Total Synthesis and Complete Structural Assignment of Yaku’amide A

Coordinating activation strategy enables 1,2-alkylamidation of alkynes

The radical 1,2-difunctionalization reaction of alkynes has been evolved into a versatile approach for expeditiously increasing the complexity of the common feedstock alkyne. However, intermolecular 1,2-carboamidation with general alkyl groups is an unsolved problem. Herein, we show that a coordinating activation strategy could act as an efficient tool for enabling radical 1,2-alkylamidation of alkynes. With the employment of diacyl peroxides as both alkylating reagents and internal oxidants, a large library of β-alkylated enamides is constructed in a three-component manner from readily accessible amides and alkynes. This protocol exhibits broad substrate scope with good functional group compatibility and is amenable for late-stage functionalization of natural molecules and biologically compounds.

Total syntheses of surugamides and thioamycolamides toward understanding their biosynthesis

Peptidic natural products have received much attention as potential drug leads, and biosynthetic studies of peptidic natural products have contributed to the field of natural product chemistry over the past several decades. However, the key biosynthetic intermediates are generally not isolated from natural sources, and this can hamper a detailed analysis of biosynthesis. Furthermore, reported unusual structures, which are targets for biosynthetic studies, are sometimes the results of structural misassignments. Chemical synthesis techniques are imperative in solving these problems. This review focuses on the chemical syntheses of surugamides and thioamycolamides toward understanding their biosynthesis. These studies can provide the key biosynthetic intermediates that can reveal the biosynthetic pathways and/or true structures of these natural products.

Solid-phase total synthesis and structural confirmation of antimicrobial longicatenamide A

Longicatenamides A–D are cyclic hexapeptides isolated from the combined culture of Streptomyces sp. KUSC_F05 and Tsukamurella pulmonis TP-B0596. Because these peptides are not detected in the monoculture broth of the actinomycete, they are key tools for understanding chemical communication in the microbial world. Herein, we report the solid-phase total synthesis and structural confirmation of longicatenamide A. First, commercially unavailable building blocks were chemically synthesized with stereocontrol. Second, the peptide chain was elongated via Fmoc-based solid-phase peptide synthesis. Third, the peptide chain was cyclized in the solution phase, followed by simultaneous cleavage of all protecting groups to afford longicatenamide A. Chromatographic analysis corroborated the chemical structure of longicatenamide A. Furthermore, the antimicrobial activity of synthesized longicatenamide A was confirmed. The developed solid-phase synthesis is expected to facilitate the rapid synthesis of diverse synthetic analogues.

[Total Synthesis and Functional Analysis of Complex Peptidic Natural Products and Their Artificial Analogues]

This review focuses on a new solid-phase synthetic strategy for an anticancer natural product yaku'amide B (1) and its target identification and structure-function relationship study using synthetic analogues and probes. To realize the Fmoc-based solid-phase synthesis of 1, we developed new synthetic methods for enamide formation. Namely, modified traceless Staudinger ligation using alkenyl azides and newly designed phosphinophenol esters enabled stereoselective construction of the (E)- and (Z)-ΔIle moieties. Furthermore, resin-cleavage and C-terminus modification were simultaneously achieved with an ester-amide exchange reaction using C-terminal amine and AlMe₃, which successfully afforded 1 via a full solid-phase route. The developed strategy was applied to the construction of seven E/Z isomers of 1. In the target identification of 1, fluorescent imaging study and affinity pull-down assay using the synthetic probes revealed that 1 exerts potent cytostatic activity by binding to subunits α and β of mitochondrial F_oF₁-ATP synthase. On the basis of the mode of action of 1, we conducted biological evaluation of the seven E/Z-isomers of 1. Assessment of growth inhibition activity and the effect on F_oF₁-ATP synthase indicates that the E/Z-stereochemistry of the three ΔIle residues controls the magnitude of biological functions of 1.

Synthesis and evaluation of potent yaku'amide A analogs

Two full-length analogs of the anticancer peptide yaku'amide A (1a) and four partial structures have been synthesized. These analogs were identified by computational studies in which the three E- and Z-ΔIle residues of the natural product were replaced by the more accessible dehydroamino acids ΔVal and ΔEnv. Of the eight possible analogs, modeling showed that the targeted structures 2a and 2b most closely resembled the three-dimensional structure of 1a. Synthesis of 2a and 2b followed a convergent route that was streamlined by the absence of ΔIle in the targets. Screening of the compounds against various cancer cell lines revealed that 2a and 2b mimic the potent anticancer activity of 1a, thereby validating the computational studies.

