Sequence specific recognition of DNA by tailor-made hairpin conjugates of achiral \u3cem\u3eseco\u3c/em\u3e-cyclopropaneindoline-2-benzofurancarboxamide and pyrrole-imidazole polyamides

Hairpin conjugates of achiral seco-cyclopropaneindoline-2-benzofurancarboxamide (achiral seco-CI-Bf) and three diamides (ImPy 1, PyIm 2, and PyPy 3, where Py is pyrrole, and Im is imidazole), linked by a gamma-aminobutyrate group, were synthesized. The sequence-specific covalent alkylation of the achiral CI moiety with adenine-N3 in the minor groove was ascertained by thermally induced DNA cleavage experiments. The results provide evidence that hairpin conjugates of achiral seco-CI-Bf-gamma-polyamides could be tailored to target specific DNA sequences according to a set of general rules: the achiral CI moiety selectively reacts with adenine-N3, a stacked pair of imidazole/benzofuran prefers a G/C base pair, and a pyrrole/benzofuran prefers an A/T or T/A base pair. Models for the binding of hairpin conjugates 1-3 with sequences 5\u27-TCA(888)G-3\u27, 5\u27-CAA(857)C-3\u27, and 5\u27-TTA(843)C-3\u27 are proposed

A Novel Achiral Seco-cyclopropylpyrido[e]indolone (CPyI) Analog of CC-1065 and the Duocarmycins: Synthesis, DNA Interactions, in Vivo Anticancer and Anti-parasitic Evaluation

The synthesis of an achiral seco-hydroxy-aza-CBI-TMI analog (8) of the duocarmycins is reported. Its specificity for the DNA minor groove of AT-rich sequences and covalent bonding to adenine-N3 was ascertained by a thermal cleavage assay. Compound 8 was found to be cytotoxic in the nanomolar range against murine and human cancer cells. It was further demonstrated that compound 8 was active against murine melanoma (B16-F0) grown in C57BL/6 mice. Compound 8 was also shown to inhibit the growth of the protozoan parasites Leishmania donovani, Leishmania mexicana, Trypanosoma brucei, and Plasmodium falciparum in culture

A novel achiral \u3cem\u3eseco\u3c/em\u3e-amino-cyclopropylindoline (CI) analog of CC-1065 and the duocarmycins: design, synthesis and biological studies

The design, synthesis and DNA binding properties of a novel achiral and amino-containing seco-cyclopropylindoline analog (seco-amino-CI-TMI, 1) of the duocarmycins are described. Thermal induced DNA cleavage studies on pUC18 DNA revealed compound 1 to preferentially bind in the minor groove and to covalently react with AT-rich sequences, particularly at the underlined adenine-N3 group of 5\u27-AAAAA(865)-3\u27. This sequence specificity is similar to adozelesin and CC-1065. Using a 4-day continuous exposure, compound 1 inhibited the growth of K562 human chronic myeloid leukemia cells in culture. Compound 1 has appreciable cytotoxicity (IC50 value of 1.30 microM) relative to compound 2 (0.15 microM), the corresponding racemic and hydroxy-seco-CI-TMI analog. These results indicate that the aminophenethyl chloride group present in compound 1 has similar sequence specific and cytotoxic properties to the hydroxy-containing seco-precursors of CC-1065 and the duocarmycins. Moreover, the results suggest that the chiral center present in the natural products is not absolutely necessary for biological activity. The novel aminophenethyl halide moiety is, therefore, a useful template from which to develop future achiral analogs of CC-1065 and the duocarmycins

Design, synthesis, and biological evaluation of achiral analogs of duocarmycin SA

The design, synthesis, as well as biochemical and biological evaluation of two novel achiral analogs of duocarmycin SA (DUMSA), 1 and 2, are described. Like CC-1065 and adozelesin, compounds 1 and 2 covalently reacted with adenine-N3 in AT-rich sequences and led to the formation of DNA strand breaks upon heating. The cytotoxicity of compounds 1 and 2 against human cancer cells (K562, LS174T) was determined using a MTT assay giving IC(50) values in the low nanomolar. Further cytotoxicity screening of compound 2 conducted by the NCI against a panel of 60 different human cancer cell lines indicated that it was particularly active against several solid tumor cells lines derived from the lung, colon, CNS, skin, and breast

Targeting the ICB2 Site of the Topoisomerase II Alpha Promoter with a Formamido-pyrrole-imidazole-pyrrole H-pin Polyamide

The synthesis, DNA binding characteristics and biological activity of an N-formamido pyrrole-and imidazole-containing H-pin polyamide (f-PIP H-pin, 2) designed to selectively target the ICB2 site on the topoII alpha promoter, is reported herein. Thermal denaturation, circular dichroism, isothermal titration calorimetry, surface plasmon resonance and DNase I footprinting studies demonstrated that 2 maintained the selectivity of the unlinked parent monomer f-PIP (1) and with a slight enhancement in binding affinity (K-eq = 5 x 10(5) M-1) to the cognate site (5 \u27-TACGAT-3 \u27). H-pin 2 also exhibited comparable ability to inhibit NF-Y binding to 1, as demonstrated by gel shift studies. However, in stark contrast to monomer 1, the H-pin did not affect the up-regulation of topoisomerase II alpha (topoII alpha) in cells (Western blot), suggesting that the H-pin does not enter the nucleus. This study is the first to the authors\u27 knowledge that reports such a markedly different cellular response between two compounds of almost identical binding characteristics

