Facile one-step synthesis of 2,5-diketopiperazines

Mechanistic Study of Diketopiperazine Formation during Solid-Phase Peptide Synthesis of Tirzepatide

This study focused on investigating diketopiperazine (DKP) and the formation of associated double-amino-acid deletion impurities during linear solid-phase peptide synthesis (SPPS) of tirzepatide (TZP). We identified that the DKP formation primarily occurred during the Fmoc-deprotection reaction and post-coupling aging of the unstable Fmoc-Pro-Pro-Ser-resin active pharmaceutical ingredient (API) intermediate. Similar phenomena have also been observed for other TZP active pharmaceutical ingredient (API) intermediates that contain a penultimate proline amino acid, such as Fmoc-Ala-Pro-Pro-Pro-Ser-resin, Fmoc-Pro-Pro-Pro-Ser-resin, and Fmoc-Gly-Pro-Ser-Ser-Gly-Ala-Pro-Pro-Pro-Ser-resin, which are intermediates for both hybrid and linear synthesis approaches. During post-coupling aging, it is found that Fmoc deprotection can proceed in dimethylformamide (DMF), dimethyl sulfoxide (DMSO), N-methyl-2-pyrrolidone (NMP), and acetonitrile (ACN) solvents without any piperidine addition. Density functional theory (DFT) calculations showed that a peptide that has a penultimate proline stabilizes the transition state through the C-H···π interaction during Fmoc decomposition, which causes those peptides to be more prone to cascade-deprotection reactions. Pseudo-reaction pathways are then proposed, and a corresponding macrokinetics model is developed to allow accurate prediction of the TZP peptide intermediate self-deprotection and DKP formation rate. Based on those studies, control strategies for minimizing DKP formation were further investigated and an alternative to Fmoc protection was identified (Bsmoc-protected amino acids), which eliminated the formation of the DKP byproducts. In addition, the use of oxyma additives and lower storage temperature was demonstrated to markedly improve the peptide intermediate stability to DKP degradation pathways.

Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide

Dipeptides, the prototype peptides, exist in both linear (l-) and cyclo (c-) structures. Since the first mass spectrometry experiments, it has been observed that some l-structures may turn into the cyclo ones, likely via a temperature-induced process. In this work, combining several different experimental techniques (mass spectrometry, infrared and Raman spectroscopy, and thermogravimetric analysis) with tight-binding and ab initio simulations, we provide evidence that, in the case of l-phenylalanyl-l-alanine, an irreversible cyclization mechanism, catalyzed by water and driven by temperature, occurs in the condensed phase. This process can be considered as a very efficient strategy to improve dipeptide stability by turning the comparatively fragile linear structure into the robust and more stable cyclic one. This mechanism may have played a role in prebiotic chemistry and can be further exploited in the preparation of nanomaterials and drugs.

Synthesis of bifacial Peptide Nucleic Acids with diketopiperazine backbones

We report herein synthesis of bifacial peptide nucleic acids (bPNAs) with novel diketopiperazine (DKP) backbones that display unnatural melamine (M) bases as well as native bases. To examine the structure-function scope of diketopiperazine bPNAs, we synthesized a set of bPNAs using diaminopropionic acid, diaminobutyric acid, ornithine and lysine derivatives to display the base-tripling motifs, which result in 1, 2, 3, and 4 carbons linking alpha carbon to sidechain amine, respectively. Thermal denaturation of DNA hybrids with these bPNAs revealed that the optimal sidechain linkage was 4 carbons, corresponding to the lysine derivative. Accordingly, monomers displaying two bases per sidechain were prepared via double reductive alkylation of the ε-amine of Fmoc-Lysine with acetaldehyde derivatives of adenine, cytidine, uridine and melamine. With these building blocks in hand, diketopiperazine bPNAs were prepared to display a combination of native and synthetic (melamine) bases. Preliminary melting studies indicate binding signatures of cytidine and melamine-displaying bPNAs to T-rich DNAs, though full characterization of this behavior is ongoing. We anticipate that the straightforward synthetic methodology developed herein will enable further studies on noncanonical nucleic acid hybridization with diketopiperazine backbones.

