抗表皮生长因子受体噬菌体抗体库的构建筛选及单链抗体可溶性表达

近年来的研究表明,表皮生长因子受体 (epidermal growth factor receptor, EGFR) 是肿瘤治疗中一个很重要的靶点。本研究应用噬菌体展示技术筛选EGFR特异性单链抗体 (single chain Fv, scFv)。利用高表达EGFR的人鳞状上皮癌细胞A431免疫小鼠,提取脾细胞mRNA,RT-PCR扩增VH和VL基因并拼装成scFv基因。将scFv基因连接到噬菌粒pCANTAB 5E中,电击转化E.coli TG1细胞,构建了库容为2.5×10⁷的噬菌体单链抗体库。用纯化的EGFR为靶抗原对噬菌体抗体库进行5轮富集筛选,得到次级抗体库6F-10。挑取48个克隆进行ELISA测定,45个克隆为阳性。取阳性值最高的克隆感染E.coli HB2151,IPTG诱导scFv的表达。scFv (约27 kD) 以可溶形式存在于细胞质及细胞周质中,并可分泌至上清液。测序结果表明,scFv基因序列全长768 bp,编码256个氨基酸。VH为与小鼠Ig同源的重链可变区基因,VL为κ型轻链可变区基因;VH和VL均由3个抗原互补决定区和4个框架区构成。免疫印迹和细胞免疫荧光显示,可溶性scFv可分别与纯化的EGFR抗原以及细胞表面的EGFR发生特异性结合。抗EGFR特异性scFv的获得,为研制靶向EGFR的抗体药物与研究生物治疗提供导向载体分子。     

Small molecule complementarity as a source of novel pharmaceutical agents and combination therapies

Many examples of specific binding between small molecules are known that are associated with modified physiological and pharmacological activities. Conversely, the antagonism or synergism of small molecules is often correlated with specific binding between the molecules. It follows that small molecule binding can be used as a relatively quick, easy, and specific screen for functionally useful drug actions and interactions. These actions and interactions may manifest themselves as functional antagonisms; binding may correlate with enhancement or synergism; the formation of some complexes may yield clues about how drugs may be targeted to specific cell types in vivo and provide leads for the development of antidotes for drug overdoses or poisoning; the binding of one molecule to another may mimic receptor binding; and complexation may provide novel ways of protecting and delivering drugs. Relevant examples from each type of application are reviewed involving peptide-peptide interactions; peptide-aromatic compound interactions; aromatic-aromatic compound interactions; vitamin-aromatic compound interactions; and polycyclic compound interactions. We argue that screening for molecular complementarity of small molecules turns ligands such as neurotransmitters and their metabolites, hormones, and drugs themselves, into direct targets of drug development that can augment screening new compounds for activity against receptors and second messenger systems. We believe that the small molecule complementarity approach is novel, fruitful and under-utilized.     

Putative Secondary Structure at 5’UTR as a Potential Antiviral Target against SARS-CoV-2

SARS-CoV-2 is an enveloped positive-sense single-stranded RNA coronavirus that causes COVID-19, of which the current outbreak has resulted in a high number of cases and fatalities throughout the world, even vaccine doses are being administered. The aim of this work was to scan the SARS-CoV-2 genome in search for therapeutic targets. We found a sequence in the 5’UTR (NC\_045512:74-130), consisting of a typical heptamer next to a structured region that may cause ribosomal frameshifting. The potential biological value of this region is relevant through its low similarity with other viruses, including coronaviruses related to SARS-CoV, and its high sequence conservation within multiple SARSCoV-2 isolates. We have predicted the secondary structure of the region by means of different bioinformatic tools. We have suggested a most probable secondary structure to proceed with a 3D reconstruction of the structured segment. Finally, we carried out virtual docking on the 3D structure to look for a binding site and then for drug ligands from a database of lead compounds. Several molecules that could be probably administered as oral drugs show promising binding affinity within the structured region, and so it could be possible interfere its potential regulatory role.     

