Solution-phase combinatorial synthesis and evaluation of piperazine-2,5-dione derivatives

Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold

Cyclic dipeptides, also know as diketopiperazines (DKP), the simplest cyclic forms of peptides widespread in nature, are unsurpassed in their structural and bio-functional diversity. DKPs, especially those containing proline, due to their unique features such as, inter alia, extra-rigid conformation, high resistance to enzyme degradation, increased cell permeability, and expandable ability to bind a diverse of targets with better affinity, have emerged in the last years as biologically pre-validated platforms for the drug discovery. Recent advances have revealed their enormous potential in the development of next-generation theranostics, smart delivery systems, and biomaterials. Here, we present an updated review on the biological and structural profile of these appealing biomolecules, with a particular emphasis on those with anticancer properties, since cancers are the main cause of death all over the world. Additionally, we provide a consideration on supramolecular structuring and synthons, based on the proline-based DKP privileged scaffold, for inspiration in the design of compound libraries in search of ideal ligands, innovative self-assembled nanomaterials, and bio-functional architectures.

Synthesis of Symmetrically 1,4-disubstituted piperazine-2,5-diones: A New Class of Antileishmanial Agents

A series of 1,4-diphenyl-2,5-dioxopiperazine derivatives were synthesised in one pot sequence. The compounds demonstrated appreciable cytotoxic activity against Leishmania donovani on both forms of the parasite, and the results suggested that some derivatives (4, 11 and 12) could be exploited as antileishmanial agents.

Phenotype-Guided Natural Products Discovery Using Cytological Profiling

Phenotype-guided natural products discovery is emerging as a useful new discovery tool that addresses challenges in early, unbiased natural product biological annotation. These high-content approaches yield screening results that report directly on the impact of test compounds on cellular processes in target organisms and can be used to predict the modes of action of bioactive constituents from primary screening data. In this study we explored the use of our recently implemented cytological profiling platform for the isolation of compounds with a specific, predefined mode of action, namely, induction of mitotic arrest. Screening of a microbially derived extract library revealed six extracts whose cytological profiles clustered closely with those of known antimitotic agents from the pure compound training set. Subsequent examination of one of these extracts revealed the presence of two separate bioactive constituents, each of which possessed a unique cytological profile. The first, diketopiperazine XR334 (3), recapitulated the observed antimitotic phenotype of the original extract, demonstrating that cytological profiling can be used for the targeted isolation of compounds with specific modes of action. The second, nocapyrone L (6), possessed a cytological profile that clustered with known calcium channel modulators, in line with previous published activities for this compound class, indicating that cytological profiling is a flexible and powerful platform for the de novo characterization of compound modes of action.

A Unified Strategy to 6-5-6-5-6-Membered Epipolythiodiketopiperazines: Studies towards the Total Synthesis of Scabrosin Diacetate and Haematocin

The family of epipolythiodiketopiperazine (ETP) natural products consists of over 200 members possessing a wide diversity of structures and biological activity. Recently, the subgroup of 6-5-6-5-6-membered ETPs has gained substantial attention, which has resulted in several total syntheses. Despite all the efforts that have been invested into accessing these complex structures, no synthesis of scabrosin diacetate (1 a) and its related esters has been reported. Herein, our attempts towards scabrosin diacetate (1 a) and haematocin (3) starting from diketopiperazine 12 a as a late-stage intermediate are presented. Diketopiperazine 12 a can be conveniently accessed in multigram quantities from aldehyde 18 and diketopiperazine 21 and was envisioned to serve as a general platform for the synthesis of 6-5-6-5-6-membered ETPs.

Design, synthesis and biological evaluation of soluble 2,5-diketopiperazines derivatives as potential antifouling agents

Based on the natural product cyclo-(l-Phe-l-Pro), a library of environmentally friendly 2,5-diketopiperazines were designed, synthesized and showed strong antifouling activities.

Synthesis and structure-activity relationship study of antimicrotubule agents phenylahistin derivatives with a didehydropiperazine-2,5-dione structure

Plinabulin (11, NPI-2358) is a potent microtubule-targeting agent derived from the natural diketopiperazine "phenylahistin" (1) with a colchicine-like tubulin depolymerization activity. Compound 11 was recently developed as VDA and is now under phase II clinical trials as an anticancer drug. To develop more potent antimicrotubule and cytotoxic derivatives based on the didehydro-DKP skeleton, we performed further modification on the tert-butyl or phenyl groups of 11, and evaluated their cytotoxic and tubulin-binding activities. In the SAR study, we developed more potent derivatives 33 with 2,5-difluorophenyl and 50 with a benzophenone in place of the phenyl group. The anti-HuVEC activity of 33 and 50 exhibited a lowest effective concentration of 2 and 1 nM for microtubule depolymerization, respectively. The values of 33 and 50 were 5 and 10 times more potent than that of CA-4, respectively. These derivatives could be a valuable second-generation derivative with both vascular disrupting and cytotoxic activities.

