n an ever-increasing domain of activity, Amino Acids, Peptides and Proteins provides an annual compilation of the world’s research effort into this important area of biological chemistry. Comprising a comprehensive review of significant developments at this biology/chemistry interface, each volume opens with an overview of amino acids and their applications. Work on peptides is reviewed over several chapters, ranging from current trends in their synthesis and conformational and structural analysis, to peptidomimetics and the discovery of peptide-related molecules in nature. The application of advanced techniques in structural elucidation is incorporated into all chapters, whilst periodic chapters on metal complexes of amino acids, peptides and beta-lactams extend the scope of coverage. Efficient searching of specialist topics is facilitated by the sub-division of chapters into discrete subject areas, allowing annual trends to be monitored. All researchers in the pharmaceutical and allied industries, and at the biology/chemistry interface in academia will find this an indispensable reference source. Volume 36 covers literature published during 2003.

Amino Acids, Peptides and Proteins Volume 36

A Review of the Literature Published During 2003–2004

By D.T. Elmore, E. Farkas, B. Penke, I. Sóvágó, G. Tóth, G. Váradi, M. Zarandi, J.S. Davies

The Royal Society of Chemistry

Copyright © 2007 The Royal Society of Chemistry
All rights reserved.
ISBN: 978-0-85404-252-4

Contents

Preface John S. Davies, 7,
Amino acids Marta Zarandi, 19,
Peptide synthesis Donald T. Elmore, 82,
Analogue and conformational studies on peptides, hormones and other biologically active peptides Botond Penke, Gábor Tóth and Györgyi Váradi, 131,
Cyclic, modified and conjugated peptides John S. Davies, 227,
Metal complexes of amino acids and peptides E. Farkas and I. Sóvágó, 287,

CHAPTER 1

Amino acids

Marta Zarandi

DOI: 10.1039/b700152p

1. Introduction

The occurrence, chemistry, and analysis of amino acids contained in the literature of 2003 and partly 2004 are reviewed in this Chapter which is arranged in sections similar to previous Volumes in this Specialist Periodical report. Scientific Papers published during 2003 (and 2004) have been sourced mainly from the Web of Science databases on the internet and from scanning a selection of major journals.

2. Naturally occuring amino acids

2.1 Occurrence of amino acids in nature

Amino acids have been produced with the aid of microorganisms for nearly 50 years. The economic importance of these cellular building blocks is significant. When compared to chemical methods, fermentative production has the advantage of yielding the optically active and biologically required L-form of amino acids from cheap carbon and nitrogen sources. In the review of Tryfona and Bustard, a brief historic background of Coryneform bacteria, which are central to the industrial production of amino acids and the various strategies used for strain improvement are discussed.

Acidic methanolic, whole body extracts of larval Tenebrio molitor (Insecta, Coleoptera) and other juvenile insects are highly toxic to adults of the same species and other species: injection causes instant paralysis to death. Referring to their dramatic effect in mature insects, the responsible compounds have been designated as “paralysins”. Two paralysins have already been identified in the flesh fly, Neobellieria bullata, i.e., β-alanyl-tyrosine (BAY) and 3-hydroxykynurenine (3HK). The isolation of two additional paralysins from larval T. molitor was reported: (i) the essential amino acid, Trp and (ii) the saturated β-carboline, 1,2,3,4-tetrahydro-β-carboline-3-carboxylic acid (THCA).

2.2 New amino acids and derivatives

In recent years there has been an increasing interest in new methods that access novel non-proteinogenic α-amino acid derivatives. Although many routes to amino acids have been developed, the Petasis reaction provides a concise and convergent approach that allows structure variability and facile incorporation of functional groups. A novel one pot Petasis reaction/palladium catalysed process is described involving 2-iodo/bromo benzylamine, ethyl glyoxalate and aryl/heteroaryl boronic acids. The reaction in the presence of CO or allenes resulted in isoindolone- or 4-methylene-3,4-dihydroisoquinoline α-amino acid (Scheme 1) derivatives, respectively in good yield.

A pyrroline nitroxide based cyclic tetrasubstituted α-amino acid and paramagnetic homoPro and their derivatives have been described. Introduction of a new para-magnetic protecting group to follow the incorporation of an amino acid into peptides is also suggested.