Selection of novel nickel-binding peptides from flagella displayed secondary peptide library

Nickel (Ni) performs its biological or toxic functions in nickel-protein coordination form. Novel Ni-binding peptides were isolated from a random dodecapeptide library displayed on the flagella of Escherichia coli against immobilized ions. On the basis of isolated sequences rich in histidine residues, two secondary libraries were constructed respectively. By consequent selection, more Ni-chelating peptides were identified and the consensus motif RHXHR (where X was always H) was deduced. The result suggested that not only histidine, but also arginine, play an important role in Ni-binding. Furthermore, two selected clones (1035 and 2022) were chosen for further identification. They exhibited similar relative binding affinity, which was about nine times that of the original library derived clones and statistically much more significant than the positive control with polyhistidine insert. Free nickel ions could almost completely inhibit the binding of the clones 1035 and 2022 to immobilized nickel, implicating that the peptides were able to chelate nickel ions. These studies reveal that bacterial surface displayed peptide libraries may have promising future potential for the development of metal bioadsorbents. Furthermore, novel Ni-binding peptides may provide lead molecules for Ni-chelation and applications thereof.     

A novel interleukin‐13 receptor alpha 2‐targeted hybrid peptide for effective glioblastoma therapy

We previously designed and reported a novel class of drugs, namely hybrid peptides, which are chemically synthesized and composed of a targeted binding peptide and a lytic‐type peptide containing cationic amino acid residues that cause cancer cell death. In the present study, we screened for peptides that bind to interleukin‐13 receptor alpha 2 (IL‐13Rα2) by using a T7 random peptide phage display library system and isolated several positive phage clones. The A2b11 peptide, which was one of the positive clones, was shown to bind to IL‐13Rα2 protein by Biacore analysis and a binding assay using glioblastoma (GB) cell lines. This peptide was linked with a lytic peptide containing a linker sequence to form the IL‐13Rα2–lytic hybrid peptide. The IL‐13Rα2–lytic hybrid peptide showed cytotoxic activity against GB cell lines in vitro. The IL‐13Rα2–lytic hybrid peptide also affected Akt and Erk1/2 activation following treatment with interleukin‐13 and induced rapid ATP dynamics in GB cells. Anti‐tumor activity of the IL‐13Rα2–lytic hybrid peptide was observed in vivo after intratumoral injection in a mouse xenograft model of human GB cells. These results suggest that the IL‐13Rα2–lytic hybrid peptide might be a potent therapeutic option for patients with GB.     

A GAL4-based yeast three-hybrid system for the identification of small molecule-target protein interactions

We report the development of a yeast strain designed for assaying compound-protein interactions through activation of reporter gene expression. Activation of lacZ expression, driven by the GAL4 promoter, has been demonstrated for precedented compound-protein interactions between FK506 and FK506 binding protein 12 (FKBP12) and also between methotrexate (MTX) and dihydrofolate reductase (DHFR). Reporter gene expression was completely abrogated in a competitive manner by the presence of excess FK506 or MTX, respectively. In addition, a strain expressing a mutated DHFR clone with decreased binding affinity for MTX was not capable of activating reporter gene expression. While strain sensitivity is compound-dependent, the minimum compound concentration necessary to drive reporter gene expression was 20 nM for the FK506-FKBP12 interaction. The utility of this strain as a tool for identifying unknown compound-binding proteins has been demonstrated by screening a mouse cDNA library for clones that encode proteins capable of binding MTX. Four library clones of mouse DHFR were identified after screening 5 x 10(6) clones. The screen background was low and false positives were easily identified, making this yeast system particularly amenable for use in a screening context for novel compound-protein interactions.     

