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. 2024 Nov 25;15(12):2225-2230.
doi: 10.1021/acsmedchemlett.4c00510. eCollection 2024 Dec 12.

Structure-Activity Relationship Study of Splicing Modulators on Hsh155/SF3B1 through Chemical Synthesis and Yeast Genetics

Jacob P Beard  1 , Sierra L Love  2   3 , John C Schmitz  4   5 , Aaron A Hoskins  2   6 , Kazunori Koide  1   5
Affiliations

Structure-Activity Relationship Study of Splicing Modulators on Hsh155/SF3B1 through Chemical Synthesis and Yeast Genetics

Jacob P Beard et al. ACS Med Chem Lett. .

Abstract

Meayamycins are synthetic analogs of the natural product FR901464 and exhibit potent anticancer activity against human cancers. They bind SF3B1 and PHF5A, components of the human spliceosome, and they alter pre-mRNA splicing. Detailed analysis of the active site led us to investigate a narrow pocket within the binding site that surrounds the α,β-unsaturated amide portion of meayamycin. We describe the synthesis and biological activity of two new analogs bearing a methyl substituent on the α or β position of the amide. With these analogs, we investigated the discrete interactions within the narrow region of SF3B1 using a human/yeast chimeric SF3B1 protein and found that the V1078 residue of SF3B1 affects compound binding at the amide moiety.

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Conflict of interest statement

The authors declare no competing financial interest.

Figures

Figure 1
Figure 1
Structures of FR901464 (natural product) and synthetic analogs.
Figure 2
Figure 2
SF3B1 binding pocket occupied by SSA (PDB: 7B9C).
Scheme 1
Scheme 1. Synthesis of 2′-Me Meayamycin D
Conditions: (a) diisobutylaluminum hydride (DIBALH), CH2Cl2, −78 °C, 2 h; then (b) 9, KOtBu, tetrahydrofuran (THF), −78 °C to rt, 20 h, 52% (E:Z = 6:94); (c) NaOH, MeOH, 0 °C to rt, 16 h, quant.; (d) 10, HATU, diisopropylethylamine, CH2Cl2, 0 °C to rt, 42 h, inseparable mixture; (e) methacrolein, nitro-Grela catalyst, 50 °C, 20 h, 39% for 2 steps; (f) Ph3PCH3Br, KOtBu, THF, 0 °C to rt, 18 h, 78%; (g) 7, nitro-Grela catalyst, dichloroethane (DCE), 50 °C, 8 h, 8%; (h) DIBALH, THF, −78 °C, 1.5 h, 68%.
Scheme 2
Scheme 2. Synthesis of 3′-Me Meayamycin D
Conditions: (i) LiOH, MeOH, H2O, 3 h, 0 °C, 84%; (j) trimethylacetyl chloride, triethylamine, CH2Cl2, 0 °C, 1.5 h; then (k) N,O-dimethylhydroxylamine hydrochloride, triethylamine, CH2Cl2, 0 °C to rt, 20 h, 83%; (l) Mg, MeI, Et2O, 0 °C, 2.5 h, 88%; (m) 20, KOtBu, THF, 0 °C to rt, 18 h, 50% (E:Z = 15:85); (n) NaOH, MeOH, 0 °C, 3.5 h, quant.; (o) 10, HATU, diisopropylamine, CH2Cl2, 0 °C to rt, 40 h, inseparable mixture; (p) methacrolein, nitro-Grela catalyst, 50 °C, 18 h, 32% for 2 steps; (q) Ph3PCH3Br, KOtBu, THF, 0 °C, 1.5 h, 82%; (r) 7, nitro-Grela catalyst, DCE, 45 °C, 14 h, 8%; (s) DIBALH, THF, −78 °C, 2 h, 79%.
Figure 3
Figure 3
Western blot analysis of HCT116 cells treated with meayamycin D (MAMD), 3′-Me MAMD, and 2′-Me MAMD.
Figure 4
Figure 4
Proximal residues to the C2’ and C3′ position in the SSA-SF3B1 crystal structure (PDB: 7B9C, residues H1091–T1122 omitted for clarity).
Figure 5
Figure 5
Growth inhibition of S. cerevisiae with chimeric Hs5–16 mutation V1078A in the presence of meayamycin D (MAMD), 2′-Me MAMD, and 3′-Me MAMD. Each point represents the average of n = 3 biological replicates, ± SD.
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