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PubMed2004

Design of bioactive and structurally well-defined peptides from conformationally restricted libraries.

Libraries of peptides and proteins can be categorized according to the function of their origin in gene- and synthetic-based libraries. Both kinds of libraries have the potential to generate the same grade of molecular diversity, although the limits imposed by the synthetic methods have been lately a matter of discussion. However, the use of synthetic strategies allows incorporation of non-natural amino acids. The development of conformationally restricted synthetic peptide libraries can be considered as a point of convergence of the two methodologies. In these libraries the diversity is grafted into scaffolds that are defined by stable secondary structural motifs, and the deconvolution protocols can be directed towards the identification of biologically active molecules and the analysis of determinants of folding of protein domains.

Amino Acid Sequence↗
PubMed2001

[Immunity against Schistosoma japonicum induced by phage display peptides mimicking antigenic epitopes of Trichinella spiralis].

OBJECTIVE: To obtain the short peptides mimicking antigenic epitopes of Trichinella spiralis (T. s.), and explore their cross protective immunity against Schistosoma japonicum (S.j.) in mice. METHODS: IgG antibodies were purified from sera of mice infected with T.s.. The purified IgG was used to immunoscreen a phage random peptide library of 7 amino-acid residues displayed as a fusion to protein of filamentous phage. Positive clones were obtained by affinity selection, the reactivity of each clone binding to specific IgG was detected by ELISA. Kunming mice were immunized subcutaneously three times with mixed phage clones. The mice were sacrificed 45 days after challenge. The worms and the liver eggs were counted. RESULTS: After three rounds of panning, the relevant phages had been enriched approximately 150 times in production as compared to those from the first round. Of 24 phage clones randomly selected from the third round biopanning, 21 clones were shown to actually bind to the specific IgG. As compared with the control group, the worm and the liver egg reduction rates in vaccination group were 42.8% and 66.3% (P < 0.001), respectively. CONCLUSION: The above results demonstrate that antigenic epitopes of T. s. can be prepared by immunoscreening phage random peptide library and a significant protective immunity against S. j. can be induced by these epitopes in mice.

Animals↗
PubMed2005

RshA mimetic peptides inhibiting the transcription driven by a Mycobacterium tuberculosis sigma factor SigH.

SigH, an alternative sigma factor in Mycobacterium tuberculosis, is a central regulator in responses to the oxidative and heat stress. This SigH activity is specifically controlled by an anti-sigma factor RshA during expression of stress-related genes. Thus, the specific interaction (k(on)=1.15x10(5) (M(-1) s(-1)), k(off)=1.7x10(-3) (s(-1)), KD=15 nM, determined in this study) between SigH and RshA is crucial for the survival and pathogenesis of M. tuberculosis. Using phage-display peptide library, we defined three specific regions on RshA responsible for SigH binding. Three RshA mimetic peptides (DAHADHD, AEVWTLL, and CTPETRE) specifically inhibited the transcription initiated by SigH in vitro. One of them (DAHADHD) diminished the extent of binding of RshA to SigH in a dose-dependent manner. The binding affinity (KD) of this peptide to SigH was about 1.2 microM. These findings might provide some insights into the development of new peptide-based drugs for TB.

Amino Acid Sequence↗
PubMed2005

DNA vaccine expressing the mimotope of GD2 ganglioside induces protective GD2 cross-reactive antibody responses.