Isolation of leptin‐binding peptides from a random peptide phage library

Abstract: Leptin plays a role in regulating the body weight in mice. Injection of recombinant mouse leptin expressed in Escherichia coli reduced the food intake and body weight in normal, ob/ob and diet‐induced obesity mice. Hyperglycemia, hyperinsulinemia and hypothermia can also be corrected inob/ob mice after leptin injection. Leptin is a 16‐kDa secretory protein comprising 167 amino acids produced in adipose tissue and is secreted to blood stream. In this study, a recombinant mouse leptin was generated and purified from a baculovirus expression system. This protein was used to identify putative ligands using a phage library of random peptides. Three leptin‐binding phage clones were found, which were characterized by DNA sequencing and ELISA methods. The amino acid sequences of the reactive peptides are: LAYCSDPVRCLVWWY, MFWISAVSFVDHALV and LVLVLSAFLCCGVG. All three clones bound to recombinant human and mouse leptins. These peptides may be useful tools to study leptin–receptor interaction, food intake and body weight regulation.     

抗人B-淋巴细胞刺激因子噬菌体单链抗体库的构建

目的构建抗人B-淋巴细胞刺激因子噬菌体单链抗体库。方法从B-淋巴细胞刺激因子免疫小鼠的脾细胞中抽提总RNA,经逆转录聚合酶反应合成cDNA,分别扩增小鼠重链可变区基因和轻链可变区基因。通过重叠延伸拼接法将重链可变区基因和轻链可变区基因组装成单链抗体基因,重组于载体pFUSE5,电转化E.coliXL 1-Blue。在辅助噬菌体援救下,构建成噬菌体单链抗体库。采用聚合酶链反应、核苷酸序列测定和酶联免疫分析鉴定单链抗体库的特征。结果本抗体库的噬菌体库容量约1×106,单链抗体基因插入效率为93%,存在序列差异性并含有抗B-淋巴细胞刺激因子单链抗体。结论成功地构建了抗人B-淋巴细胞刺激因子单链噬菌体抗体库,为筛选抗B-淋巴细胞刺激因子单链抗体药物奠定了良好的基础。     

晚期糖基化终产物受体胞外段的原核表达及其相互作用蛋白的筛选

目的构建晚期糖基化终产物受体(receptor for ad-vanced glycation end-product,RAGE)胞外段基因的原核表达载体并诱导表达,应用噬菌体展示技术筛选其相互作用蛋白。方法用RT-PCR方法扩增人RAGE胞外段cDNA,构建于原核表达载体pET14b,转化大肠杆菌BL21,IPTG诱导RAGE胞外段融合蛋白表达,用Ni2+-NTA亲和层析柱进行纯化并行Western blot鉴定。以重组RAGE胞外段蛋白为靶分子,进行3轮噬菌体展示环七肽库的筛选,从第3轮洗脱物中随机挑选分隔良好的噬菌体克隆扩增后进行ELISA鉴定。对获得的阳性噬菌体克隆分别进行扩增、纯化,提取DNA测序后翻译为氨基酸序列,用BLAST软件搜索Gen-Bank中的同源序列。结果成功构建并表达、纯化了RAGE胞外段融合蛋白。经过3轮筛选后,随机挑取的24个噬菌体克隆中11个可与RAGE胞外段结合。对11个噬菌体测序后用BLAST软件搜索同源序列,得到14个编码蛋白。结论应用噬菌体展示技术筛选到与RAGE胞外段相互作用的蛋白,为进一步研究其功能和作用机制提供新线索。     

Spectroscopic studies of rat mast cells,mouse mastocytoma cells,and compound 48/80—III: Evidence for a protein binding site for compound 48/80

