鼠抗人纤维蛋白抗体单链Fv片段的人源化分子设计

产生免疫原性的残基都是位于蛋白表面的暴露残基,为了消除鼠抗体对人的免疫原性,利用表面再塑方法对本室克隆的鼠抗人纤维蛋白抗体单链Fv片断进行了人源化分子设计。首先确定了鼠及人Fv表面残基,在此基础上分析了鼠与人Fv间表面残基的差异,将有差异的鼠表面残基换成人的。提出了残基最高频率人源化及最相似链人源化两种人源化方案。人源化后鼠抗人纤维蛋白抗体单链Fv的结构经Profile-3D验证是合理的,置换的表面残基溶液可及性未变,且未影响CDRs的结构,应不会影响与纤维蛋白的亲和力,为鼠抗体人源化实验研究奠定了基础。     

鼠抗人纤维蛋白抗体单链Fv片段的人源化分子设计

产生免疫原性的残基主要是位于蛋白表面的暴露残基,为了消除鼠抗体对人的免疫原性,利用表面再塑的方法对本室克隆的鼠抗人纤维蛋白抗体单链Ｆｖ片段进行了人源化分子设计．首先确定了鼠及人Ｆｖ片段的表面残基,在此基础上分析了鼠与人抗体Ｆｖ片段表面残基的差异,将存在差异的鼠抗体的表面残基换成人的,从而实现鼠抗体的人源化．提出了残基最高频率人源化及最相似链人源化两种分子设计方案．人源化的鼠抗人纤维蛋白抗体单链Ｆｖ片段的结构经Ｐｒｏｆｉｌｅｓ－３Ｄ检测证明合理,替换的表面残基的溶剂可及性未变,而且未对ＣＤＲｓ的空间构象产生明显影响,应不会影响与纤维蛋白的亲和力,为鼠抗体人源化实验研究奠定了基础．     

鼠抗人纤维蛋白抗体单链Fv片断的三维结构模建

用Biosym公司开发的计算机辅助分子设计系统模建了鼠抗人纤维蛋白抗体Fv片断的三维结构。Fv是由重链可变区(Vh)和轻链可变区(Vl)两个结构域组成的具有抗原结合能力的最小抗体片断。先分别模建了Vh和Vl两个结构域,然后搭建出Fv片断的整体三维结构,并对模建的结构进行了分子力学和动力学优化。对结构的合理性验证显示模建结构是合理的。本研究为鼠抗人纤维蛋白抗体Fv片断的人源化的分子设计打下了基础。     

鼠抗人纤维蛋白抗体单链Fv片段的人源化分子

产生免疫原性的残基主要是位于蛋白表面的暴露残基,为了消除鼠抗体对人的免疫原性,利用表面再塑的方法对本室克隆的鼠抗人纤维蛋白抗体链Ｆｖ片段进行了人源化分子设计。首先确定了鼠及人Ｆｖ片段的表面残基,在此基础上分析了鼠与人抗体Ｆｖ表面残基的差异,将存在差异的鼠抗体表面残基换成人的,从而实现鼠抗体的人源化。     

血管内皮生长因子特异性鼠源单链抗体的人源化

以抗体阻断血管生成信号来治疗实体肿瘤显示了很好的前景,但鼠源抗体首先必须经人源化改造以降低其免疫原性才能应用于人体。本研究以同源模建预测了一体人血管内皮生长因子（VEGF）特异性鼠源单链抗体E11的三维结构,以结构数据为基础并采取单个最相似框架区替代法对其进行人源化设计;合成并组装了人源化单链抗体基因并在大肠杆菌中表达,包含体形式的产物以凝胶柱色谱法复性,经ELISA检测表明,人源化后的单链抗体保持了与天然VEGF结合的活性,表明采取的人源化路线具有可行性。     

鼠单克隆抗体人源化

鼠源性单克隆抗体应用于临床由于HAMA反应的存在而受到阻碍。以CDR移植为核心,以同源分析及分子模建为辅助设计的人源化方案已成为克服HAMA反应的主要手段。本文结合单抗人源化的最新进展对该领域的工作作一综述。     