The GD2 ganglioside expressed on neuroectodermally derived tumors, including neuroblastoma and melanoma, is weakly immunogenic in tumor-bearing patients and induces predominantly immunoglobulin (Ig)-M antibody responses in the immunized host. Here, we investigated whether interconversion of GD2 into a peptide mimetic form would induce GD2 cross-reactive IgG antibody responses in mice. Screening of the X(15) phage display peptide library with the anti-GD2 monoclonal antibody (mAb) 14G2a led to isolation of mimetic peptide 47, which inhibited the binding of 14G2a antibody to GD2-positive tumor cells. The peptide was also recognized by GD2-specific serum antibodies from a patient with neuroblastoma, suggesting that it bears an internal image of GD2 ganglioside expressed on the tumor cells. The molecular basis for antigenicity of the GD2 mimetic peptide, established by molecular modeling and mutagenesis studies, led to the generation of a 47-LDA mutant with an increased mimicry to GD2. Immunization of mice with peptide 47-LDA-encoded plasmid DNA elicited GD2 cross-reactive IgG antibody responses, which were increased on subsequent boost with GD2 ganglioside. The vaccine-induced antibodies recognized GD2-positive tumor cells, mediated complement-dependent cytotoxicity, and exhibited protection against s.c. human GD2-positive melanoma growth in the severe combined immunodeficient mouse xenograft model. The results from our studies provide insights into approaches for boosting GD2 cross-reactive IgG antibody responses by minigene vaccination with a protective epitope of GD2 ganglioside.

Amino Acid Sequence↗
PubMed2005

Phage displaying peptides mimic schistosoma antigenic epitopes selected by rat natural antibodies and protective immunity induced by their immunization in mice.

AIM: To obtain the short peptides mimic antigenic epitopes selected by rat natural antibodies to schistosomes, and to explore their immunoprotection against schistosomiasis in mice. METHODS: Adults worm antigens (AWA) were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and enzyme-linked transferred immunoblotting methods with normal SD rat sera (NRS). The killing effects on schistosomula with fresh and heat-inactivated sera from SD rats were observed. Then the purified IgG from sera of SD rats was used to biopan a phage random peptide library and 20 randomly selected positive clones were detected by ELISA and 2 of them were sequenced. Sixty female mice were immunized thrice with positive phage clones (0, 2nd), 4th wk). Each mouse was challenged with 40 cercariae, and all mice were killed 42 d after challenge. The worms and the liver eggs were counted. RESULTS: NRS could specifically react to the molecules of 75,000, 47,000, 34,500 and 23,000 of AWA. Sera from SD rats showed that the mortality rate of schistosomula was 76.2%, and when the sera were heat-inactivated in vitro, the mortality rate was decreased to 41.0% after being cultured for 48 h. The specific phages bound to IgG were enriched about 300-folds after three rounds of biopanning. Twenty clones were detected by ELISA, 19 of them bound to the specific IgG of rat sera. Immunization with these epitopes was carried out in mice. Compared with the control groups, the mixture of two mimic peptides could induce 34.9% (P=0.000) worm reduction and 67.6% (P=0.000) total liver egg reduction in mice. Two different mimic peptides could respectively induce 31.0% (P=0.001), 14.5% (P=0.074) worm reduction and 61.2% (P=0.000), 35.7% (P=0.000) total liver egg reduction. The specific antibody could be induced by immunization of the mimic peptides, and the antibody titer in immunized mice reached more than 1:6,400 as detected by ELISA. CONCLUSION: Specific peptides mimic antigenic molecules can be obtained by biopanning the phage random peptide library and a partially protective immunity against schistosome infection can be stimulated by these phage epitopes in mice.

Animals↗
PubMed1999

A phage-displayed mimotope inhibits tumour necrosis factor-alpha-induced cytotoxicity more effectively than the free mimotope.

A phage-displayed peptide library was screened by direct interaction with human tumour necrosis factor-alpha (TNF-alpha) to identify novel antagonistic molecules of its biological activities. After several rounds of affinity selection, a phage displaying a mimotope sequence was shown to strongly inhibit, in a dose-dependent fashion, both mouse and human TNF-alpha-mediated cytotoxicity in L929 cells. The identified mimotope did not bear any sequence homology to the primary structures of the extracellular domains of either the 55 000 MW or the 75 000 MW TNF-alpha receptors, suggesting that it represents or mimics a conformational epitope involved with binding to TNF-alpha. The free 15-mer mimotope weakly inhibited TNF-alpha-induced cytotoxicity in vitro, and it did not bind to TNF-alpha as assessed by surface plasmon resonance, demonstrating the importance of mimotope presentation for its biological activities. In conclusion, this study highlights the potential of random combinatorial peptide libraries for the identification of novel inhibitors, which may serve as important tools in research that could lead to the development of TNF-alpha antagonists with therapeutic potential.