The interaction of compound 48/80 with mast cells, mastocytoma cells, isolated membranes and liposomes has been studied using electron spin resonance (e.s.r.) and light-scattering techniques. Unlike spin-labeled stearic acid, spin-labeled 48/80 (SL-48/80) bound to mastocytoma cells in a manner that was unaffected by the non-ionic detergent, Triton X-100. In contrast, sodium dodecylsulfate (SDS), a protein denaturant, altered the SL-48/80 binding site(s), causing an apparent increase in the motion of the spin label. Treatment of SL-48/80-labeled mast cells with trypsin also increased the apparent motion of the bound label. Binding of 48/80 to mast cells, mastocytoma cells, erythrocyte ghosts, and isolated mastocytoma cell membranes increased their respective light-scattering properties. In contrast, the Rayleigh scatter of protein-free liposomes was unaffected by 48/80 treatment. Cationic, anionic, and non-ionic detergents also increased the light-scattering properties of mastocytoma cells, in contrast to the effect of several other cationic drugs, including histamine liberators. Increased light-scattering occurred after 48/80 treatment of inhibited mast cells (treated at 5°), indicating that the effect was not a consequence of degranulation. Untreated cells heated above 40° showed a similar increase in light scattering that became irreversible after reaching 45°. This indicates that cells treated with 48/80 resemble those in which the proteins have been denatured by heat. The light-scattering and the e.s.r. data, therefore, are consistent with the hypothesis that 48/80 binds to proteins in biological membranes.     

A Back-to-Front Fragment-Based Drug Design Search Strategy Targeting the DFG-Out Pocket of Protein Tyrosine Kinases

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Rapid identification of inhibitors that interfere with poliovirus replication using a cell-based assay

A small molecule library containing 480 known bioactive compounds was screened for antiviral activity against poliovirus (PV) using a cellular fluorescence resonance energy transfer (FRET) assay for viral protease activity. The infected reporter cells treated with the viral replication-suppressing compounds were examined via fluorescence microscope 7.5 h postinfection. Twelve molecules showed moderate to potent antiviral activity at concentrations less than 32 microM during the primary screening. Three compounds, anisomycin, linoleic acid, and lycorine, were chosen for validation. A dose-dependent cytotoxicity assay and a secondary screening using conventional plaque assay were conducted to confirm the results. The developed method can be used for rapid screening for molecules with antiviral activity.     

DNA编码化合物库技术新进展及其在生物医药领域的应用与展望

随着医药领域对靶向调节特定生命活动过程的新分子化合物的需求日益增加,高效、低成本地发现亲和配体分子的新型小分子药物筛选技术——DNA编码的化合物库(DNA encoded compound library,DEL)筛选技术应运而生。DEL作为组合化合物库,可以是简单小分子化合物的集合,也可以是具有高级空间结构的复杂小分子库,每个化合物都以共价方式与特异的DNA序列偶联,因而可将库中所有化合物与靶标蛋白进行合并筛选,随后使用高通量测序对DNA编码序列进行测序来鉴定结合的配体分子。近年来,应用DEL技术筛选开发候选药物的例子已越来越多地被报道,本文回顾和总结了DEL技术的实施流程,特别是DEL库构建和亲和筛选方法的最新研究进展,展示了利用DEL技术筛选开发的最新亲和配体分子,并对DEL技术在生命科学领域的应用前景作了展望。     

Generation of cell lines for drug discovery through random activation of gene expression: application to the human histamine H3 receptor

Target-based high-throughput screening (HTS) plays an integral role in drug discovery. The implementation of HTS assays generally requires high expression levels of the target protein, and this is typically accomplished using recombinant cDNA methodologies. However, the isolated gene sequences to many drug targets have intellectual property claims that restrict the ability to implement drug discovery programs. The present study describes the pharmacological characterization of the human histamine H3 receptor that was expressed using random activation of gene expression (RAGE), a technology that over-expresses proteins by up-regulating endogenous genes rather than introducing cDNA expression vectors into the cell. Saturation binding analysis using [125I]iodoproxyfan and RAGE-H3 membranes revealed a single class of binding sites with a K(D) value of 0.77 nM and a B(max) equal to 756 fmol/mg of protein. Competition binding studies showed that the rank order of potency for H3 agonists was N(alpha)-methylhistamine approximately (R)-alpha- methylhistamine > histamine and that the rank order of potency for H3 antagonists was clobenpropit > iodophenpropit > thioperamide. The same rank order of potency for H3 agonists and antagonists was observed in the functional assays as in the binding assays. The Fluorometic Imaging Plate Reader assays in RAGE-H3 cells gave high Z' values for agonist and antagonist screening, respectively. These results reveal that the human H3 receptor expressed with the RAGE technology is pharmacologically comparable to that expressed through recombinant methods. Moreover, the level of expression of the H3 receptor in the RAGE-H3 cells is suitable for HTS and secondary assays.     

