Synthesis at the molecular frontier

A concise synthesis of (+)-batzelladine B from simple pyrrole-based starting materials

Alkaloids, secondary metabolites that contain basic nitrogen atoms, are some of the most well-known biologically active natural products in chemistry and medicine¹. Although the efficient laboratory syntheses of alkaloids would enable researchers to study and optimize their biological properties,² the basicity and nucleophilicity of nitrogen, its susceptibility to oxidation, and its ability to alter reaction outcomes in unexpected ways – for example, through stereochemical instability and neighboring group participation – complicates their preparation in the laboratory. Efforts to address these issues have led to the invention of a large number of protecting groups that temper the reactivity of nitrogen³; however, the use of protecting groups typically introduce additional steps and obstacles into the synthetic route. Alternatively, the use of aromatic nitrogen heterocycles as synthetic precursors can attenuate the reactivity of nitrogen and streamline synthetic strategies⁴. In this manuscript, we use such an approach to achieve a synthesis of the complex anti-HIV alkaloid (+)-batzelladine B in nine steps (longest-linear sequence) from simple pyrrole-based starting materials. The route employs several key transformations that would be challenging or impossible to implement using saturated nitrogen heterocycles and highlights some of the advantages conferred by the use of aromatic starting materials.

Lessons from the synthetic chemist nature

This conceptual review examines the ideal multistep synthesis from the perspective of nature. We suggest that besides step- and redox economies, one other key to efficiency is steady state processing with intermediates that are immediately transformed to the next intermediate when formed. We discuss four of nature's strategies (multicatalysis, domino reactions, iteration and compartmentation) that commonly proceed via short-lived intermediates and show that these strategies are also part of the chemist's portfolio. We particularly focus on compartmentation which in nature is found microscopically within cells (organelles) and between cells and on a molecular level on multiprotein scaffolds (e.g. in polyketide synthases) and demonstrate how compartmentation is manifested in modern multistep flow synthesis.

Preparation and synthetic value of π-bond-rich branched hydrocarbons

The two simplest branched acyclic structures comprising only conjugated C═C units, namely, [3]dendralene (3-methylene-1,4-pentadiene) and [4]dendralene (3,4-dimethylene-1,5-hexadiene), were first reported in 1955 and 1962, respectively. No higher members of the series were described in the literature until 2000. This Account describes the modern phase of dendralene chemistry, driven to a large extent by research performed within the author's group. The first synthesis of the parent dendralene family allowed access to the hydrocarbons in batches of up to 5 mg. The synthetic approach took into account the prevailing dogma of the time, specifically that these compounds would be very reactive species and hence difficult to handle in the laboratory. As such, a route involving the cheleotropic elimination of SO2 from stable, and generally insoluble, 3-sulfolene-masked precursors was devised. Our second-generation approach was of significantly higher value in preparative terms, allowing the syntheses of the first six members of the unsubstituted [n]dendralenes (i.e., n = 3-8) directly, on scales of hundreds of milligrams to decagrams, using commercially available precursors and standard laboratory equipment and methods. This work demonstrated that the assumed high reactivity and instability this family of compounds was erroneous and ultimately led to the development of syntheses of structurally related cross-conjugated systems including substituted dendralenes, tetravinylethylene, 1,1-divinylallene, and furan-containing analogues of the dendralenes. Cross-coupling reactions feature strongly in the syntheses of these compounds, and methods involving single- to multifold Stille, Kumada, and Negishi couplings are mainstays of this work. The even parity [n]dendralenes were shown to exhibit enhanced stability over the odd parity congeners, a result that can be attributed to conformational effects. π-Bond-rich branched hydrocarbons are demonstrated to have significant value in the rapid generation of structural complexity. Pericyclic processes are particularly useful in this regard, with the dendralenes and their relatives serving as multidienes, participating in diene-transmissive cycloaddition sequences, sometimes in combination with electrocyclizations, to generate fused and bridged multicyclic systems containing many new covalent bonds. The outcomes of exploratory investigations into pericyclic sequences involving dendralenes are presented, along with methods developed to control chemoselectivity, regioselectivity, and stereoselectivity. Distinct from their use in diene-transmissive sequences, the dendralenes also serve as multialkenes, for the direct synthesis of polyols and oligo-cyclopropanes. Finally, the deployment of π-bond-rich branched hydrocarbons in the shortest total synthesis of a pseudopterosin natural product is summarized, as a prelude to future prospects in the areas of hydrocarbon chemistry and target synthesis.

