In organic chemistry, peptide synthesis is the production of peptides, compounds where multiple amino acids are linked via amide bonds, also known as peptide bonds. Peptides are chemically synthesized by the condensation reaction of the carboxyl group of one amino acid to the amino group of another. Protecting group strategies are usually necessary to prevent undesirable side reactions with the various amino acid side chains. Chemical peptide synthesis most commonly starts at the carboxyl end of the peptide (C-terminus), and proceeds toward the amino-terminus (N-terminus). Protein biosynthesis (long peptides) in living organisms occurs in the opposite direction.
The chemical synthesis of peptides can be carried out using classical solution-phase techniques, although these have been replaced in most research and development settings by solid phase methods (see below). Solution phase synthesis retains its usefulness in production of small peptides for industrial purposes.
Chemical peptide synthesis facilitates the production of peptides that are difficult to express in bacteria, the incorporation of unnatural amino acids, peptide/protein backbone modification, and the synthesis of peptides containing D-amino acids.
Solid phase peptide synthesis The established method for the production of synthetic peptides is known as solid phase peptide synthesis (SPPS). Pioneered by Robert Bruce Merrifield, SPPS allows facile assembly of a target peptide by stepwise addition of amino acids while the growing peptide chain is attached to a macroscopically insoluble solvent-swollen beaded resin support.
Characteristics of solid supports The solid support consists of small (~50-to-100 micron diameter), polymeric resin beads functionalized with reactive groups (such as amine or hydroxyl groups) that can be used to attach the nascent peptide chain to the resin polymer. Most often, linker molecules are used to hold the peptide chains and resin together during synthesis. The peptide remains covalently attached to the resin support throughout the synthesis; after the chemical steps involved in adding each amino acid, excess reagents and soluble by-products can be removed by simple solvent washing and filtration. This approach circumvents the chromatographic isolation of the product peptide after each reaction step that is required when using conventional solution phase synthesis. Upon complete peptide synthesis, the linker molecule can be cleaved selectively to release the peptide.
General SPPS procedure Stepwise SPPS proceeds from the C-terminal amino acid residue of the target peptide chain covalently attached to the resin support. Each amino acid to be coupled to the N-terminus of the resin bound nascent peptide chain must be protected on its alpha amino group using protecting groups such as Boc (acid-labile) or Fmoc (base-labile), depending on the protection strategy used (see below).
The general SPPS procedure is one of repeated cycles of alternate N-terminal deprotection and peptide bond-forming 'coupling' reactions. The resin is washed with organic solvent between each chemical reaction step. Reactions in SPPS are conducted as follows:
The N-alpha amine of the C-terminal amino acid of the target peptide is protected with Fmoc or Boc group Protected amino acid is coupled with free amino groups attached to resin beads Protecting group is removed (see: Protecting groups schemes) The second amino acid with an N-protecting group is coupled with the first one. Coupling reagents facilitate peptide bond formation. The above cycle is repeated until the desired sequence has been synthesized Optionally, the N-terminal amino group undergoes capping, thereby preventing residual unreacted resin-bound peptides from further reaction The linker holding the peptide and resin together is cleaved chemically to release the peptide The crude product is purified using either: reverse-phase high-performance liquid chromatography (HPLC) multicolumn countercurrent solvent gradient purification (MCSGP) which is utilised mainly in the case of longer peptides, due to accumulation of numerous minor byproducts that have similar properties to the desired peptide product. This process is used to maximise the yield without sacrificing purity.
SPPS is limited by reaction yields due to the exponential accumulation of by-products, and typically peptides and proteins in the range of 40 or 50 amino acid residues are pushing the limits of synthetic accessibility of SPPS products as homogeneous molecules of defined chemical structure. Synthetic difficulty also is sequence dependent; typically aggregation-prone sequences such as amyloids are difficult to make. Longer peptides can be accessed by using approaches such as native chemical ligation, where two unprotected synthetic peptides can be covalently condensed in aqueous solution.
Amino acid coupling reagents
An important feature that has enabled the broad application of SPPS is the generation of extremely high yields in the coupling step. In stepwise peptide synthesis by SPPS, highly efficient amide bond-formation conditions are required because all resin-bound peptide products are carried over into the final crude product released from the resin. To illustrate the impact of sub-optimal coupling yields for peptide synthesis, consider the case where each coupling step were to have at least 99% yield: this would result in a 77% overall crude yield for a 26-amino acid peptide (assuming 100% yield in each deprotection); if each coupling were 95% efficient, the overall yield would be 25%. In attempts to maximize coupling yields, often a large excess of each amino acid (between 2- and 10-fold) is used in each SPPS coupling reaction. The minimization of amino acid racemization during coupling is also of vital importance to avoid epimerization in the final peptide product.
Amide bond formation between an amine and carboxylic acid requires 'coupling reagents' to activate the carboxyl group of the N-alpha protected amino acid reactant. A wide range of coupling reagents exist, due in part to their varying effectiveness for particular couplings, many of these reagents are commercially available.
