Enediynes, enyne-allenes, their reactions, and beyond

Technologies for Targeted RNA Degradation and Induced RNA Decay

The vast majority of the human genome codes for RNA, but RNA-targeting therapeutics account for a small fraction of approved drugs. As such, there is great incentive to improve old and develop new approaches to RNA targeting. For many RNA targeting modalities, just binding is not sufficient to exert a therapeutic effect; thus, targeted RNA degradation and induced decay emerged as powerful approaches with a pronounced biological effect. This review covers the origins and advanced use cases of targeted RNA degrader technologies grouped by the nature of the targeting modality as well as by the mode of degradation. It covers both well-established methods and clinically successful platforms such as RNA interference, as well as emerging approaches such as recruitment of RNA quality control machinery, CRISPR, and direct targeted RNA degradation. We also share our thoughts on the biggest hurdles in this field, as well as possible ways to overcome them.

Triggered Crosslinking of Main-Chain Enediyne Polyurethanes via Bergman Cyclization

Crosslinking chemistries occupy an important position in polymer modification with a particular importance when triggered in response to external stimuli. Enediyne (EDY) moieties are used as functional entities in this work, known to undergo a pericyclic Bergman cyclization (BC) to induce a triggered crosslinking of polyurethanes (PU) via the intermediately formed diradicals. Diamino-EDYs, where the distance between the enyne-moieties is known to be critical to induce a BC, are placed repetitively as main-chain structural elements in isophorone-based PUs to induce reinforcement upon heating, compression, or stretching. A 7-day compression under room temperature results in a ≈69% activation of the BC, together with the observation of an increase in tensile strength by 62% after 25 stretching cycles. The occurrence of BC is further proven by the decreased exothermic values in differential scanning calorimetry, together with characteristic peaks of the formed benzene moieties via IR spectroscopy. Purely heat-induced crosslinking contributes to 191% of the maximum tensile strength in comparison to the virgin PU. The BC herein forms an excellent crosslinking strategy, triggered by heat or force in PU materials.

Targeted Discovery of Cryptic Enediyne Natural Products via FRET-Coupled High-Throughput Elicitor Screening

Enediyne antibiotics are a striking family of DNA-cleaving natural products with high degrees of cytotoxicity and structural complexity. Microbial genome sequences, which have recently accumulated, point to an untapped trove of "cryptic" enediynes. Most of the cognate biosynthetic gene clusters (BGCs) are sparingly expressed under standard growth conditions, making it difficult to characterize their products. Herein, we report a fluorescence-based DNA cleavage assay coupled with high-throughput elicitor screening for the rapid, targeted discovery of cryptic enediyne metabolites. We applied the approach to Streptomyces clavuligerus, which harbors two such BGCs with unknown products, identified steroids as effective elicitors, and characterized 10 cryptic enediyne-derived natural products, termed clavulynes A-J with unusual carbonate and terminal olefin functionalities, with one of these congeners matching the recently reported jejucarboside. Our results contribute to the growing repertoire of enediynes and provide a blueprint for identifying additional ones in the future.

Inorganic Bergman Cyclization: An Appeal From Theory

The scope of Bergman cyclization is expanded computationally by exploring the cyclization in inorganic B, N substituted derivative. This substitution has introduced polarity into the transition state, which resulted in dramatic lowering of the activation barrier. Natural charge distribution throughout the reaction profile has ascertained this hypothesis. Single B and N atom substitution at 1 and 6 terminal positions lowers the activation barrier by almost half of the original value which becomes even lower in the complete B, N analogue. The parent Bergman and single B, N substituted products were characterized by significant biradical character while the complete B, N substituted analogue was characterized by significant zwitterionic character. Reduction in electron delocalization is also observed in the complete B, N substituted analogue.