Formation and in situ reactions of hypervalent iodonium alkynyl triflates to form cyanocarbenes

The conversion of readily available silylalkynes, iodobenzene diacetate, and azide anions was utilized to form and react cyanocarbenes. A copper(II)-catalyzed reaction was found to react in a different manner. Both of these methods benefit from the formation and in situ reaction of hypervalent iodonium alkynyl triflates in O-H insertion reactions.

A Practical, Multi-gram Synthesis of (±)-Herbindole A, (±)-Herbindole B, and (±)-Herbindole C from a Common Intermediate via 6,7-Indole Aryne Cycloaddition and Pd(0)-Catalyzed Cross-Coupling Reactions

A practical, multi-gram 10-step synthesis of racemic herbindole A, B, and C from a common intermediate is described. The key step features a remarkably regioselective C-7 metal-halogen exchange and elimination from a Bartoli-generated N-t-butyldimethylsilyl-4,6,7-tribromo-5-methylindole scaffold to afford the 6,7-indole aryne. Cycloaddition with cyclopentadiene, oxidative cleavage, and Fujimoto reduction gave a common intermediate from which all three herbindoles were readily derived. A final Pd(0)-catalyzed Negishi and Stille cross-coupling reaction at the C-4 bromide afforded each of the herbindoles on a multigram scale.

Tetramethyleneethane Equivalents: Recursive Reagents for Serialized Cycloadditions

New reactions and reagents that allow for multiple bond-forming events per synthetic operation are required to achieve structural complexity and thus value with step-, time-, cost-, and waste-economy. Here we report a new class of reagents that function like tetramethyleneethane (TME), allowing for back-to-back [4 + 2] cycloadditions, thereby amplifying the complexity-increasing benefits of Diels–Alder and metal-catalyzed cycloadditions. The parent recursive reagent, 2,3-dimethylene-4-trimethylsilylbutan-1-ol (DMTB), is readily available from the metathesis of ethylene and THP-protected 4-trimethylsilylbutyn-1-ol. DMTB and related reagents engage diverse dienophiles in an initial Diels–Alder or metal-catalyzed [4 + 2] cycloaddition, triggering a subsequent vinylogous Peterson elimination that recursively generates a new diene for a second cycloaddition. Overall, this multicomponent catalytic cascade produces in one operation carbo- and heterobicyclic building blocks for the synthesis of a variety of natural products, therapeutic leads, imaging agents, and materials. Its application to the three step synthesis of a new solvatochromic fluorophore, N-ethyl(6-N,N-dimethylaminoanthracene-2,3-dicarboximide) (6-DMA), and the photophysical characterization of this fluorophore are described.

Unified total synthesis of the natural products endiandric acid A, kingianic acid E, and kingianins A, D, and F

A measure of the strength of a synthetic strategy is its versatility: specifically, whether it allows structurally distinct targets to be prepared. Herein we disclose a unified approach for the total synthesis of natural products of three distinct structural types, all of which occur naturally as racemic mixtures. The point of divergence involves the terminal alkylation of a conjugated tetrayne, and culminates in a significantly shortened synthesis of endiandric acid A (8 steps), the first total synthesis of kingianic acid E (8 steps), and a second-generation synthesis of kingianins A, D, and F (11 steps). Evidence for redox catalysis in the biosynthesis of kingianic acid E is presented.