Carbodiimides
Carbodiimides such as dicyclohexylcarbodiimide (DCC) and diisopropylcarbodiimide (DIC) are frequently used for amide bond formation. The reaction proceeds via the formation of a highly reactive O-acylisourea. This reactive intermediate is attacked by the peptide N-terminal amine, forming a peptide bond. Formation of the O-acylisourea proceeds fastest in non-polar solvents such as dichloromethane.
DIC is particularly useful for SPPS since as a liquid it is easily dispensed, and the urea byproduct is easily washed away. Conversely, the related carbodiimide 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) is often used for solution-phase peptide couplings as its urea byproduct can be removed by washing during aqueous work-up.
Carbodiimide activation opens the possibility for racemization of the activated amino acid. Racemization can be circumvented with 'racemization suppressing' additives such as the triazoles 1-hydroxy-benzotriazole (HOBt), and 1-hydroxy-7-aza-benzotriazole (HOAt). These reagents attack the O-acylisourea intermediate to form an active ester, which subsequently reacts with the peptide to form the desired peptide bond. Ethyl cyanohydroxyiminoacetate (Oxyma), an additive for carbodiimide coupling, acts as an alternative to HOAt.
Amidinium and phosphonium salts
To avoid epimerization through the O-acylisourea intermediate formed when using a carbodiimide reagent, an amidinium- or phosphonium-reagent can be employed These reagents have two parts: an electrophilic moiety which deoxygenates the carboxylic acid (blue) and masked nucleophilic moiety (red). Nucleophilic attack of the carboxylic acid on the electrophilic amidinium or phosphonium moiety leads to a short lived intermediate which is rapidly trapped by the unmasked nucleophile to form the activated ester intermediate and either a urea or phosphoramide by-product. These cationic reagents have non-coordinating counteranions such as a hexafluorophosphate or a tetrafluoroborate. The identity of this anion is typically indicated by the first letter in the reagent's acronym, although the nomenclature can be inconsistent. For example HBTU is a hexafluorophosphate salt while TBTU is a tetrafluoroborate salt. In addition to HBTU and HATU other common reagents include HCTU (6-ClHOBt), TCFH (chloride) and COMU (ethyl cyano(hydroxyimino)acetate). Amidinium reagents incorporating hydroxybenzotriazole moieties can exist in an N-form (guanadinium) or an O-form (uronium), but the N-form is generally more stable. Phosphonium reagents include BOP (HOBt), PyBOP (HOBt) and PyAOP (HOAt). Although these reagents can lead to the same activated ester intermediates as a carbodiimide reagent, the rate of activation is higher due to the high electrophilicity of these cationic reagents. Amidinium reagents are capable of reacting with the peptide N-terminus to form an inactive guanidino by-product, whereas phosphonium reagents are not. Propanephosphonic acid anhydride Since late 2000s, propanephosphonic acid anhydride, sold commercially under various names such as "T3P", has become a useful reagent for amide bond formation in commercial applications. It converts the oxygen of the carboxylic acid into a leaving group, whose peptide-coupling byproducts are water-soluble and can be easily washed away. In a performance comparison between propanephosphonic acid anhydride and other peptide coupling reagents for the preparation of a nonapeptide drug, it was found that this reagent was superior to other reagents with regards to yield and low epimerization.
Solid supports
Solid supports for peptide synthesis are selected for physical stability, to permit the rapid filtration of liquids. Suitable supports are inert to reagents and solvents used during SPPS and allow for the attachment of the first amino acid. Swelling is of great importance because peptide synthesis takes place within the solvent-swollen resin beads.
The primary type of solid supports is suspension polymerized copoly(1% m-divinyl + styrene)beaded resin. Improvements to solid supports used for peptide synthesis enhance their ability to withstand the repeated use of TFA during the deprotection step of SPPS. Two primary resins are used, based on whether a C-terminal carboxylic acid or amide is desired. The Wang resin was, , the most commonly used resin for peptides with C-terminal carboxylic acids.
Protecting groups schemes
As described above, the use of N-terminal and side chain protecting groups is essential during peptide synthesis to avoid undesirable side reactions, such as self-coupling of the activated amino acid leading to (polymerization). This would compete with the intended peptide coupling reaction, resulting in low yield or even complete failure to synthesize the desired peptide.
Two principle protecting group schemes are typically used in solid phase peptide synthesis: so-called Boc/benzyl and Fmoc/tert-butyl approaches. The Boc/Bzl strategy utilizes TFA-labile N-terminal Boc protection alongside side chain protection that is removed using anhydrous hydrogen fluoride during the final cleavage step (with simultaneous cleavage of the peptide from the solid support). Fmoc/tBu SPPS uses base-labile Fmoc N-terminal protection, with side chain protection and a resin linkage that are acid-labile (final acidic cleavage is carried out via TFA treatment). Both approaches, including the advantages and disadvantages of each, are outlined in more detail below.
Boc/Bzl SPPS