白色念珠菌羊毛甾醇14α-去甲基化酶三维结构分子模型研究

基于四种原核细胞色素Ｐ４５０晶体蛋白Ｐ４５０ＢＭ３、Ｐ４５０ｃａｍ、Ｐ４５０ｔｅｒｐ、Ｐ４５０ｅｒｙＦ模建白色念珠菌羊毛甾醇１４α－去甲基化酶三维结构。序列匹配采用四种晶体结构比较结果基础之上提出的细胞色素Ｐ４５０超家族蛋白基于结构知识的序列匹配方法。以Ｐ４５０ＢＭ３晶体结构坐标模建目标蛋白结构保守区主链结构,结构保守区侧链构象来源于四种晶体蛋白与模建蛋白对应残基同源性得分最高残基构象。模建结果用分子力学和分子动力学进行结构优化,模建结果蛋白采用Ｐｒｏｆｉｌｅ－３Ｄ图、Ｒａｍａｃｈａｎｄｒａｎ图和疏水图分析确证结构的合理性。并根据模型推测与血红素辅基相互作用的残基、与氧化还原偶联蛋白作用和参与电子传递的残基、底物进出通道和活性位点的残基。这些研究结果为定点突变研究、抗多肽抗体结合实验等提供理论依据,为高效低毒抗真菌药物合理设计提供靶标。     

人源抗体筛选和表达载体的构建

目的:构建一个可供抗体CDR(决定簇互补区)进行自由替换、筛选、表达的通用载体,并对其生物学功能进行鉴定.方法:在已构建好的具有Fc段的完全人源抗狂犬病病毒抗体表达栽体基础上,利用PCR介导的定点突变技术,引入2个可供CDR3区进行自由替换的限制性酶切位点,构建出通用表达载体.体外合成人源、鼠源抗乳腺癌Her2抗体的CDR3区,克隆至已构建的通用载体,在毕赤酵母中诱导表达.应用ELISA和Western Blotting技术对亲本抗体和新抗体进行生物学及免疫学分析.结果:PCR、Western Blotting等试验表明具有Her2抗原结合活性的人源和鼠源突变型抗体获得成功表达,通过对表达产物的免疫学及功能学检测证明所表达出的抗体具有抗原中和活性,而且鼠源抗体的活性要稍高于人源抗体.结论:成功构建了可用于功能性抗体筛选和表达的通用载体,对抗体的体外亲和力成熟及抗体的人源化有重要意义.     

β淀粉样肽单克隆抗体可变区基因的5′RACE扩增及序列分析

目的:克隆并分析抗β淀粉样肽单克隆抗体轻链与重链可变区基因。方法:从分泌抗β淀粉样肽单克隆抗体的杂交瘤细胞株A8中提取总RNA,根据恒定区序列设计基因特异性引物,通过5′RACE法扩增抗体的轻链和重链可变区基因,测定并分析可变区基因序列,并克隆入pMD18-T载体。结果:重链可变区基因序列全长450bp,编码150个氨基酸残基;轻链可变区基因序列全长429bp,编码143个氨基酸残基。在GeneBank中对氨基酸序列进行比对分析,二者均符合小鼠IgG可变区基因的特征。根据Kabat法则对A8抗体轻链和重链可变区氨基酸序列基因进行分析并确定了3个抗原互补决定区(CDR)、4个框架区(FR)和信号肽。结论:通过5′RACE法得到了抗β淀粉样肽单克隆抗体轻链与重链可变区基因,为进一步研究抗体三维结构,以及对该抗体进行人源化改造奠定了基础。     

肺炎链球菌双组份系统中的组氨酸激酶(YycG)的同源模建与分析

对肺炎链球菌双组份系统中的组氨酸激酶YycG进行同源模建, 并分析其与底物ADP的相互作用, 为寻找特异性的激酶抑制剂提供了理论依据。采用同源模建的方法构建YycG蛋白的三维结构, 并用ProCheck、Profile_3D软件对此结构模型的合理性进行验证; 用Autodock4.0软件将结构模型与ADP进行自动对接, 分析二者之间的相互作用。序列比对结果显示肺炎链球菌YycG蛋白与Thermotoga maritima X-ray晶体结构序列的同一性达33%; YycG模建后的结构与模板能很好的叠合; 在活性口袋处的保守的氨基酸残基Asn145、Asn149、Lys152以及口袋内部的疏水残基在结合、水解底物ADP的过程中发挥重要作用。组氨酸激酶YycG的模建合理, 该结构模型可作为设计抗菌药的研究起点。     

