Mechanisms of DNA damage by leinamycin

Bivalent Ni(II), Co(II) and Cu(II) complexes of [(E)-[(2-methyl-1,3-thiazol-5-yl)methylidene]amino]thiourea: synthesis, spectral characterization, DNA and in-vitro anti-bacterial studies

The present work describes the preparation of bivalent Ni(II), Co(II) and Cu(II) complexes of [(E)-[(2-methyl-1,3-thiazol-5-yl)methylidene]amino]thiourea (MTHC) by mixing in 1:2 ratio of corresponding metal salt and Schiff base ligand in ethanolic medium. The prepared ligand and its complexes are confirmed using elemental analysis, magnetic moments, FT-IR, NMR, electronic and ESR spectroscopy techniques. The spectroscopic data reveals that metal complexes are in square planar in nature. In DNA binding studies, the higher intrinsic binding constants (K_b) of Ni(II), Co(II) and Cu(II) complexes are 2.713 × 10⁶ M⁻¹, 5.529 × 10⁶ M⁻¹ and 2.950 × 10⁶ M⁻¹ respectively, evident that complexes are avid binder with DNA base pairs. The moderate anti-bacterial activity (in-vitro) against staphylococcus epidermidis, Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli bacterial culture may be due to the high electron density of ligand which prevents the charge reduction of metal ion. In the presence and absence of H₂O_2, it is notified that there is no appreciable DNA cleavage activity of Ni(II) and Co(II) complexes except Cu(II) complex which is due to aprotonation in the medium.

P450-Catalyzed Tailoring Steps in Leinamycin Biosynthesis Featuring Regio- and Stereoselective Hydroxylations and Substrate Promiscuities

Leinamycin (LNM) is a potent antitumor antibiotic produced by Streptomyces atroolivaceus S-140. Both in vivo and in vitro characterization of the LNM biosynthetic machinery have established the formation of the 18-membered macrolactam backbone and the C-3 alkyl branch; the nascent product, LNM E1, of the hybrid nonribosomal peptide synthetase (NRPS)-acyltransferase (AT)-less type I polyketide synthase (PKS); and the generation of the thiol moiety at C-3 of LNM E1. However, the tailoring steps converting LNM E1 to LNM are still unknown. Based on gene inactivation and chemical investigation of three mutant strains, we investigated the tailoring steps catalyzed by two cytochromes P450 (P450s), LnmA and LnmZ, in LNM biosynthesis. Our studies revealed that (i) LnmA and LnmZ regio- and stereoselectively hydroxylate the C-8 and C-4' positions, respectively, on the scaffold of LNM; (ii) both LnmA and LnmZ exhibit substrate promiscuity, resulting in multiple LNM analogs from several shunt pathways; and (iii) the C-8 and C-4' hydroxyl groups play important roles in the cytotoxicity of LNM analogs against different cancer cell lines, shedding light on the structure-activity relationships of the LNM scaffold and the LNM-type natural products in general. These studies set the stage for future biosynthetic pathway engineering and combinatorial biosynthesis of the LNM family of natural products for structure diversity and drug discovery.

Oxidative activation of leinamycin E1 triggers alkylation of guanine residues in double-stranded DNA

It may be useful to develop prodrugs that are selectively activated by oxidative stress in cancer cells to release cell-killing reactive intermediates. However, relatively few chemical strategies exist for the activation of prodrugs under conditions of oxidative stress. Here we provide evidence for a novel process in which oxidation of a thiol residue in the natural product leinamycin E1 by H₂O₂ and other byproducts of cellular oxidative stress initiates generation of an episulfonium ion that selectively alkylates guanine residues in duplex DNA.

Properties and reactivity of nucleic acids relevant to epigenomics, transcriptomics, and therapeutics

Developments in epigenomics, toxicology, and therapeutic nucleic acids all rely on a precise understanding of nucleic acid properties and chemical reactivity. In this review we discuss the properties and chemical reactivity of each nucleobase and attempt to provide some general principles for nucleic acid targeting or engineering. For adenine-thymine and guanine-cytosine base pairs, we review recent quantum chemical estimates of their Watson-Crick interaction energy, π-π stacking energies, as well as the nuclear quantum effects on tautomerism. Reactions that target nucleobases have been crucial in the development of new sequencing technologies and we believe further developments in nucleic acid chemistry will be required to deconstruct the enormously complex transcriptome.

Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis

Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.