Simplified full-length analogs of yaku'amide A were designed with the aid of computations and then synthesized. The analog that was predicted to most closely resemble the structure of the natural product mimicked its anticancer activity.

Versatile Access to Tetrasubstituted 2-Amidoacroleins through Formal Silylformylation of Ynamides

In this paper we are reporting the first regio- and stereoselective silylformylation of ynamides. This reaction is tolerant to a wide range of functional groups around the ynamides. The substitution of CO by an isocyanide makes this reaction safer and more practical than standard silylformylation reactions. It overall represents a versatile and rapid access to various tetrasubstituted 3-silyl-2-amidoacrolein derivatives. The synthetic potential of these new building blocks has been evaluated by performing several postfunctionalization.

Generation and Biological Evaluation of Degraded Derivatives of the Three E/Z-Isomers of Yaku'amide B

Potently cytostatic yaku'amide B (1) is a highly unsaturated linear tridecapeptide. During our synthetic studies of the E/Z-isomers of the α,β-dehydroisoleucines of 1, an unexpected retro-aldol reaction proceeded to transform E/Z-isomers 2, 3, and 4 into 2a, 3a, and 4a/4b, respectively. Compounds 2a, 3a, and 4a have a glycine at residue-1 instead of β-hydroxyisoleucine, and the β-hydroxyvaline at residue-8 in 4a is further replaced by glycine in 4b. Evaluation of the growth inhibition activities against MCF-7 cells revealed that 4b was approximately 10-fold weaker than the equipotent 2-4 and 2a-4a, demonstrating the biological importance of a bulky side chain at residue-8.

Highly Sensitive Determination of Amino Acids by LC-MS under Neutral Conditions

Peptide drug leads possess unusual structural features that allow them to exert their unique biological activities and ideal physicochemical properties. In particular, these peptides often have D-amino acids, and therefore the absolute configurations of the component amino acids have to be elucidated during the structural determination of newly isolated peptide drug leads. Recently, we developed the highly sensitive labeling reagents D/L-FDVDA and D/L-FDLDA for the structural determination of the component amino acids in peptides. In an LC-MS-based structural study of peptides, these reagents enabled us to detect infinitesimal amounts of amino acids derived from mild degradative analysis of the samples. Herein, we firstly report the improved LC-MS protocols for the highly sensitive analyses of amino acids. Second, two new labeling reagents were synthesized and their detection sensitivities evaluated. These studies increase our understanding of the structural basis of these highly sensitive labeling reagents, and should provide opportunities for future on-demand structural modifications of the reagents to enhance their hydrophobicity, stability, and affinity for applications to specialized HPLC columns.

Longicatenamides A-D, Two Diastereomeric Pairs of Cyclic Hexapeptides Produced by Combined-culture of Streptomyces sp. KUSC_F05 and Tsukamurella pulmonis TP-B0596

Longicatenamides A-D, two diastereomeric pairs of new cyclic hexapeptides, were isolated from the combined-culture of Streptomyces sp. KUSC_F05 and Tsukamurella pulmonis TP-B0596. Their planar structures were determined by spectroscopic analysis including extensive 2D NMR and MS analysis. The absolute configurations of their component amino acids were determined by the use of highly sensitive reagents we recently developed; the highly sensitive-advanced Marfey's method (HS-advanced Marfey's method), which led us to reduce the sample loss and prevent incorrect structural determination. Particularly, the C_β-stereochemistry of hyGlu in longicatenamides A and C was assigned without any use of C_β-Marfey's methods. Longicatenamide A exhibited weak but preferential antimicrobial activity against Bacillus subtilis.

Convergent Total Synthesis of Yaku'amide A

Total synthesis of the anticancer peptide natural product yaku'amide A is reported. Its β-tert-hydroxy amino acids were prepared by regioselective aminohydroxylation involving a chiral mesyloxycarbamate reagent. Stereospecific construction of the E- and Z-ΔIle residues was accomplished through a one-pot reaction featuring anti dehydration, azide reduction, and O→N acyl transfer. Alkene isomerization was negligible during this process. These methods enabled a highly convergent and efficient synthetic route to the natural product.