Functionalized 10-Membered Aza- and Oxaenediynes through the Nicholas Reaction

The scope and limitations of the Nicholas-type cyclization for the synthesis of 10-membered benzothiophene-fused heterocyclic enediynes with different functionalities were investigated. Although the Nicholas cyclization through oxygen could be carried out in the presence of an ester group, the final oxaenediyne was unstable under storage. Among the N-type Nicholas reactions, cyclization via an arenesulfonamide functional group followed by mild Co-deprotection was found to be the most promising, yielding 10-membered azaendiynes in high overall yields. By contrast, the Nicholas cyclization through the acylated nitrogen atom did not give the desired 10-membered cycle. It resulted in the formation of a pyrroline ring, whereas cyclization via an alkylated amino group resulted in a poor yield of the target 10-membered enediyne. The acylated 4-aminobenzenesulfonamide nucleophilic group was found to be the most convenient for the synthesis of functionalized 10-membered enediynes bearing a clickable function, such as a terminal triple bond. All the synthesized cyclic enediynes exhibited moderate activity against lung carcinoma NCI-H460 cells and had a minimal effect on lung epithelial-like WI-26 VA4 cells and are therefore promising compounds in the search for novel antitumor agents that can be converted into conjugates with tumor-targeting ligands.

Intramolecular Nicholas Reactions in the Synthesis of Heteroenediynes Fused to Indole, Triazole, and Isocoumarin

The applicability of an intramolecular Nicholas reaction for the preparation of 10-membered O- and N-enediynes fused to indole, 1,2,3-triazole, and isocoumarin was investigated. The general approach to acyclic enediyne precursors fused to heterocycles includes inter- and intramolecular buta-1,3-diyne cyclizations with the formation of iodoethynylheterocycles, followed by Sonogashira coupling. The nature of both a heterocycle and a nucleophilic group affects the possibility of a 10-membered ring closure by the Nicholas reaction. Among oxacycles, an isocoumarin-fused enediyne was obtained. In the case of O-enediyne annulated with indole, instead of the formation of a 10-membered cycle, BF₃-promoted addition of an OH-group to the proximal triple bond at the C3 position afforded dihydrofuryl-substituted indole. For 1,2,3-triazole-fused analogues, using NH-Ts as a nucleophilic functional group allowed obtaining 10-membered azaenediyne, while the substrate with a hydroxyl group gave only traces of the desired 10-membered oxacycle. An improved method for the deprotection of Co-complexes of cyclic enediynes using tetrabutylammonium fluoride in an acetone/water mixture and the investigation of the 10-membered enediynes' reactivity in the Bergman cyclization are also reported. In the solid state, all synthesized iodoethynylheterocycles were found to be involved in halogen bond (XB) formation with either O or N atoms as XB acceptors.

The Outliers: Metal-Mediated Radical Reagents for Biological Substrate Degradation

The predictable and controllable interaction of small organic or peptidic molecules with biological substrates is the primary reason most pharmaceuticals are narrowly decorated carbon frameworks. The inhibition or activation binding models are measurable and without side reactions that can cause pathological angst. Yet many diseases, especially those involving rapid proliferation of cells (i.e., cancer) or aggregation of peptides (e.g., heart disease, Alzheimer's disease) have not yet been cured by inhibition therapeutics. Additionally, interventional medicine is often required to alleviate such maladies by physical removal first, followed by molecular-level therapy as a second stage. Thus, there appears to be a niche for more aggressive therapeutics that may employ harsher chemical processes to realize clinical efficacy, albeit without causing catastrophic side effects. Molecules that may be considered for this challenge are not typically biomimetic, nor do they fit the traditional pharmaceutical paradigm. They may have unusual modes of action or undesired reactivity that can be lethal if not controlled. These are the outliers; potential pharmacophores that biology does not know how to manage or adapt to. This is why they may be an intriguing class of agents that needs continuous development. In this Account, we connect the under-developed enediyne family of compounds and our metalloenediyne derivatives to existing radical-based therapeutics such as bleomycin and doxorubicin to illustrate that controlled diradical reactivity, although an outlier mechanism, has a place in the therapeutic portfolio. This is self-evident in that of the 11 natural product enediynes known, 2 have clinical impact, a strong ratio. We expand on the chemical diversity of potential enediyne constructs and focus on the accessible trigger mechanisms to activate diradical formation as a method to control toxicity. Moreover, we further illustrate how electromagnetic fields can be employed to activate both molecular and larger nanomaterial constructs that carry highly concentrated payloads of reactive reagent. Finally, we describe how controlled diradical reactivity can reach beyond traditional therapeutic targets such as DNA, to peptide aggregates found in blood clots, neural fibrils, and membrane scaffolds. It is our belief that cleverly constructed frameworks with well-designed and controlled activation/reaction schemes can lead to novel therapeutics that can challenge evolving viral and bacterial invaders. From this evangelical perspective, our hope is that the conceptual framework, if not the specific designs in this Account, stimulate the readership to develop out-of-the-box therapeutic designs that may combat resistant disease targets.