SDR grafting--a new approach to antibody humanization

A major impediment to the clinical utility of the murine monoclonal antibodies is their potential to elicit human anti-murine antibody (HAMA) response in patients. To circumvent this problem, murine antibodies have been genetically manipulated to progressively replace their murine content with the amino acid residues present in their human counterparts. To that end, murine antibodies have been humanized by grafting their complementarity determining regions (CDRs) onto the variable light (V(L)) and variable heavy (V(H)) frameworks of human immunoglobulin molecules, while retaining those murine framework residues deemed essential for the integrity of the antigen-combining site. However, the xenogeneic CDRs of the humanized antibodies may evoke anti-idiotypic (anti-Id) response in patients. To minimize the anti-Id response, a procedure to humanize xenogeneic antibodies has been described that is based on grafting, onto the human frameworks, only the specificity determining residues (SDRs), the CDR residues that are most crucial in the antibody-ligand interaction. The SDRs are identified through the help of the database of the three-dimensional structures of the antigen-antibody complexes of known structures or by mutational analysis of the antibody-combining site. An alternative approach to humanization, which involves retention of more CDR residues, is based on grafting of the 'abbreviated' CDRs, the stretches of CDR residues that include all the SDRs. A procedure to assess the reactivity of the humanized antibody to sera from patients who had been administered the murine antibody has also been described.     

Structural correlates of an anticarcinoma antibody: identification of specificity-determining residues (SDRs) and development of a minimally immunogenic antibody variant by retention of SDRs only

Clinical utility of murine mAbs is limited because many elicit Abs to murine Ig constant and variable regions in patients. An Ab humanized by the current procedure of grafting all the complementarity determining regions (CDRs) of a murine Ab onto the human Ab frameworks is likely to be less immunogenic, except that its murine CDRs could still evoke an anti-variable region response. Previous studies with anticarcinoma mAb CC49 showed that light chain LCDR1 and LCDR2 of humanized CC49 could be replaced with the corresponding CDRs of a human Ab with minimal loss of Ag-binding activity. The studies reported in this paper were undertaken to dissect the CC49 Ag-binding site to identify 1) specificity determining residues (SDRs), the residues of the hypervariable region that are most critical in Ag-Ab interaction, and 2) those residues that contribute to the idiotopes that are potential targets of patients' immune responses. A panel of variants generated by genetic manipulation of the murine CC49 hypervariable regions were evaluated for their relative Ag-binding affinity and reactivity to sera from several patients who had been immunized with murine CC49. One variant, designated HuCC49V10, retained only the SDRs of CC49 and does not react with the anti-variable region Abs of the sera from the murine CC49-treated patients. These studies thus demonstrate that the genetic manipulation of Ab variable regions can be accomplished by grafting only the SDRs of a xenogeneic Ab onto human Ab frameworks. This approach may reduce the immunogenicity of Abs to a minimum.     

从抗TNF抗体的CDR肽库中获得拮抗TNF的短肽

为设计来自抗体的短肽 ,以抗肿瘤坏死因子 (TNF)嵌合抗体 (cA2 )CDRs为模板 ,在其两侧各加 3个随机氨基酸残基 ( X3 CDR X3 ) ,构建了 6个以CDR为基础的肽库 .经过 3轮亲和选择 ,挑取单克隆 ,进一步经ELISA检测TNF阳性噬菌体克隆 ,分离得到 7个ELISA阳性较好的噬菌体肽克隆 ,分别命名为CDR2L1、CDR2L2、CDR2L3、CDR1L1、CDR2H1、CDR3H1、CDR3H 2 .应用MTT方法 ,检测 7个克隆对TNF生物学活性的拮抗作用 .结果显示 :来自CDR2L ,CDR3H肽库中的CDR2L2、CDR2L3,CDR3H2噬菌体肽具有明显的拮抗TNF诱导L92 9细胞的细胞毒作用 ,其中以CDR2L2噬菌体肽的拮抗活性最强 .而来源于CDR1L ,CDR2H肽库的CDR1L1和CDR2H1噬菌体肽和来自CDR2L ,CDR3H肽库中的CDR2L1和CDR3H1噬菌体肽没有明显的拮抗TNF作用 .研究结果初步表明 :从cA2抗体CDR肽库中筛选得到的噬菌体CDR模拟肽具有亲本抗体相似的结合活性和生物学效应 ,从而为开发已知抗体 (特别是治疗用抗体 )CDR为基础的肽药物创建一个技术平台奠定基础     

Fundamental characteristics of the immunoglobulin VH repertoire of chickens in comparison with those of humans, mice, and camelids