Patent Evaluation: Human serotonin receptor 5-HTIE clone

Novelty: A human serotonin receptor of the 5-HT_1E subtype is claimed. The cloned receptor could be used for the screening of novel agonists or antagonists. Serotonin and serotonin receptors are involved in many functions in the body including behavioural functions, pain perception, sleep, aggression and sexual activity.

Biology: A human placental genomic library was screened using oligonucleotides derived from the known sequence of the 5-HT_1Dβ receptor gene. DNA sequencing of the positive clones showed one to be a different sub-class to those already known. DNA sequences of this clone were used as probes in the screening of a cDNA library and an expression vector expressing the 5-HT_1E receptor in transfected Y1 cells showed an increase in CAMP production after pargyline incubation. The disclosure also claims antibodies specific for this receptor which could be used in analysis of tissues or in drug development. Antisense RNA is claimed which could be used to inhibit the expression of this class of receptor in neuronal tissue.     

Rapid discovery of death ligands with one-bead-two-compound combinatorial library methods

The one-bead-one-compound (OBOC) technology enables one to generate thousands to millions of chemical molecules on resin beads (90 μm diameter) such that each bead displays 10(13) copies of the same chemical entity. Whole-cell binding assays have been developed to screen OBOC combinatorial libraries for ligands that bind to specific cell surface receptors. While very powerful, this screening method does not address the downstream cell signaling properties of the binding ligand. We have modified the OBOC technology by introducing a fixed known cell adhesion ligand to the outer layer of each bead. This one-bead-two-compound (OB2C) library configuration allows the bound cells to interact with the random immobilized chemical molecules on each bead. The bound cells can then be probed for specific cellular responses such as apoptosis and activation or inhibition of a specific cell signaling pathway. To validate this concept, an OB2C combinatorial library was created such that a random hexapeptide plus a high affinity lymphoma targeting ligand LLP2A were displayed on each bead. This LLP2A-X(6) OB2C library was then screened with human T-cell leukemia cells (Molt-4) for cell death responses. After 5 days of incubation, propidium iodide was added to the bead library to stain dead cells. Beads coated by red fluorescent cells were isolated for sequence analysis. Two ligands identified by this method, when added to the lymphoid cancer cells, were able to induce cell death.     

Using Ligand-Based Virtual Screening to Allosterically Stabilize the Activated State of a GPCR

G-protein coupled receptors play an essential role in many biological processes. Despite an increase in the number of solved X-ray crystal structures of G-protein coupled receptors, capturing a G-protein coupled receptor in its activated state for structural analysis has proven to be difficult. An unexplored paradigm is stabilization of one or more conformational states of a G-protein coupled receptor via binding a small molecule to the intracellular loops. A short tetrazole peptidomimetic based on the photoactivated state of rhodopsin-bound structure of Gt_α(340–350) was previously designed and shown to stabilize the photoactivated state of rhodopsin, the G-protein coupled receptor involved in vision. A pharmacophore model derived from the designed tetrazole tetrapeptide was used for ligand-based virtual screening to enhance the possible discovery of novel scaffolds. Maybridge Hitfinder and National Cancer Institute diversity libraries were screened for compounds containing the pharmacophore. Forty-seven compounds resulted from virtually screening the Maybridge library, whereas no hits resulted with the National Cancer Institute library. Three of the 47 Maybridge compounds were found to stabilize the MII state. As these compounds did not inhibit binding of transducin to photoactivated state of rhodopsin, they were assumed to be allosteric ligands. These compounds are potentially useful for crystallographic studies where complexes with these compounds might capture rhodopsin in its activated conformational state.     