A New Cross-Link for an Old Cross-Linking Drug: The Nitrogen Mustard Anticancer Agent Mechlorethamine Generates Cross-Links Derived from Abasic Sites in Addition to the Expected Drug-Bridged Cross-Links

Nitrogen mustard anticancer drugs generate highly reactive aziridinium ions that alkylate DNA. Monoadducts arising from reaction with position N7 of guanine residues are the major DNA adducts generated by these agents. Interstrand cross-links in which the drug bridges position N7 of two guanine residues are formed in low yields relative to those of the monoadducts but are generally thought to be central to medicinal activity. The N7-alkylguanine residues generated by nitrogen mustards are depurinated to yield abasic (Ap) sites in duplex DNA. Here, we show that Ap sites generated by the nitrogen mustard mechlorethamine lead to interstrand cross-links of a type not previously associated with this drug. Gel electrophoretic data were consistent with early evolution of the expected drug-bridged cross-links, followed by the appearance of Ap-derived cross-links. The evidence is further consistent with a reaction pathway involving alkylation of a guanine residue in a 5'-GT sequence, followed by depurination to generate the Ap site, and cross-link formation via reaction of the Ap aldehyde residue with the opposing adenine residue at this site [Price, N. E., Johnson, K. M., Wang, J., Fekry, M. I., Wang, Y., and Gates, K. S. (2014) J. Am. Chem. Soc. 136, 3483-3490]. The monofunctional DNA-alkylating agents 2-chloro-N,N-diethylethanamine 5, (2-chloroethyl)ethylsulfide 6, and natural product leinamycin similarly were found to induce the formation of Ap-derived cross-links in duplex DNA. This work provides the first characterization of Ap-derived cross-links at sequences in which a cytosine residue is located directly opposing the Ap site. Cross-linking processes of this type could be relevant in medicine and biology because Ap sites with directly opposing cytosine residues occur frequently in genomic DNA via spontaneous or enzymatic depurination of guanine and N7-alkylguanine residues.

Characterization of LnmO as a pathway-specific Crp/Fnr-type positive regulator for leinamycin biosynthesis in Streptomyces atroolivaceus and its application for titer improvement

The cyclic adenosine monophosphate (cAMP) receptor protein/fumarate and nitrate reductase regulatory protein (Crp/Fnr) family of transcriptional regulators are pleiotropic transcriptional regulators that control a broad range of cellular functions. Leinamycin (LNM) is a potent antitumor antibiotic produced by Streptomyces atroolivaceus S-140. We previously cloned and characterized the lnm biosynthetic gene cluster from S. atroolivaceus S-140. We here report inactivation of lnmO in S. atroolivaceus S-140 and overexpression of lnmO in the S. atroolivaceus S-140 wild-type and ∆lnmE mutant SB3033 to investigate its role in LNM biosynthesis. Bioinformatics analysis revealed LnmO as the only regulator within the lnm gene cluster, exhibiting high sequence similarity to known Crp/Fnr family regulators. The inactivation of lnmO in S. atroolivaceus S-140 completely abolished LNM production but caused no apparent morphological changes, supporting that LnmO is indispensable and specific to LNM biosynthesis. Overexpression of lnmO in S. atroolivaceus S-140 and SB3033 resulted in three- and fourfold increase in LNM and LNM E1 production, respectively, supporting that LnmO acts as a positive regulator. While all of the Crp/Fnr family regulators studied to date appeared to be pleiotropic, our results support LnmO as the first Crp/Fnr family regulator that is pathway-specific. LnmO joins the growing list of regulators that could be exploited to improve secondary metabolite production in Streptomyces. Engineered strains overproducing LNM and LNM E1 will facilitate further mechanistic studies and clinical evaluation of LNM and LNM E1 as novel anticancer drugs.

Persulfides: current knowledge and challenges in chemistry and chemical biology

Recent studies conducted in hydrogen sulfide (H2S) signaling have revealed potential importance of persulfides (RSSH) in redox biology. The inherent instability of RSSH makes these species difficult to study and sometimes controversial results are reported. In this review article we summarize known knowledge about both small molecule persulfides and protein persulfides. Their fundamental physical and chemical properties such as preparation/formation and reactivity are discussed. The biological implications of persulfides and their detection methods are also discussed.

Synthesis and evaluation of 8,4'-dideshydroxy-leinamycin revealing new insights into the structure-activity relationship of the anticancer natural product leinamycin

Leinamycin (LNM, 1) is a novel antitumor antibiotic produced by Streptomyces atroolivaceus S-140 and features an unusual 1,3-dioxo-1,2-dithiolane moiety that is spiro-fused to a thiazole-containing 18-membered lactam ring. The 1,3-dioxo-1,2-dithiolane moiety of LNM is essential for its antitumor activity via an episulfonium ion-mediated DNA alkylation upon reductive activation in the presence of cellular thiols. We recently isolated leinamycin E1 (LNM E1, 2) from an engineered strain S. atroolivaceus SB3033, which lacks the 1,3-dioxo-1,2-dithiolane moiety. Here we report the chemical synthesis of 8,4'-dideshydroxy-LNM (5) from 2 and determination of the cytotoxicity of 5 against selected cancer cell lines in comparison with 1; 5 exhibits comparable activity as 1 with the EC50 values between 8.21 and 275 nM. This work reveals new insight into the structure-activity relationship of LNM and highlights the synergy between metabolic pathway engineering and medicinal chemistry for natural product drug discovery.

