Total Synthesis and Determination of the Absolute Configuration of Rakicidin A

Rakicidin J and K, two cytotoxic and antibacterial cyclic depsipeptides from the marine bacterium Micromonospora chalcea

Rakicidin J (1) and rakicidin K (2), two new cyclic depsipeptides, were isolated from culture broth of Micromonospora chalcea FIM-R150103. Their structures were elucidated by extensive analysis of NMR, HR-ESI-MS, and electronic circular dichroism (ECD) data. The two compounds showed strong cytotoxic activity against human colon carcinoma HCT-8 and human pancreatic cancer PANC-1 cells under normoxic and hypoxic conditions in the range of IC50 values from 0.024 to 0.79 μg/mL. Moreover, compounds 1 and 2 also showed moderate antibacterial activity against ten Gram-positive bacterial strains with MIC values ranging from 4 to more than 32 μg/mL. Structure-activity relationship of these two compounds with a close analogue, rakicidin B1, is also discussed.

Two new rakicidin derivatives from marine Micromonospora chalcea FIM-R160609

The establishment of structure activity relationship (SAR) for rakicidin derivatives is pretty vital to develop rakicidins as a new type of anti-cancer agents. Herein, two novel rakicidin derivatives, compounds B1-1 (1) and B1-2 (2), a cyclic depsipeptide and a chain lipopeptide, respectively, were isolated from culture broth of Micromonospora chalcea FIM-R160609, and their structures were elucidated clearly by extensive NMR and HR-ESI-MS analyses. Following, their cytotoxic activities were evaluated against HCT-8 and PANC-1 human cancer cell lines under hypoxic and normoxic conditions. Their activities were significantly decreased when compared with that of rakicidin B1. These results demonstrated that the double bond located on the position 9 and 10 of conjugated diene unit and cycle-type structure plays an important role in keeping the biological activity of rakicidins. Furthermore, the positive effect of double bond and cycle form on the anti-bacterial activities were also confirmed by testing their inhibitory activities against gram positive bacteria. This work will definitely diversify the SAR of rakicidins and provide the guidance for the design of new potent rakicidin analogues.

Dual hypoxia-responsive supramolecular complex for cancer target therapy

The prognosis with pancreatic cancer is among the poorest of any human cancer. One of the important factors is the tumor hypoxia. Targeting tumor hypoxia is considered a desirable therapeutic option. However, it has not been translated into clinical success in the treatment of pancreatic cancer. With enhanced cytotoxicities against hypoxic pancreatic cancer cells, BE-43547A2 (BE) may serve as a promising template for hypoxia target strategy. Here, based on rational modification, a BE prodrug (NMP-BE) is encapsulated into sulfonated azocalix[5]arene (SAC5A) to generate a supramolecular dual hypoxia-responsive complex NMP-BE@SAC5A. Benefited from the selective load release within cancer cells, NMP-BE@SAC5A markedly suppresses tumor growth at low dose in pancreatic cancer cells xenograft murine model without developing systemic toxicity. This research presents a strategy for the modification of covalent compounds to achieve efficient delivery within tumors, a horizon for the realization of safe and reinforced hypoxia target therapy using a simple approach.

Development of a drug discovery approach from microbes with a special focus on isolation sources and taxonomy

After the successful discoveries of numerous antibiotics from microorganisms, frequent reisolation of known compounds becomes an obstacle in further development of new drugs from natural products. Exploration of biological sources that can provide novel scaffolds is thus an urgent matter in drug lead screening. As an alternative source to the conventionally used soil microorganisms, we selected endophytic actinomycetes, marine actinomycetes, and actinomycetes in tropical areas for investigation and found an array of new bioactive compounds. Furthermore, based on the analysis of the distribution pattern of biosynthetic gene clusters in bacteria together with available genomic data, we speculated that biosynthetic gene clusters for secondary metabolites are specific to each genus. Based on this assumption, we investigated actinomycetal and marine bacterial genera from which no compounds have been reported, which led to the discovery of a variety of skeletally novel bioactive compounds. These findings suggest that consideration of environmental factor and taxonomic position is critically effective in the selection of potential strains producing structurally unique compounds.

