Structure–Activity Relationship Study of Rakicidins: Overcoming Chronic Myeloid Leukemia Resistance to Imatinib with 4‑Methylester-Rakicidin A

Natural product rakicidin A induces cell death in TKI-resistant chronic myelogenous leukemia (CML) cells. Therefore, 14 rakicidin A analogues were synthesized via a highly efficient combinatorial strategy and were evaluated against CML cell lines. The conjugated diene moiety was found to be crucial for the anti-CML activity of rakicidin A, and the changes in the configuration(s) at C-2, C-3, C-14, C-15, and C-16 resulted in lower levels of anti-CML activity. The most promising compound was 4-methylester rakicidin A (<b>1a</b>). Compared with rakicidin A, <b>1a</b> exhibited 2.8-fold greater potency against the imatinib-resistant cell line K562/G⁺ and approximately 100-fold enhanced potency compared with that of imatinib. Furthermore, compound <b>1a</b> demonstrated a significantly lower resistance index against Ba/F3 cells expressing BCR-ABL^T315I than bosutinib, dasatinib, nilotinib, and ponatinib, while <b>1a</b> exhibited less effect on normal hematopoietic cells. Preliminary results indicated that <b>1a</b> down-regulated caspase-3 and PARP, which contributes to its K562 cell inhibitory activity

Total Synthesis and Determination of the Absolute Configuration of Rakicidin A

Rakicidin A is a cyclic depsipeptide that has exhibited unique growth inhibitory activity against chronic myelogenous leukemia stem cells. Furthermore, rakicidin A has five chiral centers with unknown stereochemical assignment, and thus, can be represented by one of 32 possible stereoisomers. To predict the most probable stereochemistry of rakicidin A, calculations and structural comparison with natural cyclic depsipeptides were applied. A total synthesis of the proposed structure was subsequently completed and highlighted by the creation of a sterically hindered ester bond (C1–C15) through trans-acylation from an easily established isomer (C1–C13). The analytic data of the synthetic target were consistent with that of natural rakicidin A, and then the absolute configuration of rakicidin A was assigned as 2<i>S</i>, 3<i>S</i>, 14<i>S</i>, 15<i>S</i>, 16<i>R</i>. This work suggests strategies for the determination of unknown chiral centers in other cyclic depsipeptides, such as rakicidin B, C, D, BE-43547, and vinylamycin, and facilitates the investigations of rakicidin A as an anticancer stem cell agent