C-S bond cleavage by a polyketide synthase domain

Leinamycin (LNM) is a sulfur-containing antitumor antibiotic featuring an unusual 1,3-dioxo-1,2-dithiolane moiety that is spiro-fused to a thiazole-containing 18-membered lactam ring. The 1,3-dioxo-1,2-dithiolane moiety is essential for LNM's antitumor activity, by virtue of its ability to generate an episulfonium ion intermediate capable of alkylating DNA. We have previously cloned and sequenced the lnm gene cluster from Streptomyces atroolivaceus S-140. In vivo and in vitro characterizations of the LNM biosynthetic machinery have since established that: (i) the 18-membered macrolactam backbone is synthesized by LnmP, LnmQ, LnmJ, LnmI, and LnmG, (ii) the alkyl branch at C-3 of LNM is installed by LnmK, LnmL, LnmM, and LnmF, and (iii) leinamycin E1 (LNM E1), bearing a thiol moiety at C-3, is the nascent product of the LNM hybrid nonribosomal peptide synthetase (NRPS)-acyltransferase (AT)-less type I polyketide synthase (PKS). Sulfur incorporation at C-3 of LNM E1, however, has not been addressed. Here we report that: (i) the bioinformatics analysis reveals a pyridoxal phosphate (PLP)-dependent domain, we termed cysteine lyase (SH) domain (LnmJ-SH), within PKS module-8 of LnmJ; (ii) the LnmJ-SH domain catalyzes C-S bond cleavage by using l-cysteine and l-cysteine S-modified analogs as substrates through a PLP-dependent β-elimination reaction, establishing l-cysteine as the origin of sulfur at C-3 of LNM; and (iii) the LnmJ-SH domain, sharing no sequence homology with any other enzymes catalyzing C-S bond cleavage, represents a new family of PKS domains that expands the chemistry and enzymology of PKSs and might be exploited to incorporate sulfur into polyketide natural products by PKS engineering.

Leinamycin E1 acting as an anticancer prodrug activated by reactive oxygen species

Leinamycin (LNM) is a potent antitumor antibiotic produced by Streptomyces atroolivaceus S-140, featuring an unusual 1,3-dioxo-1,2-dithiolane moiety that is spiro-fused to a thiazole-containing 18-membered lactam ring. Upon reductive activation in the presence of cellular thiols, LNM exerts its antitumor activity by an episulfonium ion-mediated DNA alkylation. Previously, we have cloned the lnm gene cluster from S. atroolivaceus S-140 and characterized the biosynthetic machinery responsible for the 18-membered lactam backbone and the alkyl branch at C3 of LNM. We now report the isolation and characterization of leinamycin E1 (LNM E1) from S. atroolivacues SB3033, a ΔlnmE mutant strain of S. atroolivaceus S-140. Complementary to the reductive activation of LNM by cellular thiols, LNM E1 can be oxidatively activated by cellular reactive oxygen species (ROS) to generate a similar episulfonium ion intermediate, thereby alkylating DNA and leading to eventual cell death. The feasibility of exploiting LNM E1 as an anticancer prodrug activated by ROS was demonstrated in two prostate cancer cell lines, LNCaP and DU-145. Because many cancer cells are under higher cellular oxidative stress with increased levels of ROS than normal cells, these findings support the idea of exploiting ROS as a means to target cancer cells and highlight LNM E1 as a novel lead for the development of anticancer prodrugs activated by ROS. The structure of LNM E1 also reveals critical new insights into LNM biosynthesis, setting the stage to investigate sulfur incorporation, as well as the tailoring steps that convert the nascent hybrid peptide-polyketide biosynthetic intermediate into LNM.

Enzyme-catalysed oxidation of 1,2-disulfides to yield chiral thiosulfinate, sulfoxide and cis-dihydrodiol metabolites

Oxidative biotransformations of 1,2-disulfides using bacterial whole cells and pure enzymes yielded an unexpectedly wide range of products including thiolactones and chiral thiosulfinate, sulfoxide, cis-diol and metabolites.