Late-Stage Functionalization: Total Synthesis of Beauveamide A and Its Congeners and Their Anticancer Activities

Asymmetric total synthesis of cyclotetradepsipeptide beauveamide A has been achieved for the first time. A macrolactamization strategy involving two possible sites has been explored to find the most effective route for cyclization. A late-stage functionalization approach has been adopted for easy access of non-natural analogues of beauveamide A for further biological evaluation. Interestingly, the anticancer activity of one of the synthesized analogues was better than that of the parent natural product.

Divergent synthesis of biologically active L-threo-β-hydroxyaspartates from common trans-oxazolidine dicarboxylate

A divergent synthetic strategy starting from a common trans-oxazolidine dicarboxylate intermediate has been successful to produce several non-proteinogenic L-threo-β-hydroxyaspartate derivatives efficiently with high stereoselectivity. Three bioactive α-amino-β-hydroxy acids, L-threo-β-hydroxyaspartic acid, L-threo-β-hydroxyasparagine, and L-threo-β-benzyloxyaspartic acid, were synthesized in good yields (58-83%) from the common chiral intermediate, and the chemoselective peptide bond formation at the α-amino group, β-hydroxy group, or α-carboxylic acid of the common intermediate was possible to afford the corresponding dipeptide, tripeptide, or didepsipeptide intermediate in 46~77% yields (in three-to-four steps) due to the orthogonal protective groups on the chiral intermediate.

Micromonospora: A Prolific Source of Bioactive Secondary Metabolites with Therapeutic Potential

Micromonospora, one of the most important actinomycetes genera, is well-known as the treasure trove of bioactive secondary metabolites (SMs). Herein, together with an in-depth genomic analysis of the reported Micromonospora strains, all SMs from this genus are comprehensively summarized, containing structural features, bioactive properties, and mode of actions as well as their biosynthetic and chemical synthesis pathways. The perspective enables a detailed view of Micromonospora-derived SMs, which will enrich the chemical diversity of natural products and inspire new drug discovery in the pharmaceutical industry.

Total synthesis and stereochemical assignment of rakicidin F

Total synthesis of rakicidin F was accomplished in 20 linear steps (0.68% overall yield), which enabled the configural determination of its six stereogenic centers as 2R, 15R, 16R, 17S, 19S, and 21S. The macrolactonization of the rakicidin linear precursor was investigated and the unsuccessful results might be attributed to the steric hindrance near C16-OH.

Toward the synthesis of the hypoxia selective anticancer agent BE-43547 A2

A short and enantioselective synthesis of the 19-epi-BE-43547 A2 chiral framework has been achieved in a high yield. The challenging key C15 tertiary stereocenter was derived from D-glucose. The synthetic strategy involves a Julia-Kocienski olefination to install the lipophilic side chain. An efficient protocol for Z to E isomerization of olefin was developed using a novel UV flow reactor. In addition, an unprecedented oxygen mediated hydroboration and the Krapcho decarboxylation of β-keto lactone were observed.

Total Synthesis and Determination of the Absolute Configuration of Rakicidin C

The absolute configuration of rakicidin C was predicted by comparison of optical rotation data and absolute configuration of APD-cyclic depsipeptides and further determined by total synthesis. The absolute configuration of five chiral centers was determined as 2R, 15R, 16R, 17S, and 19S. Our efficient route involves 19 longest linear steps with an overall yield of 1.49%.

Total Synthesis and Structure Revision of Boholamide A

The 15-membered cyclic depsipeptide boholamide A and an epimer were prepared by total synthesis for the first time, thus leading to a revision of C6 stereochemistry in the originally proposed structure of natural boholamide A. This convergent route features achievement of a macro-lactamization step in a gram scale. The revised boholamide A was sythesized with 16 linear steps in 5.46% overall yield. This work facilitates the investigations of boholamide A as a potential hypoxia-selective anticancer agent.

