Yatakemycin: total synthesis, DNA alkylation, and biological properties

DNA-binding small molecules are an important source of anticancer therapeutics that display a diverse array of mechanisms of action. Synthetic studies on the new DNA-alkylating natural product yatakemycin, detailed in this Highlight, have served to reassign its structure, assign the absolute stereochemistry, and provide access to yatakemycin and a series of structural analogues for biological evaluation. Studies on the DNA alkylation properties of (+)-and ent-(-)-yatakemycin and related analogues have demonstrated the enhanced DNA alkylation properties of this class of agents and provided insight into their interaction with DNA.     

Systematic exploration of the structural features of yatakemycin impacting DNA alkylation and biological activity

A systematic examination of the impact of the yatakemycin left and right subunits and their substituents is detailed along with a study of its unique three subunit arrangement (sandwiched vs extended and reversed analogues). The examination of the ca. 50 analogues prepared illustrate that within the yatakemycin three subunit structure, the subunit substituents are relatively unimportant and that it is the unique sandwiched arrangement that substantially increases the rate and optimizes the efficiency of its DNA alkylation reaction. This potentiates the cytotoxic activity of yatakemycin and its analogues overcoming limitations typically observed with more traditional compounds in the series (CC-1065, duocarmycins). Moreover, a study of the placement of the alkylation subunit within the three subunit arrangement (sandwiched vs extended and reversed analogues) indicates that it not only has a profound impact on the rate and efficiency of DNA alkylation but also controls and establishes the DNA alkylation selectivity as well, where both enantiomers of such sandwiched agents alkylate the same adenine sites exhibiting the same DNA alkylation selectivity independent of their absolute configuration.     

Asymmetric total synthesis of (+)- and ent-(-)-yatakemycin and duocarmycin SA: evaluation of yatakemycin key partial structures and its unnatural enantiomer

Complementary to studies that provided the first yatakemycin total synthesis resulting in its structure revision and absolute stereochemistry assignment, a second-generation asymmetric total synthesis is disclosed herein. Since the individual yatakemycin subunits are identical to those of duocarmycin SA (alkylation subunit) or CC-1065 (central and right-hand subunits), the studies also provide an improvement in our earlier total synthesis of CC-1065 and, as detailed herein, have been extended to an asymmetric total synthesis of (+)-duocarmycin SA. Further extensions of the studies provided key yatakemycin partial structures and analogues for comparative assessments. This included the definition of the DNA selectivity (adenine central to a five-base-pair AT sequence, e.g., 5'-AAAAA), efficiency, relative rate, and reversibility of ent-(-)-yatakemycin and its comparison with the natural enantiomer (identical selectivity and efficiency), structural characterization of the adenine N3 adduct confirming the nature of the DNA reaction, and comparisons of the cytotoxic activity of the natural product (L1210, IC50 = 5 pM) with those of its unnatural enantiomer (IC50 = 5 pM) and a series of key partial structures including those that probe the role of the C-terminus thiomethyl ester. The only distinguishing features between the enantiomers is that ent-(-)-yatakemycin alkylates DNA at a slower rate (krel = 0.13) and is reversible, whereas (+)-yatakemycin is not. Nonetheless, even ent-(-)-yatakemycin alkylates DNA at a faster rate and with a greater thermodynamic stability than (+)-duocarmycin SA, illustrating the unique characteristics of such "sandwiched" agents.     

DFT study of conformational and spectroscopic properties of yatakemycin

Molecular structure and conformational preferences of yatakemycin, a novel and exceptionally potent antitumor agent, have been investigated using the density functional theory (DFT) formalism. From the relative stability of various possible conformations, it is found that two conformers are nearly isoenergetic and markedly more stable than the others in the gas phase. To test the effect of polar mediums, the relative energies have been recalculated using the self-consistent reaction field method. Thus, the most stable conformer of the isolated molecule in the gas phase is expected to be still more preferred in solution. The molecular structure of yatakemycin has also been studied by means of its spectroscopic properties. The DFT results satisfactorily reproduce the experimental data and corroborate the reliability of the structural characterization advanced for yatakemycin. The lowest-energy electronic transitions have been interpreted with time-dependent DFT calculations. Notably, the strong IR band observed at 2852 cm(-1) is unambiguously assigned to the O-H stretching of the (C7)O-H...O(C12) fragment, linked by a strong intramolecular H-bond, and may be viewed as a distinctive fingerprint of yatakemycin. Furthermore, the calculated set of NMR chemical shifts of carbonyl carbon atoms and indole protons, the most sensitive to stereoelectronic factors, is consistent with experiment. The effects of both protonation and oxidation on the geometry of the most stable conformer have also been studied. With reference to yatakemycin's DNA alkylation properties, the structure of the yatakemycin-adenine adduct has been theoretically modeled and found to be consistent with experimental spectroscopic evidence.     

