Improved deprotection of cysteine‐containing peptides in HF

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Abstract
The deprotection of S‐4‐methylbenzyl‐cysteine in HF was studied as a function of acidity and scavengers employed and a highly effective procedure was developed. Under conditions of low acidity which promote SN2 deprotection of benzyl alcohol‐derived protecting groups of amino acid side‐chain functionalities, i.e. low HF (HF:DMS, 1:3, v/v), little or no deprotection of S‐4‐methylbenzyl cysteine was observed. Under conditions of high acidity (90% HF), recovery of cysteine was only 79% using the conventional scavenger, anisole. However a combination of the scavengers p‐cresol and p‐thiocresol provided nearly quantitative recovery of the cysteine thiol, with the preferred deprotection conditions being HF:p‐cresol:p‐thiocresol (90:5:5, v/v), 0°C, 1 h. The possibility that the sulfoxide of the protected cysteine thioether was involved in cysteine side reactions was investigated. The formation of the sulfoxide was found to be low (0.15% per residue added) under standard solid‐phase peptide synthesis conditions. Since the sulfoxide derivative was resistant to deprotection in high HF, two methods for the reduction of the molecule to the thioether were developed. One method involved the reduction of the sulfoxide in HF at intermediate acidity levels (HF:DMS, 40:60, v/v), 0°, 4h. The other method involved a mixture of TFA, DMS and CH2Cl2 (45:10:45, v/v) containing (Et)4 NCl ˜ H2O (50 equiv. per cysteine residue) which efficiently reduced both free and resin‐bound S‐4‐methylbenzyl cysteine sulfoxide (t1/2= 35 min). Both methods also reduced methionine sulfoxide to methionine.