Synthesis and characterization of a small analogue of the anticancer natural product leinamycin

Leinamycin (1) is a Streptomyces-derived natural product that displays nanomolar IC(50) values against human cancer cell lines. In the work described here, we report the synthesis and characterization of a small leinamycin analogue 19 that closely resembles the 'upper-right quadrant' of the natural product, consisting of an alicyclic 1,2-dithiolan-3-one 1-oxide heterocycle connected to an alkene by a two-carbon linker. The results indicate that this small analogue contains the core set of functional groups required to enable thiol-triggered generation of both redox active polysulfides and an episulfonium ion intermediate via the complex reaction cascade first seen in the natural product leinamycin. The small leinamycin analogue 19 caused thiol-triggered oxidative DNA strand cleavage in a manner similar to the natural product, but did not alkyate duplex DNA effectively. This highlights the central role of the 18-membered macrocycle of leinamycin in driving efficient DNA alkylation by the natural product.

The macrocycle of leinamycin imparts hydrolytic stability to the thiol-sensing 1,2-dithiolan-3-one 1-oxide unit of the natural product

Reaction of cellular thiols with the 1,2-dithiolan-3-one 1-oxide moiety of leinamycin triggers the generation of DNA-damaging reactive intermediates. Studies with small, synthetic analogues of leinamycin reveal that the macrocyclic portion of the natural product imparts remarkable hydrolytic stability to the 1,2-dithiolan-3-one 1-oxide heterocycle without substantially compromising its thiol-sensing property.

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.

Harmful and beneficial effects of organic monosulfides, disulfides, and polysulfides in animals and humans

Many organic sulfides (mono-, di-, and polysulfides) are present in our environment. Simple derivatives are produced by some plants and animals, while complex sulfides are secondary metabolites of several genera of bacteria and fungi. Sulfides play an important role in the smell and taste of food, and many such compounds are used as food flavorings. Some sulfides are toxic, and there is evidence that such toxicity is caused by the ability of these substances to generate reactive oxygen species. Some sulfides, however, have been shown to protect against toxicants and carcinogens. These beneficial effects are believed to involve, at least in part, the ability of sulfides to inhibit the enzymatic activation of pro-toxicants and to increase tissue activities of enzymes that protect against electrophiles. Some sulfides also have potential as cancer chemotherapeutics. In this review, the toxic and beneficial effects of sulfides in animals are described, and the possible value of sulfides in cancer chemoprotection and cancer chemotherapy is discussed.

Thiol-activated DNA damage by α-bromo-2-cyclopentenone

Some biologically active chemicals are relatively stable in the extracellular environment but, upon entering the cell, undergo biotransformation into reactive intermediates that covalently modify DNA. The diverse chemical reactions involved in the bioactivation of DNA-damaging agents are both fundamentally interesting and of practical importance in medicinal chemistry and toxicology. The work described here examines the bioactivation of α-haloacrolyl-containing molecules. The α-haloacrolyl moiety is found in a variety of cytotoxic natural products including clionastatin B, bromovulone III, discorahabdins A, B, and C, and trichodenone C, in mutagens such as 2-bromoacrolein and 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX), and in the anticancer drug candidates brostallicin and PNU-151807. Using α-bromo-2-cyclopentenone (1) as a model compound, the activation of α-haloacrolyl-containing molecules by biological thiols was explored. The results indicate that both low molecular weight and peptide thiols readily undergo conjugate addition to 1. The resulting products are consistent with a mechanism in which initial addition of thiols to 1 is followed by intramolecular displacement of bromide to yield a DNA-alkylating episulfonium ion intermediate. The reaction of thiol-activated 1 with DNA produces labile lesions at deoxyguanosine residues. The sequence specificity and salt dependence of this process is consistent with involvement of an episulfonium ion intermediate. The alkylated guanine residue resulting from the thiol-triggered reaction of 1 with duplex DNA was characterized using mass spectrometry. The results provide new insight regarding the mechanisms by which thiols can bioactivate small molecules and offer a more complete understanding of the molecular mechanisms underlying the biological activity of cytotoxic, mutagenic, and medicinal compounds containing the α-haloacrolyl group.

Characterization of DNA damage induced by a natural product antitumor antibiotic leinamycin in human cancer cells

Leinamycin is a structurally novel Streptomyces-derived natural product that displays very potent activity against various human cancer cell lines (IC(50) values in the low nanomolar range). Previous in vitro biochemical studies have revealed that leinamycin alkylates DNA, generates apurinic (AP) sites and reactive oxygen species (ROS), and causes DNA strand breaks. However, it is not clear whether these events occur inside cells. In the present study, we have determined the endogenous amount of AP sites and DNA strand breaks in genomic DNA and the amount of oxidative stress in a human pancreatic carcinoma cell line, MiaPaCa, treated with leinamycin by utilizing the aldehyde-reactive probe assay, the comet assay, and fluorescent probes, respectively. We demonstrated that AP sites are formed rapidly following exposure to leinamycin, and the number of AP sites was increased up to seven-fold in a dose-dependent manner. However, only 25-50% of these sites remain 2 h after media containing drug molecules were aspirated and replaced with fresh media. We also observed leinamycin-induced ROS generation and a concomitant increase in apoptosis of MiaPaCa cells. Because both AP sites and ROS have the potential to generate strand breaks in cellular DNA, the comet assay was utilized to detect damage to nuclear DNA in leinamycin-treated MiaPaCa cell cultures. Both alkaline and neutral electrophoretic analysis revealed that leinamycin produces both single- and double-stranded DNA damage in drug-treated cells in a dose-dependent manner. Taken together, the results suggest that rapid conversion of leinamycin-guanine (N7) adducts into AP sites to produce DNA strand breaks, in synergy with leinamycin-derived ROS, accounts for the exceedingly potent biological activity of this natural product.

