Small molecules that mimic the thiol-triggered alkylating properties seen in the natural product leinamycin

Reaction of the antitumor agent leinamycin with cellular thiols results in conversion of the natural product to a DNA-alkylating episulfonium alkylating agent via an intriguing sequence of chemical reactions. To establish whether the chemistry first seen in leinamycin represents a general motif that can function in various molecular frameworks, construction of greatly simplified analogues containing only the "core" funcional groups anticipated to be necessary for thiol-triggered generation of an alkylating agent was undertaken. For this purpose, the "stripped-down" leinamycin analogue 7-(3-methyl-but-2-enyl)-1-oxo-1H-lambda4-benzo[1,2]dithiol-3-one (4) was synthesized. Treatment of 4 with thiol under several different conditions results in efficient conversion of the compound to cyclized 2,3-dihydro-benzo[b]thiophene-7-carboxylic acid products (13) that are envisioned to arise from Markovnikov addition of solvent to an intermediate episulfonium ion (14). Thus, the relatively simple molecule 4 is able to mimic the thiol-triggered alkylating properties displayed by the natural product leinamycin. This work helps define why the core functional groups required thiol-accelerated generation of an alkylating intermediate from leinamycin and indicates that substantially altered analogues of the natural product may retain alkylating properties. In a broader context, the results provide evidence that the unique cascade of chemical reactions first seen in the context of leinamycin represents a general motif that can operate in a variety of molecular frameworks.     

Activation of leinamycin by thiols: a theoretical study

Reaction of thiols with the 1,2-dithiolan-3-one 1-oxide heterocycle found in leinamycin (1) results in the conversion of this antitumor antibiotic to a DNA-alkylating episulfonium ion (5). While the products formed in this reaction have been rationalized by a mechanism involving initial attack of thiol on the central sulfenyl sulfur (S2') of the 1,2-dithiolan-3-one 1-oxide ring, the carbonyl carbon (C3') and the sulfinyl sulfur (S1') of this heterocycle are also expected to be electrophilic. Therefore, it is important to consider whether nucleophilic attack of thiol at these sites might contribute either to destruction of the antibiotic or conversion to its episulfonium ion form. To address this question, we have used computational methods to examine the attack of methyl thiolate on each of the three electrophilic centers in a simple analogue of the 1,2-dithiolan-3-one 1-oxide heterocycle found in leinamycin. Calculations were performed at the MP2/6-311+G(3df,p)//B3LYP/6-31G level of theory with inclusion of solvent effects. The results indicate that the most reasonable mechanism for thiol-mediated activation of leinamycin involves initial attack of thiolate at the S2'-position of the antibiotic's 1,2-dithiolan-3-one 1-oxide heterocycle, followed by conversion to the 1,2-oxathiolan-5-one intermediate (3).     

DFt study of the regioselectivity of addition of sulfenylchloride to ethenes

The electrophilic addition reactions of methylsulfenyl chloride to the double bonds of functionalized ethenes have been studied theoretically. Density functional theory (DFT) calculations have been applied for starting species and ethene‐based sulfonium intermediates bearing substitutes at α‐carbon atom to study geometrical parameters and electronic states of plausible intermediate forms. The quantum chemical optimizations of intermediates indicate that the episulfonium ion is the most likely methyl‐ or carboxyl‐substituted ethane‐based intermediate. However, with phenyl substituents the intermediate is more like a carbonium than an episulfonium ion. The role of sulfur appears to be that of directing the stereochemistry of the addition reaction of chloride, forming the trans product upon nucleophilic attack on the C—C bond of the episulfonium ion. The regioselectivity features of the opening of the episulfonium ion by the chloride anion depend on the LUMO and LUMO+1 of the episulfonium ion and the approaching HOMO of chlorine. The results of the theoretical investigations are in agreement with experiment. © 2007 Wiley Periodicals, Inc. Heteroatom Chem 18:695–703, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/hc.20378     

Noncovalent DNA binding drives DNA alkylation by leinamycin: evidence that the Z,E-5-(thiazol-4-yl)-penta-2,4-dienone moiety of the natural product serves as an atypical DNA intercalator

