Deprotection

Almost universally, SPPS grows the peptide by anchoring the acid terminus and growing the peptide using N-Fmoc-protected AA synthons. Thus, after each amide coupling step, deprotection is required before the next coupling. Deprotection reagents need to ensure Fmoc removal to the highest efficiency and cause no undesired side reactions with the peptide, e.g., racemization, at a reasonable reaction rate.
Most SPPS Fmoc deprotections use a large excess of piperidine as a base catalyst to effect deprotection. Typically, a large excess (20-30% v/v solution is employed).
Excess, piperidine can be recovered and recycled.
DMF is typically used as solvent to give a fast reaction rate. Greener alternatives like EtOAc do work, but when used neat show much slower deprotection kinetics hence are often used as mixtures with a small amount of a more polar solvent – suggestions above.
Other reagents and solvent combinations employed are:

  • NaOH in 2-MeTHF/MeOH
  • Lower quantities of piperazine with DBU
  • Lower quantities of 4-methylpiperidine (5% vs. 20% v/v piperidine)

Přibylka, A.; Krchňák, V.; Schütznerová, E. Environmentally friendly SPPS I. Application of NaOH in 2-MeTHF/methanol for Fmoc removal. Green Chem. 2019, 21, 775–779.

Ralhan, K.; KrishnaKumar, V. G.; Gupta, S. Piperazine and DBU: a safer alternative for rapid and efficient Fmoc deprotection in solid phase peptide synthesis. RSC Adv. 2015, 5, 104417–104425.

Jad, Y. E.; Govender, T.; Kruger, H. G.; El-Faham, A.; de la Torre, B. G.; Albericio, F. Green Solid-Phase Peptide Synthesis (GSPPS) 3. Green Solvents for Fmoc Removal in Peptide Chemistry. Org. Process Res. Dev. 2017, 21, 365–369.

Hachmann, J.; Lebl, M. Alternative to Piperidine in Fmoc Solid-Phase Synthesis. J. Comb. Chem. 2006, 8, 149.

Zinieris, N.; Leondiadis, L.; Ferderigos, N. Nα-Fmoc Removal from Resin-Bound Amino Acids by 5% Piperidine Solution. J. Comb. Chem. 2005, 7, 4–6.

Lobo-Ruiz, A.; Tulla-Puche, J. General Fmoc-Based Solid-Phase Synthesis of Complex Depsipeptides Circumventing Problematic Fmoc Removal. Eur. J. Org. Chem. 2020, 183–192.
© 2015 Green Chemistry Institute Pharmaceutical Roundtable. All rights reserved.