Structural Basis of Splicing Modulation by Antitumor Macrolide Compounds

Abstract

SF3B is a multi-protein complex essential for branch site (BS) recognition and selection during pre-mRNA splicing. Several splicing modulators with antitumor activity bind SF3B and thereby modulate splicing. Here we report the crystal structure of a human SF3B core in complex with pladienolide B (PB), a macrocyclic splicing modulator and potent inhibitor of tumor cell proliferation. PB stalls SF3B in an open conformation by acting like a wedge within a hinge, modulating SF3B's transition to the closed conformation needed to form the BS adenosine-binding pocket and stably accommodate the BS/U2 duplex. This work explains the structural basis for the splicing modulation activity of PB and related compounds, and reveals key interactions between SF3B and a common pharmacophore, providing a framework for future structure-based drug design.

Human co-transcriptional splicing kinetics and coordination revealed by direct nascent RNA sequencing

“…To explore this issue, we investigated the impact of the small molecule pladienolide B (PlaB), which competitively binds to SF3B1 (Cretu et al, 2018;Kotake et al, 2007). Consistent with previous studies of SF3B1 inhibitors, RT-PCR analysis revealed that PlaB treatment caused no detectable changes in splice isoforms of cytosolic transcripts ( Figure 3A).…”

Mutations in spliceosome genes and therapeutic opportunities in myeloid malignancies

“…This was validated in a more recent study that identified a series of acquired mutations in SF3B1 (K1071 and V1078) in addition to R1074H, and in PHF5A Y36C that also conferred resistance to pladienolides . The crystal structure of pladienolide B bound to the human SF3B complex was recently solved and confirmed that, in addition to SF3B1, pladienolide B also interacts with PHF5A, a PHD‐finger‐like domain containing member of the SF3B complex . Structural analysis showed that pladienolide B fits into a hinge area that prevents the transition to a closed confirmation and precludes recognition of the branchpoint adenosine.…”

“…116 The crystal structure of pladienolide B bound to the human SF3B complex was recently solved and confirmed that, in addition to SF3B1, pladienolide B also interacts with PHF5A, a PHDfinger-like domain containing member of the SF3B complex. 117 Structural analysis showed that pladienolide B fits into a hinge area that prevents the transition to a closed confirmation and precludes recognition of the branchpoint adenosine. This work is consistent with previous RNA sequencing data that showed intron retention as the major splicing alteration upon exposure to small molecule spliceosome inhibitors.…”

The SF3b complex: splicing and beyond

“…The BS-A pocket likely accommodates other inhibitors that target SF3b1. For instance, pladienolide B, another SF3b1 inhibitor with a distinct structure, was also found to occupy this pocket [53]. These splicing modulators, therefore, inhibit splicing by interfering with the formation of the U2/BPS duplex and blocking the correct BS-A configuration in the spliceosome [54,55].…”