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Author : Jennifer Marie Brown
Publisher :
Page : 64 pages
File Size : 10,38 MB
Release : 2010
Category : Combinatorial chemistry
ISBN :
Author : Shmuel Cabilly
Publisher : Springer Science & Business Media
Page : 320 pages
File Size : 14,85 MB
Release : 2008-02-02
Category : Science
ISBN : 1592595715
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 : Günther Jung
Publisher : John Wiley & Sons
Page : 571 pages
File Size : 37,88 MB
Release : 2008-09-26
Category : Science
ISBN : 3527614907
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 : Lisa B. English
Publisher : Springer Science & Business Media
Page : 380 pages
File Size : 18,90 MB
Release : 2008-02-04
Category : Science
ISBN : 1592592856
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 : Peng Wang
Publisher :
Page : pages
File Size : 49,74 MB
Release : 2003
Category : Ligands
ISBN :
Abstract: A method for the rapid identification of high-affinity ligands was used to study the specificity of the interaction between FHA2 domain of Rad53 and phosphotyrosyl peptide. A phosphotyrosyl (pY) peptide library containing completely randomized residues at positions -2 to +3 relative to the pY was synthesized on TentaGel resin, with a unique peptide sequence on each resin bead. The library was screened against the biotinylated FHA2 domains, and the beads that carry high-affinity ligands of the FHA2 domains were identified using an enzyme-linked assay. Peptide ladder sequencing of the hundreds of selected beads using MALDI-TOF revealed consensus sequences for FHA2 domains. A new method was developed to rapidly sequence support-bound peptides derived from combinatorial peptide library. Support-bound peptides isolated from one-bead-one-compound libraries are subjected to partial Edman degradation in the presence of an N-terminal blocking agent (5% phenyl isocyanate). Repetition of the degradation reaction results in a series of sequence-specific truncation products (a peptide ladder). The sequence of the full-length peptide is determined by MALDI-TOF analysis of the peptide ladder. During screening of combinatorial libraries for optimal enzyme substrates, the challenge is to differentiate a reaction product(s) from a complex mixture of substrates. We have overcome this problem by partially labeling the substrates with a heavier isotope (heavy/normal isotope = 1:1), so that each member of the substrate library appears as a doublet in ESI-MS spectrum whereas the products appear as singlets in the spectrum, allowing for their unambiguous identification. The strategy has been successfully demonstrated by peptide deformylase screening. This method was further perfected in the screening of the pY library against the catalytic domain of SHP-1. Limited treatment of the library with a PTP removed phosphoryl group from the most preferred substrates to generate products as singlet peaks, which were readily identified in ESI-FTICR-MS spectrum and sequenced by tandem mass spectrometry. Several selected peptides were individually synthesized and assayed against SHP-1 and the kinetic data confirmed the screening results.
Author : Sejal Sampat Hall
Publisher : ProQuest
Page : 276 pages
File Size : 32,25 MB
Release : 2008
Category :
ISBN : 9780549702900
An auto-fluorescent bacterial display peptide library was used to isolate red blood cell (RBC) binding ligands which were used to attach nanoparticles to the RBC surface to develop novel long circulating drug delivery vehicles. Bacterial display was also employed to isolate tissue targeting ligands in vivo. Finally, multi-color FACS was used to quantitatively isolate highly-specific peptides and further optimize their specificity for a target antibody present at a 10,000 - 100,000 fold dilution in serum IgG. The method was employed to screen serum antibodies of patients with Celiac Disease to identify potential biomarker candidates. The method developed here enables quantitative screening and evolution of specificity, enhancing the current repertoire of screening methods available in protein engineering.