Antitumor compounds from actinomycetes: from gene clusters to new derivatives by combinatorial biosynthesis

Covering: up to October 2008. Antitumor compounds produced by actinomycetes and novel derivatives generated by combinatorial biosynthesis are reviewed (with 318 references cited.) The different structural groups for which the relevant gene clusters have been isolated and characterized are reviewed, with a description of the strategies used for the generation of the novel derivatives and the activities of these compounds against tumor cell lines.

Evidence for a Morin type intramolecular cyclization of an alkene with a phenylsulfenic acid group in neutral aqueous solution

Sulfenic acids (RSOH) are among the most common sulfur-centered reactive intermediates generated in biological systems. Given the biological occurrence of sulfenic acids, it is important to explore the reactivity of these intermediates under physiological conditions. The Morin rearrangement is a synthetic process developed for the conversion of penicillin derivatives into cephalosporins that proceeds via nucleophilic attack of an alkene on a sulfenic acid intermediate. In its classic form, the Morin reaction involves initial elimination of a sulfenic acid from a cyclic sulfoxide, followed by intramolecular cyclization of the resulting alkene and sulfenic acid groups to generate an episulfonium ion intermediate that undergoes further reaction to yield ring-expanded products. On the basis of the existing literature, it is difficult to assess whether the reaction between an alkene and a sulfenic group can occur under mild conditions because the conditions required to generate the sulfenic acid from the sulfoxide precursor in the Morin reaction typically involve high temperatures and strong acid. In the work described here, beta-sulfinylketone precursors were used to generate a "Morin type" sulfenic acid intermediate under mild conditions. This approach made it possible to demonstrate that the intramolecular cyclization of an alkene with a phenylsulfenic acid to generate an episulfonium ion intermediate can occur in neutral aqueous solution at room temperature.

Possible chemical mechanisms underlying the antitumor activity of S-deoxyleinamycin

Though less potent than the parent natural product leinamycin, S-deoxyleinamycin displays activity against human cancer cell lines that is comparable to many clinically used agents. The results reported here suggest that the 1,2-dithiolan-3-one heterocycle found in S-deoxyleinamycin reacts with thiols to generate a persulfide intermediate (RSS(-)) that could deliver biologically active polysulfides, hydrogen sulfide, and reactive oxygen species (O2*-, H(2)O(2), and HO*) to the interior of cells.

Planar Chirality due to a Polysulfur Ring in Natural Pentathiepin Cytotoxins. Implications of Planar Chirality for Enantiospecific Biosynthesis and Toxicity

A low-energy pathway for pentathiepin racemization has been found using density functional theory (DFT) calculations. 3-[1,2,3,4,5]pentathiepin-6-yl-propylamine served as a model compound for tunicate-derived pentathiepins. Pentathiepin racemization becomes a low-energy process in the presence of a thiolate ion nucleophile. It is unknown whether the biosynthetic process for pentathiepins is enantiospecific (Bentley, R. (2005) Chem. Soc. Rev. 34, 609) or whether toxicity differs between enantiomers. However, the ease of thiolate ion attack on the polysulfur ring suggests that nucleophiles may induce optical instability on the laboratory time scale. The DFT study predicts that enantiospecific behaviors such as toxicity differences between P- and M-pentathiepins would be difficult to determine experimentally. The computed results fit into a broader picture that nucleophiles assist in ring-opening and equilibration reactions of polysulfanes.

Entering the leinamycin rearrangement via 2-(trimethylsilyl)ethyl sulfoxides

Attack of cellular thiols on the antitumor natural product leinamycin is believed to generate a sulfenate intermediate that undergoes subsequent rearrangement to a DNA-alkylating episulfonium ion. Here, 2-(trimethylsilyl)ethyl sulfoxides were employed in a fluoride-triggered generation of sulfenate anions related to the putative leinamycin-sulfenate. The resulting sulfenates enter smoothly into a leinamycin-type rearrangement reaction to afford an episulfonium ion alkylating agent. The results provide evidence that the sulfenate ion is, indeed, a competent intermediate in the leinamycin rearrangement. Further, the molecules examined here may provide a foundation for the design of functional leinamycin analogues that bypass the unstable and synthetically challenging 1,2-dithiolan-3-one 1-oxide moiety found in the natural product.