Molecular recognition and chemical modification of DNA are important in medicinal chemistry, toxicology, and biotechnology. Historically, natural products have revealed many interesting and unexpected mechanisms for noncovalent DNA binding and covalent DNA modification. The studies reported here characterize the molecular mechanisms underlying the efficient alkylation of duplex DNA by the Streptomyces-derived natural product leinamycin. Previous studies suggested that alkylation of duplex DNA by activated leinamycin (2) is driven by noncovalent association of the natural product with the double helix. This is striking because leinamycin does not contain a classical noncovalent DNA-binding motif, such as an intercalating unit, a groove binder, or a polycation. The experiments described here provide evidence that leinamycin is an atypical DNA-intercalating agent. A competition binding assay involving daunomycin-mediated inhibition of DNA alkylation by leinamycin provided evidence that activated leinamycin binds to duplex DNA with an apparent binding constant of approximately 4.3 ± 0.4 × 10(3) M(-1). Activated leinamycin caused duplex unwinding and hydrodynamic changes in DNA-containing solutions that are indicative of DNA intercalation. Characterization of the reaction of activated leinamycin with palindromic duplexes containing 5'-CG and 5'-GC target sites, bulge-containing duplexes, and 5-methylcytosine-containing duplexes provided evidence regarding the orientation of leinamycin with respect to target guanine residues. The data allow construction of a model for the leinamycin-DNA complex suggesting how a modest DNA-binding constant combines with proper positioning of the natural product to drive efficient alkylation of guanine residues in the major groove of duplex DNA.     

The first oxygen-bonded sulfenate ion: crystal and molecular structures of bis(ethylenediamine)(2-pyridinesulfenato-O)cobalt(III) and bis(ethylenediamine)(2-pyridinesulfinato-O)cobalt(III)

The first O-bonded sulfenate species [Co(en)2(py-SO-O)]2+ has been synthesized by isomerization of its S-bonded linkage isomer, [Co(en)2(pyridine-2-sulfenate-S]2+. The sulfenate ion in both forms is stabilized by coordination to the electropositive cobalt(III) ion. The driving force for the formation of the O-bonded sulfenate linkage isomer comes from the four to five membered ring expansion which accompanies the rearrangement. Crystal structures of the green O-sulfenate confirm the formulation and reveal varying amounts of a cocrystallized O-bonded sulfinate diastereomer. The cations have essentially identical structures except for the extra oxygen in the O-sulfinate. Differences in packing of cations and perchlorates give rise to two different structural types for the salts, corresponding to sulfenate-rich and sulfinate-rich phases.     

Synthesis and noncovalent DNA-binding properties of thiazole derivatives related to leinamycin

A series of compounds related to the macrocyclic portion of the DNA-damaging antitumor agent leinamycin were prepared as tools to characterize noncovalent DNA binding by this natural product. Acyclic (Z,E)-dienes were assembled via a Sonogashira coupling followed by partial hydrogenation. A Stille coupling was used in the cyclization step leading to a macrocyclic thiazole-diene analogue. Results obtained using the synthetic analogues reported here indicate that the extended π-system on the `left-hand side' of leinamycin is required for noncovalent association of the natural product with duplex DNA.     

Stereospecific alkyl and alkynyl substitution reactions of epoxy sulfides with organoaluminums with double inversion of the configuration

A regioselective and stereospecific substitution reaction of 1-(phenylthio)-2,3-epoxyalkanes was achieved by using organoaluminum reagents as a nucleophile. Under the influence of trimethyl- or triethylaluminum, a 1-(phenylthio)-2,3-epoxyalkane underwent substitution at the C2 position to give a product with retention of the configuration. The reaction proceeds through an episulfonium ion intermediate, which gives rise to the C2-substitution products with double inversion of the configuration. Introduction of an alkynyl group was also accomplished by the reaction with dimethyl[2-(trimethylsilyl)ethynyl]aluminum in dichloromethane.     

Enantioselective total synthesis of (+)-salvileucalin B

An enantioselective total synthesis of the diterpenoid natural product (+)-salvileucalin B is reported. Key findings include a copper-catalyzed arene cyclopropanation reaction to provide the unusual norcaradiene core and a reversible retro-Claisen rearrangement of a highly functionalized norcaradiene intermediate.     

A one-pot synthesis of beta-C-glucopyranosides from exo-glucal,p-tolylsulfenyl chloride,an alpha-methoxyalkene,and an external nucleophile

[formula: see text] beta-C-Glycosides were synthesized in one-pot experiments using the following sequence of four reactions: (i) addition of p-TolSCl to an alpha-methoxyalkene, (ii) generation of the episulfonium ion from a beta-(arylsulfanyl)alkyl chloride, (iii) reaction of the episulfonium intermediate with benzylated exo-D-glucal to form a cyclic five-membered sulfonium salt, and (iv) quenching of the sulfonium salt with the external nucleophile: H2O, CH3OH, or NaCNBH3.     