A molecular understanding of mast cell activation and the promise of anti-allergic therapeutics

Mast cells are central to allergic disease. Their immediate (exocytosis of granule-stored allergic-mediators) and delayed (de novo synthesis of inflammatory mediators) response to an allergen underlies the symptoms seen in acute; and chronic allergic disease. Thus, intervention in the allergen-mediated activation of mast cells is a long sought after goal in the treatment and management of allergic disease. The recent gain in deciphering the molecular mechanisms underlying immunoglobulin E (IgE)-mediated mast cell activation has provided optimism for the development of new therapeutic strategies. Among the most promising is the use of humanized anti-IgE antibodies that inhibit binding of IgE to its high affinity receptor (FcepsilonRI) on the mast cell. Other strategies target molecules proximal to FcepsilonRI, whose activities are central in mast cell activation. One such molecule, Syk kinase, has been targeted by various approaches including a small molecule inhibitor that specifically abrogates mast cell degranulation. More recently, various molecules that function to promote protein-protein interactions (adapters) were demonstrated as essential to mast cell degranulation and cytokine production. It remains to be seen if these molecules hold therapeutic promise for disease intervention. Additional studies identifying molecules required for mast cell granule fusion and content exocytosis also bodes well for discovery of new therapeutic targets. While our understanding of IgE-mediated mast cell activation is still at its inception, the modest success in identifying molecules essential to this process affords some confidence for better treatment of allergic disease.     

DiSSiMiL: Diverse Small Size Mini‐Libraries applied to simple and rapid epitope mapping of a monoclonal antibody

Abstract: Methods for screening protein–protein interactions are useful in protein science and for the generation of drug leads. We set out to develop a simplified assay to rapidly test protein–protein interactions, with a library of 400 pentapeptides comprising the 20 natural amino acids at two variable positions followed by three glycines (NH₂‐X₁X₂GGG). The library was used to identify the epitope of monoclonal antibody (mAb) 10D11 directed against the HOXD4 protein. Three pentapeptide ‘hits’ were selected (VYGGG, PWGGG and WKGGG) from direct binding assays screening for pentapeptide?mAb interactions; and from assays using pentapeptides in solution to competitively block HOXD4?mAb interactions. Alignment of the three ‘hit’ pentapeptides to the HOXD4 sequence predicts the mAb 10D11 epitope as NH₂‐VYPWMK. Synthesis of NH₂‐VYPWMK hexapeptide confirmed this prediction; and an alanine scan of HOXD4 ablated binding by mAb 10D11 when amino acids in the putative epitope were mutated. We propose that these simplified but diverse libraries can be used for rapid epitope mapping of some mAbs, and for generating lead small peptide analogs that interfere with receptor–ligand or other protein–protein interactions, or with enzymatic activity.     

Molecular Modelling of β Turns in a Cyclic Melanotropin

α-Melanocyte stimulating hormone (α-MSH) is a tridecapeptide which interacts with a family of G protein-coupled receptors, the melanocortin receptors, to cause its biological effects. We have modelled the low energy conformations of the α-MSH derivatives as part of a project to probe the receptor binding conformation of melanocortins, and also to design ligands for targeting cytotoxic drugs to MC1 receptors expressed by melanoma cells. H***ere we report a molecular dynamics study of β turns in a cyclic lactam analogue [Nle⁴, ***Asp⁵, D-Phe⁷, Lye***¹⁰]α-MSH. The data show that it is possible for a β turn to exist in the ring portion of this molecule which contains the melanocortin conserved sequence -His-Phe-Arg-Trp-, even though the lowest energy conformers lack a β turn.