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.

Domino reactions of 1,2-diimidoyl-1,2-dichloroethanes. Synthesis of 3-imino-1,2-dithia-3h-cyclopent-4-enes, 3-amino-2-thioxo-2,5H-pyrrol-5-ones, 2,3-diamino-4-thioxo-4H-thiopyrans, and 6-imino-6H-1,3-oxazines

The reaction of mono- and dilithiated ethyl thioglycolate with 1,2-diimidoyl-1,2-dichloroethanes, aza-analogues of oxalyl chloride, afforded (depending on the reaction conditions) 3-imino-1,2-dithia-3H-cyclopent-4-enes, 3-amino-2-thioxo-2,5H-pyrrol-5-ones, and 2,3-diamino-4-thioxo-4H-thiopyrans. The reaction of the dianion of ethyl hippurate with 1,2-diimidoyl-1,2-dichloroethanes afforded 6-imino-6H-1,3-oxazines.

Synthesis and Cytotoxicity of Leinamycin Antibiotic Analogues

A simple synthesis of 1,2-dithiolan-3-ones from alpha,beta-unsaturated thiophenyl esters is reported. Introduction of the biologically active 1,2-dithiolan-3-one-1-oxide moiety of leinamycin into aldehydo-d-arabinose 11, the uridine derivative 16, and the deoxythymidine 21 was established. An extended bioactive part of leinamycin carrying a carbon-carbon triple bond was also synthesized. All of these analogues of leinamycin showed cytotoxic activity against HeLa3 tumor cells. Interestingly, the lipophilic, silyl group-containing derivatives proved to be more active than the hydrophilic counterparts.

Reaction of thioketones with propiolic acids

The reaction of adamantane-2-thione with propiolic acid afforded a novel type of cycloadduct, spiro[adamantane-2,2'-6'H-[1,3]-oxathiin]-6'-one (3a), in quantitative yield. The reaction of thiobenzophenone with propiolic acid gave 2,2-diphenyl-6'H-[1,3]-oxathiin]-6'-one and 4-phenyl-3-thia-3,4-dihydronaphthoic acid in 34% and 35% yields, respectively. The reaction might proceed through a concerted process, as confirmed by kinetics. The reaction of adamantane-2-thione with 2-butynoic acid or phenylpropiolic acid gave the corresponding adducts regioselectively. Interestingly, only one isomer was obtained by the reaction of thiofenchone with propiolic acid, suggesting that the reaction proceeded diastereospecifically. Oxidation of adducts by dimethyldioxirane or m-chloroperoxybenzoic acid gave the corresponding sulfoxides and sulfones. The sulfoxides were thermally decomposed to give disulfide or another type of 1,3-oxathiin-6-one.

A scent of therapy: pharmacological implications of natural products containing redox-active sulfur atoms

A range of sulfur-containing natural products from plants, fungi, bacteria and animals have recently been investigated to determine their therapeutic potential. Preliminary in vitro and in vivo studies of compounds such as ergothioneine, ovothiols, allicin, leinamycin, varacin, lenthionine and diallyltetrasulfide have provided evidence for antioxidant, antibacterial, antimicrobial, antifungal and anticancer properties. The biological activity of these compounds is the result of specific chemical properties which converge in chemotypes such as thiols, disulfides, sulfenic and sulfinic acids,thiosulfinates, sulfoxides, sulfones and polysulfides. Redox-activity, catalysis, metal binding, enzyme inhibition and radical generation allow reactive sulfur species to interact with oxidative stressors, to affect the function of redox-sensitive cysteine proteins and to disrupt the integrity of DNA and cellular membranes. In some cases, the biological activity of sulfur-containing plant products depends on initial enzymatic activation, which allows thiosulfinates and isothiocyanates to be generated with high target selectivity. Not surprisingly, research into the biochemical and pharmacological properties of the lesser known sulfur chemotypes is rapidly gathering momentum.

DNA Damage by Fasicularin

Fasicularin is a structurally novel thiocyanate-containing alkaloid isolated from the ascidian Nephteis fasicularis. Early biological experiments suggested that this compound's cytotoxic properties may stem from its ability to damage cellular DNA. Sequence gel analysis reveals that treatment of a 5'-32P-labeled DNA duplex with fasicularin in pH 7.0 buffer causes strand cleavage selectively at guanine residues. Further experiments indicate that production of these base-labile lesions in DNA involves alkylation of guanine residues by a fasicularin-derived aziridinium ion. This work reveals fasicularin as the first natural product found to generate a DNA-alkylating aziridinium ion via a mechanism analogous to the clinically used anticancer drugs mechlorethamine, melphalan, and chlorambucil.

