Protecting peptide synthesis

Primary and secondary amines are susceptible to oxidation and replacement reactions involving the N—H bonds. Within the development of peptide synthesis numerous protective groups for N—H bonds have been found (M, Bodanszky, 1976 L.A. Carpino, 1973), and we shall discuss five of the more general methods used involving the reversible formation of... 

A major trend in organic synthesis, however, is the move towards complex systems. It may happen that one needs to combine a steroid and a sugar molecule, a porphyrin and a carotenoid, a penicillin and a peptide. Also the specialists in a field have developed reactions and concepts that may, with or without modifications, be applied in other fields. If one needs to protect an amino group in a steroid, it is advisable not only to search the steroid literature but also to look into publications on peptide synthesis. In the synthesis of corrin chromophores with chiral centres, special knowledge of steroid, porphyrin, and alkaloid chemistry has been very helpful (R.B. Woodward, 1967 A. Eschenmoser, 1970). 

The phenolic hydroxyl group of tyrosine, the imidazole moiety of histidine, and the amide groups of asparagine and glutamine are often not protected in peptide synthesis, since it is usually unnecessary. The protection of the hydroxyl group in serine and threonine (O-acetylation or O-benzylation) is not needed in the azide condensation procedure but may become important when other activation methods are used. 

In each step of the usual C-to-N peptide synthesis the N-protecting group of the newly coupled amino acid must be selectively removed under conditions that leave all side-chain pro-teaing groups of the peptide intact. The most common protecting groups of side-chains (p. 229) are all stable towards 50% trifluoroacetic acid in dichloromethane, and this reagent is most commonly used for N -deprotection. Only /ert-butyl esters and carbamates ( = Boc) are solvolyzed in this mixture. 

Sections 27 15 through 27 17 describe the chemistry associated with the protection and deprotection of ammo and carboxyl functions along with methods for peptide bond formation The focus m those sections is on solution phase peptide synthesis Section 27 18 shows how these methods are adapted to solid phase synthesis... 

Several of the ammo acids listed m Table 27 1 bear side chain functional groups which must also be protected during peptide synthesis In most cases protecting groups are available that can be removed by hydrogenolysis... 

The actual process of solid phase peptide synthesis outlined m Figure 27 15 begins with the attachment of the C terminal ammo acid to the chloromethylated polymer m step 1 Nucleophilic substitution by the carboxylate anion of an N Boc protected C terminal... 

These methodologies have been reviewed (22). In both methods, synthesis involves assembly of protected peptide chains, deprotection, purification, and characterization. However, the soHd-phase method, pioneered by Merrifield, dominates the field of peptide chemistry (23). In SPPS, the C-terminal amino acid of the desired peptide is attached to a polymeric soHd support. The addition of amino acids (qv) requires a number of relatively simple steps that are easily automated. Therefore, SPPS contains a number of advantages compared to the solution approach, including fewer solubiUty problems, use of less specialized chemistry, potential for automation, and requirement of relatively less skilled operators (22). Additionally, intermediates are not isolated and purified, and therefore the steps can be carried out more rapidly. Moreover, the SPPS method has been shown to proceed without racemization, whereas in fragment synthesis there is always a potential for racemization. Solution synthesis provides peptides of relatively higher purity however, the addition of hplc methodologies allows for pure peptide products from SPPS as well. 

In these cases, it is better to protect the carboxyl group. Optimized conditions for A/-acetylation have been studied (78). A/-Acylation can be utilized for protecting the amino group in the reaction of amino acids, for example in peptide synthesis. 

Protected Amino Acids. Various types of protected amino acids for peptide synthesis are available commercially (243). 

Polypeptide Synthesis and Analysis. Sihca or controUed-pore glass supports treated with (chloromethyl)phenylethyltrimethoxysilane [68128-25-6] or its derivatives are replacing chloromethylated styrene—divinylbenzene (Merrifield resin) as supports in polypeptide synthesis. The sdylated support reacts with the triethyl ammonium salt of a protected amino acid. Once the initial amino acid residue has been coupled to the support, a variety of peptide synthesis methods can be used (34). At the completion of synthesis, the anchored peptide is separated from the support with hydrogen bromide in acetic acid (see Protein engineering Proteins). 

Amino Acids. Chloroformates play a most important role for the protection of the amino group of amino acids (qv) during peptide synthesis (32). The protective carbamate formed by the reaction of benzyl chloroformate and amino acid (33) can be cleaved by hydrogenolysis to free the amine after the carboxyl group has reacted further. The selectivity of the amino groups toward chloroformates results in amino-protected amino acids with the other reactive groups unprotected (34,35). Methods for the preparation of protected amino acids on an industrial scale have been developed (36,37). A wide variety of chloroformates have been used that give various carbamates that are stable or cleaved under different conditions. 

The most frequendy used technique to shift the equiUbrium toward peptide synthesis is based on differences in solubiUty of starting materials and products. Introduction of suitable apolar protective groups or increase of ionic strength decreases the product solubiUty to an extent that often allows neady quantitative conversions. Another solubiUty-controUed technique is based on introduction of a water-immiscible solvent to give a two-phase system. Products preferentially partition away from the reaction medium thereby shifting the equiUbrium toward peptide synthesis. 