Amycolapeptins A and B, Cyclic Nonadepsipeptides Produced by Combined-culture of Amycolatopsis sp. and Tsukamurella pulmonis

Two nonapeptide natural products, amycolapeptins A (1) and B (2) with a 22-membered cyclic depsipeptide skeleton, β-hydroxytyrosine, and a highly modified side chain, which were not produced in a monoculture of the rare actinomycete Amycolatopsis sp. 26-4, were discovered in broth of its combined-culture with Tsukamurella pulmonis TP-B0596. The planar structures were elucidated by spectroscopic analyses (extensive 2D-NMR and MALDI-TOF MS/MS). The absolute configurations of component amino acids were unambiguously determined by the highly sensitive advanced Marfey's method we recently developed. Additionally, the structures of unstable/unusual moieties were corroborated by chemical synthesis and CD analysis.

Application of the highly sensitive labeling reagent to the structural confirmation of readily isomerizable peptides

Thioamycolamide A (1) is a biosynthetically unique cytotoxic cyclic microbial lipopeptide that bears a D-configured thiazoline, a thioether bridge, a fatty acid side chain, and a reduced C-terminus. It has gained attention for its unique structure, and very recently we reported the total synthesis of 1 via a biomimetic route. The NMR spectra of synthetic 1 agreed with those of natural 1. However, structural identity between peptidic natural and synthetic compounds is often difficult to confirm by comparison of NMR spectra because their NMR spectra vary depending on the conditions in the NMR tube, which often result in the structural misassignment of peptidic compounds. Especially, our total synthesis based on the putative biomimetic route potentially gives 1 as a diastereomixture at the final step. The problem is that the diastereomers of peptidic mid-sized molecules often exhibit similar properties (such as NMR spectra and bioactivities), and their separation procedures are often laborious. Herein we report the structural confirmation of synthetic 1 by the LC-MS-based chromatographic comparison with the use of our highly sensitive labeling reagent L-FDVDA; the highly sensitive-advanced Marfey's method (HS-advanced Marfey's method). This work demonstrated the utility of our highly sensitive labeling reagent for the structural determination of not only scarce natural products but also readily isomerizable synthetic compounds.

Total Synthesis and Structural Revision of Kasumigamide, and Identification of a New Analogue

Kasumigamide is an antialgal hybrid peptide-polyketide isolated from the freshwater cyanobacterium Microcystis aeruginosa (NIES-87). The biosynthetic gene cluster was identified from not only the cyanobacterium but also Candidatus "Entotheonella", associated with the Japanese marine sponge Discodermia calyx. Therefore, kasumigamide is considered to play a key role in microbial ecology, regardless of the terrestrial and marine habitats. We now report synthetic studies on this intriguing natural product that have led to a structural revision and the first total synthesis. During this study, a new analogue, deoxykasumigamide, was also isolated and structurally validated. This study confirmed the presence of the unusual pathway in the biosynthesis of a hybrid peptide-polyketide natural product.

Highly Sensitive Labeling Reagents for Scarce Natural Products

Scarce natural products that possess unique biological activities have been ideal drug leads for decades. However, their identification and structural determinations are problematic owing to sample amount limitation. Inspired by an extremely rare natural product yaku'amide B (10), highly sensitive labeling reagents that would be powerful tools for scarce natural product chemistry were designed and synthesized in this study. By fusion with the key structural motif for the structural revision of 10, the detection sensitivities of amino acid labeling reagents were drastically enhanced in LC-MS analysis. These advanced labeling reagents enabled the detection of infinitesimal amounts of amino acids and peptide hydrolysates. This sensitivity-enhancement design concept was also applicable to reagents for labeling saccharides and reactivity-guided isolation of electrophilic natural products. Details of these reagents, including their practical preparations and extended applications, are also provided.

Silver-Promoted Direct Phosphorylation of Bulky C(sp2)-H Bond to Build Fully Substituted β-Phosphonodehydroamino Acids

A general and practical cross-dehydrogenative coupling protocol between readily available trisubstituted α,β-dehydro α-amino carboxylic esters and H-phosphites is described. This C(sp²)-H phosphorylation reaction proceeds with absolute Z-selectivity promoted by silver salt in a radical relay manner. The bulky tetrasubstituted β-phosphonodehydroamino acids were obtained in grams and added new modules to the toolkit for peptide modifications.