Animals↗
PubMed1995

Isolation of a kidney-specific peptide recognized by alloreactive HLA-A3-restricted human CTL.

The molecular nature of tissue-specific Ags involved in MHC-restricted CTL responses is as yet undefined. To determine the specificity of these peptides, their function, and their possible relationship to allograft rejection, we have utilized human kidney-specific CD8+ CTL clones to screen reversed-phase HPLC (RP-HPLC)-separated self peptides presented by allo-class I molecules. One of these clones is HLA-A3-restricted and the other HLA-B62-restricted, lysing human kidney cell lines but not MHC identical B lymphoblastoid cells which express the appropriate HLA molecules. We have identified a biologically active RP-HPLC fraction containing self peptides eluted from affinity-purified MHC molecules from HLA-A3+ kidney. This peptide is not expressed in HLA-A3+ spleen. Similarly, a HLA-B62-associated peptide fraction was identified in kidney but not in spleen using the HLA-B62-restricted CTL clone. Sequence analysis of the biologically active fraction from HLA-A3 kidney revealed multiple peptides. Because of the ambiguity of the peptide sequence, a mixed peptide library corresponding to this sequence was synthesized that included the HLA-A3 binding motif. The biologically active peptide library was RP-HPLC fractionated and the fraction containing HLA-A3-restricted CTL activity was sequenced. The resulting sequence of the alloreactive HLA-A3-restricted peptide epitope is GPPGVTIVK. By using this unique strategy, we describe the successful isolation and sequencing of an antigenic peptide that is recognized by a human alloreactive kidney-specific CTL clone.

Amino Acid Sequence↗
PubMed2005

Screening of peptide affinity tags using immobilised metal affinity chromatography in 96-well plate format.

A method for high throughput screening of Green Fluorescent Proteins carrying metal binding tags in bacteria was developed. A random four amino acids tag-peptide library was successfully generated in E. coli. A 96-microtiter plate assembled with metal-iminodiacetic acid small cryogel columns was used for library screening. For the first time we were able to simultaneously screen a metal binding peptide tags library obtained from E. coli against different metal ions. From screening 25 different tags, three clones were able to bind to all metal ions studied (Ni2+, Zn2+, Co2+ and Cd2+). It was clearly demonstrated that the new construct could facilitate the screening of large peptide libraries.

Affinity Labels↗
PubMed2005

Affinity selection to papain yields potent peptide inhibitors of cathepsins L, B, H, and K.

Endogenous cysteine proteases were given much attention lately, as their role in a variety of pathophysiological disorders became evident. Amongst them cathepsins, which are thought to be implicated in mediation of osteoporosis, cancer progression, atherosclerosis, and many other conditions, are of considerable interest as drug targets. In the presented work, papain was chosen as a model cysteine protease and panning protocol was optimized for selection of papain-binding phage-displayed peptides from a commercially available combinatorial peptide library. Different selection strategies were applied in order to select high-affinity binders. Ultimately, five cyclic peptides (CNWAAGYNCGGGS-NH2, CWSMMGFQCGGGS-NH2, CWEWGGWHCGGSS-OH, CNWTLGGYKCGGGS-NH2 (all cyclized through formation of intramolecular disulphide bond), and GNWTLGGYKGG (cyclized head-to-tail)) were synthesized and tested for inhibitory activity towards papain and human cathepsins L, B, H, and K. The peptides possess inhibitory constants in the low micromolar to mid-nanomolar range and exhibit certain selectivity for different lysosomal cysteine proteases included in this study.

Amino Acid Sequence↗
PubMed2004

Characterization of BoHV-1 gE envelope glycoprotein mimotopes obtained by phage display.