Aeruginosins constitute a new group of structurally related cyanobacterial peptides, bearing a C-6 functionalized cis-octahydroindole-2-carboxylic acid derivative as their common structural feature. An efficient and stereoselective route to a new α-amino acid has been reported (Scheme 2), which is the proposed core of aeruginosins 205.

New bicyclic acidic amino acids, which are conformationally constrained-homologues of Glu, were prepared via a strategy based on a 1,3-dipolar cycloaddition.

The increasing interest of modified peptides in the chemical engineering of proteins and also as therapeutic agents has refreshed research towards the development of new methodologies for the stereoselective production of natural and unnatural α-amino acids. A new method for the stereoselective synthesis of protected nonproteinogenic α-amino acids, having the structure of a branched bis-homoSer (Scheme 3) or proline can be prepared stereoselectively by hetero-Diels–Alder addition of ethyl 2-nitrosoacrylate to electron-rich alkenes, such as enol ethers and allylsilanes, and a further two or three step manipulation of the resulting oxazine.

2.3 Miscellaneous

Over the last 25 years, significant efforts have been devoted to the development of polymeric biomaterials. These materials have to be biologically inert and stable under physiological conditions. Since polyamino acids are structurally related to natural proteins, the synthesis of amino-acid-based polymers was explored as a potential source of new biomaterials. The phenolic hydroxyl group of the natural amino acid L-Tyr makes it possible to use derivatives of Tyr dipeptide as a motif to generate diphenolic monomers, which are important building blocks for the design of biodegradable polymers. Particularly useful monomers are desaminotyrosyl-Tyr alkyl esters. Using this approach, a wide variety of polymers (tyrosine-derived polycarbonates, polyarylates, and polyethers) have been synthesized and are reviewed with special emphasis on recent developments.

In the past 20 years, a large number of compounds have been developed as β-turn mimics, but previously, there was no general method for keeping all the side chain functions of the natural β-turns, which limits the ability of the motifs to mimic natural turns. The 3-substituted prolines and particularly the cis isomers with the appropriate side chain can be used to mimic type I, II or III β-turns and incorporate the side chain functionalities on both the i + 1 and i + 2 positions of β-turns.

A number of experimental evidences suggested that acivicin [(αS,5S)-α-amino-3-chloro-4,5-dihydro-isoxazol-5-yl acetic acid] could be potentially useful in the treatment of certain tumors, i.e. myeloid leukemia. However, a number of severe side effects associated with the use of acivicin emerged during clinical trials. Therefore, acivicin represents an excellent lead for the design of new, structurally related amino acid derivatives with an improved selectivity and a reduced toxicity. A set of conformationally constrained analogues of acivicin has been designed and synthesized.

In α-cyclodextrin six D-glucose units are covalently linked to form a torus shaped molecule with a rigid cavity. Cucurbit[6]uril is a highly symmetric molecule like α-cyclodextrin. It is formed from urea, glyoxal, and formaldehyde during an acid-catalysed reaction. Six glycoluril units form a rigid molecule with a cavity. Both the natural and the synthetic ligand are closely related and are able to enclose a large number of guest molecules within their cavities. The complex stabilities and the thermodynamic data for the complexation of α-cyclodextrin and cucurbit[6]uril with some amino acids (Gly, L-Ala, L-Val, L-Phe, 6-amino hexanoic acid, 8-amino octanoic acid, 11-amino undecanoic acid) and dipeptides have been determined in aqueous solution by calorimetric titrations. The stabilities of the complexes formed are of the same order of magnitude. In case of α-cyclodextrin, the hydrophobic interactions are responsible for the observed values. For cucurbit[6]uril, ion–dipole interactions are the important factor.

Nonnatural amino acid mutagenesis makes possible the site-specific incorporation of synthetic amino acids and allows detailed studies of ion channels with admirable molecular precision in a cellular environment. The ability to incorporate synthetic amino acids allows systematic structure-function studies, furnishing a chemical-scale precision at the level of single atoms and bonds. The methodology permits study in a cellular system, allowing direct and relevant functional analysis of the mutated channels.