A Fast and Efficient Route to 5-Chloromethyl-1,4,7,10-Tetrathiacyclotridecane and its Behavior in a Chloroform Solution

Chlorination of [14]aneS4-ol (1,4,8,11-tetrathiacyclotetradecan-6-ol) by a one pot reaction in 3 min produces quantitatively the ring-contracted product [13]aneS4-CH₂Cl (5-chloromethyl-1,4,7,10-tetrathiacyclotridecane). In a chloroform solution, [13]aneS4-CH₂Cl is slowly converted to an isomer [14]aneS4-Cl (6-chloro-1,4,8,11-tetrathiacyclotetradecane) until an equilibrium takes place. These results are discussed and a reaction mechanism involving an episulfonium ion intermediate is proposed.     

Concise Approach to 1,4-Dioxygenated Xanthones via Novel Application of the Moore Rearrangement

The rapid synthesis of 1,4-dioxygenated xanthones and related natural products employing the Moore rearrangement as a key transformation has been developed. The approach features an acetylide stitching step to unite a substituted squaric acid with a protected hydroxy benzaldehyde derivative to provide a key intermediate that undergoes facile Moore rearrangement to deliver a hydroxymethyl aryl quinone. Subsequent oxidation, hydroxy group deprotection and cyclization then affords highly functionalized xanthones. The utility of the approach was demonstrated by its application to a concise and efficient synthesis of the naturally-occurring xanthone 1. The structure of a natural product that had been named dulcisxanthone C was also corrected to that of the xanthone 1.     

Generation of cyclohexene-s-phenylepisulfonium fluoborate and its reaction with nucleophilic reagents

Conclusions It was shown that a stable intermediate of the episulfonium ion type can be generated by the reaction of cyclohexene with phenylsulfenyl fluoborate, and its reactions with nucleophilic reagents were studied.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 12, pp. 2832–2834, December, 1974.     

An ester enolate-Claisen rearrangement route to substituted 4-alkylideneprolines. studies toward a definitive structural revision of lucentamycin A

Substituted 4-alkylideneprolines represent a rare class of naturally occurring amino acids with promising biological activities. Lucentamycin A is a cytotoxic, marine-derived tripeptide that harbors a 4-ethylidine-3-methylproline (Emp) residue unique among known peptide natural products. In this paper, we examine the synthesis of Emp and related 4-alkylideneprolines employing a versatile ester enolate-Claisen rearrangement. The scope and selectivity of the key rearrangement reaction are described with a number of diversely substituted glycine ester substrates. Treatment of the allyl esters with excess NaHMDS at ambient temperature gives rise to highly substituted α-allylglycine products with good to excellent diastereoselectivities. Resolution of dipeptide diastereomers and cyclization to form the pyrrolidine rings provide rapid access to stereopure prolyl dipeptides. We have applied this strategy to the synthesis of four Emp-containing isomers of lucentamycin A in pursuit of a definitive stereochemical revision of the natural product. Our studies indicate that the Emp stereogenic centers are not the source of structural misassignment. The current strategy should find broad utility in the synthesis of additional natural product analogues and related 3-alkyl-4-alkylidene prolines.     

Regiochemical control in intramolecular cyclizations of 2,3-epoxysulfides mediated by solvent effects

The regioselectivity of cyclization in methylene-interrupted epoxydiols with a thiophenyl ether group adjacent to the epoxide can be controlled by the appropriate choice of reaction conditions. Thus, while the 5-exo mode of cyclization is observed under protic conditions with polar solvents, the intermediacy of an episulfonium ion generated in non-polar solvents lead to a regioisomeric THF product.     

Stereocontrolled Total Synthesis of (+)‐trans‐Dihydronarciclasine

A highly stereoselective and efficient total synthesis of trans‐dihydronarciclasine from a readily available chiral starting material was developed. The synthesis defines two of the five stereogenic centers of the natural product by an amino acid ester–enolate Claisen rearrangement. The other three stereogenic centers are created in a highly stereocontrolled fashion via a six‐ring vinylogous ester intermediate, which is generated from the γ,δ‐unsaturated ester functional group of the Claisen rearrangement product in an efficient three‐step sequence. This concise total synthesis exemplifies the use of a highly regioselective Friedel–Crafts‐type cyclization to form the B ring via an isocyanate intermediate derived from an N‐Boc group, which is superior to the conventional method using an imino triflate intermediate. This same N‐Boc group is employed to give high selectivity in the Claisen rearrangement earlier in the sequence.     