Cytotoxicity and sequence specificity of C- and N-terminus conjugates of N-methylpyrrole polyamides with \u3cem\u3eseco\u3c/em\u3e-cyclopropaneindoline

The cytotoxicity and covalent DNA sequence specificity of three novel conjugates of polyamides and seco-cyclopropaneindoline (or seco-CI), a minimum alkylating pharmacophore of CC-1065 are reported. Compounds 1 and 2 consist of a seco-Cl group attached to the C-terminus of either one or two N-methylpyrrole units, respectively. In compound 3, the seco-Cl group is attached to the N-terminus of a one pyrrole-containing analog of distamycin. Following a one-hour exposure of human chronic myeloid leukemia K562 cells, compounds 1 and 2 gave a similar level of cytotoxicity (IC(50) 1-2 rectangleM). Compound 3 was considerably less active (IC(50) \u3e30 rectangleM), despite the fact that it and compound 1 contain one-pyrrole unit each. Using Taq polymerase stop assay, the sequence specificity of the target compounds was determined. Like CC- 1065 and the duocarmycins, compounds 1 and 2 retained the preferential alkylation for the 5\u27-AAAA(865)A-3\u27 sequence. Compound 3 was less sequence discriminating and showed a preference for alkylation at a 5\u27-TTTTA(843)-3\u27 sequence over the 5\u27AAAA(865)A-3\u27 site

Novel diamino imidazole and pyrrole-containing polyamides: Synthesis and DNA binding studies of mono- and diamino-phenyl-ImPy*Im polyamides designed to target 5 \u27-ACGCGT-3 \u27

Pyrrole- and imidazole-containing polyamides are widely investigated as DNA sequence selective binding agents that have potential use as gene control agents. The key challenges that must be overcome to realize this goal is the development of polyamides with low molar mass so the molecules can readily diffuse into cells and concentrate in the nucleus. In addition, the molecules must have appreciable water solubility, bind DNA sequence specifically, and with high affinity. It is on this basis that the orthogonally positioned diamino/dicationic polyamide Ph-ImPy*Im 5 was designed to target the sequence 5\u27-ACGCGT-3\u27. Py* denotes the pyrrole unit that contains a N-substituted aminopropyl pendant group. The DNA binding properties of diamino polyamide 5 were determined using a number of techniques including CD, Delta T(M), DNase I footprinting, SPR and ITC studies. The effects of the second amino moiety in Py* on DNA binding affinity over its monoamino counterpart Ph-ImPylm 3 were assessed by conducting DNA binding studies of 3 in parallel with 5. The results confirmed the minor groove binding and selectivity of both polyamides for the cognate sequence 5\u27-ACGCGT-3\u27. The diamino/dicationic polyamide 5 showed enhanced binding affinity and higher solubility in aqueous media over its monoamino/monocationic counterpart Ph-ImPylm 3. The binding constant of 5, determined from SPR studies, was found to be 1.5 x 10(7) M(-1), which is similar to 3 times higher than that for its monoamino analog 3 (4.8 x 10(6) M(-1)). The affinity of 5 is now approaching that of the parent compound f-ImPyIm 1 and its diamino equivalent 4. The advantages of the design of diamino polyamide 5 over 1 and 4 are its sequence specificity and the ease of synthesis compared to the N-terminus pyrrole analog 2. (C) 2011 Elsevier Ltd. All rights reserved

Cytotoxicity and sequence specificity of C- and N-terminus conjugates of N-methylpyrrole polyamides with \u3cem\u3eseco\u3c/em\u3e-cyclopropaneindoline

The cytotoxicity and covalent DNA sequence specificity of three novel conjugates of polyamides and seco-cyclopropaneindoline (or seco-CI), a minimum alkylating pharmacophore of CC-1065 are reported. Compounds 1 and 2 consist of a seco-Cl group attached to the C-terminus of either one or two N-methylpyrrole units, respectively. In compound 3, the seco-Cl group is attached to the N-terminus of a one pyrrole-containing analog of distamycin. Following a one-hour exposure of human chronic myeloid leukemia K562 cells, compounds 1 and 2 gave a similar level of cytotoxicity (IC(50) 1-2 rectangleM). Compound 3 was considerably less active (IC(50) \u3e30 rectangleM), despite the fact that it and compound 1 contain one-pyrrole unit each. Using Taq polymerase stop assay, the sequence specificity of the target compounds was determined. Like CC- 1065 and the duocarmycins, compounds 1 and 2 retained the preferential alkylation for the 5\u27-AAAA(865)A-3\u27 sequence. Compound 3 was less sequence discriminating and showed a preference for alkylation at a 5\u27-TTTTA(843)-3\u27 sequence over the 5\u27AAAA(865)A-3\u27 site