A phage-displayed peptide library was screened using four mAbs directed against bovine herpesvirus 1 (BoHV-1) gE glycoprotein to identify peptides mimicking this glycoprotein. The selected mimotopes allowed us to characterize the epitopes corresponding to the mAbs as continuous and proteinic and to consider using these peptides in further studies. One epitope has been clearly located at the C-terminus of the protein (amino-acids 561-569). The three other mAbs enabled us to stress the immunogenic relevance of the proline-rich motifs of gE. Selected peptides showed no clear sequence identity with gE, but there is a clear link between gE proline-rich regions and the amino-acid composition of the mimotopes. The proline-rich motifs of gE are potentially located in flanking regions involved in the gE/gl glycoprotein complex formation. N-terminal fusion to pill or pVIII filamentous phage protein, C-terminal fusion to the T7 phage capsid protein, biotinylated synthetic peptides and insertion between the non-cleaved CX leader sequence and the C-terminal part of Caulobacter crescentus RsaA protein have been tested in order to increase the valency of a model peptide. We have diverted the C. crescentus expression system and proven its usefulness using the RsaA protein as a scaffold displaying the peptides of interest. Comparison between these different display systems in an indirect ELISA, indicates that the C. crescentus expression and the T7 phage display systems have some major advantages.

Amino Acid Sequence↗
PubMed2000

Rapid identification of key amino-acid-DNA contacts through combinatorial peptide synthesis.

BACKGROUND: Basic helix-loop-helix (bHLH) transcription factors are characterized by a conserved four-helix bundle that recognizes a specific hexanucleotide DNA sequence in the major groove. Previous studies have shown that amino acids in the basic region make base-specific contacts, whereas the HLH region is responsible for dimerization. Structural data suggest that portions of the loop region may be proximal to the DNA; however, the role of the loop in DNA-binding affinity and specificity has not been investigated. RESULTS: Protein-DNA recognition by the Drosophila bHLH transcription factor Deadpan was probed using combinatorial solid-phase peptide synthesis methods. A series of bHLH peptide libraries that modulate amino acid content and length in the loop region was screened with DNA and peptide affinity columns, and analyzed using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). A functional bHLH peptide with reduced loop length was found, and Lys80 was unambiguously identified as the sole loop residue critical for DNA binding. Unnatural amino acids were substituted at this position to assess contributions of the terminal amino group and the alkyl chain length to DNA-binding affinity and specificity. CONCLUSIONS: Using combinatorial solid-phase peptide synthesis methods and MALDI-MS, we were able to rapidly identify a key amino acid involved in DNA binding by a bHLH protein. Our approach provides a powerful alternative to current recombinant DNA methods to identify and probe the energetics of protein-DNA interactions.

Amino Acid Sequence↗
PubMed2002

Anti-neovascular therapy using novel peptides homing to angiogenic vessels.

Cancer chemotherapy targeted to angiogenic vessels is expected to cause indirect tumor regression through the damage of the neovasculature without the induction of drug resistance. To develop a tool for neovasculature-specific drug delivery, we isolated novel peptides homing to angiogenic vessels formed by a dorsal air sac method from a phage-displayed peptide library. Three distinct phage clones that markedly accumulated in murine tumor xenografts presented PRPGAPLAGSWPGTS-, DRWRPALPVVLFPLH- or ASSSYPLIHWRPWAR-peptide respectively. After the determination of the epitope sequences of these peptides, we modified liposomes with epitope penta-peptides. Liposome modified with APRPG-peptide showed high accumulation in murine tumor xenografts, and APRPG-modified liposome encapsulating adriamycin effectively suppressed experimental tumor growth. Finally, specific binding of APRPG-modified liposome to human umbilical endothelial cells, and that of PRP-containing peptide to angiogenic vessels in human tumors, i.e., islet cell tumor and glioblastoma, were demonstrated. The present study indicates the usefulness of APRPG-peptide as a tool for anti-neovascular therapy, a novel modality of cancer treatment.

Amino Acid Sequence↗
PubMed2002

Monoclonal antibodies selective for low molecular weight neurofilaments.

Neurofilaments are necessary for the maintenance of axonal caliber and structural organization of nerve cells. The low molecular weight form of neurofilament, the neurofilament light protein, which serves as the core of the filament, was used as immunogen for generation of hybridomas with selective reactivity with this form of the filament. Six hybridomas, out of approximately 100 tested clones, were highly discriminatory. All involved epitopes were localized to the rod region of the antigen, as determined by alpha-chymotrypsin digestion of the purified filament and enzymatic peptide mapping. Synthetic peptides (20 mers) covering the entire rod region did not react with the antibodies. A phage display peptide library was used to identify four consensus sequences for the antibodies. The results indicate that all epitopes were of conformational type. Pair-wise BIAcore data furthermore indicated that the epitopes were independent. The access to such specific reagents is a prerequisite for further elucidation of the biology of the low molecular weight form of neurofilaments proteins.