Microwave-assisted solution-phase synthesis and DART-mass spectrometric monitoring of a combinatorial library of indolin-2,3-dione schiff bases with potential antimycobacterial activity

A combinatorial library composed of eleven hydrazides A-K and eleven indolin-1,2-dione derivatives 1-11 has been designed to formally generate sublibraries of 22 mixtures, M₁-M₂₂ comprising of 121 Schiff bases, A-K(1-11). The designed library has been synthesized by the solution-phase method and microwave-assisted synthetic techniques. The formation of individual compounds of each mixture was confirmed by Direct Analysis in Real Time (DART) as ionization technique connected to an Ion Trap as a mass detector. The synthesized mixtures were evaluated for their antimycobacterial activity against four Mycobacterium strains; M. intercellulari, M. xenopi, M. cheleneoi and M. smegmatis. Variable antimycobacterial activity was revealed with the investigated mixtures and maximum activity was shown by M₈, M₁₀, M₁₁, and M₁₅ with MIC values of 1.5, 3.1, 6.2 and 0.09 μg/mL, respectively. Application of the indexed method of analysis on these active mixtures revealed that compounds D₈, D₁₀ and D₁₁ may contribute to the activity of the tested mixtures.

Fragmentation of deprotonated cyclic dipeptides by electrospray ionization mass spectrometry

The fragmentation pathways of deprotonated cyclic dipeptides have been studied by electrospray ionization multi-stage mass spectrometry (ESI-MSn) in negative mode. The results showed that the fragmentation pathways of deprotonated cyclic dipeptides depended significantly on the different substituents, the side chains of amino acid residues at the diketopiperazine ring. In the spectra of deprotonated cyclic dipeptides, the ion [M-H-substituent radical]- was firstly observed in the ESI mode. The characteristic fragment ions [M-H-substituent radical]- and [M-H-(substituent-H)]- could be used as the symbols of particular cyclic dipeptides. The hydrogen/deuterium (H/D) exchange experiment, the high-resolution mass spectrometry (Q-TOF) and theoretical calculations were used to rationalize the proposed fragmentation pathways and to verify the differences between the fragmentation pathways. The relative Gibbs free energies (DeltaG) of the product ions and possible fragmentation pathways were estimated using the B3LYP/6-31++G(d, p) model. The results have some potential applications in the structural elucidation and interpretation of the mass spectra of homologous compounds and will enrich the gas-phase ESI-MS ion chemistry of cyclic dipeptides.

Solid-phase total synthesis of (-)-Phenylhistine and (-)-Aurantiamine. Synthesis of a diverse dehydro-2,5-diketopiperazine library. Part II

The preparation of solid supported glycine phosphonate and its utilization for the total synthesis of two natural products is presented. The proposed protocol combines diversity with accessibility and speed, which makes this scaffold suitable for automated parallel synthesis and combinatorial chemistry. The preparation of a small library of dehydro-2,5-diketopiperazines, combining several natural amino acids with diverse heterocycles (including thiazoles, pyridines, indoles and imidazoles), is also demonstrated.

Exploring privileged structures: the combinatorial synthesis of cyclic peptides

Head-to-tail cyclic peptides have been reported to bind to multiple, unrelated classes of receptor with high affinity. They may therefore be considered to be privileged structures. This review outlines the strategies by which both macrocyclic cyclic peptides and cyclic dipeptides or diketopiperazines have been synthesised in combinatorial libraries. It also briefly outlines some of the biological applications of these molecules, thereby justifying their inclusion as privileged structures.

Diketopiperazines in peptide and combinatorial chemistry

Diketopiperazines (DKPs), the smallest cyclic peptides, represent an important class of biologically active natural products and their research has been fundamental to many aspects of peptide chemistry. The advent of combinatorial chemistry has revived interest in DKPs for two reasons: firstly, they are simple heterocyclic scaffolds in which diversity can be introduced and stereochemically controlled at up to four positions; secondly, they can be prepared from readily available alpha-amino acids using very robust chemistry. Here synthetic methods, conformation, as well as applications of DKPs are summarized and discussed critically.

Exploring privileged structures: the combinatorial synthesis of cyclic peptides

Head-to-tail cyclic peptides have been reported to bind to multiple, unrelated classes of receptor with high affinity. They may therefore be considered to be privileged structures. This review outlines the strategies by which both macrocyclic cyclic peptides and cyclic dipeptides or diketopiperazines have been synthesised in combinatorial libraries. It also briefly outlines some of the biological applications of these molecules, thereby justifying their inclusion as privileged structures.