Total synthesis, structure revision, and absolute configuration of (+)-yatakemycin

The total synthesis of the reported structure 2 for yatakemycin, an exceptionally potent, naturally occurring antitumor agent disclosed in 2003, and its lack of correlation with the natural product are detailed. On the basis of spectroscopic distinctions between 2 and yatakemycin, the natural product structure was reformulated as 3, now bearing a thiomethyl ester versus thioacetate in the left-hand subunit. Total synthesis of 3 provided a compound nearly identical to but still subtly distinct from the natural product. A second reformulation of the yatakemycin structure as 1, incorporating the alternatively substituted right-hand subunit as well as the initial thiomethyl ester reformulation, was confirmed by total synthesis of both (+)- and ent-(-)-1 in studies that also unambiguously established the absolute configuration of the natural product.     

Regioselective Formation of Enediynes via Intramolecular Trapping of Allylic Cations

Enediynes are a novel class of naturally occurring antitumor antibiotics capable of causing DNA strand cleavage by hydrogen atom abstraction from the deoxyribose backbone. During the past decade, numerous synthetic methods have been developed to synthesize the naturally occurring and the "designed" enediynes for biomedical studies. Recently, we have succeeded in assembling the cis-enediynes 2 by a novel and high-yielding allylic rearrangement under mild reaction conditions (Eq 1).^1-3 This methodology has been used to synthesize a 10-membered ring enediyne³ which exhibits DNA cleavage activity.     

Lewis Acid Assisted Nickel‐Catalyzed Cross‐Coupling of Aryl Methyl Ethers by C−O Bond‐Cleaving Alkylation: Prevention of Undesired β‐Hydride Elimination

In the presence of trialkylaluminum reagents, diverse aryl methyl ethers can be transformed into valuable products by C?O bond‐cleaving alkylation, for the first time without the limiting β‐hydride elimination. This new nickel‐catalyzed dealkoxylative alkylation method enables powerful orthogonal synthetic strategies for the transformation of a variety of naturally occurring and easily accessible anisole derivatives. The directing and/or activating properties of aromatic methoxy groups are utilized first, before they are replaced by alkyl chains in a subsequent coupling process.     

The First Total Synthesis of 16-Hydroxygeranylgeraniol

Facile synthesis of 16-hydroxygeranylgeranio 1,a naturally occurring alicyclic diterpene,by alkylation reaction of allylic iodide 3 with phenyl sulfone 4,is described.     

First synthesis and absolute configuration of decaturin D

The first synthesis of (+)-decaturin D (1), an antiinsectant diterpenoid isolated from Penicillium thiersii, was accomplished by employing our original spiro-cyclization reaction as the key step. The absolute configuration of the naturally occurring 1 was determined.     

Depurinating acylfulvene-DNA adducts: characterizing cellular chemical reactions of a selective antitumor agent

Acylfulvenes (AFs) are a class of semisynthetic agents with high toxicity toward certain tumor cells, and for one analogue, hydroxymethylacylfulvene (HMAF), clinical trials are in progress. DNA alkylation by AFs, mediated by bioreductive activation, is believed to contribute to cytotoxicity, but the structures and chemical properties of corresponding DNA adducts are unknown. This study provides the first structural characterization of AF-specific DNA adducts. In the presence of a reductive enzyme, alkenal/one oxidoreductase (AOR), AF selectively alkylates dAdo and dGuo in reactions with a monomeric nucleoside, as well as in reactions with naked or cellular DNA, with 3-alkyl-dAdo as the apparently most abundant AF-DNA adduct. Characterization of this adduct was facilitated by independent chemical synthesis of the corresponding 3-alkyl-Ade adduct. In addition, in naked or cellular DNA, evidence was obtained for the formation of an additional type of adduct resulting from direct conjugate addition of Ade to AF followed by hydrolytic cyclopropane ring-opening, indicating the potential for a competing reaction pathway involving direct DNA alkylation. The major AF-dAdo and AF-dGuo adducts are unstable under physiologically relevant conditions and depurinate to release an alkylated nucleobase in a process that has a half-life of 8.5 h for 3-alkyladenine and less than approximately 2 h for dGuo adducts. DNA alkylation further leads to single-stranded DNA cleavage, occurring exclusively at dGuo and dAdo sites, in a nonsequence-specific manner. In AF-treated cells that were transfected with either AOR or control vectors, the DNA adducts identified match those from in vitro studies. Moreover, a positive correlation was observed between DNA adduct levels and cell sensitivity to AF. The potential contributing roles of AOR-mediated bioactivation and adduct stability to the cytotoxicity of AF are discussed.     

