(−)-Sandramycin: Total Synthesis and Characterization of DNA Binding Properties

Full details of the total synthesis of the potent
antitumor antibiotic (−)-sandramycin (1), a
cyclic
decadepsipeptide possessing a 2-fold axis of symmetry, is described and
constitutes the first total synthesis of a
member of the growing class of naturally occurring agents now including
the luzopeptins and quinaldopeptin. Key
strategic elements of the approach include the late stage introduction
of the heteroaromatic chromophore thereby
providing access to analogs possessing altered intercalation
capabilities, symmetrical pentadepsipeptide coupling
and 32-membered macrocyclization conducted at the single secondary
amide site in superb conversion (90%), and
a convergent assemblage of the precursor pentadepsipeptide in which the
potentially labile ester linkage was introduced
in the final key coupling reaction. This approach also provided
the cyclic decadepsipeptides 24−26 lacking
both
chromophores and was extended to provide 32 lacking one of
the two chromophores. The characterization of the
DNA-binding properties of sandramycin vs 25 and
32 is detailed. The largest share of the binding is
derived from
the cyclic decadepsipeptide (ΔG° = −6.0 kcal/mol)
and the incremental addition of each chromophore increases
the
binding approximately 3.2 and 1.0 kcal/mol, respectively. This is
consistent with the representation of sandramycin
and the luzopeptins as minor groove binding cyclic decadepsipeptides
incrementally stabilized by mono and
bisintercalation. Following the same trends, sandramycin and
luzopeptin A were found to be nearly equivalent,
exceptionally potent cytotoxic agents (6−0.02 nM), 500−1000× more
potent than the cyclic decadepsipeptide 32
possessing a single chromophore, and ≥105× more potent
than the cyclic decadepsipeptides 24 and 25
lacking both
chromophores. DNase I footprinting studies revealed that
sandramycin and luzopeptin A behave comparably and
appear to bind best to regions containing alternating A and T residues.
Binding at other and perhaps all sites is
observed at modest agent concentrations with a perceptible preference
for 5‘-AT dinucleotide sequences many of
which were preceded by a 5‘-C, i.e. 5‘-CAT. Preliminary
studies of the 1:1 complex of sandramycin with 5‘-d(GCATGC)2 revealed that it maintains the 2-fold axis of
symmetry of the components with the agent sandwiching
the central two AT base pairs and adopting a compact conformation in
which the interchromophore distance is 10.1
Å. The cyclic decadepsipeptide is positioned in the minor groove
and the adopted conformation permits a rich array
of complementary hydrophobic contacts extending over much of the
interacting surface.