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

Abstract

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.

A short enantioselective total synthesis of (R)- and (S)-pipecolic acid

“…To a solution of the salt from above step in 3 N H 2 SO 4 (4.5 mL) at 10°C, was slowly added KMnO 4 (0.12 g, 0.744 mmol) and the reaction mixture was stirred at room temperature for 3 h, filtered through a pad of Celite and concentrated. (S)-Pipecolic acid 1 was isolated after elution on a Dowex 50 W-X4 ion-exchange column (NH 4 …”

Methods for the Chemical Synthesis of Noncoded α‐Amino Acids found in Natural Product Peptides

“…It is isolated as a secondary metabolite from some plants and fungi [75]. Also, it is found to be incorporated in pharmaceutically important natural products such as immunosuppressors FK506 [76] and rapamycin [77], oxytocin antagonist L-356209 [78], antiprotozal agent ampicidin [79], antifungal agent petriellin A [80], and antitumor antibiotic sandramycin [81]. Although pipecolic acid is available commercially, the enantiomerically pure form of it is quite expensive, which can be a problem when large quantities are needed.…”

Molecular characterization of lysine 6-dehydrogenase from Achromobacter denitrificans

“…The crystallization of the A. denitrificans enzyme will help in the establishment of the three-dimensional structure of Lys 6-DH. Recently, much attention has been paid to the asymmetric synthesis of L-pipecolate (18,19), a key component of the immunosuppressant rapamycin (20) and the antitumor agent sandramycin (21). L-Pipecolate can be derived from P-6-C (18).…”