Approaches to Cyclophane-Types of Cyclopeptide Alkaloids.

The cyclopeptide alkaloids are cyclic depsipeptides incorporating cyclophanes with polyamide units 13-, 14- and 15-membered macrocyclic systems. Although various pharmacological activities have been ascribed to cyclopeptide alkaloids from plants of the Rhamnacea family, these studies have been hampered by their low availability due to the lack of reasonable amounts distributed in nature. Therefore, novel and efficient synthetic approaches should be an important aim, which inspired us to examine how to diversely construct the unique structures of this type of natural products. In this account, several typical strategies are presented in terms of efficient, stereocontrolled and regioselective synthesis of cyclopeptide alkaloids.

A Transannular Rearrangement Reaction of a Pyrroloindoline Diketopiperazine.

Oxaline, glandicoline, and meleagrin contain a unique triazaspirocyclic structure. Attracted by their biological activities, we attempted a novel strategy, mimicking a proposed biosynthetic pathway for glandicoline B in Penicillium chrysogenum and Penicillium oxalicum and using a transannular rearrangement to the desired triazaspirocycle 15.

Total synthesis of the reported structure of ceanothine D via a novel macrocyclization strategy.

The first total synthesis of the reported structure of ceanothine D, a cyclopeptide alkaloid found in red root, was achieved using a highly convergent synthetic strategy. Highlights of the synthesis include the first concomitant macrocyclization and formation of the unique chiral tertiary alkyl-aryl ether bond with complete regio- and stereo-control in the presence of a sensitive Z-enamide moiety to access the strained para-cyclophane present in its structure. This synthetic strategy may be broadly applicable in the generation of other structurally similar cyclopeptide alkaloids, enabling further biological and chemical investigations.

Canvass: A Crowd-Sourced, Natural-Product Screening Library for Exploring Biological Space.

Natural products and their derivatives continue to be wellsprings of nascent therapeutic potential. However, many laboratories have limited resources for biological evaluation, leaving their previously isolated or synthesized compounds largely or completely untested. To address this issue, the Canvass library of natural products was assembled, in collaboration with academic and industry researchers, for quantitative high-throughput screening (qHTS) across a diverse set of cell-based and biochemical assays. Characterization of the library in terms of physicochemical properties, structural diversity, and similarity to compounds in publicly available libraries indicates that the Canvass library contains many structural elements in common with approved drugs. The assay data generated were analyzed using a variety of quality control metrics, and the resultant assay profiles were explored using statistical methods, such as clustering and compound promiscuity analyses. Individual compounds were then sorted by structural class and activity profiles. Differential behavior based on these classifications, as well as noteworthy activities, are outlined herein. One such highlight is the activity of (-)-2(S)-cathafoline, which was found to stabilize calcium levels in the endoplasmic reticulum. The workflow described here illustrates a pilot effort to broadly survey the biological potential of natural products by utilizing the power of automation and high-throughput screening.

OxaD: A Versatile Indolic Nitrone Synthase from the Marine-Derived Fungus Penicillium oxalicum F30.

Indole alkaloids are a diverse class of natural products known for their wide range of biological activities and complex chemical structures. Rarely observed in this class are indolic nitrones, such as avrainvillamide and waikialoid, which possess potent bioactivities. Herein the oxa gene cluster from the marine-derived fungus Penicillium oxalicum F30 is described along with the characterization of OxaD, a flavin-dependent oxidase that generates roquefortine L, a nitrone-bearing intermediate in the biosynthesis of oxaline. Nitrone functionality in roquefortine L was confirmed by spectroscopic methods and 1,3-dipolar cycloaddition with methyl acrylate. OxaD is a versatile biocatalyst that converts an array of semisynthetic roquefortine C derivatives bearing indoline systems to their respective nitrones. This work describes the first implementation of a nitrone synthase as a biocatalyst and establishes a novel platform for late-stage diversification of a range of complex natural products.

Joining Forces: Fermentation and Organic Synthesis for the Production of Complex Heterocycles.

Commercial application of many promising heterocyclic natural products is limited by their natural abundance. While organic synthesis provides access to many natural products, total synthesis of numerous complex molecules is not economically feasible. In recent years, the combination of fermentation and organic synthesis has provided a new route for the production of complex heterocycles that are inaccessible by typical synthetic methods. This JOCSynopsis will review examples of how this union of disciplines has overcome obstacles in both academia and industry.

Triazaspirocycles: Occurrence, Synthesis, and Applications.