Computational Investigation of the Selective Cleavage of Diastereotopic Cyclopropane Bonds in 5-Spirocyclopropane Isoxazolidines Rearrangement

The complete path of the Brandi-Guarna rearrangement of 5-spirocyclopropane isoxazolidines has been investigated by means of density functional theory calculations to rationalize the competing formation of tetrahydropyridones and enaminones by the determination of the minimum energy reaction paths. Our calculations confirm that the rearrangement is triggered by the homolysis of the isoxazolidine N-O bond followed by cleavage of one of the two C-CH₂ cyclopropane bonds as previously proposed by the Fabian group [ Eur. J. Org. Chem. 2001, 2001, 4223]. In addition, the results of this work suggest that in the presence of a stereogenic center at isoxazolidine C-4', the formation of a piperidinone or an enaminone as the final product depends on which of the two diastereotopic C-CH₂ bonds of cyclopropane is cleaved in the second step of the process. The result can be of great interest for the understanding of other processes involving the opening of a cyclopropane ring.

Effect of Extended Benzannelation Orientation on Bergman and Related Cyclizations of Isomeric Quinoxalenediynes

A combined computational and experimental study was conducted to examine the effect of extended benzannelation orientation on C¹-C⁵ and C¹-C⁶ cyclization of acyclic quinoxalenediynes. Calculations (mPW1PW91/cc-pVTZ//mPW1PW91/6-31G(d,p)) on terminal and phenylethynyl-substituted 5,6-diethynylquinoxaline and 6,7-diethynylquinoxaline showed C¹-C⁶ Bergman cyclization as the favored thermodynamic reaction pathway, with larger C¹-C⁶ preference for the angular quinoxalenediynes due to gain of a new aromatic sextet. Kinetic studies, as a function of 1,4-cyclohexadiene concentration, revealed retro-Bergman ring opening predominates over hydrogen atom abstraction (k_-1 > k₂) for 6,7-diethynylquinoxaline while 5,6-diethynylquinoxaline undergoes irreversible Bergman cyclization indicative of a large retro-Bergman ring opening barrier (k₂ > k_-1). The effect of extended linear versus angular benzannelation on reaction pathway shows in the contrasting photocyclizations of phenylethynyl derivatives. While angular 5,6-diethynylquinoxalines gave exclusive C¹-C⁶ photocyclization, linear 6,7-diethynylquinoxaline afforded C¹-C⁵ fulvene products. Computed singlet-triplet gaps and biradical stabilization energies indicated weak interaction between the nitrogen lone pair and proximal radical center in angular 5,6-diethynylquinoxalines. The overall data indicates extended angular benzannelation effectively renders Bergman cyclization irreversible due to favorable aromatic stabilization energy, while extended linear benzannelation results in increased retro-Bergman ring opening, allowing C¹-C⁵ cyclization to become a competitive reaction channel.