Solid-Phase Total Synthesis of Yaku'amide B Enabled by Traceless Staudinger Ligation

We report a solid-phase strategy for total synthesis of the peptidic natural product yaku'amide B (1), which exhibits antiproliferative activity against various cancer cells. Its linear tridecapeptide sequence bears four β,β-dialkylated α,β-dehydroamino acid residues and is capped with an N-terminal acyl group (NTA) and a C-terminal amine (CTA). To realize the Fmoc-based solid-phase synthesis of this complex structure, we developed new methods for enamide formation, enamide deprotection, and C-terminal modification. First, traceless Staudinger ligation enabled enamide formation between sterically encumbered alkenyl azides and newly designed phosphinophenol esters. Second, application of Eu(OTf)₃ led to chemoselective removal of the enamide Boc groups without detaching the resin linker. Finally, resin-cleavage and C-terminus modification were simultaneously achieved with an ester-amide exchange reaction using CTA and AlMe₃ to deliver 1 in 9.1 % overall yield (24 steps from the resin).

Total synthesis of thioamycolamide A via a biomimetic route

A concise total synthesis of thioamycolamide A was accomplished as a key step of thio-Michael addition via a biomimetic route.

Insights into base-free OsO4-catalyzed aminohydroxylations employing chiral ligands

Attempts to perform the OsO4-catalyzed enantioselective base-free aminohydroxylation of β,β-disubstituted enoates are described. Low yields and racemic products were obtained in the presence of standard chiral ligands, suggesting the occurrence of a "Second Cycle" process due to slow hydrolysis of the amino alcohol product from the Os metal center. Support for this hypothesis was provided by the slightly improved enantioselectivity (60:40 er) obtained with an amino alcohol ligand. Based on density functional theory calculations, it is proposed that the lack of significant enantioselectivity is due to a low-energy (3 + 2) oxo/imido cycloaddition transition state without the chiral ligand in the Second Cycle that outcompetes protonolysis in the First Cycle.

Total synthesis of the reported structure of ceanothine D via a novel macrocyclization strategy

The first total synthesis of the reported structure of ceanothine D, a cyclopeptide alkaloid found in red root, was achieved using a highly convergent synthetic strategy. Highlights of the synthesis include the first concomitant macrocyclization and formation of the unique chiral tertiary alkyl-aryl ether bond with complete regio- and stereo-control in the presence of a sensitive Z-enamide moiety to access the strained para-cyclophane present in its structure. This synthetic strategy may be broadly applicable in the generation of other structurally similar cyclopeptide alkaloids, enabling further biological and chemical investigations.

Bulky Dehydroamino Acids Enhance Proteolytic Stability and Folding in β-Hairpin Peptides

The bulky dehydroamino acids dehydrovaline (ΔVal) and dehydroethylnorvaline (ΔEnv) can be inserted into the turn regions of β-hairpin peptides without altering their secondary structures. These residues increase proteolytic stability, with ΔVal at the (i + 1) position having the most substantial impact. Additionally, a bulky dehydroamino acid can be paired with a d-amino acid (i.e., d-Pro) to synergistically enhance resistance to proteolysis. A link between proteolytic stability and peptide structure is established by the finding that a stabilized ΔVal-containing β-hairpin is more highly folded than its Asn-containing congener.

Conformational preferences and synthesis of isomers Z and E of oxazole-dehydrophenylalanine

Dehydrophenylalanine, ΔPhe, is the most commonly studied α,β-dehydroamino acid. In nature, further modifications of the α,β-dehydroamino acids were found, for example, replacement of the C-terminal amide group by oxazole ring. The conformational properties of oxazole-dehydrophenylalanine residue (ΔPhe-Ozl), both isomers Z and E, were investigated. To determine all possible conformations, theoretical calculations were performed using Ac-(Z/E)-ΔPhe-Ozl(4-Me) model compounds at M06-2X/6-31++G(d,p) level of theory. Ac-(Z/E)-ΔPhe-Ozl-4-COOEt compounds were synthesized and the conformational preferences of each isomer, Z and E, were investigated using FTIR and NMR-NOE in solutions of increasing polarity (CHCl3 , DMSO-d6). The solid-state low-temperature structures of Ac-(Z)-ΔPhe-Ozl-4-COOEt and its intermediate analog Ac-(Z)-ΔPhe-Ozn(4-OH)-4-COOEt were also determined. In a weakly polar environment, the ΔPhe-Ozl residue has a tendency to adopt the conformation β2 with the calculated φ and ψ angles of -127° and 0° for the isomer Z and -170° and 26° for the isomer E. The increase of environment polarity favors the helical conformation α and the beta-turn like conformation β, but the conformation β2 seems to be still accessible. The (E)-ΔPhe-Ozl residue can be obtained from the isomer Z in photoisomerization reaction. However, hydroxyl-oxazoline-dehydrophenylalanine ΔPhe-Ozn(4-OH) decomposes in such conditions. Alternatively, (E)-ΔPhe-NH2 can be applied as a substrate in the Hantzsch reaction. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 283-294, 2016.