One of the main strategies applied to address the AIDS epidemic consists of the inhibition of the virally encoded enzyme human immunodeficiency virus (HIV) aspartyl protease. Simple and potent anti-HIV protease compounds were fashioned from the amino acid L-lysine. A series of Nα-isobutyl-Nα-arylsulfonamido-(Nε-acyl) Lys and lysinol (1) derivatives were prepared and evaluated as inhibitors of HIV protease and wild type virus. A simple original synthesis was devised to form Nα-(arylsulfonamide)-Nα-isobutyl Lys, which could be easily acylated with carboxylic acids at the Nε position. A two-atom spacer was found to be optimal between this acyl group and a phenyl yielding compounds of sub-nanomolar potency on purified enzyme.

The synthesis of ε-Poly-L-Lys (ε-PL), a unique homopolypeptide, has been investigated in a cell-free system. It has been suggested that its synthesis is similar to that of poly-(γ-D-Glu) in terms of adenylation of the substrate amino acid.

More than 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive and redox active amino acids, glycosylated and heavy atom derived amino acids in addition to those with keto, azido and acetylene chains.

3. Chemical synthesis and resolution of amino acids

3.1 General methods

Benzyloxycarbonyl (Z) group is a widely utilized amine protecting group in peptide chemistry. Hydrogen in the presence of Pd/C catalyst is often used for its removal. An alternate method for the removal of the Z group involves the use of acids, such as trifluoroacetic acid/thioanisole; however, this method can potentially damage other acid-labile groups. In view of the current interest in environmentally benign organic synthetic methodologies, much attention has been paid to the development of highly efficient heterogeneous catalysts for removal of the Z group with functional group tolerance. Hydroxyapatite-bound Pd catalyst was found to be highly effective for the deprotection of the Z group from amino acids in the presence of molecular hydrogen. The catalyst was also applicable to the hydrogenolysis of a sterically encumbered core-Z-protected poly(amido amine) dendrimer. Fluorous carboben-zyloxy ((F)Cbz) reagents RfCH2CH2C6H4CH2OC(O)OSu (where Su is succinimidoyl and Rf is C6F13 and C8F17) have been used to make (F)Cbz derivatives of 18 of the 20 natural amino acids.

The formyl protecting group in combination with a tert-butyl ester group is useful in preparing highly functionalized peptide derivatives, but standard N-formylation is incompatible with tert-butyl groups. A simple and useful methodology has been developed for the preparation of N-formyl amino acid esters using the inexpensive, readily available, and environmentally acceptable reagent ammonium formate. Amino acid ester hydrochlorides were reacted with ammonium formate to give N-formyl amino acid esters.

The synthesis of mixed anhydrides of polyamino-polycarboxylic acids, amino acids, and phosphoric acid was presented. The obtained compounds were effective as flame retardants at low concentrations where classical fire retardants are not effective.

Photolysis of the amino acid derived symmetrical and unsymmetrical diacyl peroxides at 254 nm at low temperature (-78 to -196 °C) generates various bis(amino acids) in a concise manner (Scheme 4) and with orthogonal protection. The methodology was applied to the synthesis of (4R)-5-propyl-L-Leu.

Synthesis of Fmoc-/Boc-/Z-β-amino acids viaArndt-Eistert homologation of Fmoc-/Boc-/Z-α-amino acids employing BOP and PyBOP as a coupling agent to the corresponding β-amino acids and synthesizing the key intermediate α-diazoke-tones as crystalline solids in good yield were described. The synthesis of optically active amino acid over Pd catalysts impregnated on mesoporous support has been described. These catalysts afford a high level of enantio-selectivity in the asymmetric hydrogenation of α-keto acids to corresponding amino acids. A series of new 4-[2′-(6′-nitro)benzimidazolyl]benzoyl amino acids and peptides have been synthesized by coupling the 4-[2′-(6′-nitro)benzimidazolyl]benzoic acid with amino acid methyl esters/dipeptides using DCC as the coupling agent.

Although solid-supported reagents and scavengers have been used in organic synthesis for decades, it was the development of combinatorial and parallel high throughput synthesis techniques that brought this class of reagents to wider attention. A convenient and general procedure is described with the application of the polystyrylsulfonyl-3-nitro-1H-1,2,4-triazolide-resin which is readily available from the corresponding commercially available polystyryl sulfonyl chloride resin. The new resin was used for the formation of esters of Fmoc-protected α-amino acids in high yields and purity with a low level of racemisation. When compared to polystyryl sulfonyl chloride resin, the new solid-supported reagent reduces considerably the amount of racemisation. All by-products can be removed by simple filtration and extraction work-up without the need for chromatography.

