Mini-Reviews in Organic Chemistry - Volume 8, Issue 2, 2011

Protein-protein and protein-nucleic acid interactions are of key importance in cellular biology and thus in the context of basic as well as applied life science. Roughly, five interaction partners for any given cellular protein have been predicted illustrating the complexity of the formed network. In this context, the parallel synthesis of oligopeptide arrays on cellulose membrane supports (SPOT method) fills the gap between application of a global systematic empirical search and a focused iterative rational design to investigate protein-protein and proteinnucleic acid interactions. Many novel applications for the method and improvements of the method itself have appeared recently. The reviews within this issue of Mini Reviews in Organic Chemistry cover the broad variety of applications of peptide arrays. The first section of the issue deals with the production of peptide arrays, which had been continuously optimized including the implementation of novel array formats with drastically increased spot density (chapters 1-4); the second part summarizes the great potential of peptide arrays in order to screen for protein-protein interaction sites such as antibody epitopes, to profile enzyme targeting sites, and to screen for novel antibiotic peptides and their derivatives for clinical applications (chapters 5-8). Finally, the last chapter of the issue summarizes recent achievements to apply peptide arrays to screen with whole cells for peptides which are toxic to tumor cells or might be applied for technical applications such as scaffold for cell growth in cell culture. Beside the great potential of the method and its many successful applications we also discuss limitations and pitfalls of the technique and their circumvention. All of the articles were written by leading experts in the field whose work is gratefully acknowledged. Moreover, I like to thank the Editorial Board of Mini Reviews in Organic Chemistry for their trust and the opportunity to serve as a guest-editor for this issue. Finally, I like to thank Miss Qurrat-ul-Ain Khan for her support and cooperation.

A detailed knowledge on how proteins interact with other proteins or nucleic acids is essential for basic research as well as for the development of drugs and therapeutic leads. In this context, peptide arrays represent a powerful tool to analyze individual interactions within complex protein networks. Moreover, peptide arrays allow for incorporation of artificial building blocks during synthesis and secondary modification of amino acid side chains after synthesis, which makes them even more versatile. Within this review, we summarize the spectrum of applications of solid-supported peptide arrays generated by the SPOT method and provide an introduction into the entire volume dedicated to the topic.

The SPOT technique is one of the most frequently used methods for synthesis and screening of peptides on arrays. Materials such as polypropylene and glass are used for the preparation of peptide arrays, however the most commonly used material for SPOT membranes is cellulose. This paper focuses on materials and procedures used in the SPOT synthesis on cellulose membranes as a special type of solid phase peptide synthesis. In particular, different strategies for the modification of cellulose are described which make it more suitable for solid-phase peptide synthesis. This review also provides a short overview of the synthesis procedures including some important types of peptide modification.

Nowadays, lithographic methods facilitate the combinatorial synthesis of >50.000 oligonucleotides per cm2, an achievement that revolutionized the whole field of genomics. High-density peptide arrays might spark a similar development for the field of proteomics, but all lithographic methods have a peptide specific disadvantage that impairs their use for peptide synthesis: Each monomer must be coupled separately to the solid support. This adds up to an excessive number of coupling cycles, especially when comparing the 4 x 20 coupling cycles that would generate an array of 20meric oligonucleotides, to the 20 x 20 cycles that would yield an array of 20meric peptides. This review mainly discusses one recent development that leads to very high-density peptide arrays: the combinatorial chemical synthesis based on electrically charged solid amino acid particles. Either a colour laser printer or a chip addresses the different charged amino acid particles to a solid support, where the whole layer of solid amino acid particles is melted. Hitherto immobilized amino acids then start to diffuse to the support, where all the 20 different amino acids couple in a spatially defined manner, and in one single coupling reaction to the support. The method should allow for the translation of entire genomes into sets of overlapping peptides to be used in proteome research.

Peptide arrays are useful tools to characterize antibodies, to determine sequence specificities of enzymes, or to find interaction partners to given peptide sequences. One widely-used format for such arrays is a cellulose sheet with hundreds of synthetic peptides bound to it. These SPOT arrays have been used successfully in a broad range of applications since their invention at the beginning of the nineties. The simplicity and robustness of this method along with the fully automated synthesis to generate custom arrays with high peptide densities made the SPOT method popular. A drawback of the SPOT method is the use of large reagent volumes and the limited throughput with only one copy of the library. CelluSpots represent a new method that retains the advantages of the SPOT method but allows the production of hundreds of identical copies on microscope slides for parallel screenings with low sample volumes.