Total Syntheses of Nannocystins A and A0, Two Elongation Factor 1 Inhibitors

Asymmetric total syntheses of nannocystins A and A0 were achieved in a convergent route starting from simple materials. Nannocystin family natural products bear potent anticancer activity as elongation factor 1 inhibitors. In this synthesis, the challenging tertiary amide bond was constructed by peptide coupling between an acyl chloride and a secondary amine. A late-stage ring-closing metathesis reaction successfully rendered the macrocycle. This efficient synthetic strategy should be applicable to other nannocystins and analogues and therefore should benefit future structure-activity relationship studies.

Studies on the synthesis of peptides containing dehydrovaline and dehydroisoleucine based on copper-mediated enamide formation

The preparation of peptide fragments containing dehydrovaline and dehydroisoleucine moieties present in the antibiotic myxovalargin is reported. Peptide formation is based on a copper-mediated C–N cross-coupling protocol between an acyl amide and a peptidic vinyl iodide. The presence of a neighboring arginine in the vinyl iodide posed a challenge with respect to the choice of the protecting group and the reaction conditions. It was found that ornithine – a suitable precursor – is better suited than arginine for achieving good yields for the C–N cross-coupling reaction. The optimized conditions were utilized for the synthesis of peptides 32, 33, 39 and 40 containing a neighboring ornithine as well as for the tripeptide 44 containing dehydroisoleucine with the correct stereochemistry.

Broad Scope Aminocyclization of Enynes with Cationic JohnPhos-Gold(I) Complex as the Catalyst

A practical aminocyclization of 1,6-enynes with a wide variety of substituted anilines, including N-alkyl anilines, has been achived by using cationic [JohnPhosAu(MeCN)]SbF₆ as a general purpose catalyst. The resulting adducts can be easily converted into polycyclic compounds by palladium- and gold-catalyzed reactions.

A concise total synthesis of sespenine, a structurally unusual indole terpenoid from Streptomyces

A ten-step (the longest linear sequence) total synthesis of sespenine was accomplished.

The stereoselective construction of E- and Z-Δ-Ile from E-dehydroamino acid ester: the synthesis of the phomopsin A tripeptide side chain

The synthesis of the phomopsin A tripeptide side chain was achieved by the stereoselective construction of E-Δ-Ile and E-Δ-Asp using α-(diphenylphosphono)glycine.

The total synthesis and functional evaluation of fourteen stereoisomers of yaku'amide B. The importance of stereochemistry for hydrophobicity and cytotoxicity

Yaku'amide B is a highly unsaturated linear tridecapeptide and an extremely potent cytotoxin.

Marine natural products

This review covers the literature published in 2013 for marine natural products (MNPs), with 982 citations (644 for the period January to December 2013) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1163 for 2013), together with the relevant biological activities, source organisms and country of origin. Reviews, biosynthetic studies, first syntheses, and syntheses that lead to the revision of structures or stereochemistries, have been included.

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

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.

Chemoselective Catalytic Oxidation of 1,2-Diols to α-Hydroxy Acids Controlled by TEMPO-ClO2 Charge-Transfer Complex

Chemoselective catalytic oxidation from 1,2-diols to α-hydroxy acids in a cat. TEMPO/cat. NaOCl/NaClO2 system has been achieved. The use of a two-phase condition consisting of hydrophobic toluene and water suppresses the concomitant oxidative cleavage. A study of the mechanism suggests that the observed selectivity is derived from the precise solubility control of diols and hydroxy acids as well as the active species of TEMPO. Although the oxoammonium species TEMPO(+)Cl(-) is hydrophilic, the active species dissolves into the organic layer by the formation of the charge-transfer (CT) complex TEMPO-ClO2 under the reaction conditions.