[PDF] Synthetic Combinatorial Peptide Libraries And Their Application In Decoding Biological Interactions eBook

Author : Michael Cameron Sweeney
Publisher :
Page : pages
File Size : 32,38 MB
Release : 2005
Category : Amino acid sequence
ISBN :

GET BOOK

Abstract: The synthesis of peptides was revolutionized by the adoption of solid-phase synthetic techniques. Subsequent improvement, evolution, and refinement of this chemical technique has allowed research into areas of biology not previously accessible with such speed and breadth. Because of the efficiency and flexibility of the chemistry involved in peptide synthesis, libraries representing millions of unique natural, modified, or unnatural peptides can be constructed rapidly and in high enough purity as to obviate the need for purification. In this work, libraries were synthesized for screening against individual protein domains in an effort to both determine the preferred peptidyl binding partner types for each, as well as to establish an optimized, broadly applicable methodology for screening other domains. One of the problems encountered during the development of the screening methodology was the low success-rate of sequence determination for the peptides selected by each domain. Herein we report the successful modification of the peptide ladder mass spectrometry sequencing technique referred to as partial Edman degradation (PED). Success-rates were improved to greater than 90% for full-length sequencing determination of peptide up to 8-mers, even for more difficult phosphotyrosine (pY)-containing peptides. As a result of this improvement, three pY-binding Src Homology 2 (SH2) domains and two N-terminus binding Baculoviral Inhibitor-of-Apoptosis Repeat (BIR) domains were screened against their respective libraries and the preferred ligand types for each was determined. The advantage of sequencing by the PED method became especially clear in the case of the N-terminal SH2 (N-SH2) domain of Src Homology 2 Protien Tyrosine Phosphatase 2 (SHP-2) as previously unidentified sub-classes of binding consensus motifs were distinguishable due to the discreet nature of the sequencing technique. This work demonstrates the usefulness and potential generality of peptide library screening by this method.

Author : Shmuel Cabilly
Publisher : Springer Science & Business Media
Page : 320 pages
File Size : 10,13 MB
Release : 2008-02-02
Category : Science
ISBN : 1592595715

GET BOOK

During the course of evolution, an imbalance was created between the rate of vertebrate genetic adaptation and that of the lower forms of living organisms, such as bacteria and viruses. This imbalance has given the latter the advantage of generating, relatively quickly, molecules with unexpected structures and features that carry a threat to vertebrates. To compensate for their weakness, vertebrates have accelerated their own evolutionary processes, not at the level of whole organism, but in specialized cells containing the genes that code for antibody molecules or for T-cell receptors. That is, when an immediate requirement for molecules capable of specific interactions arose, nature has preferred to speed up the mode of Darwinian evolution in pref- ence to any other approach (such as the use of X-ray diffraction studies and computergraphic analysis). Recently, Darwinian rules have been adapted for test tube research, and the concept of selecting molecules having particular characteristics from r- dom pools has been realized in the form of various chemical and biological combinatorial libraries. While working with these libraries, we noticed the interesting fact that when combinatorial libraries of oligopeptides were allowed to interact with different selector proteins, only the actual binding sites of these proteins showed binding properties, whereas the rest of the p- tein surface seemed "inert. " This seemingly common feature of protein- having no extra potential binding sites--was probably selected during evolution in order to minimize nonspecific interactions with the surrounding milieu.

Author : Lisa B. English
Publisher : Springer Science & Business Media
Page : 380 pages
File Size : 30,6 MB
Release : 2008-02-04
Category : Science
ISBN : 1592592856

GET BOOK

The continued successes of large- and small-scale genome sequencing projects are increasing the number of genomic targets available for drug d- covery at an exponential rate. In addition, a better understanding of molecular mechanisms—such as apoptosis, signal transduction, telomere control of ch- mosomes, cytoskeletal development, modulation of stress-related proteins, and cell surface display of antigens by the major histocompatibility complex m- ecules—has improved the probability of identifying the most promising genomic targets to counteract disease. As a result, developing and optimizing lead candidates for these targets and rapidly moving them into clinical trials is now a critical juncture in pharmaceutical research. Recent advances in com- natorial library synthesis, purification, and analysis techniques are not only increasing the numbers of compounds that can be tested against each specific genomic target, but are also speeding and improving the overall processes of lead discovery and optimization. There are two main approaches to combinatorial library production: p- allel chemical synthesis and split-and-mix chemical synthesis. These approaches can utilize solid- or solution-based synthetic methods, alone or in combination, although the majority of combinatorial library synthesis is still done on solid support. In a parallel synthesis, all the products are assembled separately in their own reaction vessels or microtiter plates. The array of rows and columns enables researchers to organize the building blocks to be c- bined, and provides an easy way to identify compounds in a particular well.

Author : Günther Jung
Publisher : John Wiley & Sons
Page : 571 pages
File Size : 48,9 MB
Release : 2008-09-26
Category : Science
ISBN : 3527614907

GET BOOK

With combinatorial chemistry millions of organic compounds can be produced simultaneously, quickly, and in most cases by automated procedures. These compound libraries are a cost-effective resource for the pharmaceutical industry in their search for biologically active lead structures. Furthermore simultaneous parallel synthesis of single peptides and peptide libraries solve the problem of the worldwide increasing demand for peptides. The synthetic methods described here in detail contribute to a forward-looking technology that has a high impact for industrial and academic research. Fast and efficient analytical techniques are essential for using the complicated product mixtures and detecting by-products. Various synthetic approaches and technologies, mass spectrometry, and screening assays are discussed extensively. This book is a must and an indispensible source of information for every researcher in this rapidly developing field, which spans organic synthesis, biochemistry, biotechnology, pharmaceutical, medicinal, and clinical chemistry.