Spirotetronate polyketides as leads in drug discovery

The discovery of chlorothricin (1) defined a new family of microbial metabolites with potent antitumor antibiotic properties collectively referred to as spirotetronate polyketides. These microbial metabolites are structurally distinguished by the presence of a spirotetronate motif embedded within a macrocyclic core. Glycosylation at the periphery of this core contributes to the structural complexity and bioactivity of this motif. The spirotetronate family displays impressive chemical structures, potent bioactivities, and significant pharmacological potential. This review groups the family members based on structural and biosynthetic considerations and summarizes synthetic and biological studies that aim to elucidate their mode of action and explore their pharmacological potential.

Function through synthesis-informed design

In 1996, a snapshot of the field of synthesis was provided by many of its thought leaders in a Chemical Reviews thematic issue on “Frontiers in Organic Synthesis”. This Accounts of Chemical Research thematic issue on “Synthesis, Design, and Molecular Function” is intended to provide further perspective now from well into the 21st century. Much has happened in the past few decades. The targets, methods, strategies, reagents, procedures, goals, funding, practices, and practitioners of synthesis have changed, some in dramatic ways as documented in impressive contributions to this issue. However, a constant for most synthesis studies continues to be the goal of achieving function with synthetic economy. Whether in the form of new catalysts, reagents, therapeutic leads, diagnostics, drug delivery systems, imaging agents, sensors, materials, energy generation and storage systems, bioremediation strategies, or molecules that challenge old theories or test new ones, the function of a target has been and continues to be a major and compelling justification for its synthesis. While the targets of synthesis have historically been heavily represented by natural products, increasingly design, often inspired by natural structures, is providing a new source of target structures exhibiting new or natural functions and new or natural synthetic challenges. Complementing isolation and screening approaches to new target identification, design enables one to create targets de novo with an emphasis on sought-after function and synthetic innovation with step-economy. Design provides choice. It allows one to determine how close a synthesis will come to the ideal synthesis and how close a structure will come to the ideal function.

In this Account, we address studies in our laboratory on function-oriented synthesis (FOS), a strategy to achieve function by design and with synthetic economy. By starting with function rather than structure, FOS places an initial emphasis on target design, thereby harnessing the power of chemists and computers to create new structures with desired functions that could be prepared in a simple, safe, economical, and green, if not ideal, fashion. Reported herein are examples of FOS associated with (a) molecular recognition, leading to the first designed phorbol-inspired protein kinase C regulatory ligands, the first designed bryostatin analogs, the newest bryologs, and a new family of designed kinase inhibitors, (b) target modification, leading to highly simplified but functionally competent photonucleases—molecules that cleave DNA upon photoactivation, (c) drug delivery, leading to cell penetrating molecular transporters, molecules that ferry other attached or complexed molecules across biological barriers, and (d) new reactivity-regenerating reagents in the form of functional equivalents of butatrienes, reagents that allow for back-to-back three-component cycloaddition reactions, thus achieving structural complexity and value with step-economy. While retrosynthetic analysis seeks to identify the best way to make a target, retrofunction analysis seeks to identify the best targets to make. In essence, form (structure) follows function.

Catalytic Efficiency Is a Function of How Rhodium(I) (5 + 2) Catalysts Accommodate a Conserved Substrate Transition State Geometry: Induced Fit Model for Explaining Transition Metal Catalysis

The origins of differential catalytic reactivities of four Rh(I) catalysts and their derivatives in the (5 + 2) cycloaddition reaction were elucidated using density functional theory. Computed free energy spans are in excellent agreement with known experimental rates. For every catalyst, the substrate geometries in the transition state remained constant (<0.1 Å RMSD for atoms involved in bond-making and -breaking processes). Catalytic efficiency is shown to be a function of how well the catalyst accommodates the substrate transition state geometry and electronics. This shows that the induced fit model for explaining biological catalysis may be relevant to transition metal catalysis. This could serve as a general model for understanding the origins of efficiencies of catalytic reactions.

