One-pot synthesis of 2,5-diketopiperazine with high titer and versatility using adenylation enzyme

2,5-Diketopiperazine (DKP) is a cyclic peptide composed of two amino acids and has been recently reported to exhibit various biological activities. DKPs have been synthesized using various methods. In chemical synthesis, a multi-step reaction requiring purification and racemization is problematic. Although enzymatic synthesis can overcome these problems, there has been no example of a general-purpose synthesis of DKPs with high titers. Therefore, we propose a chemoenzymatic method that can synthesize DKPs in a general-purpose manner with high efficiency under mild conditions. The adenylation domain of tyrocidine synthetase A (TycA-A) catalyzes the adenylation reaction of amino acids, and various amides can be synthesized by a nucleophilic substitution reaction with any amine. On the other hand, DKPs can be produced via intramolecular cyclization reactions from dipeptide esters. Based on these observations, we expected a one-pot synthesis of DKPs via dipeptide ester synthesis by TycA-A and cyclization reactions. This method enabled the synthesis of more than 128 types of DKPs without racemization. Importantly, the intramolecular cyclization reaction proceeded largely depending on the pH. In particular, the cyclization reaction proceeded well in the pH range of 6.5-9.5. Based on these results, we constructed a bioreactor with pH-stat for purified enzyme reaction; cyclo(L-Trp-L-Pro) was produced at 4.07 mM by controlling the reaction pH over time using this reactor. The DKPs obtained using this method will provide deeper insights into their structures and functions in future studies. KEY POINTS: • Adenylation enzyme enabled one-pot synthesis of arbitrary 2,5-diketopiperazine. • Little or no racemization occurred during 2,5-diketopiperazine synthesis. • Bioreactor with pH-stat for purified enzymes improved the reaction rate.

Analysis of the isomerization of diketopiperazine consisting of proline and aromatic amino acid residues using nuclear magnetic resonance

Under different concentrations of the base potassium deuteroxide KOD, the progress of reactions, such as enolization, D-substitution, isomerization, and conformational changes of diketopiperazine cyclo(L-Pro-L-Xxx) and cyclo(D-Pro-L-Xxx) (Xxx = Phe, Tyr) in D2O solution, was investigated by 1H nuclear magnetic resonance (NMR). Cyclo(L-Pro-L-Xxx) is mostly isomerized to cyclo(D-Pro-L-Xxx) in D2O solution, whereas cyclo(D-Pro-L-Xxx) is only slightly isomerized to cyclo(L-Pro-L-Xxx) even under stronger basic conditions. After adding a deuterated organic solvent (CD3COCD3, CD3SOCD3 or CD3OD) to a D2O solution of cyclo(L-Pro-L-Xxx), cyclo(D-Pro-L-Xxx), or increasing the temperature of the D2O solution, CH-π interaction between H9 and the benzene ring of cyclo (D-Pro-L-Xxx) was stronger than that between H8α and the benzene ring of cyclo(L-Pro-L-Xxx).

Conformational Change and Epimerization of Diketopiperazines Containing Proline Residue in Water

In water, diketopiperazines cyclo(L-Pro-L-Xxx) and cyclo(L-Pro-D-Xxx) (Xxx=Phe, Tyr) formed an intramolecular hydrophobic interaction between the main skeleton part and their benzene ring, and both cyclo(L-Pro-L-Xxx) and cyclo(L-Pro-D-Xxx) took a folded conformation. The conformational changes from folded to extended conformation by addition of several deuterated organic solvents (acetone-d₆, metanol-d₄, dimethyl sulfoxide-d₆ (DMSO-d₆)) and the temperature rise were investigated using ¹H-NMR spectra. The results suggested that the intrarmolecular hydrophobic interaction of cyclo(L-Pro-D-Xxx) formed more strongtly than that of cyclo(L-Pro-L-Xxx). Under a basic condition of 1.0×10^-1 mol/L potassium deuteroxide, enolization of O₁-C₁-C₉-H₉ moiety of cyclo(L-Pro-L-Xxx) occurred, while that of the O₄-C₄-C₃-H₃ moiety did not. Cyclo(L-Pro-L-Xxx) epimerized to cyclo(D-Pro-L-Xxx), while cyclo(L-Pro-D-Xxx) did not change.