Author : Xinxia Liang
Publisher :
Page : 173 pages
File Size : 28,52 MB
Release : 2016
Category :
ISBN :

GET BOOK

A great number of cellular and biological processes depend, at some level, on protein-protein interactions (PPI). Their manipulation with chemical compounds has provided a great potential for the discovery of new drugs. Despite the increasing demand for molecules able to interrupt specific PPI, the development of small PPI inhibitors is beset by a number of challenges such as the large size of the interaction interface. Based on the interface's nature, the ability to mimic protein secondary structures is very important to bind a protein and inhibit PPI. With their interesting peptidomimetic abilities and pharmacological properties, cyclic peptides are very promising templates to discover protein ligands and development new PPI inhibitors. To fully exploit the great diversity accessible with cyclic peptides, the one-bead-one-compound (OBOC) combinatorial method is certainly the most accessible and powerful approach. Unfortunately, the use of cyclic peptides in OBOC libraries is limited by difficulties in sequencing hit compounds after the screening. Lacking a free N-terminal amine, Edman degradation cannot be used on cyclic peptides and complicated fragmentation patterns are obtained by tandem mass spectrometry (MS/MS). In this regard we have designed and developed new convenient ring-opening approaches to prepare and decode OBOC cyclic peptide libraries. Our strategy was to introduce a cleavable residue in the macrocycle and as a linker to allow linearization of peptides and their release from the beads for sequencing by MS/MS. First, amino acid residues sensible to nucleophiles, ultraviolet irradiation or cyanogens bromide were introduced in a model cyclic peptide. Afterward, the most promising residues were used to design and develop tandem ring-opening/cleavage approaches to decode OBOC cyclic peptide libraries. In the first approach a methionine residue was introduced in the macrocycle and as a linker to allow a simultaneous ring-opening and cleavage from the beads upon treatment with cyanogens bromide. In the second approach, a photosensitive residue was used in the macrocycle and as a linker for a dual ring-opening/cleavage upon UV irradiation. The linear peptide generated by these approaches can be efficiently sequenced by tandem mass spectrometry. Finally, an OBOC library has been prepared and screened against the HIV-1 Nef protein to identify selective ligands. The development of these methodologies will prompt the use of macrocyclic compounds in OBOC libraries and be an important contribution in medicinal chemistry for the discovery of protein ligands and the development of PPI inhibitors.

Author : Thi Ba Trinh
Publisher :
Page : pages
File Size : 20,21 MB
Release : 2014
Category :
ISBN :

GET BOOK

Combinatorial chemistry is a powerful tool in medicinal chemistry as well as chemical biology. In this work, we have applied combinatorial chemistry toward the analysis of peptide cyclization, specificity profiling of protein kinases and the identification of novel inhibitors against medicinally important protein targets.

Author : Joachim Koch
Publisher : Springer Science & Business Media
Page : 192 pages
File Size : 14,27 MB
Release : 2013-03-09
Category : Science
ISBN : 3662092298

GET BOOK

Proteins interacting with diverse ligands - proteins, peptides or DNA - are the basic principles underlying many biological processes, such as antigen-antibody binding, signal transduction or receptor binding. The technique of oligopeptide synthesis on a cellulose membrane and the subsequent binding assays allow the investigation of protein interactions. A particular advantage of these peptide arrays (SPOT - technology) is the high number of oligopeptide probes that can be tested in parallel. Detailed protocols for peptide synthesis, and the analysis of protein-protein, protein-DNA interactions as well as epitope mapping are presented in this manual. It is ideally suited not only for basic research laboratories but also for diagnostic and therapeutic applications since many diseases are related to dysfunctions in protein recognition and binding.

Author : Irwin M. Chaiken
Publisher :
Page : 346 pages
File Size : 30,48 MB
Release : 1996
Category : Medical
ISBN :

GET BOOK

Reports progress on chemical, enzymatic, phage, and cell-derived libra ries. Discusses synergy between structure-based design and combinatori al libraries. Presents applications of combinatorial libraries to drug discovery and new synthetic catalysis. Reports library screening appr oaches, including the use of NMR. Presents recent advances in solid-ph ase organic synthesis, liquid-phase organic synthesis, and high-throug hput combinatorial organic synthesis. Discusses automation of organic synthesis as well as new methodologies for monitoring solid-phase orga nic synthesis.

Author : Amit Thakkar
Publisher :
Page : pages
File Size : 18,6 MB
Release : 2009
Category :
ISBN :

GET BOOK

We have also successfully synthesized and sequenced support-bound cyclic peptoids, a novel class of compounds. By using a one-bead, two-compound approach, we have spatially segregated TentaGel microbeads (90 um) and synthesized a cyclic peptoid on the bead exterior to be used for biological screenings and a linear peptoid on the bead interior for sequencing by PED/MS. Cyclic peptoid libraries were used to investigate potential protein inhibitors and determine streptavidin ligands.