Synthesis of key sandramycin analogs: systematic examination of the intercalation chromophore

Abstract

The preparation and examination of 2–22 constituting a systematic study of the chromophore of sandramycin ( 1) are detailed. Fluorescence quenching studies were used to establish binding constants for 1–24 within calf thymus DNA, within a single high affinity bis-intercalation binding site 5′-d(GCATGC) 2, and to establish the preference for sandramycin binding to 5′-d(GCXXGC) 2 where XX=AT, TA, GC, and CG. From the latter studies, sandramycin was found to exhibit a preference that follows the order: 5′-d(GCATGC) 2 > 5′- d(GCGCGC) 2, δδG° = 0.3 kcal/mol > 5′-d(GCTAGC) 2, 5′-d(GCCGGC) 2, δδG° = 0.6 kcal/mol although it binds with high affinity to all four deoxyoligonucleotides. The two highest affinity sequences constitute repeating 5′-PuPy motifs with each intercalation event occurring at a 5′-PyPu step. The most effective sequence constitutes the less stable duplex, contains the sterically most accessible minor groove central to the bis-intercalation site, and the ability to accept two gly-NG/T C2 carbonyl H-bonds identified in prior NMR studies. Similarly, the contribution of the individual structural features of the chromophore were assessed with the high affinity duplex sequence 5′-d(GCATGC) 2. To a first approximation, the cytotoxic properties were found to parallel trends established in the DNA binding affinities. The exception to this generalization was 4 which lacks the sandramycin chromophore phenol. Although typically 4–10 × less potent than sandramycin against leukemia cell lines, it proved to be 1–10,000 × more potent against melanomas, carcinomas, and adenocarcinomas exhibiting IC 50 values of 1 pM−10 nM placing it among the most potent agents identified to date. Additionally, the first disclosure of the HIV-1 reverse transcriptase inhibitory activity of sandramycin ( 1) as well as that of its key analogs are described and define the chromophore structural features required for their exceptional potency. Two analogs, 18 and 3, roughly maintain the HIV-1 reverse transcriptase inhibitory potency of 1 but exhibit substantially diminished cytotoxic activity (10 2–10 3x).