A de novo enantioselective total synthesis of (-)-laulimalide

An enantioselective total synthesis of the naturally occurring anticancer agent (-)-laulimalide is described. The synthesis is characterized by extensive use of new reaction methodologies based on catalytic asymmetric acyl halide-aldehyde cyclocondensation (AAC) reactions and transformations of the derived enantioenriched beta-lactones. The synthesis also incorporates a unique allenylstannane glycal acetate alkylation and chemoselective ring-closing metathesis reaction.     

Synthesis and absolute configuration of brevione B, an allelochemical isolated from Penicillium sp.

Breviones A-E (1-5), allelochemicals isolated from Penicillium brevicompactum Dierckx, are structurally unique diterpenoid derivatives. The first synthesis of both enantiomers of brevione B (2) was accomplished by employing the double S_N2′-type tandem reaction as a key step, and the absolute configuration of the naturally occurring 2 was established.     

Syntheses of two cytotoxic polyunsaturated pyrrole metabolites of the marine sponge Mycale micracanthoxea

Starting from eicosapentaenoic acid (EPA) the marine, naturally occurring, pyrrole derivatives, mycalazol 5 and mycalazal 2 have been synthesized. The Stille coupling reaction is a key step in the syntheses.     

Sequence specific alkylation of DNA by hairpin pyrrole-imidazole polyamide conjugates

BACKGROUND: Pyrrole-imidazole polyamides are synthetic ligands that recognize predetermined sequences in the minor groove of DNA with affinities and specificities comparable to those of DNA-binding proteins. As a result of their DNA-binding properties, polyamides could deliver reactive moieties for covalent reaction at specific DNA sequences and thereby inhibit DNA-protein interactions. Site-specific alkylation of DNA could be a useful tool for regulating gene expression. As a minimal first step, we set out to design and synthesize a class of hairpin polyamides equipped with DNA alkylating agents and characterize the specificity and yield of covalent modification. RESULTS: Bis(dichloroethylamino)benzene derivatives of the well-characterized chlorambucil (CHL) were attached to the gamma turn of an eight-ring hairpin polyamide targeted to the HIV-1 promoter. We found that a hairpin polyamide-CHL conjugate binds and selectively alkylates predetermined sites in the HIV promoter at subnanomolar concentrations. Cleavage sites were determined on both strands of a restriction fragment containing the HIV-1 promoter, revealing good specificity and a high yield of alkylation. CONCLUSIONS: The ability of polyamide-CHL conjugates to sequence specifically alkylate double-stranded DNA in high yield and at low concentrations sets the stage for testing their use as regulators of gene expression in cell culture and ultimately in complex organisms.     

Stereoselective synthesis of naturally occurring alpha-methylenebis-gamma-butyrolactones: an application of novel oxiranyl "remote" anions.

Stereospecific deprotonation of the epoxy proton at the beta-position of the alpha,beta-epoxy esters 5 and 6 yielded oxiranyl "remote" anions 7 and 8, which could then be used for alkylation. The anions 7 and 8 underwent a consecutive aldol lactonization to give, respectively, epoxy lactones 11 and 13 with high stereoselectivity. Generation of the remote anions as well as their stereoselective reactions served as a new synthetic route to the naturally occurring alpha-methylenebis-gamma-butyrolactones, 1.     

A palladium-catalyzed approach to allenic aromatic ethers and first total synthesis of terricollene A

A palladium-catalyzed C–O bond formation reaction between phenols and allenylic carbonates to give 2,3-allenic aromatic ethers with decent to excellent yields under mild reaction conditions has been described. A variety of synthetically useful functional groups are tolerated and the synthetic utility of this method has been demonstrated through a series of transformations of the allene moiety. By applying this reaction as the key step, the total syntheses of naturally occurring allenic aromatic ethers, eucalyptene and terricollene A (first synthesis; 4.5 g gram scale), have been accomplished.

A palladium-catalyzed C–O bond formation reaction between phenols and allenylic carbonates to give 2,3-allenic aromatic ethers with decent to excellent yields under mild reaction conditions has been described.     