Examination of 1269 unique naive chicken V(H) sequences showed that the majority of positions in the framework (FW) regions were maintained as germline, with high mutation rates observed in the CDRs. Many FW mutations could be clearly related to the modulation of CDR structure or the V(H)-V(L) interface. CDRs 1 and 2 of the V(H) exhibited frequent mutation in solvent-exposed positions, but conservation of common structural residues also found in human CDRs at the same positions. In comparison with humans and mice, the chicken CDR3 repertoire was skewed toward longer sequences, was dominated by small amino acids (G/S/A/C/T), and had higher cysteine (chicken, 9.4%; human, 1.6%; and mouse, 0.25%) but lower tyrosine content (chicken, 9.2%; human, 16.8%; and mouse 26.4%). A strong correlation (R(2) = 0.97) was observed between increasing CDR3 length and higher cysteine content. This suggests that noncanonical disulfides are strongly favored in chickens, potentially increasing CDR stability and complexity in the topology of the combining site. The probable formation of disulfide bonds between CDR3 and CDR1, FW2, or CDR2 was also observed, as described in camelids. All features of the naive repertoire were fully replicated in the target-selected, phage-displayed repertoire. The isolation of a chicken Fab with four noncanonical cysteines in the V(H) that exhibits 64 nM (K(D)) binding affinity for its target proved these constituents to be part of the humoral response, not artifacts. This study supports the hypothesis that disulfide bond-constrained CDR3s are a structural diversification strategy in the restricted germline v-gene repertoire of chickens.     

Crystal structure of HEL4, a soluble, refoldable human V(H) single domain with a germ-line scaffold

The antigen binding site of antibodies usually comprises associated heavy (V(H)) and light (V(L)) chain variable domains, but in camels and llamas, the binding site frequently comprises the heavy chain variable domain only (referred to as V(HH)). In contrast to reported human V(H) domains, V(HH) domains are well expressed from bacteria and yeast, are readily purified in soluble form and refold reversibly after heat-denaturation. These desirable properties have been attributed to highly conserved substitutions of the hydrophobic residues of V(H) domains, which normally interact with complementary V(L) domains. Here, we describe the discovery and characterisation of an isolated human V(H) domain (HEL4) with properties similar to those of V(HH) domains. HEL4 is highly soluble at concentrations of > or =3 mM, essentially monomeric and resistant to aggregation upon thermodenaturation at concentrations as high as 56 microM. However, in contrast to V(HH) domains, the hydrophobic framework residues of the V(H):V(L) interface are maintained and the only sequence changes from the corresponding human germ-line segment (V3-23/DP-47) are located in the loops comprising the complementarity determining regions (CDRs). The crystallographic structure of HEL4 reveals an unusual feature; the side-chain of a framework residue (Trp47) is flipped into a cavity formed by Gly35 of CDR1, thereby increasing the hydrophilicity of the V(H):V(L) interface. To evaluate the specific contribution of Gly35 to domain properties, Gly35 was introduced into a V(H) domain with poor solution properties. This greatly enhanced the recovery of the mutant from a gel filtration matrix, but had little effect on its ability to refold reversibly after heat denaturation. Our results confirm the importance of a hydrophilic V(H):V(L) interface for purification of isolated V(H) domains, and constitute a step towards the design of isolated human V(H) domains with practical properties for immunotherapy.     

Engineering Fully Human Monoclonal Antibodies from Murine Variable Regions

Fully human monoclonal antibodies (mAbs) derived from transgenic mice or human antibody libraries are the current state of the art for reducing the immunogenicity risk of antibody drugs. Here, we describe a novel method for generating fully human mAbs from nonhuman variable regions using information from the human germline repertoire. Central to our strategy is the rational engineering of residues within and proximal to CDRs and the V_H/V_L interface by iteratively exploring substitutions to the closest human germline sequences using semi-automated computational methods. Starting from the parent murine variable regions of three currently marketed mAbs targeting CD25, vascular endothelial growth factor, and tumor necrosis factor alpha, we have generated fully human antibodies with 59, 46, and 45 substitutions, respectively, compared to the parent murine sequences. A large number of these substitutions were in the CDRs, which are typically avoided in humanization methods. Antigen affinities of the fully human variants were comparable to the chimeric mAbs in each case. Furthermore, in vitro functional characterization indicated that all retain potency of the chimeric mAbs and have comparable activity to their respective marketed drugs daclizumab, bevacizumab, and infliximab. Based on local and global sequence identity, the sequences of our engineered mAbs are indistinguishable from those of fully human mAbs isolated from transgenic mice or human antibody libraries. This work establishes a simple rational engineering methodology for generating fully human antibody therapeutics from murine mAbs produced from standard hybridoma technology.     

