核苷酸差异≥8%,定为基因型分型标准。目前从世界不同地区分离的乙型肝炎病毒分离株已被分为A、B、C、D、E、F、G、H等8种不同的基因型[3~5]。包括中国、日本和东南亚在内的亚洲地区主要流行B、C两种基因…     

反义前S／S基因转移表达抗乙型肝炎病毒的研究

为了观察反义基因转录表达抗乙型肝炎病毒（HBV）的作用,将HBVayw前S／S基因（PreS／S）片段反向插入逆转录病毒载体质粒,构建preS／S反义基因重组体,经转染PA317细胞后,获得重组逆转录病毒颗粒。用重组病毒转导2．2．15细胞后,第3天即可见细胞培养上清HBV表面抗原（HBsAg）和e抗原（HBeAg）表达量减少,到转导后第5天,细胞培养上清中的HBsAg和HBeAg表达量降到最低水平,HBsAg抑制率为71％,HBeAg抑制率为27％,抑制作用至少可持续到转导后第11天。空载及正向插入基因的重组逆转录病毒转导对2,2．15细胞内HBV抗原表达无抑制作用。     

反义前C／C基因转移表达抗乙型肝炎病毒作用的研究

为了观察逆转录病毒载体包装细胞系统介导反义基因转移表达的抗乙型肝炎病毒（HBV）作用,将HBVayw前C／C基因（preC／C）片段反向插入逆转录病毒载体质粒。将重组体转染逆转录病毒包装细胞PA317后,获得重组逆转录病毒。用重组逆转录病毒感染2．2．15细胞后发现,感染后第3天,细胞培养上清HBV表面抗原（HBsAg）和e抗原（HBeAg）表达量即明显减少,抑制作用于感染后第5天达到高峰,其中对HBsAg表达的抑制率为27．0％,对HBeAg表达的抑制率为59.5％。反义基因重组逆转录病毒感染2.2．15细胞对HBV抗原表达的抑制作用至少可以持续到转导后的第11天。空载及正义基因重组逆转录病毒感染对2．215细胞HBV抗原表达无明显抑制作用。此外,反义基因重组逆转录病毒感染对2.2.15细胞HBVDNA复制也有抑制作用．无细胞毒性。     

人原发性肝细胞肝癌中丙型肝炎病毒C_（33c）抗原及HBxAg的分布及意义

作者应用抗ＨＣＶＮＳ３区Ｃ３３ｃ抗原２Ｂ６株单克隆抗体和抗ＨＢｘＡｇ多克隆抗体,采用ＡＢＣ法对１０２例人原发性肝细胞肝癌（ＰＨＣ）组织进行了ＨＣＶ及ＨＢＶ抗原定位研究。ＨＣＶＣ３。抗原及ＨＢｘＡｇ在ＰＨＣ中的阳性检出率分别是８１．４％及７４．５％,Ｃ３３ｃ抗原或ＨＢｘＡｇ阳性占所检病例９４．１％,相同病例二者同时阳性为６１．８％。１０２例ＰＨＣ中５０例有癌旁肝组织,其Ｃ３３ｃ抗原和ＨＢｘＡｇ的阳性检出率分别是６２％和９２％。ＨＣＶＣ３３ｃ抗原定位于肝癌细胞的胞浆内,胞核未见阳性信号。Ｃ３３ｃ抗原阳性细胞在ＰＨＣ中呈散在、局灶分布为主,在癌旁肝组织呈弥漫分布为主。本文结果提示ＨＣＶ感染在ＰＨＣ的发生中可能起重要作用。     

Association between the frequency of class II HLA antigens and the susceptibility to intrauterine infection of hepatitis B virus

Multiple factors determine the susceptibility to intrauterine hepatitis B virus (HBV) infection. These factors include the HBV structure, HBV mutation, HBV DNA level, placental barrier, the immune status of the mother, and the genetic make-ups of the newborn infants. Since HLA system is an integral component of the immune response, we hypothesized that the highly polymorphic HLA genes are the key determinants of intrauterine HBV infection. In this study, we selected newborn infants of HBsAg-positive mothers, and divided the infants into 2 groups: intrauterine infection group and non-intrauterine infection group according to the status whether or not they were infected at birth. Each infected infant was compared with 2 controls from the same birth cohort. HLA-DR allele typing was performed using a PCR-sequence specific primer (PCR-SSP) for 24 subjects with intrauterine infection and 48 controls without infection. We found that, among the fifteen (15) HLA-DR alleles assessed, HLA-DRB1*07 was the one, and the only one, significantly in excess (OR = 6.66, P = 0.004) in the intrauterine infection group compared to the non-intrauterine infection group. Our findings thus suggest that high frequency of HLA class II molecules, e.g. HLA-DRB1*07, is associated with the susceptibility of the infants to intrauterine HBV infection.     

针对不同基因靶位的锤头状核酶对HBV的抑制作用研究

前基因组mRNA是HBV(Hepatitis B virus)基因表达和复制的重要中间产物,全长的前基因组mRNA分子具有复杂易变的二级结构,是设计抑制HBV的核酶时所必须考虑的因素.我们使用多个最新的计算机软件对HBV前基因组mRNA二级结构进行模拟、分析,在全面分析核酶的可作用位点的基础上设计三个针对不同基因靶位的锤头状核酶,并对它们在细胞中对HBV的抑制作用进行研究.结果表明在HBV前基因组mRNA上存在几个高度复杂二级结构的区域,可能对核酶完全不敏感,而S、C、X基因的编码区是合适的核酶作用位点,都可达到对HBV的有效抑制,而且X基因位点的核酶对HBV的各种mRNA的抑制作用最为明显,是设计针对HBV核酶时应该优先考虑的位点.     

Effects of Dimethyl Sulfoxide on Tetrahymena pyriformis GL. Fine Structural Changes and Their Reversibility*

SYNOPSIS. Fine-structural changes are induced in Tetrahymena by exposure to 7.5% dimethyl sulfoxide (DMSO) in the presence of growth medium. Some of these changes (nucleolar, mitochondrial, peroxisomal) resemble those seen during starvation, in agreement with the previously reported inhibitory effect of DMSO on food-vacuole formation; however, changes such as helical formations of polyribosomes indicate additional internal actions of the reagent. The effects vary to some extent within the same group of cells, suggesting that sensitivity to the reagent may differ with the stage in the cell cycle. The structural changes induced by a 1-hr exposure to DMSO are reversible, but recovery of the cells after removal of the reagent is slower than that seen after starvation. The observations suggest that the recovery is associated with renewed synthesis.