Animals↗
PubMed2004

Indolactam and benzolactam compounds as new medicinal leads with binding selectivity for C1 domains of protein kinase C isozymes.

Protein kinase C (PKC) isozymes (alpha, betaI, betaII, gamma, delta, epsilon, eta, theta) are major receptors of tumor promoters and also play a crucial role in cellular signal transduction via the second messenger, 1,2-diacyl-sn-glycerol (DG). Each isozyme of PKC is involved in diverse biological events, indicating that it serves as a novel therapeutic target. Since PKC isozymes contain two possible binding sites of tumor promoters and DG (C1A and C1B domains), the design of agents with binding selectivity for individual PKC C1 domains is a pressing need. We developed a synthetic C1 peptide library of all PKC isozymes for high-throughput screening of new ligands with such binding selectivity. This peptide library enabled us to determine that indolactam and benzolactam compounds bound to the C1B domains of novel PKC isozymes (delta, epsilon, eta, theta) in some selective manner, unlike phorbol esters and DG. Simpler in structure and higher in stability than the other potent tumor promoters, a number of indolactam and benzolactam derivatives have been synthesized to develop new PKC isozyme modulators by several groups. We focused on the amide function of these compounds because recent investigations revealed that both the amide hydrogen and carbonyl oxygen of indolactam-V (ILV) are involved in hydrogen bonding with the C1B domains of PKCdelta. Synthesis of several conformationally fixed analogues of ILV led to the conclusion that the trans-amide restricted analogues with a hydrophobic chain at an appropriate position (2,7) are promising leads with a high binding selectivity for novel PKC isozyme C1B domains. We also developed a new lactone analogue of benzolactam-V8 (17) which shows significant binding selectivity for the C1B domains of PKCepsilon and PKCeta. Furthermore, our synthetic approach with the PKC C1 homology domains clarified that diacylglycerol kinase beta and gamma are new targets of phorbol esters.

Amino Acid Sequence↗
PubMed2001

The development and application of a novel safety-catch linker for BOC-based assembly of libraries of cyclic peptides.

Cyclic peptides are appealing targets in the drug-discovery process. Unfortunately, there currently exist no robust solid-phase strategies that allow the synthesis of large arrays of discrete cyclic peptides. Existing strategies are complicated, when synthesizing large libraries, by the extensive workup that is required to extract the cyclic product from the deprotection/cleavage mixture. To overcome this, we have developed a new safety-catch linker. The safety-catch concept described here involves the use of a protected catechol derivative in which one of the hydroxyls is masked with a benzyl group during peptide synthesis, thus making the linker deactivated to aminolysis. This masked derivative of the linker allows BOC solid-phase peptide assembly of the linear precursor. Prior to cyclization, the linker is activated and the linear peptide deprotected using conditions commonly employed (TFMSA), resulting in deprotected peptide attached to the activated form of the linker. Scavengers and deprotection adducts are removed by simple washing and filtration. Upon neutralization of the N-terminal amine, cyclization with concomitant cleavage from the resin yields the cyclic peptide in DMF solution. Workup is simple solvent removal. To exemplify this strategy, several cyclic peptides were synthesized targeted toward the somatostatin and integrin receptors. From this initial study and to show the strength of this method, we were able to synthesize a cyclic-peptide library containing over 400 members. This linker technology provides a new solid-phase avenue to access large arrays of cyclic peptides.

Combinatorial Chemistry Techniques↗
PubMed2001

Immunoglobulin cross-reactivity examined by library screening, crystallography and docking studies.