Generation of reactive oxygen species by a persulfide (BnSSH)

Hydropersulfides (RS(x)SH) have been implicated as important intermediates in the cell-killing action of the anticancer natural products leinamycin and varacin. It has been suggested that persulfides can mediate the conversion of molecular oxygen to reactive oxygen species (O2*-, H2O2, and HO*). Here, experiments with synthetic benzyl hydrodisulfide (BnSSH) provide direct evidence that persulfides readily decompose to produce reactive oxygen species under physiologically relevant conditions.

Substituent Effects on the Reactivity of Benzo-1,2-dithiolan-3-one 1-Oxides and Their Possible Application to the Synthesis of DNA-Targeting Drugs

The efficiency of polysulfane product generation has been investigated for n-propyl thiol reactions with ortho- and para-substituted benzo-1,2-dithiolan-3-one 1-oxides in acetonitrile-water (7:3) mixtures. The reaction is facilitated by reducing the electron density at the para position or by placing substituents bearing lone pair electrons ortho to the dithiolanone-oxide (S1) reaction center. Through-space and through-bond effects both contribute to the conversion of polysulfane products.

Sequence-selective DNA recognition: natural products and nature's lessons

Biologically active, therapeutically useful, DNA binding natural products continue to reveal new paradigms for sequence-selective recognition, to enlist beautiful mechanisms of in situ activation for DNA modification, to define new therapeutic targets, to exploit new mechanisms to achieve cellular selectivity, and to provide a rich source of new drugs. These attributes arise in compact structures of complex integrated function.

A fluorimetric assay for the spontaneous release of an N7-alkylguanine residue from duplex DNA

A fluorimetric assay for monitoring depurination of the N7-alkylguanine adduct derived from the anticancer natural product leinamycin is described. This general approach could potentially provide the foundation for a high throughput assay that detects DNA-alkylating agents or a convenient continuous fluorimetric assay for base excision repair enzymes.

Cellular response and molecular mechanism of antitumor activity by leinamycin in MiaPaCa human pancreatic cancer cells

Previous in vitro biochemical studies have revealed that the antitumor drug leinamycin causes oxidative DNA damage and DNA alkylation. However, it is still not clear whether the same mechanism(s) of action operate in cultured human tumor cells. Here, we evaluated the effects of leinamycin in the human pancreatic carcinoma cell line MiaPaCa. Leinamycin was highly toxic to MiaPaCa cells in vitro, with an IC50 value of 50 nM, and extensive DNA fragmentation was observed in leinamycin-treated MiaPaCa cells. Flow cytometric experiments showed that leinamycin was able to disrupt normal cell cycle progression, resulting in an initial arrest of the cells in S phase. With increased time or at higher concentrations of leinamycin, the population of cells in the sub-G1 phase gradually increased, indicative of apoptotic cell death due to DNA damage. Mammalian Chk2, but not Chk1 kinase, was found to be activated in MiaPaCa cells treated with leinamycin, indicating that cellular responses to leinamycin could be attributed to DNA strand break formation rather than DNA adduct formation. Like other DNA-damaging anticancer drugs, the downregulation of telomerase activity was also observed in MiaPaCa cells at cytotoxic concentrations. However, leinamycin failed to induce DNA ligase I expression in MiaPaCa cells, unlike other DNA-damaging agents, which are known to inhibit DNA replication by arresting DNA replication forks. Taken together, the results from our study indicate that the DNA strand breakage caused by the oxidative DNA-damaging property of leinamycin is directly related to the cellular responses of this drug in MiaPaCa cells over the DNA alkylation property in a dose-responsive manner.

Leinamycin Biosynthesis Revealing Unprecedented Architectural Complexity for a Hybrid Polyketide Synthase and Nonribosomal Peptide Synthetase

A 135,638 bp DNA region that encompasses the leinamycin (LNM) biosynthetic gene cluster was sequenced from Streptomyces atroolivaceus S-140. The boundaries of the lnm cluster were defined by systematic inactivation of open reading frames within the sequenced region. The lnm cluster spans 61.3 kb of DNA and consists of 27 genes encoding nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), hybrid NRPS-PKS, resistance, regulatory, and tailoring enzymes, as well as proteins of unknown function. A model for LNM biosynthesis is proposed, central to which is the LNM hybrid NRPS-PKS megasynthetase consisting of discrete (LnmQ and LnmP) and modular (LnmI) NRPS, acyltransferase-less PKS (LnmG, LnmI, and LnmJ), and PKS modules with unusual domain organization. These studies unveil an unprecedented architectural complexity for the LNM hybrid NRPS-PKS megasynthetase and set the stage to investigate the molecular basis for LNM biosynthesis.