Total synthesis of the proposed structure of the anthrapyran metabolite delta-indomycinone

The first total synthesis of the proposed structure of delta-indomycinone has been accomplished. The key steps involve the Diels-Alder reaction of a bromonaphthoquinone (6) and 1-methoxy-3-methyl-1-trimethylsiloxy-1,3-butadiene (7) to access the anthraquinone skeleton, representing a common building block of other naturally occurring anthraquinone antibiotics, regioselective bromination of anthraquinone (14) and a highly diastereoselective alkylation of enantiomerically pure dioxolanone 8. The reported synthetic approach has the advantage of high yields, excellent selectivity and a remarkable general applicability for the total synthesis of other anthrapyran natural products. The spectroscopic data obtained for the synthetic compounds 2 and 36 are not in agreement with those reported for the natural product, and therefore revision of the assigned structure is required.     

A Convergent Synthesis of the O-Benzyl Derivative of Enantio-Ineupatoriol From a Carbohydrate Precursor

The trans-2,3-disubstituted tetrahydropyran 7, obtained in eight steps from methyl α-D-glucoside, and the phosphonium salt 10, obtained from thiophene in six steps, were successfully combined in a Wittig reaction to form 11, the O-benzyl enantiomer of the naturally occurring thiophene ineupatoriol.     

6,7-Seco-ent-kaurane-type diterpenoids from Isodon eriocalyx var. laxiflora

Twenty nine 6,7-seco-ent-kaurane-type diterpenoids including 18 new ones, laxiflorolides C–T (1–18), along with 21 known ones were obtained from Isodon eriocalyx var. laxiflora. Laxiflorolides E–G (3–5) are the first identified naturally occurring 6,7-seco-ent-kauranoids that feature a 3,6-epoxy unit, and laxiflorolide M (11) is the first identified naturally occurring 6-nor-6,7-seco-ent-kauranoid. The absolute configurations of compounds 1, 3, 6, and 11 were determined by single-crystal X-ray diffraction analyses. The cytotoxic activity of the isolates was evaluated by an MTT assay.     

Synthesis and evaluation of 1,2,8, 8a-Tetrahydrocyclopropa[c]pyrrolo[3,2-e]indol-4(5H)-one, the parent alkylation subunit of CC-1065 and the duocarmycins: impact of the alkylation subunit substituents and its implications for DNA alkylation catalysis

The synthesis of 1,2,8,8a-tetrahydrocyclopropa[c]pyrrolo[3, 2-e]indol-4(5H)-one (CPI), the parent CC-1065 and duocarmycin SA alkylation subunit, is detailed. The parent CPI alkylation subunit lacks the C7 methyl substituent of the CC-1065 alkylation subunit and the C6 methoxycarbonyl group of duocarmycin SA, and their examination permitted the establishment of the impact of these natural product substituents. The studies revealed a CPI stability comparable to the CC-1065 alkylation subunit but which was 6x more reactive than the (+)-duocarmycin SA alkylation subunit, and it displayed the inherent reaction regioselectivity (4:1) of the natural products. The single-crystal X-ray structure of (+)-N-BOC-CPI depicts a near identical stereoelectronic alignment of the cyclopropane accounting for the identical reaction regioselectivity and a slightly diminished vinylogous amide conjugation relative to (+)-N-BOC-DSA suggesting that the stability distinctions stem in part from this difference in the vinylogous amide as well as alterations in the electronic nature of the fused pyrrole. Establishment of the DNA binding properties revealed that the CPI-based agents retain the identical DNA alkylation selectivities of the natural products. More importantly, the C6 methoxycarbonyl group of duocarmycin SA was found to increase the rate (12-13x) and efficiency (10x) of DNA alkylation despite its intrinsic lower reactivity while the CC-1065 C7 methyl group was found to slow the DNA alkylation rate (4x) and lower the alkylation efficiency (ca. 4x). The greater DNA alkylation rate and efficiency for duocarmycin SA and related analogues containing the C6 methoxycarbonyl is proposed to be derived from the extended length that the rigid C6 methoxycarbonyl provides and the resulting increase in the DNA binding-induced conformational change which serves to deconjugate the vinylogous amide and activate the alkylation subunit for nucleophilic attack. The diminished properties resulting from the CC-1065 C7 methyl group may be attributed to the steric impediment this substituent introduces to DNA minor groove binding and alkylation. Consistent with this behavior, the duocarmycin SA C6 methoxycarbonyl group increases biological potency while the CC-1065 C7 methyl group diminishes it.