Among the new challenges of chemistry are macromolecular entities composed of many identical components, arranged to serve as receptors for given binding units or ligands. Multifunctionality of receptor molecules reflects a current trend towards ‘smart’ materials, informationally rich molecular devices, and nanofabrication. A modular strategy towards receptor macromolecules is presented, which combines synthetically diverse peptide synthesis with highly functional calixarene chemistry. The design and synthesis of calix[4]arene amino acids (calix-lysines) are described (Scheme 5), which were used as construction blocks to assemble nanoscale, multivalent entities — calix-peptides and calix-peptide-dendrimers.

3-(7,8-dihydroxyquinolin-5-yl)-L-Ala (2) can be expected to form metal complexes. In addition, it can participate in electron transfer reactions and may be regarded as a biosynthetic precursor of the cytotoxic marine alkaloid halitulin. An efficient synthesis of this interesting amino acid has been described from L-Tyr.

3.2 Asymmetric and stereoselective synthesis

In addition to the 20 natural α-amino acids, there are many other α-amino acids found in various natural products. Although a large number of methods are available for the synthesis of α-amino acids, there is always scope for the development of new and more efficient methods that could be useful for the synthesis of many of the natural and unusual α-amino acids. Broad review of recent developments in the catalytic asymmetric synthesis of α- and β-amino acids has been appeared, and the use of aziridines and oxazolines as valuable intermediates in the synthesis of unusual amino acids has also been summarized.

The catalytic asymmetric addition of organic nucleophiles to α-imino esters has emerged as one of the most promising and intensely investigated routes to optically enriched α- and β-amino acid derivatives as highlighted in a recent review. Preparation of L-α-amino acids has been easily accomplished simply by exchanging the position of the lactone group of a chiral template from C-2 to C-3. Alkylation of iminolactone afforded the α-monosubstituted products in good yields and excellent diastereoselectivities (>98%). Hydrolysis of the alkylated iminolactones furnished the desired L-α-amino acids in good yields. A high degree of stereocontrol in radical addition to glyoxylic nitrone provided a new method for asymmetric synthesis of α-amino acids.

Since nowadays enantiomeric purity is one of the major issues in α-amino acid synthesis, tremendous efforts have been put into the development of asymmetric versions of Strecker’s protocol. Carbocyclic α-amino acids as representatives of the α,α-disubstituted α-amino acid family are widely used in the isosteric replacement of proteinogenic amino acids resulting in specific backbone conformations and increased stability towards chemical and enzymatic degradations. The synthesis of the bicyclic imides as conformationally restricted templates, which mimic folded conformations of Glu has been reported. The application of the asymmetric Strecker protocol followed by a ring closure addition-elimination reaction between an amide nitrogen and the ester functionality led to the synthesis of the previously unknown 1R, 2S– and 1S, 2R-1-amino-cis-3-azabicyclo[4.4.0]decan-2,4-dione hydro- chlorides (bicyclic Glu derivatives). The synthesis of a series of optically active α,α—disubstituted α-amino acids has been summarized starting with an achiral or a racemic α-hydroxy or α-diazo ketone. Some problematic processes that remained in the Strecker synthesis, i.e. preparation of the starting α-acyloxy ketone and oxidative conversion of alpha-amino nitrile into α-imino nitrile, are much improved as regards efficiency by the development of a Cu-catalyzed insertion of α-diazo ketone into N-protected α-amino acid, and as regards yields by the use of ozone as the oxidant. With these methods, various types of α,α-disubstituted α-amino acids have been synthesized including cyclic analogs as a conformational variant of Ser.

(Continues…)Excerpted from Amino Acids, Peptides and Proteins Volume 36 by D.T. Elmore, E. Farkas, B. Penke, I. Sóvágó, G. Tóth, G. Váradi, M. Zarandi, J.S. Davies. Copyright © 2007 The Royal Society of Chemistry. Excerpted by permission of The Royal Society of Chemistry.
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