Peptide Synthesis Reagents
Peptide synthesis reagents can be sorted into several smaller categories, namely coupling reagents, protecting/labeling reagents and deprotection/ cleavage reagents. Coupling reagents are the largest subset of peptide synthesis reagents and the most important.
Peptide coupling reagents activate the acid group of the protected amino acids for forming a new peptide amide bond. These reagents are also often used to attach the first amino acid of a peptide sequence to the peptide synthesis resin. The most peptide coupling reagents belong to one of these catagories:
Carbodiimides are usually used with an additive such as HOBt to form activated ester intermediates. Ureas are the byproducts formed from carbodiimides. N,N'-dicyclohexylurea, the byproduct from DCC (N,N'-dicyclohexylcarbodiimide), is not soluble in most organic solvents and forms a precipitate when DCC is used. DCC is useful in manual synthesis, but is not suitable for automated peptide instruments. The urea byproduct of DIC (N,N'-diisopropylcarbodiimide) is soluble in peptide synthesis solvents and DIC can be utilized in automated peptide synthesizers. EDC and its urea byproduct are water soluble and are often used to conjugate smaller molecules to proteins.
Some of the first coupling reagents developed were phosphonium salts. Phosphonium salts and related phosphorus compounds are very efficient, highly reactive and cause very little racemization. PyAOP and PyBrOP are the recommended reagents for coupling to N-methyl amino acids and alpha, alpha-disubstituted glycines.
When these reagents were introduced, they were believed to have a uronium structure. Later structure studies revealed that these reagents actually have aminium structure. They are very efficient peptide coupling reagents with little racemization. Coupling reactions are complete in as little as six minutes and when HOBt is added, racemization can be reduced to insignificant levels.
Uronium salts are very efficient coupling reagents. They are not as widely utilized as HBTU and HATU, but are used in special applications, especially in difficult reactions or where racemization must be minimized.
When used with carbodiimide reagents, these compounds form activated esters. Used with other coupling reagents, they suppress racemization.
Protecting groups are temporarily applied to keep reactive functional groups on the amino acids and peptides from interfering in the peptide synthesis reactions and producing unwanted side products. At the approriate point in the synthesis, the protecting groups are removed to expose the functional group.
Labels are small molecules attached to a peptide to assist in later identification or manipulation of the peptide. Typical labels are dye or fluorescent compounds.
Primarily two types of deprotection reagents are used in solid phase peptide synthesis. The first type are N-deprotection reagents. These remove only the N-terminal protection group of the peptide attached to the resin. These are trifluoroacetic acid (TFA) in Boc chemistry and piperidine in Fmoc chemistry. DBU may also be used to selectively remove Fmoc groups when deprotection with piperidine is sluggish.
Cleavage reagents are the secon type of deprotection reagents utilized in solid phase peptide synthesis. Cleavage reagents typically cleave the peptide product from the resin and at the same time, remove all of the side chain protection groups producing the free peptide. In Boc chemistry, typical cleavage reagents are HF, TFMSA and TMSOTf. In Fmoc chemistry, TFA is utilized.
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