Author : Michael Cameron Sweeney
Publisher :
Page : pages
File Size : 34,28 MB
Release : 2005
Category : Amino acid sequence
ISBN :
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 : Tao Liu
Publisher :
Page : pages
File Size : 43,79 MB
Release : 2011
Category :
ISBN :
Abstract: Cyclic peptides are widely produced in nature and possess a broad range of biological activities. Their enhanced proteolytic stability in vivo and improved receptor binding affinity/specificity makes them excellent drug candidates, molecular probes and targeting agents. In fact, many cyclic peptides are clinically used therapeutic agents. Combinatorial library approaches provide powerful tools for the rapid identification of compounds with desired properties from large pools in biological and biomedical studies. However, the synthesis and screening of cyclic peptide libraries in a combinatorial format has been challenging. To overcome the issue, we have successfully developed one-bead-two-compound (OBTC) libraries with a cyclic peptide displayed on the bead surface accessible for protein targets screening, while the bead interior contains the corresponding linear peptide served as an encoding tag for hit identification. The primary goal of my research is to identify novel biologically active cyclic peptides, beyond what nature has provided us. By applying cyclic peptide library approach, we have successfully identified high affinity ligands against various biological targets, including: extracellular protein receptors (human prolactin receptor), intracellular protein domains (the capsid domain of HIV-1 Gag polyprotein and calcineurin catalytic domain) and enzymes (Pin1 catalytic domains). In the meantime, we have continued to improve the methodologies associated with combinatorial chemistry. To facilitate the process and improve the screening results, such as avoiding false positives, we have developed many cyclic library approaches including libraries on different solid supports, reduced surface density libraries, high diversity libraries with different ring sizes and library compatible with rapid solution phase validation. These new approaches greatly facilitate the ligands discovery process. My final work focused on the intracellular delivery of cyclic peptides. Little is known about how cyclization would affect peptides membrane permeability and the results from existing studies are controversial. With a combination of biophysical approaches and cell based studies, we have found that cyclization has a dramatic effect on the cell permeation of peptides with certain residues. By applying the rules, we were able to design cell permeable cyclic peptide inhibitors against various intracellular protein targets. Our studies provide guiding principles for designing membrane penetrating cyclic peptidyl drugs.
Author : P. Gopalakrishnakone
Publisher : Springer
Page : 0 pages
File Size : 12,34 MB
Release : 2019-09-11
Category : Medical
ISBN : 9789400764514
In recent years, the field of Toxinology has expanded substantially. On the one hand it studies venomous animals, plants and micro organisms in detail to understand their mode of action on targets. While on the other, it explores the biochemical composition, genomics and proteomics of toxins and venoms to understand their three interaction with life forms (especially humans), development of antidotes and exploring their pharmacological potential. Therefore, Toxinology has deep linkages with biochemistry, molecular biology, anatomy and pharmacology. In addition, there is a fast developing applied subfield, clinical toxinology, which deals with understanding and managing medical effects of toxins on human body. Given the huge impact of toxin-based deaths globally, and the potential of venom in generation of drugs for so-far incurable diseases (for example, Diabetes, Chronic Pain), the continued research and growth of the field is imminent. This has led to the growth of research in the area and the consequent scholarly output by way of publications in journals and books. Despite this ever growing body of literature within biomedical sciences, there is still no all-inclusive reference work available that collects all of the important biochemical, biomedical and clinical insights relating to Toxinology. The Handbook of Toxinology aims to address this gap and cover the field of Toxinology comprehensively.
Author : Ratmir Derda
Publisher : Humana
Page : 0 pages
File Size : 12,68 MB
Release : 2016-09-24
Category : Science
ISBN : 9781493946426
This volume provides an overview of modern and emerging methods for production, analysis, and utility of peptide libraries. Chapter focus on methods and techniques for synthesis, genetic expression, hybrid synthesis-expression, examples of modern utility of these libraries, de novo discovery of reactions, hybrid organic-inorganic materials and, emerging tools for the analysis of these libraries by method of genetic selection and next-generation sequencing. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Peptide Libraries: Methods and Protocols seeks to serve both professionals and novices with its well-honed methodologies.