Cyclo(l-proline-l-serine) Dipeptide Suppresses Seed Borne Fungal Pathogens of Rice: Altered Cellular Membrane Integrity of Fungal Hyphae and Seed Quality Benefits

Five proline-containing diketopiperazines (Pro-DKPs) produced by antagonistic microorganisms as secondary metabolites were selected and synthesized under laboratory conditions. Out of five synthesized Pro-DKPs, cyclo(l-Pro-l-Ser) (DKP-6) revealed the best inhibition of fungal pathogens (Fusarium verticillioides and Fusarium fujikuroi) of rice under in vitro conditions with effective doses lower than standard fungicide carbendazim. DKP-6 induced stress on the fungal cell membrane integrity, which was revealed by calcofluor white and propidium iodide assays, endorsed by ultra-microscopic details and soluble protein leakage assays. In vivo seed treatment of infested rice seeds with DKP-6 at 2000 μg/mL for 10 h of seed treatment inflicted best reduction in seed rot and seedling blight with respect to control and carbendazim. Significant enhancement in seedling quality parameters were also observed. The work presented the strong influence of cyclo(l-Pro-l-Ser) as a mycocidal seed treatment agent better than synthetic toxic fungicides for rice.

Cyclic Dipeptide: A Privileged Molecular Scaffold to Derive Structural Diversity and Functional Utility

Cyclic dipeptides (CDPs) are the simplest form of cyclic peptides with a wide range of applications from therapeutics to biomaterials. CDP is a versatile molecular platform endowed with unique properties such as conformational rigidity, intermolecular interactions, structural diversification through chemical synthesis, bioavailability and biocompatibility. A variety of natural products with the CDP core exhibit anticancer, antifungal, antibacterial, and antiviral activities. The inherent bioactivities have inspired the development of synthetic analogues as drug candidates and drug delivery systems. CDP plays a crucial role as conformation and molecular assembly directing core in the design of molecular receptors, peptidomimetics and fabrication of functional material architectures. In recent years, CDP has rapidly become a privileged scaffold for the design of advanced drug candidates, drug delivery agents, bioimaging, and biomaterials to mitigate numerous disease conditions. This review describes the structural diversification and multifarious biomedical applications of the CDP scaffold, discusses challenges, and provides future directions for the emerging field.

Self-Assembly of Cyclic Dipeptides: Platforms for Functional Materials

Supramolecular self-assembled functional materials comprised of cyclic dipeptide building blocks have excellent prospects for biotechnology applications due to their exceptional structural rigidity, morphological flexibility, ease of preparation and modification. Although the pharmacological uses of many natural cyclic dipeptides have been studied in detail, relatively little is reported on the engineering of these supramolecular architectures for the fabrication of functional materials. In this review, we discuss the progress in the design, synthesis, and characterization of cyclic dipeptide supramolecular nanomaterials over the past few decades, highlighting applications in biotechnology and optoelectronics engineering.

2,5-diketopiperazines mitigate the amount of advanced glycation end products accumulated with age in human dermal fibroblasts

OBJECTIVE

Glycation is a common non-enzymatic reaction between proteins and sugars, resulting in the formation of advanced glycation end products (AGEs) in the human body. As can be seen in diabetic patients, the accumulation of AGEs in the skin has aesthetic consequences (wrinkles, brown spots and yellowish complexion). Therefore, the objective of this work was to find compounds isolated from natural sources that could eliminate the final AGEs accumulated in the skin with ageing.

METHODS AND RESULTS

A preliminary screening performed on a bank of microbial extracts and pure compounds showed that 2,5-Diketopiperazines (DKPs), as well as the extract of Sphingobacterium sp (SNB-CN13), reduced the presence of AGEs in fibroblasts by -28% and -23%, respectively. In this article, we present the dereplication approach used to reveal the presence of 26 different DKPs in the crude extract of Sphingobacterium sp. Bioguided fractionation has led to the isolation of 12 of them, whose identity has been confirmed by HRMS and NMR. A green synthesis approach has been developed to synthesize 3 symmetrical DKPs. The biological activity of all DKPs was evaluated by the development of an in vitro test using immunocytochemistry to reveal the presence of AGE carboxymethyl-lysine in human dermal fibroblasts.

CONCLUSION

Our work shows for the first time that DKPs decrease the amount of carboxymethyl-lysine AGE in elderly human dermal fibroblasts grown in vitro. Therefore, diketopiperazines can be considered as compounds of interest for dermatological and cosmetic applications with an anti-ageing aim.