Four new alkylating N-methylpyrrole-N-methylimidazole (PI) polyamide conjugates (1-4) with seven-base-pair (bp) recognition ability were synthesized. Evaluation of their DNA-alkylating activity clearly showed accurate alkylation at match site(s). The cytotoxicities of conjugates 1-4 were determined against six human cancer cell lines, and the effect of these conjugates on the expression levels of the whole human genome in A549 cells were also investigated. A few genes among the top 20 genes were commonly downregulated by each conjugate, which reflects their sequence specificity. Conversely, many of the top 10 genes were commonly upregulated, which may have been caused by alkylation damage to DNA. Moreover, the antitumor activities of the PI polyamide conjugates 2 and 3 were investigated using nude mice transplanted with DU145 or A549. The intravenous administration of each liposomal conjugate in water yielded tumor-suppressing effects specifically toward DU145 cells and not A549 cells, which was pertinent to cytotoxicity.

Pyrrole-imidazole (PI) polyamides are small DNA-binding molecules that can recognize predetermined DNA sequences with high affinity and specificity. Hairpin PI polyamides have been studied intensively; however, cyclic PI polyamides have received less attention, mainly because of difficulties with their synthesis. Here, we describe a novel cyclization method for producing PI polyamides using cysteine and a chloroacetyl residue. The cyclization reaction is complete within 1 h and has a high conversion efficiency. The method can be used to produce long cyclic PI polyamides that can recognize 7 bp DNA sequences. A cyclic PI polyamide containing two β-alanine molecules had higher affinity and specificity than the corresponding hairpin PI polyamide, demonstrating that the cyclic PI polyamides can be used as a new type of DNA-binding molecule.

Convergent synthetic routes for N-methylpyrrole (P) and N-methylimidazole (I) seco-1-chloromethyl-5-hydroxy-1,2-dihydro-3H-benz[e]indole (CBI) conjugates with a vinyl linker were developed. New hairpin polyamide-seco-CBI conjugates, compounds 16-19, were synthesized, and their DNA sequence-specific alkylating activities were evaluated via high-resolution denaturing gel electrophoresis and high-performance liquid chromatography (HPLC) product analysis. The new synthetic route for PI conjugates with a vinyl linker consisted of the introduction of a vinylpyrrole unit (8-11) into the C terminal of a PI polyamide synthesized by (fluorenylmethoxy)carbonyl solid-phase peptide synthesis (SPPS), followed by liquid-phase coupling with seco-CBI. The yield of the conjugates was significantly improved compared with that of the method reported previously, which allows us to synthesize various substituted conjugates containing a vinyl linker. Conjugates 16-19 were designed to investigate the substituent effect of the vinyl linker, and conjugate 16S was synthesized to evaluate the reactivity between racemic and S enantiomers of the seco-CBI derivative. The results of high-resolution denaturing gel electrophoresis using 208 bp DNA fragments indicated that alkylation by compounds 16 and 17, in which the H of the vinyl linker of compound 16 was replaced with F, occurred predominantly at the A of the 5'-TTTGTCA-3' sequence at nanomolar concentrations. In clear contrast, compounds 18 and 19, which were methyl or Br derivatives of compound 16, did not exhibit any DNA alkylating activity. Moreover, HPLC product analysis using synthetic oligonucleotides demonstrated that alkylation occurred between the N3 of the adenine of the oligomer and the cyclopropane ring of 16S. Density functional calculation of substituted vinylpyrrole seco-CBI units indicated that methyl and Br substituents led to a significantly distorted geometry of the vinyl group with the pyrrole ring compared with H and F derivatives. Molecular modeling studies offered the additional information that steric hindrance reduced the DNA alkylating activity of these derivatives.

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A modular strategy for the synthesis of a variety of axially chiral dicarboxylic acids bearing 3,3′‐disilyl groups has been developed. Dehydrogenative silalactonization and subsequent Grignard addition offered a straightforward way towards axially chiral 3,3′‐disilyl dicarboxylic acids in good yields (see scheme; LiTMP=lithium 2,2,6,6‐tetramethylpiperidide).