Elucidation and Total Synthesis of the Correct Structures of Tridecapeptides Yaku’amides A and B. Synthesis-Driven Stereochemical Reassignment of Four Amino Acid Residues

Abstract

Yaku'amides A (1) and B (2) possess four α,β-dehydroamino acid residues in their linear tridecapeptide sequence and differ in their residue-3 (Gly for 1 and Ala for 2). The highly unsaturated peptide structure, characteristic cytotoxicity profile, and extreme scarcity from natural sources motivated us to launch synthetic studies of 1 and 2. Here, we report the total synthesis of the originally proposed structure of yaku'amide B (2a) by applying the route to 1a, which was previously established in our group. However, this accomplishment only proved that 2a and natural 2 were structurally different and prompted investigations directed toward determining the true structure of 2. Extensive Marfey's analyses of minute amounts of natural 2 and its degradation products presented us the possible stereoisomers, all of which were synthetically prepared for chromatographic comparison with the authentic fragments of 2. Based on this detective work, we proposed a corrected structure for yaku'amide B (2c), in which the orders of residues-7 and -8 and residues-11 and -12 are reversed. Finally, the total synthesis of 2c led to confirmation of its structural identity. Moreover, the revised structure of yaku'amide A (1c) was constructed by switching Ala-3 to Gly-3 and was found to be chromatographically matched with the re-isolated natural 1. The present work demonstrated the high reliability and sensitivity of the MS- and LC-based structural analyses and the indispensable role of chemical synthesis in structural elucidation of scarce natural products.

Total Synthesis of the Nonribosomal Peptide Surugamide B and Identification of a New Offloading Cyclase Family

“…[10] Finally, treatment of 11 with TFA/i-Pr 3 SiH/H 2 O(95:2.5:2.5) afforded crude 2,with minimal Ca epimerization at the C-terminal d-Leu (d.r. After ODS-HPLC purification to remove the small amount of the epimer, 2 was obtained in 34 %y ield over 18 steps.T he NMR spectra and the HPLC retention time of the synthetic 2 were identical to those of the natural 2 ( Figures S2 and S7), [11] and the absolute configurations were confirmed by Marfeys analysis ( Figure S11). After ODS-HPLC purification to remove the small amount of the epimer, 2 was obtained in 34 %y ield over 18 steps.T he NMR spectra and the HPLC retention time of the synthetic 2 were identical to those of the natural 2 ( Figures S2 and S7), [11] and the absolute configurations were confirmed by Marfeys analysis ( Figure S11).…”

“…=> 25:1, Figure S1 in the Supporting Information). After ODS-HPLC purification to remove the small amount of the epimer, 2 was obtained in 34 %y ield over 18 steps.T he NMR spectra and the HPLC retention time of the synthetic 2 were identical to those of the natural 2 ( Figures S2 and S7), [11] and the absolute configurations were confirmed by Marfeys analysis ( Figure S11). [12] Theaverage yield per step in the total synthesis was 94 %.…”

Marine natural products

“…The compounds of mixed biosynthesis was a tranche comprised of a chromene, 746 528 The proposed, unprecedented syn-cis-anti arrangement for the A/B/C ring system in the cyclic meroditerpenoid, O,C(3)-seco-9-ene-6b-taondiol 752 was based on NOESY data and supported the notion that the folding patterns of the presumed biosynthetic precursor, 2-geranylgeranyl-6methylhydroquinone, are exible during biosynthesis leading to different classes of metabolites related to the taondiol group. [528][529][530][531] The isolation and characterisation of >20 acyclic meroditerpenoids from a collection of seven Australian brown algae (and one red alga) included ve new diterpenoids (747,748,(749)(750)(751). This is an excellent example of the use of HPLC-NMR for the isolation and identication of unstable compounds (see 748 as a representative example).…”

Diastereoselective Total Synthesis and Structural Confirmation of Surugamide F

“…Furthermore, the planar structure and stereochemistries of all amino acids except for AMPA, were validated by chemical synthesis. 6,7) Specifically, peptide 1 was chemically constructed by 9-fluorenylmethyloxycarbonyl (Fmoc)-based solid-phase peptide synthesis using racemic Fmoc-AMPA (9) as a building block, to yield the diastereomers (Chart 1a), which were separated by reversedphase HPLC. The stereochemically pure peptides were chromatographically and spectroscopically compared with natural 1 by LC-MS (Chart 1b) and NMR, respectively.…”