Toward ideality: the synthesis of (+)-kalkitoxin and (+)-hydroxyphthioceranic acid by assembly-line synthesis

The iterative homologation of boronic esters using chiral lithiated benzoate esters and chloromethyllithium has been applied to the highly efficient syntheses of two natural products, (+)-kalkitoxin and (+)-hydroxyphthioceranic acid. The chiral lithiated benzoate esters (>99% ee) were generated from the corresponding stannanes, which themselves were prepared by Hoppe-Beak deprotonation of ethyl 2,4,6-triisopropyl-benzoate with s-BuLi in the presence of (+)- or (-)-sparteine and trapping with Me3SnCl followed by recrystallization. In addition, it was found that purification between several homologations could be avoided, substantially increasing both chemical and manpower efficiency. In the case of (+)-kalkitoxin, six iterative homologations were conducted on commercially available p-MeOC6H4CH2Bpin to build up the core of the molecule before the C-B bond was converted into the desired C-N bond, without purification of intermediates. In the case of (+)-hydroxyphthioceranic acid, 16 iterative homologations were conducted on p-MeOC6H4Bpin with only four intermediate purifications before oxidation of the C-B bond to the desired alcohol. The stereocontrolled and efficient syntheses of these complex molecules highlight the power of iterative chemical synthesis using boronic esters.

Copper-catalyzed aerobic oxidative cleavage of C–C bonds in epoxides leading to aryl nitriles and aryl aldehydes

Novel copper-catalyzed aerobic synthesis of aryl nitriles and aldehydes from epoxides via C–C single bond cleavage has been discovered.

Reactivity and chemoselectivity of allenes in Rh(I)-catalyzed intermolecular (5 + 2) cycloadditions with vinylcyclopropanes: allene-mediated rhodacycle formation can poison Rh(I)-catalyzed cycloadditions

Allenes are important 2π building blocks in organic synthesis and engage as 2-carbon components in many metal-catalyzed reactions. Wender and co-workers discovered that methyl substituents on the terminal allene double bond counterintuitively change the reactivities of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with vinylcyclopropanes (VCPs). More sterically encumbered allenes afford higher cycloadduct yields, and such effects are also observed in other Rh(I)-catalyzed intermolecular cycloadditions. Through density functional theory calculations (B3LYP and M06) and experiment, we explored this enigmatic reactivity and selectivity of allenes in [Rh(CO)2Cl]2-catalyzed intermolecular (5 + 2) cycloadditions with VCPs. The apparent low reactivity of terminally unsubstituted allenes is associated with a competing allene dimerization that irreversibly sequesters rhodium. With terminally substituted allenes, steric repulsion between the terminal substituents significantly increases the barrier of allene dimerization while the barrier of the (5 + 2) cycloaddition is not affected, and thus the cycloaddition prevails. Computation has also revealed the origin of chemoselectivity in (5 + 2) cycloadditions with allene-ynes. Although simple allene and acetylene have similar reaction barriers, intermolecular (5 + 2) cycloadditions of allene-ynes occur exclusively at the terminal allene double bond. The terminal double bond is more reactive due to the enhanced d-π* backdonation. At the same time, insertion of the internal double bond of an allene-yne has a higher barrier as it would break π conjugation. Substituted alkynes are more difficult to insert compared with acetylene, because of the steric repulsion from the additional substituents. This leads to the greater reactivity of the allene double bond relative to the alkynyl group in allene-ynes.

Function through bio-inspired, synthesis-informed design: step-economical syntheses of designed kinase inhibitors†Dedicated to Max Malacria, a friend and scholar whose science and creative contributions to step-economical synthesis have inspired us all and moved the field closer to the ideal.‡Electronic supplementary information (ESI) available: Synthetic procedures and spectral data. See DOI: 10.1039/c4qo00228hClick here for additional data file

We describe here step-economical, function-oriented strategies towards the syntheses of potent kinase inhibitors inspired by the natural product staurosporine.

The human kinome comprises over 500 protein kinases. When mutated or over-expressed, many play critical roles in abnormal cellular functions associated with cancer, cardiovascular disease and neurological disorders. Here we report a step-economical approach to designed kinase inhibitors inspired by the potent, but non-selective, natural product staurosporine, and synthetically enabled by a novel, complexity-increasing, serialized [5 + 2]/[4 + 2] cycloaddition strategy. This function-oriented synthesis approach rapidly affords tunable scaffolds, and produced a low nanomolar inhibitor of protein kinase C.