Antibodies are extremely diverse with respect to their specificities and affinities for target molecules. Despite rigorous selection, some antibodies are cross-reactive whereby they recognize their natural antigens along with other molecules. In this review, we discuss our efforts toward understanding the cross-reactivity of selected immunoglobulins. Investigations that are discussed employed screens of combinatorial peptide libraries, crystallography of ligand-protein complexes, and computer-based peptide docking simulations. In the first example, two different antibodies (NC6.8 and NC10.14) bound the same trisubstituted guanidine (NC174) with similar affinities, but utilized predominantly dissimilar binding strategies. However, there was one common binding strategy, in which the cyanophenyl portion of NC174 was inserted end-on into the binding crevices of the NC6.8 and NC10.14 antibodies. In the second example, scanning of peptide libraries and X-ray crystallography were used to design and test synthetic peptides for binding to the Mcg L chain dimer. Again, end-on insertion was favored for all peptides larger than dipeptides in the voluminous Mcg binding cavity. Finally, automated docking was used for rapid predictions of complexes for the Fv molecule from a broadly cross-reactive human IgM (Mez) and nearly two thousand peptides. Certain amino acids, including the aromatic residues Trp and Phe, functioned as anchoring groups in automated docking. Anchoring groups acted in most of the peptides that were otherwise accommodated by a variety of binding strategies in the docked complexes. We suggest that anchoring of at least a portion of a ligand in a binding site is a common mechanism for antibody recognition.

Binding Sites, Antibody↗
PubMed2003

Exploring protein-protein interactions with phage display.

Protein-protein interactions mediate essentially all biological processes. A detailed understanding of these interactions is thus a major goal of modern biological chemistry. In recent years, genome sequencing efforts have revealed tens of thousands of novel genes, but the benefits of genome sequences will only be realized if these data can be translated to the level of protein function. While genome databases offer tremendous opportunities to expand our knowledge of protein-protein interactions, they also present formidable challenges to traditional protein chemistry methods. Indeed, it has become apparent that efficient analysis of proteins on a proteome-wide scale will require the use of rapid combinatorial approaches. In this regard, phage display is an established combinatorial technology that is likely to play an even greater role in the future of biology. This article reviews recent applications of phage display to the analysis of protein-protein interactions. With combinatorial mutagenesis strategies, it is now possible to rapidly map the binding energetics at protein-protein interfaces through statistical analysis of phage-displayed protein libraries. In addition, naïve phage-displayed peptide libraries can be used to obtain small peptide ligands to essentially any protein of interest, and in many cases, these binding peptides act as antagonists or even agonists of natural protein functions. These methods are accelerating the pace of research by enabling the study of complex protein-protein interactions with simple molecular biology methods. With further optimization and automation, it may soon be possible to study hundreds of different proteins in parallel with efforts comparable to those currently expended on the analysis of individual proteins.

Animals↗
PubMed2002

Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries.

Novel statistical methods have been developed and used to quantitate and annotate the sequence diversity within combinatorial peptide libraries on the basis of small numbers (1-200) of sequences selected at random from commercially available M13 p3-based phage display libraries. These libraries behave statistically as though they correspond to populations containing roughly 4.0+/-1.6% of the random dodecapeptides and 7.9+/-2.6% of the random constrained heptapeptides that are theoretically possible within the phage populations. Analysis of amino acid residue occurrence patterns shows no demonstrable influence on sequence censorship by Escherichia coli tRNA isoacceptor profiles or either overall codon or Class II codon usage patterns, suggesting no metabolic constraints on recombinant p3 synthesis. There is an overall depression in the occurrence of cysteine, arginine and glycine residues and an overabundance of proline, threonine and histidine residues. The majority of position-dependent amino acid sequence bias is clustered at three positions within the inserted peptides of the dodecapeptide library, +1, +3 and +12 downstream from the signal peptidase cleavage site. Conformational tendency measures of the peptides indicate a significant preference for inserts favoring a beta-turn conformation. The observed protein sequence limitations can primarily be attributed to genetic codon degeneracy and signal peptidase cleavage preferences. These data suggest that for applications in which maximal sequence diversity is essential, such as epitope mapping or novel receptor identification, combinatorial peptide libraries should be constructed using codon-corrected trinucleotide cassettes within vector-host systems designed to minimize morphogenesis-related censorship.

Amino Acids↗