Addition/oxidative rearrangement of 3-furfurals and 3-furyl imines: new approaches to substituted furans and pyrroles

Furans and pyrroles are important synthons in chemical synthesis and are commonly found in natural products, pharmaceutical agents, and materials. Introduced herein are three methods to prepare 2-substituted 3-furfurals starting from 3-furfural, 3-bromofuran, and 3-vinylfurans. Addition of a variety of organolithium, Grignard, and organozinc reagents (M-R) to 3-furfural provides 3-furyl alcohols in high yields. Treatment of these intermediates with NBS initiates a novel oxidative rearrangement that results in the installation of the R group in the 2 position of the 2-substituted 3-furfurals. Likewise, metalation of 3-bromofuran with n-BuLi and addition to benzaldehyde provides a furyl alcohol that is converted to 2-phenyl 3-furfural upon oxidative rearrangement. Enantioenriched disubstituted furans can be prepared starting with the Sharpless asymmetric dihydroxylation of 3-vinylfurans. The resulting enantioenriched diols undergo the oxidative rearrangement to furnish enantioenriched 2-substituted 3-furfurals with excellent transfer of asymmetry. This later method has been applied to the enantioselective preparation of an intermediate in Honda's synthesis of the natural product (-)-canadensolide. Mechanistic studies involving deuterium-labeled furyl alcohol suggest that the oxidative rearrangement proceeds through an unsaturated 1,4-dialdehyde intermediate. The alcohol then cyclizes onto an aldehyde, resulting in the elimination of water and rearomatization. On the basis of this proposed mechanism, we found that 3-furyl imines undergo the addition of organometallic reagents to provide furyl sulfonamides. Under the oxidative rearrangement conditions, 2-substituted 3-formyl pyrroles are formed, providing a novel route to these heterocycles. In contrast to the metalation of heterocycles, which often lead to mixtures of regioisomeric products, these new oxidative rearrangements of furyl alcohols and furyl sulfonamides generate only one regioisomer in each case.     

Stereocontrolled Total Synthesis of (+)-trans-Dihydronarciclasine

A highly stereoselective and efficient total synthesis of trans-dihydronarciclasine from a readily available chiral starting material was developed. The synthesis defines two of the five stereogenic centers of the natural product by an amino acid ester-enolate Claisen rearrangement. The other three stereogenic centers are created in a highly stereocontrolled fashion via a six-ring vinylogous ester intermediate, which is generated from the γ,δ-unsaturated ester functional group of the Claisen rearrangement product in an efficient three-step sequence. This concise total synthesis exemplifies the use of a highly regioselective Friedel-Crafts-type cyclization to form the B ring via an isocyanate intermediate derived from an N-Boc group, which is superior to the conventional method using an imino triflate intermediate. This same N-Boc group is employed to give high selectivity in the Claisen rearrangement earlier in the sequence.     

The Degradation Mechanism of an Oral Cephalosporin: Cefaclor

The degradation of cefaclor ( 1 ), an oral cephalosporin antibiotic, was studied at 37° in a neutral aqueous medium by HPLC and ¹H-NMR. Under these conditions, 1 underwent intramolecular aminolysis by the 7-side-chain NH₂ group on the β-lactam moiety to give a piperazine-2,5-dione. The most prominent peak in the HPLC profile of a degradation solution from 1 was isolated by prep. HPLC. Mechanistically, the formation of this degradation product cis- 11 from 1 involves the contraction from a six-membered cephem ring to a five-membered ring, which presumably takes place via a common episulfonium ion intermediate 9 (see Scheme). Loss of the Cl-atom from 3-chloro-3-cephem is a general reaction subsequent to β-lactam ring opening.     

ELECTROPHILIC CLEAVAGE OF SULFENATE ESTERS. I. POSSIBLE BIOLOGICAL IMPLICATIONS

Abstract

Base-assisted electrophilic cleavage of sulfenate esters was studied with reference to possible biological models. It is suggested that sulfenate esters (RSOR') may serve as intermediates in oxidations involving alcohol dehydrogenases. Models for the biological oxidation of alcohols via sulfenate ester intermediates are presented. The lipoic acid catalyzed dehydrogenation step in the actions of α-ketoacid oxidases (e.g., pyruvic acid dehydrogenase and α-keto glutarate dehydrogenase) is also explained in terms of a possible sulfenate ester intermediate.

In the interaction of alcohols and amines, with membrane proteins, the possibility of reversible formation of sulfenate esters and of sulfenamide formation is suggested. Experimental support is given for the formation of carbonyl compounds, from alcohols via sulfenate esters and subsequent electrophilic attack by N-iodosuccinimide on the esters. Such reactions of sulfenyl esters open virtually unexplored areas of chemistry and of the related biological implications. Methyl fluorosulfate (‘magic methyl’) in presence of base is also effective for the cleavage reaction.