Solution structure of a llama single-domain antibody with hydrophobic residues typical of the VH/VL interface

The three-dimensional structure of a llama single-domain antibody BrucD4-4 was established by use of solution NMR spectroscopy. BrucD4-4 has Val, Gly, Leu, and Trp residues at positions 37, 44, 45, and 47, which are considered to be a hallmark to distinguish llama VH from V(H)H fragments at the germline level. In contrast to the murine and human VHs, BrucD4-4 has sufficient solubility, is monomeric in solution, and displays high-quality NMR spectra characteristic of well-structured proteins. Amide proton/deuterium exchange and the (15)N relaxation data showed that BrucD4-4 has a classic protein structure with a well-packed core and comparatively mobile surface loops. The three-dimensional architecture of BrucD4-4 is analogous to that of VHs from murine and human F(v)s and camelid V(H)Hs with two pleated beta-sheets formed by four and five beta-strands. A canonical and undistorted beta-barrel exposes a number of hydrophobic residues into the solvent on the surface of the three-dimensional structure. The eight-residue H3 loop folds over the side chain of Val37 similarly to that in llama V(H)Hs; however, this interaction may be transient due to the H3 conformational flexibility. Overall, the surface characteristics of BrucD4-4 with respect to hydrophobicity appear to lie between the human VH domain from Fv Pot and the llama V(H)H fragment HC-V, which may explain its enhanced solubility allowing NMR structural analysis.     

Automated identification of complementarity determining regions (CDRs) reveals peculiar characteristics of CDRs and B cell epitopes

Exact identification of complementarity determining regions (CDRs) is crucial for understanding and manipulating antigenic interactions. One way to do this is by marking residues on the antibody that interact with B cell epitopes on the antigen. This, of course, requires identification of B cell epitopes, which could be done by marking residues on the antigen that bind to CDRs, thus requiring identification of CDRs. To circumvent this vicious circle, existing tools for identifying CDRs are based on sequence analysis or general biophysical principles. Often, these tools, which are based on partial data, fail to agree on the boundaries of the CDRs. Herein we present an automated procedure for identifying CDRs and B cell epitopes using consensus structural regions that interact with the antigens in all known antibody-protein complexes. Consequently, we provide the first comprehensive analysis of all CDR-epitope complexes of known three-dimensional structure. The CDRs we identify only partially overlap with the regions suggested by existing methods. We found that the general physicochemical properties of both CDRs and B cell epitopes are rather peculiar. In particular, only four amino acids account for most of the sequence of CDRs, and several types of amino acids almost never appear in them. The secondary structure content and the conservation of B cell epitopes are found to be different than previously thought. These characteristics of CDRs and epitopes may be instrumental in choosing which residues to mutate in experimental search for epitopes. They may also assist in computational design of antibodies and in predicting B cell epitopes.     

Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides

By analyzing the human antibody repertoire in terms of structure, amino acid sequence diversity and germline usage, we found that seven V(H) and seven V(L) (four Vkappa and three Vlambda) germline families cover more than 95 % of the human antibody diversity used. A consensus sequence was derived for each family and optimized for expression in Escherichia coli. In order to make all six complementarity determining regions (CDRs) accessible for diversification, the synthetic genes were designed to be modular and mutually compatible by introducing unique restriction endonuclease sites flanking the CDRs. Molecular modeling verified that all canonical classes were present. We could show that all master genes are expressed as soluble proteins in the periplasm of E. coli. A first set of antibody phage display libraries totalling 2x10(9) members was created after cloning the genes in all 49 combinations into a phagemid vector, itself devoid of the restriction sites in question. Diversity was created by replacing the V(H) and V(L) CDR3 regions of the master genes by CDR3 library cassettes, generated from mixed trinucleotides and biased towards natural human antibody CDR3 sequences. The sequencing of 257 members of the unselected libraries indicated that the frequency of correct and thus potentially functional sequences was 61 %. Selection experiments against many antigens yielded a diverse set of binders with high affinities. Due to the modular design of all master genes, either single binders or even pools of binders can now be rapidly optimized without knowledge of the particular sequence, using pre-built CDR cassette libraries. The small number of 49 master genes will allow future improvements to be incorporated quickly, and the separation of the frameworks may help in analyzing why nature has evolved these distinct subfamilies of antibody germline genes.     

1H NMR assignment and secondary structural elements of human transforming growth factor alpha

The 1H NMR spectrum of human transforming growth factor alpha (hTGF-alpha) has been completely assigned, and secondary structural elements have been identified as a preliminary step in determining the structure of this protein by distance geometry methods. Many of these structural elements closely correspond to those previously found in a truncated human EGF [Cooke et al. (1987) Nature (London) 327, 339-341] and murine EGF [Montelione et al. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 5226-5230]. These include the presence of an antiparallel beta-sheet between residues G19 and C34 with a type I beta-turn at V25-D28, a type II beta-turn at H35-Y38, and another short beta-sheet between residues Y38-V39 and H45-A46.