A benzyl carbonate was prepared in 83% yield from the sodium alkoxide of glycerol and benzyl chloroformate (20°, 24 h). It is cleaved by hydrogenolysis (H2/ Pd-C, EtOH, 20°, 2 h, 2 atm, 76% yield) and electrolytic reduction (-2.7 V, R4N X, DMF, 70% yield). A benzyl carbonate was used to protect the hy-droxyl group in lactic acid during a peptide synthesis. 

Polymer-supported esters are widely used in solid-phase peptide synthesis, and extensive information for this specialized protection is reported annually. Some activated esters that have been used as macrolide precursors and some that have been used in peptide synthesis are also described in this chapter the many activated esters that are used in peptide synthesis are discussed elsewhere. A useful... 

E. Gross and J. Meinenhofer, Eds., The Peptides Analysis. Synthesis, Biology Vol. 3 Protection of Functional Groups in Peptide Synthesis, Academic Press, New York, 1981. 

The carboxamidomethyl ester was prepared for use in peptide synthesis. It is formed from the cesium salt of an A-protected amino acid and a-chloroacetamide (60-85% yield). It is cleaved with 0.5 M NaOH or NaHCOa in DMF/H2O. It is stable to the conditions required to remove BOC, Cbz, Fmoc, and r-butyl esters. It cannot be selectively cleaved in the presence of a benzyl ester of aspartic acid. ... 

The Dim ester was developed for the protection of the carboxyl function during peptide synthesis. It is prepared by transesterification of amino acid methyl esters with 2-(hydroxymethyl)-l,3-dithiane and Al(/-PrO)3 (reflux, 4 h, 75°, 12 torr, 75% yield). It is removed by oxidation [H2O2, (NH4)2Mo04 pH 8, H2O, 60 min, 83% yield]. Since it must be removed by oxidation it is not compatible with.sulfur-containing amino acids such as cysteine and methionine. Its suitability for other, easily oxidized amino acids (e.g., tyrosine and tryptophan) must also be questioned. It is stable to CF3CO2H and HCl/ether. - ... 

The Dppe group was developed for carboxyl protection in peptide synthesis. It is formed from an N-protected amino acid and the alcohol (DCC, DMAP, 3-12 h, 0°, It). It is most efficiently cleaved by quatemization with Mel followed by treatment with fluoride ion or K2CO3. The ester is stable to HBr/AcOH, BF3 Et20, and CF3CO2H. ... 

The / -(methylmercapto)phenyl ester has been prepared from an /-protected amino acid and 4-tH3SC6H40H (DCC, CH2CI2, 0°, 1 h 20°, 12 h, 60-70% yield). The p-(methylmercapto)phenyl ester serves as an unactivated ester that is activated on oxidation to the sulfone (H2O2, AcOH, 20°, 12 h, 60-80% yield) which then serves as an activated ester in peptide synthesis. ... 

The pentaaminecobalt(III) complex has been prepared from amino acids to protect the carboxyl group during peptide synthesis [(H20)Co(NH3)5(C104)3, 70 , H2O,... 

Carbamates can be used as protective groups for ammo acids to minimize race-mization in peptide synthesis. Raccmi/ation occurs during the base-catalyzed coupling reaction of an W-protected, catboxyl-uc ivated amino acid, and takes place in the intermediate oxazolone that foro S readily from an N-acyl protected amino... 

The BOC group is used extensively in peptide synthesis for amine protection. It is not hydrolyzed under basic conditions and is inert to many other nucleophilic reagents. 

Tri.-nethylsilyl triflate (TMSOTf), PhSCH, CF3COOH. These conditions also cleave the following protective groups used in peptide synthesis (MeO)Z-, Bn-, Ts-, CI2C6H3CH2-, BOM (benzyloxymethyl)-, Mts-, MBS-, r-Bu-SR, Ad-SR, but not a BnSR, Acm, or Arg(N02) group. The rate of cleavage is reported to be faster than with TfOH/TFA. 

Alkyldithio carbamates are prepared from the acid chloride (Et N, EtOAc, 0°) and amino acid, either free or as the O-silyl derivatives (70-88% yield). The N- i-propyldithio) carbamate has been used in the protection of proline during peptide synthesis. Alkyldithio carbamates can be cleaved with thiols, NaOH, Ph P/TsOH. They are stable to acid. Cleavage rates are a function of the size of the alkyl group as illustrated in the table below. 

HF) /Pyr, 25°, 60 min, 100% yield. Polyhydrogen fluoride/pyridine cleaves most of the protective groups used in peptide synthesis. 

In the second major method of peptide synthesis the carboxyl group is activated by converting it to an active ester, usually a p-nitrophenyl ester. Recall from Section 20.12 that esters react with ammonia and amines to give fflnides. p-Nitrophenyl esters are much more reactive than methyl and ethyl esters in these reactions because p-nitrophenoxide is a better (less basic) leaving group than methoxide and ethoxide. Simply allowing the active ester and a C-protected amino acid to stand in a suitable solvent is sufficient to bring about peptide bond formation by nucleophilic acyl substitution. 

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