Nickel-catalyzed intramolecular [3 + 2 + 2] cycloadditions of alkylidenecyclopropanes. A straightforward entry to fused 6,7,5-tricyclic systems

A highly diastereo- and chemoselective intramolecular nickel-catalyzed cycloaddition of alkene- and alkyne-tethered alkynylidenecyclopropanes is reported. The method constitutes the first fully intramolecular [3 + 2 + 2] alkylidenecyclopropropane cycloaddition occurring via a proximal cleavage of the cyclopropane and makes it possible to build relevant 6,7,5-tricyclic frameworks in a single-pot reaction. Importantly, the reaction outcome is highly dependent on the characteristics of the nickel ligands.

Synthesis of partially O-acetylated N-acetylneuraminic acid using regioselective silyl exchange technology

Postglycosylation acetylation of sialic acid imparts unique roles to sialoglycoconjugates in mammalian immune response making structural and functional understanding of these analogues important. Five partially O-acetylated Neu5Ac analogues have been synthesized. Reaction of per-O-silylated Neu5Ac ester with AcOH and Ac₂O in pyridine promotes regioselective silyl ether/acetate exchange in the following order: C₄ (2°) > C₉ (1°) > C₈ (2°) > C₂ (anomeric). Subsequent hydrogenolysis affords the corresponding sialic acid analogues as useful chemical biology tools.

Improved protein kinase C affinity through final step diversification of a simplified salicylate-derived bryostatin analog scaffold

Bryostatin 1, in clinical trials or preclinical development for cancer, Alzheimer’s disease, and a first-of-its-kind strategy for HIV/AIDS eradication, is neither readily available nor optimally suited for clinical use. In preceding work, we disclosed a new class of simplified bryostatin analogs designed for ease of access and tunable activity. Here we describe a final step diversification strategy that provides, in only 25 synthetic steps, simplified and tunable analogs with bryostatin-like PKC modulatory activities.

Computer-guided design, synthesis, and protein kinase C affinity of a new salicylate-based class of bryostatin analogs

Bryostatin 1 is in clinical trials for the treatment of cancer and Alzheimer’s disease and is a candidate for a first-in-class approach to HIV/AIDS eradication. It is neither readily available nor optimally suited for clinical use. Using a function oriented synthesis strategy, a new class of bryostatin-inspired analogs was designed with a simplified salicylate-derived subunit, enabling step-economical synthesis (23 total steps) of agents exhibiting bryostatin-like affinity to protein kinase C (PKC).

Total Syntheses of Lyconadins: Finding Efficiency and Diversity

Lyconadins A-C are important members of the Lycopodium alkaloid family with challenging structural features and interesting biological profile. Herein, various synthetic strategies and methods for their preparation are summarized with the focus on constructive bond formation and our efficient and divergent synthesis based on functional group pairing (FGP) strategy.

Molecular systems pharmacology: isoelectric focusing signature of protein kinase Cδ provides an integrated measure of its modulation in response to ligands

Protein kinase C (PKC), a validated therapeutic target for cancer chemotherapy, provides a paradigm for assessing structure–activity relations, where ligand binding has multiple consequences for a target. For PKC, ligand binding controls not only PKC activation and multiple phosphorylations but also subcellular localization, affecting subsequent signaling. Using a capillary isoelectric focusing immunoassay system, we could visualize a high resolution isoelectric focusing signature of PKCδ upon stimulation by ligands of the phorbol ester and bryostatin classes. Derivatives that possessed different physicochemical characteristics and induced different patterns of biological response generated different signatures. Consistent with different patterns of PKCδ localization as one factor linked to these different signatures, we found different signatures for activated PKCδ from the nuclear and non-nuclear fractions. We conclude that the capillary isoelectric focusing immunoassay system may provide a window into the integrated consequences of ligand binding and thus afford a powerful platform for compound development.