Natural products bearing a triazaspirocyclic motif have received significant attention in recent years. These compounds, which feature three nitrogen atoms attached to one quaternary carbon forming a spirocyclic scaffold, exhibit a wide range of biological activity and have promising applications in materials as well as in drug discovery. In this review article, we will discuss triazaspirocycles in Nature, their biological activity, and applications. Methods for the synthesis of triazaspirocycles as well as the reactivity of triazaspirocyclic scaffolds will be reviewed.

Incorporating Fermentation into Undergraduate Laboratory Courses.

Laboratory courses in universities have a responsibility to introduce current research practices and trends in scientific research to adequately prepare students for work in the field. One such research practice gaining popularity in recent years is that of green chemistry. Since the 1960s, increasing concern over the release of toxic chemicals into the environment has led to a push for more environmentally responsible chemistry. A growing faction of chemists has begun to adopt methods to eliminate chemical waste and support green chemistry. Fermentation is an ideal technique to demonstrate environmentally sustainable chemistry in an undergraduate laboratory class. Fermentation of complex natural products, as opposed to traditional organic synthesis, is beneficial as it supports a number of principles of green chemistry; it is conducted at ambient temperature and pressure, uses inexpensive and innocuous materials, makes use of renewable resources, and does not require a fume hood. Skills implemented during fermentation can be easily taught to upper-level Chemistry and Biochemistry undergraduate students, who typically have limited exposure to complex natural products in their coursework. Such a course would be interdisciplinary in nature, incorporating fungal biology and metabolism as well as organic chemistry. Students would learn a variety of skills, including growth media selection and preparation, inoculation of fungal cultures, extraction of natural products, and purification and characterization of metabolites. Experiments of this nature would allow for discussions of several areas of research: green chemistry, natural products and their application to medicine, identification of functional groups in complex molecules by spectroscopy, and introduction to biochemistry and metabolism. Roquefortine C, a prenylated indole alkaloid readily produced by a variety of species of Penicillia, is an excellent candidate for demonstrating fermentation in a laboratory classroom setting, owing to its ease of purification from other metabolites and its unique structural features.

Possible reason for the unusual regioselectivity in nucleophilic ring opening of trisubstituted aziridines under mildly basic conditions.

2,2,3-Trisubstituted aziridines are known to undergo ring opening at the more substituted carbon under mildly basic conditions. However, the reason for the formation of the more sterically encumbered product has never been examined. Several trisubstituted aziridines, with different substitution patterns at the C-2 and C-3 carbons, were synthesized to change the electronics of the aziridine ring system. These changes had no effect on the regioselectivity of the ring-opening reaction. Using the B3LYP/6-31G* DFT basis set it was determined that the transition state for opening at the more substituted carbon proceeds at a lower energy than the transition state at the less substituted carbon.

Structural plasticity of tubulin assembly probed by vinca-domain ligands.

Vinca-domain ligands are compounds that bind to tubulin at its inter-heterodimeric interface and favour heterogeneous protofilament-like assemblies, giving rise to helices and rings. This is the basis for their inhibition of microtubule assembly, for their antimitotic activities and for their use in anticancer chemotherapy. Ustiloxins are vinca-domain ligands with a well established total synthesis. A 2.7 Å resolution structure of ustiloxin D bound to the vinca domain embedded in the complex of two tubulins with the stathmin-like domain of RB3 (T(2)R) has been determined. This finding precisely defines the interactions of ustiloxins with tubulin and, taken together with structures of other vinca-ligand complexes, allows structure-based suggestions to be made for improved activity. These comparisons also provide a rationale for the large-scale polymorphism of the protofilament-like assemblies mediated by vinca-domain ligands based on local differences in their interactions with the two tubulin heterodimers constituting their binding site.

Didemnins, tamandarins and related natural products.

Since the discovery and isolation of the didemnin family of marine depsipeptides in 1981, the synthesis and biological activity of its congeners have been of great interest to the scientific community. The didemnins have demonstrated antitumor, antiviral, and immunosuppressive activity at low nano- and femtomolar levels. Of the congeners, didemnin B was the first marine natural product to reach phase II clinical trials in the United States, stimulating many analogue syntheses to date. About two decades later, tamandarins A and B were isolated, and were found to possess very similar structure and biological activity to that of the didemnin B. These compounds have shown impressive biological activity and some progress has been made in establishing structure-activity relationships. However, their molecular mechanism of action still remains unclear. This review highlights the long-standing study of didemnins and its critical application towards the understanding of the molecular mechanism of action of tamandarins and their potential use as therapeutic agents.