Solving the puzzling competition of the thermal C(2)-C(6) vs Myers-Saito cyclization of enyne-carbodiimides

The mechanism of the thermal cyclization of enyne-carbodiimides 7a–c has been studied computationally by applying the DFT method. The results indicate that enyne-carbodiimides preferentially follow the C²–C⁶ (Schmittel) cyclization pathway in a concerted fashion although the Myers–Saito diradical formation is kinetically preferred. The experimentally verified preference of the C²–C⁶ over the Myers–Saito pathway is guided by the inability of the Myers–Saito diradical to kinetically compete in the rate-determining trapping reactions, either inter- or intramolecular, with the concerted C²–C⁶ cyclization. As demonstrated with enyne-carbodiimide 11, the Myers–Saito channel can be made the preferred pathway if the trapping reaction by hydrogen transfer is no more rate determining.

Mechanistic Information from Nonstationary Points

The thermal cyclization of enyne-carbodiimides substituted at both the alkyne and carbodiimide terminus showed two curved Hammett correlations (log k/k0 against σp) that were fully reproduced by DFT (density functional theory) computational results. The latter suggest a concerted mechanism, but the transition state (TS) analysis failed to reveal any mechanistic insight about the reason for a curved Hammett correlation. Instead a preTS inspection, i.e., examination of the electronic and steric details on route between reactant and TS, furnished a detailed picture of the mechanism.

Mechanism of the Intramolecular Hexadehydro-Diels-Alder Reaction

Theoretical analysis of the mechanism of the intramolecular hexadehydro-Diels-Alder (HDDA) reaction, validated against prior and newly measured kinetic data for a number of different tethered yne-diynes, indicates that the reaction proceeds in a highly asynchronous fashion. The rate-determining step is bond formation at the alkyne termini nearest the tether, which involves a transition-state structure exhibiting substantial diradical character. Whether the reaction then continues to close the remaining bond in a concerted fashion or in a stepwise fashion (i.e., with an intervening intermediate) depends on the substituents at the remaining terminal alkyne positions. Computational modeling of the HDDA reaction is complicated by the significant diradical character that arises along the reaction coordinate, which leads to instabilities in both restricted singlet Kohn-Sham density functional theory (DFT) and coupled cluster theory based on a Hartree-Fock reference wave function. A consistent picture emerges, however, from comparison of broken-symmetry DFT calculations and second-order perturbation theory based on complete-active-space self-consistent-field (CASPT2) calculations.

Nonstatistical dynamics in the thermal C2-C6/diels-alder cyclization of enyne-allenes: effect of topology

The thermal C(2)-C(6) (Schmittel) cyclization of an enyne-allene with two aryl rings at the allene terminus experimentally leads to three formal Diels-Alder (DA) cycloaddition products, two of which (involving the dimethylamino phenyl unit) are shown to form in a nonstatistical process. DFT computations on the reaction paths reveal that the two aryl rings (Ph vs PhNMe2) do not interact in a dynamic manner as their minimum energy pathways (MEPs) are separated by a large barrier. The preferential formation of the more-hindered DA product 8 (ortho to the dimethylamino group) over the less-hindered product 9 (para to the dimethylamino group), despite the higher energy TS for 8, suggests the occurrence of nonstatistical dynamics in the cyclization onto the dimethylamino phenyl unit, though. Potential energy surface (PES) computations indicate that the large amount of nonstatistical dynamics (97%) arises from facile IRC dynamics (left picture) that is compared with the non-IRC dynamics of a related system (∼76%, right picture, J. Org. Chem. 2014, 79, 2368).

Gold(i)-catalyzed hydroindolylation of allenyl ethers

Nucleophilicity game: the gold(i)-catalyzed reaction/rearrangement of allenyl ethers has been investigated in the presence of indoles. The reaction outcome seems to be decided mainly by the nature of the pendant group of allenyl ether. Control experiments are indicative of an inner sphere mechanism for the hydroindolylation reaction.