Papain-catalyzed peptide bond formation: Enzyme-specific activation with guanidinophenyl esters

Roseri J.A.C. de Beer, Barbara Zarzycka, Helene I.V. Amatdjais-Groenen, Sander C.B. Jans, Timo Nuijens, Peter J.L.M. Quaedflieg, Floris L. van Delft, Sander B. Nabuurs, Floris P.J.T. Rutjes*

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


The substrate mimetics approach is a versatile method for small-scale enzymatic peptide-bond synthesis in aqueous systems. The protease-recognized amino acid side chain is incorporated in an ester leaving group, the substrate mimetic. This shift of the specific moiety enables the acceptance of amino acids and peptide sequences that are normally not recognized by the enzyme. The guanidinophenyl group (OGp), a known substrate mimetic for the serine proteases trypsin and chymotrypsin, has now been applied for the first time in combination with papain, a cheap and commercially available cysteine protease. To provide insight in the binding mode of various Z-X AA-OGp esters, computational docking studies were performed. The results strongly point at enzyme-specific activation of the OGp esters in papain through a novel mode of action, rather than their functioning as mimetics. Furthermore, the scope of a model dipeptide synthesis was investigated with respect to both the amino acid donor and the nucleophile. Molecular dynamics simulations were carried out to prioritize 22 natural and unnatural amino acid donors for synthesis. Experimental results correlate well with the predicted ranking and show that nearly all amino acids are accepted by papain.

Original languageEnglish
Pages (from-to)2201-2207
Number of pages7
Issue number14
Publication statusPublished - 19 Sept 2011
Externally publishedYes


  • Enzymatic peptide synthesis
  • Esters
  • Molecular dynamics
  • Papain
  • Substrate mimetics


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