A Systematic Comparison of Different Methods to Tackle Aspartimide Formation

A Systematic Comparison of Different Methods to Tackle Aspartimide Formation

Published on 06/09/2022

Read on for detailed information on the results of our comparative study on different methods to tackle aspartimide formation. Click here!

Aspartimide formation is still a serious challenge in peptide synthesis. This side reaction is strongly sequence dependent and preferably occurs at Asp-Aaa motifs (Aaa = Gly, Asp, Asn, Gln or Arg). In a first step, the cyclic aspartimide is formed, which can re-open in a second reaction leading to (epimerized) alpha- and beta-Asp peptides and corresponding piperidides. Thus, all in all around 10 different undesired byproducts can be formed. Over the last decades, several approaches to solve this problem have been developed.

In a joint study together with Biosyntan, we systematically compared the combination of various strategies on different aspartimide-prone model peptides, namely VKDGYI-OH, VKDDYI-OH, VKDRYI-OH, which were synthesized using 50% morpholine/0.1 M formic acid.

First, the influence of various Fmoc-cleaving reagents (DMF only, 30% piperidine, 30% piperidine/0.1 M formic acid, morpholine) was studied.

VKDGYI-OH

VKDRYI-OH

VKDDYI-OH

The effects of the tested conditions above on the degree of aspartimide/piperidide formation can be summarized as follows:

  • Sequence dependency: DG >> DR ≥ DD
  • Cleavage reagent: 30% piperidine > 30% piperidine/0.1 M formic acid > 50% morpholine
    (pKa piperidine = 11.2; pKa morpholine = 8.4)
    If a weak cleaving reagent, e.g. morpholine, is used, there is almost no aspartimide formation but sometimes this cleavage reagent is not sufficient for complete Fmoc cleavage; thus, stronger ones have to be used
  • Addition of formic acid reduces aspartimide formation (sequence dependent)

In a next step, the influence of acidic additives (formic acid, ammonium acetate, HOBt, trifluoroethanol) as well as the steric effect of different bulky Asp side chain protecting groups (OtBu, OEpe, OBno; see related products) was investigated. These results were compared with the application of dimethoxybenzyl (Dmb) as amide backbone protection and cyanosulfurylide (CSY) as side chain protection.

Effect of Acidic Additives

Steric Effect of Bulky Protecting Groups

Effect of the CSY Protecting Group

These results show that

  • Various acidic additives show similar results:
    0.1 M formic acid ~ 0.5 M formic acid ~ 0.1 M NH4OAc ~ 0.1 M HOBt ~ 0.1 M trifluoroethanol
  • The lower the steric demand of the bulky Asp protecting group, the higher the amount of aspartimide formation: Asp(OtBu) >> Asp(OEpe) > Asp(OBno)
  • The use of Asp(CSY) allows complete suppression of aspartimide formation; but the formation of side products is observed, even when using morpholine; side reactions are the oxidation of cysteine, methionine and tryptophane; besides, chlorination of tyrosine is detected upon cleavage of the CSY group with a large excess of N-chloro-succinimide

Finally, our identified optimal conditions were tested in the synthesis of other peptide sequences prone to aspartimide formation. The results are displayed in the table shown below:

Sequence

Asp-PG

Cleavage Conditions

Crude Yield/Area [%]

Isolated Yield [%]

ASYKVTLKTPDGDNVITVPD-amide

OtBu (3x)

30% piperidine

66

29

ASYKVTLKTPDGDNVITVPD-amide

OtBu (3x)

30% piperidine/0.1 M FA

71

33

ASYKVTLKTPDGDNVITVPD-amide

OBno (3x)

30% piperidine

76

42

ASYKVTLKTPDGDNVITVPD-amide

CSY (3x)

30% piperidine

73

37

NPLGFFPDHQLDPAFRANTANPDWDy-amide

OtBu (3x)

30% piperidine

53

23

NPLGFFPDHQLDPAFRANTANPDWDy-amide

OtBu (3x)

30% piperidine/0.1 M FA

58

24

NPLGFFPDHQLDPAFRANTANPDWDy-amide

OBno (3x)

30% piperidine

63

27

NPLGFFPDHQLDPAFRANTANPDWDy-amide

CSY (3x)

30% piperidine

64

14

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References:

Acid-Mediated Prevention of Aspartimide Formation in Solid Phase Peptide Synthesis; T. Michels, R. Dölling, U. Haberkorn, W. Mier; Org. Lett. 2012; 14(20): 5218-5221. https://doi.org/10.1021/ol3007925

The aspartimide problem in Fmoc-based SPPS. Part II; M. Mergler, F. Dick, B. Sax, C. Stähelin, T. Vorherr; J. Pept. Sci. 2003; 9(8): 518-526. https://doi.org/10.1002/psc.473

Prevention of aspartimide formation during peptide synthesis using cyanosulfurylides as carboxylic acid-protecting groups; K. Neumann, J. Farnung, S. Baldauf, J. W. Bode; Nat. Commun. 2020; 11: 982. https://doi.org/10.1038/s41467-020-14755-6

Preventing aspartimide formation in Fmoc SPPS of Asp-Gly containing peptides - practical aspects of new trialkylcarbinol based protecting groups; R. Behrendt, S. Huber, P. White; J. Pept. Sci. 2016; 22(2): 92-97. https://doi.org/10.1002/psc.2844

New t-butyl based aspartate protecting groups preventing aspartimide formation in Fmoc SPPS; R. Behrendt, S. Huber, R. Marti, P. White; J. Pept. Sci. 2015; 21(8): 680-687. https://doi.org/10.1002/psc.2790

2-phenyl isopropyl esters as carboxyl terminus protecting groups in the fast synthesis of peptide fragments; C. Yue, J. Thierry, P. Potier; Tetrahedron Lett. 1993; 34: 323-326. https://doi.org/10.1016/S0040-4039(00)60578-6

A new protecting group for aspartic acid that minimizes piperidine-catalyzed aspartimide formation in Fmoc solid phase peptide synthesis; A. Karlström, A. Undén; Tetrahedron Lett. 1996; 37(24): 4243-4246. https://doi.org/10.1016/0040-4039(96)00807-6

Patent EP 2 886 531 B1

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