Evolving a Peptide: Library Platforms and Diversification Strategies (original) (raw)
Related papers
BMC Genomics
Background: Recombinant peptide chips could constitute a versatile complementation to state-of-the-art in situ (chemical on-chip) synthesis, particle-based printing, or pre-manufactured peptide spotting. Bottlenecks still impeding a routine implementation-from restricted peptide lengths, low diversity and low array densities to high costs-could so be overcome. Methods: To assess overall performance, we assembled recombinant chips composed of 38,400 individual peptide spots on the area of a standard 96-well microtiter plate from comprehensive, highly diverse (>107 single clones) short random peptide libraries. Results: Screening of altogether 476,160 clones against Streptavidin uncovered 2 discrete new binders: a characteristic HPQ-motif containing VSHPQAPF and a cyclic CSGSYGSC peptide. Interactions were technically confirmed by fluorescence polarization as well as biolayer-interferometry, and their potential suitability as novel detection tags evaluated by detection of a peptide-fused exemplary test protein. Conclusion: From our data we conclude that the presented technical pipeline can reliably identify novel hits, useful as first-generation binders or templates for subsequent ligand design plus engineering.
Biopolymers, 2004
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.
Peptide Diversity in Drug Discovery
Frontiers in Drug Design & Discovery (Volume 3), 2012
Solid-phase peptide synthesis is the archetypal example of combinatorial chemistry. Advances in amino acid synthesis allow unprecedented structural diversity using automated synthesis. In this chapter we briefly introduce the history and advances in peptide synthesis and include strategies for peptidomimetic development. We highlight examples of the use of peptides in drug development, including pharmacophore extrapolation, substrate/ligand mimicry, and post-genomics target protein identification. We also describe methods for virtual combinatorial peptide construction, using databases of commercially available, non-natural amino acids, as well as strategies for high throughput virtual screening and de novo design of inhibitors. Finally, we offer suggestions for using peptide diversity for lead compound identification and optimisation, as well as a number of pitfalls in both peptide synthesis and virtual screening that need to be avoided.
Advances in Methods for Therapeutic Peptide Discovery, Design and Development
Current Pharmaceutical Biotechnology, 2011
Drug discovery and development are intense, lengthy and interdisciplinary processes. Traditionally, drugs were discovered by synthesizing compounds in time-consuming multi-step experimental investigations followed by in vitro and in vivo biological screening. Promising candidates were then further studied for their pharmacokinetic properties, metabolism and potential toxicity. Today, the process of drug discovery has been revolutionized due to the advances in genomics, proteomics, and bioinformatics. Efficient technologies such as combinatorial chemistry, high throughput screening (HTS), virtual screening, de novo design and structure-based drug design contribute greatly to drug discovery. Peptides are emerging as a novel class of drugs for cancer therapy, and many efforts have been made to develop peptide-based pharmacologically active compounds. This paper presents a review of current advances and novel approaches in experimental and computational drug discovery and design. We also present a novel bioactive peptide analogue, designed using the Resonant Recognition Model (RRM), and discuss its potential use for cancer therapeutics.
Reactive Polymers, 1994
The diversity of peptide libraries synthesized according to the "mixing and portioning" concept producing libraries containing one peptide per bead is limited by the number of beads. A method for the generation and screening of peptide libraries with increased molecular diversity by synthesis of many peptides on each of the beads is described. According to this approach, in each synthesis cycle, every portion of the beads gets a mixture of amino acids, thus the total number of peptides is larger then the number of beads in the library. The degree of heterogeneity is increases from the N-to the C-terminal. Positions close to the N-terminal include relatively few amino acids, whereas positions closer to the C-terminal include a higher number of amino acids. This structure allows generation of extensive diversity on each bead, while still retaining the ability to identify the peptide by N-terminal sequencing. The identification of the peptides on selected beads is achieved by sequencing and by using a self-encoding system. This self-encoding system allows the use of coded as well as non-coded amino acids which cannot be identified by automatic sequencers. According to this system, each non-coded amino acid is presented in a mixture with a coded amino acid. The coded amino acid serves as an indicator for the presence of the non-coded one. Only a portion of the target sequence is identified by N-terminal sequencing. Once partial sequence information is obtained, secondary libraries are synthesized in order to find out which amino acids present in each position are responsible for binding a ligand. The new approach enables generation and screening of up to about 1015 peptides per library, increasing the diversity of solid phase-screened peptides, or other non-sequenceable polymer libraries, by up to 107-fold, thereby increasing the chances of discovering structures of interest.
Strategic Approaches to Improvise Peptide Drugs as Next Generation Therapeutics
International Journal of Peptide Research and Therapeutics
In recent years, the occurrence of a wide variety of drug-resistant diseases has led to an increase in interest in alternate therapies. Peptide-based drugs as an alternate therapy hold researchers' attention in various therapeutic fields such as neurology, dermatology, oncology, metabolic diseases, etc. Previously, they had been overlooked by pharmaceutical companies due to certain limitations such as proteolytic degradation, poor membrane permeability, low oral bioavailability, shorter half-life, and poor target specificity. Over the last two decades, these limitations have been countered by introducing various modification strategies such as backbone and side-chain modifications, amino acid substitution, etc. which improve their functionality. This has led to a substantial interest of researchers and pharmaceutical companies, moving the next generation of these therapeutics from fundamental research to the market. Various chemical and computational approaches are aiding the production of more stable and long-lasting peptides guiding the formulation of novel and advanced therapeutic agents. However, there is not a single article that talks about various peptide design approaches i.e., in-silico and in-vitro along with their applications and strategies to improve their efficacy. In this review, we try to bring different aspects of peptide-based therapeutics under one article with a clear focus to cover the missing links in the literature. This review draws emphasis on various in-silico approaches and modification-based peptide design strategies. It also highlights the recent progress made in peptide delivery methods important for their enhanced clinical efficacy. The article would provide a bird's-eye view to researchers aiming to develop peptides with therapeutic applications.
A review of the utility of soluble peptide combinatorial libraries
…, 1995
This paper reviews the preparation and use ofsoluble synthetic combinatorial libraries (SCLs) made up of millions of peptide and nonpeptide .sequences,fix the identifrcation qf highly active individual compounds. First presented in I991. SCLs have been prepared in a number ofdifferent lengths andjbrmats, and are composed entirely oft.-, D-, and unnatiiral amino acids. Also, existing peptide libraries have been chemically transfirmed to yield large diversitie%s ofnonpeptidic comnpound.r. This review encompasses the pirblished work,fiom this laboratory using SCLs .for the ident$wition ojantigenic sequences recognized by monoclor?al antibodies, novel peptide agonists and antagonists to opioid receptors, new trypsin in ors, novel antibacterials, and compounds that inhibit melittin3 hemolytic uctivity. SCLs a fitndameniul, pact ical advance in the .study ofinteructions berween peptide and nonpeplide sequences and their biochemical or pharmacological targets. 0