One of the first applications of peptide arrays in general and those prepared by SPOT synthesis in particular was the mapping of antibody epitopes. In this article the diverse applications in this field are described. Different types of peptide libraries such as peptide scans, substitution analyses, truncation and deletion libraries as well as combinatorial and randomly generated libraries are briefly covered. Furthermore, their applications for antibody epitope mapping are described. These are: (i) identification of antigenic determinants within protein sequences for monoclonal and polyclonal antibodies, (ii) identification of key residues for binding, mapping of linear and discontinuous binding sites, (iii) paratope mapping, (iv) identification of mimotopes, and finally (v) the profiling of complex (auto)antibody signatures in biological fluids such as human or mice sera to identify novel biomarkers for e.g. cancer, allergy, infectious and autoimmune diseases.

Applications of peptide arrays in the field of enzyme profiling are described in detail. Focus is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimization for kinases. Additionally, several examples for reliable identification of substrates for other enzymes like lysine methyl transferases and ATP-ribosyltransferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological fluids like cell lysates or lysates of complete organisms will be analysed. All published examples of peptide arrays used for enzyme profiling are summarized comprehensively.

Developing of new lead structures against multidrug-resistant bacteria is an urgent need and cationic antimicrobial peptides (AMPs) have the potential to become such a lead structure. Here we provide an overview of a method to screen peptides for antimicrobial activity based on the SPOT synthesis. Three different strategies to study and optimize antimicrobial activity of peptides have been reported, substitution analysis of known AMPs, scrambling of known AMPs, and screening peptide libraries for novel AMP sequences. This screening method has great potential for discovery and optimization of novel antibiotics; many different peptides with low cytotoxicity and superior activity against different pathogenic bacteria have already been discovered and selected candidates were successfully tested in a mouse infection model using Staphylococcus aureus. The combination of this screening method together with quantitative structure-activity relationship (QSAR) approach led to superior active peptide against several clinical isolates of different multidrugresistant bacteria. A variant of this screening method can also be used to discover peptides that are antimicrobial when attached to surfaces, a potentially important application for prevention of implant-associated infection.

Development of array technologies started in the late 1980s, and today this technique has become a powerful tool for high throughput approaches in biology and chemistry. Progress was mainly driven by the human genome project and associated with the development of several new technologies, leading to the birth of additional “omic” topics such as proteomics, glycomics, or antibodyomics. In this review we focus strictly on peptide arrays applied to investigate protein-protein interactions, starting from single events up to complete interaction networks (interactomes). The specificities and interaction networks of protein interaction domains (PIDs) are our central theme. Picking practical examples from the literature, we review some general concepts about peptide arrays on planar supports for mapping protein-protein interactions.

Peptide arrays represent a powerful research tool, especially for the development of medical applications to screen peptides for the replacement of animal-derived proteins. This minireview focuses on the applicability of cellulose-bound peptide arrays to assay peptide- cell interactions. Moreover, the successful combination of peptide array and bioinformatics to overcome the limitation of library size in array-type screenings is reviewed.

Ionic liquids (ILs) are attracting increasing interest as a potential ecosustainable alternative to traditional volatile organic solvents (VOCs), generally used in large amounts. About the “greenness” of ILs a certain controversy still exists because their toxicity and biodegradability need to be fully assessed. Moreover, the real advantages of using this novel class of solvents should be more deeply studied in comparison with traditional media. This article presents some of the most recent findings in this field by reviewing selected examples of applications of ILs in organic synthesis and catalysis. In addition, anionic reactivity data for some organic reactions will be discussed and compared with those previously found for the same reactions in molecular solvents. Finally, updated results concerning toxicity, ecotoxicity and biodegradation of the most common ILs will be reported.

The preparation of oxime by nitrosation of active methyl and methylene groups of N-heteroaromatics is presented. The reaction of N-heteroaromatics with alkyl nitrite in the presence of a base in liq. NH3 or THF and the difference of reactivity based on E-Z geometrical isomers of oxime are discussed experimentally and theoretically.

3-Amino-2-hydroxy-4-phenylbutyric acids (AHPA or alternatively abbreviated AHPBA) serve as chiral building blocks for various bioactive compounds including aminopeptidase N (APN) inhibitors, HIV-l protease inhibitors, and renin inhibitors. The synthesis of α-hydroxy-β-amino acids has therefore attracted considerable interest in recent years and various synthetic approaches have been developed to complete their synthesis. These strategies include utilization of enantiopure starting materials like sugars and amino acids and introduction of bulky groups to achieve the desired stereoselectivity and asymmetric catalysis using enzymes or inorganic catalysts to achieve the desired stereochemistry. This review will discuss these synthetic strategies.

Salicylanilides are a well-known family of pharmacological compounds, which are under renewed investigation because of the discovery of novel interesting biological activities and mechanisms of action over the last decade. This comprehensive mini-review describes the biological and pharmacological properties of salicylanilides, their activity against atypical and multi-drug resistant mycobacterial strains, and synthetic routes for their preparation. In particular, this review focuses on the synthesis and biological properties of salicylanilides and O-substituted derivates reported between 2000 and 2010, which have displayed the highest antituberculosis or antifungal activity.