Structure-activity relationships of ustiloxin analogues.

Four novel ustiloxin D analogues were synthesized focusing on the size of the macrocyclic core, the stereochemistry at the bridgehead ether, and the enantiomer of ustiloxin D. All four were subjected to biological evaluation testing the inhibition of tubulin polymerization. Only 2,2-dimethyl-ustiloxin D retained any activity.

Facile ring-opening of azabicyclic [3.1.0]- and [4.1.0]aminocyclopropanes to afford 3-piperidinone and 3-azepinone.

Azabicyclic [3.1.0] and [4.1.0] Kulinkovich products underwent a facile reduction/fragmentation to afford a variety of 3-piperidinones and 3-azepinones, respectively, in the presence of catalytic palladium on carbon and formic acid in an atmosphere of hydrogen.

Total synthesis of Lys(3) tamandarin M: a potential affinity ligand.

The synthesis of Lys(3) tamandarin M is described. This analogue can be used as a protein affinity ligand to probe the mechanism of action of this unique class of molecules.

Ring opening of a trisubstituted aziridine with amines: regio- and stereoselective formation of substituted 1,2-diamines.

The formation of substituted 1,2-diamines via nucleophilic ring opening of a trisubstituted ethynyl aziridine was performed with complete regio- and stereoselective control. Various amines with different levels of nucleophilicity were employed and gave similar results. The ring opening reaction is not limited to ethynyl aziridines, as other alkyl trisubstituted aziridines gave the same results. This method allows for the formation of unique vicinal diamines while providing a fully substituted carbon center in a stereoselective manner under mild conditions.

An efficient synthesis of the tamandarin B macrocycle.

A reliable, high yielding cyclization protocol for the macrocycle of tamandarin B is presented. This strategy will facilitate the synthesis of side chain analogues.

Synthetic studies of tamandarin B side chain analogues.

The syntheses of three tamandarin B analogues are described. The goal of these studies was to prepare material to determine their relative therapeutic index and to gain an oversight as to their potential for clinical applications.

Total Synthesis of Isoroquefortine E and Phenylahistin.

Isoroquefortine E and phenylahistin were synthesized using the Horner-Wadsworth-Emmons reaction as the key step to build the dehydroamino acid moiety. The syntheses provide materials for the biological studies of the roquefortine-phenylahistin molecules.

Intramolecular hydrogen bonding as a determinant of the inhibitory potency of N-unsubstituted imidazole derivatives towards mammalian hemoproteins.

Enzymes involved in the mammalian microsomal metabolism of drugs are, in numerous cases, inhibited by compounds bearing an imidazolyl scaffold. However, the inhibition potency is highly dependent upon the accessibility of the imidazolyl nitrogen lone pair. In order to highlight some structural parameters of inhibitors that control this phenomenon, a series of compounds containing a nitrogen unsubstituted imidazolyl moiety with varying degrees of nitrogen lone pair accessibility was tested on human and rat hepatic cytochromes P450 and microperoxidase 8, an enzymatically active peptide derived from cytochrome c. In each case, we have shown that the accessibility of the imidazole lone pair determined the extent of inhibition. Nitrogen accessibility was tuned not only by varying the steric hindrance in the vicinity of the imidazolyl ring but also by modifying its surrounding hydrogen bonding network. Compounds in which there exists intramolecular hydrogen bonding between the imidazole moiety and an H-bond acceptor, such as an appropriately positioned amide carbonyl group, demonstrated enhanced inhibitory effects. Conversely, imidazole moieties which are in proximity to H-bond donors, such as an amide NH group, displayed reduced potency. This trend was observed in cyclo-peptide derivatives in which the intramolecular H-bond network was adjusted through the modification of the stereochemistry of a dehydrohistidine residue. It was observed that (Z)-isomers weakly bind heme, whereas (E)-isomers demonstrated higher degrees of metal binding. Therefore, enzymatic inhibition of heme-containing proteins by compounds bearing a dehydrohistidine motif seems to be closely related to its stereochemistry and hydrogen binding propensity. At neutral pH, these differences in binding affinities can be confidently attributed to the ambident H-bond properties of imidazole nitrogen atoms. This structure-activity relationship may be of use for the design of novel imidazolyl compounds as new P450 inhibitors or drug candidates.