1,2-Dithiolan-3-ones and derivatives structurally related to leinamycin. Synthesis and biological evaluation

Leinamycin, an antitumor antibiotic isolated from Streptomyces sp., shows a 1,2-dithiolan-3-one 1-oxide heterocycle that appears to be involved in the biological activity. Several derivatives related to 1,2-dithiolan-3-one 1-oxide have been prepared and their activity as antineoplastic agents have been investigated. The synthesized compounds did not display a significative antitumor or cytotoxic activity in vitro.

Covalent binding to glutathione of the DNA-alkylating antitumor agent, S23906-1

The benzoacronycine derivative, S23906-1, was characterized recently as a novel potent antitumor agent through alkylation of the N2 position of guanines in DNA. We show here that its reactivity towards DNA can be modulated by glutathione (GSH). The formation of covalent adducts between GSH and S23906-1 was evidenced by EI-MS, and the use of different GSH derivatives, amino acids and dipeptides revealed that the cysteine thiol group is absolutely required for complex formation because glutathione disulfide (GSSG) and other S-blocked derivatives failed to react covalently with S23906-1. Gel shift assays and fluorescence measurements indicated that the binding of S23906-1 to DNA and to GSH are mutually exclusive. Binding of S23906-1 to an excess of GSH prevents DNA alkylation. Additional EI-MS measurements performed with the mixed diester, S28053-1, showed that the acetate leaving group at the C1 position is the main reactive site in the drug: a reaction scheme common to GSH and guanines is presented. At the cellular level, the presence of GSH slightly reduces the cytotoxic potential of S23906-1 towards KB-3-1 epidermoid carcinoma cells. The GSH-induced threefold reduction of the cytotoxicity of S23906-1 is attributed to the reduced formation of lethal drug-DNA covalent complexes in cells. Treatment of the cells with buthionine sulfoximine, an inhibitor of GSH biosynthesis, facilitates the formation of drug-DNA adducts and promotes the cytotoxic activity. This study identifies GSH as a reactant for the antitumor drug, S23906-1, and illustrates a pathway by which GSH may modulate the cellular sensitivity to this DNA alkylating agent. The results presented here, using GSH as a biological nucleophile, fully support our initial hypothesis that DNA alkylation is the major mechanism of action of the promising anticancer drug S23906-1.

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.

The role of amine in the mechanism of pentathiepin (polysulfur) antitumor agents

A computational and experimental study is presented, which provides the first evidence that amine has an opportunity to engage in bonding with pentathiepin to promote its decomposition. The study provides mechanistic insight into the process that gives rise to pentathiepin biological activity. Primary or secondary amine will allow for an intramolecular addition to the pentathiepin ring at the nearest sulfur (S1). In contrast, tertiary amine adds reversibly to S1, because nitrogen cannot lose its positive charge by deprotonation. This precludes the amine promotion step. An energetically low-lying process is characterized, corresponding to S3-loss triggered by nucleophilic activation with a primary or secondary amine. Pentathiepin desulfurization via S3-unit transfer is supported by a trapping study with norbornene. That the amine may confer an enhanced reactivity in the natural products varacin, 1, and lissoclinotoxin A, 2, adds to the understanding of the pathway for pentathiepin activation and may provide new design concepts that have potential applications for this class of biocides.

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).

Identification and localization of the gene cluster encoding biosynthesis of the antitumor macrolactam leinamycin in Streptomyces atroolivaceus S-140

Leinamycin (LNM), produced by Streptomyces atroolivaceus, is a thiazole-containing hybrid peptide-polyketide natural product structurally characterized with an unprecedented 1,3-dioxo-1,2-dithiolane moiety that is spiro-fused to a 18-member macrolactam ring. LNM exhibits a broad spectrum of antimicrobial and antitumor activities, most significantly against tumors that are resistant to clinically important anticancer drugs, resulting from its DNA cleavage activity in the presence of a reducing agent. Using a PCR approach to clone a thiazole-forming nonribosomal peptide synthetase (NRPS) as a probe, we localized a 172-kb DNA region from S. atroolivaceus S-140 that harbors the lnm biosynthetic gene cluster. Sequence analysis of 11-kb DNA revealed three genes, lnmG, lnmH, and lnmI, and the deduced product of lnmI is characterized by domains characteristic to both NRPS and polyketide synthase (PKS). The involvement of the cloned gene cluster in LNM biosynthesis was confirmed by disrupting the lnmI gene to generate non-LNM-producing mutants and by characterizing LnmI as a hybrid NRPS-PKS megasynthetase, the NRPS module of which specifies for L-Cys and catalyzes thiazole formation. These results have now set the stage for full investigations of LNM biosynthesis and for generation of novel LNM analogs by combinatorial biosynthesis.