Total Synthesis of Natural Products Containing Enamine or Enol Ether Derivatives

Enamine and enol ethers are nucleophilic functional groups that are well known to most chemists. When enamine or enol ethers are present in natural products, they are nearly exclusively found as derivatives having a direct connection to electron-withdrawing groups for stabilization, and the resulting larger entities, such as enamides or enol acylates, can be further extended or modified in the framework of natural products. The restricted conformational space that is associated with even simple enamine and enol ether derivatives can be a strong determinant of the overall molecular structure, and the more polarized derivatives can endow some natural products with electrophilic properties and thus facilitate covalent interactions with biological targets.In this Account, I describe our efforts (published since 2016) to prepare natural products from several different classes that all feature enamine or enol ether derivatives as key functionalities. Our choice of targets has been guided by a desire to illuminate unknown biological mechanisms associated with the compounds or, alternatively, to improve upon known biological activities that appear to be promising from a biomedical perspective. In the present text, however, the exclusive focus will be on the syntheses.First, I will discuss the basic properties of the functional groups and briefly present a small collection of illustrative and inspirational examples from the literature for their construction in different complex settings. Next, I will provide an overview of our work on the macrocyclic APD-CLD natural products, rakicidin A and BE-43547A₁, involving the development of an efficient macrocyclization strategy and the development of methods to construct the hallmark APD group: a modified enamide. The synthesis of the meroterpenoid strongylophorine-26 is discussed next, where we developed an oxidative quinone methoxylation to build a vinylogous ester group in the final step of the synthesis and employed FeCl₃-mediated cascade reactions for the rapid assembly of the overall scaffold to enable a short semisynthesis from isocupressic acid. An efficient core scaffold assembly was also in focus in our synthesis of the alkaloid streptazone A with the signature enaminone system being assembled through a rhodium-catalyzed Pauson-Khand reaction. Sequential, site-selective redox manipulations were developed to arrive at strepatzone A and additional members of the natural product family. Finally, I discuss our work to prepare analogs of complex polyether ionophores featuring functionalized tetronic acids as cation-binding groups. A method for the construction of a suitably protected chloromethylidene-modified tetronate is presented which enabled its installation in the full structure through a C-acylation reaction. This work exemplifies how components of abundant polyether ionophores can be recycled and used to access new structures which may possess enhanced biological activities.

The genus Micromonospora as a model microorganism for bioactive natural product discovery

This review covers the development of the genus Micromonospora as a model for natural product research and the timeline of discovery progress from the classical bioassay-guided approaches through the application of genome mining and genetic engineering techniques that target specific products. It focuses on the reported chemical structures along with their biological activities and the synthetic and biosynthetic studies they have inspired. This survey summarizes the extraordinary biosynthetic diversity that can emerge from a widely distributed actinomycete genus and supports future efforts to explore under-explored species in the search for novel natural products.

Boholamide A, an APD-Class, Hypoxia-Selective Cyclodepsipeptide

Calcium homeostasis is implicated in some cancers, leading to the possibility that selective control of calcium might lead to new cancer drugs. On the basis of this idea, we designed an assay using a glioblastoma cell line and screened a collection of 1000 unique bacterial extracts. Isolation of the active compound from a hit extract led to the identification of boholamide A (1), a 4-amido-2,4-pentadieneoate (APD)-class peptide. Boholamide A (1) applied in the nanomolar range induces an immediate influx of Ca²⁺ in glioblastoma and neuronal cells. APD-class natural products are hypoxia-selective cytotoxins that primarily target mitochondria. Like other APD-containing compounds, 1 is hypoxia selective. Since APD natural products have received significant interest as potential chemotherapeutic agents, 1 provides a novel APD scaffold for the development of new anticancer compounds.

Dehydration reactions in polyfunctional natural products

Here, we review methods for chemical dehydration of alcohols to alkenes and discuss the potential of late-stage functionalization by direct, site- and chemo-selective dehydration of complex molecular substrates.

Comparative Genomic Insights into Secondary Metabolism Biosynthetic Gene Cluster Distributions of Marine Streptomyces

Bacterial secondary metabolites have huge application potential in multiple industries. Biosynthesis of bacterial secondary metabolites are commonly encoded in a set of genes that are organized in the secondary metabolism biosynthetic gene clusters (SMBGCs). The development of genome sequencing technology facilitates mining bacterial SMBGCs. Marine Streptomyces is a valuable resource of bacterial secondary metabolites. In this study, 87 marine Streptomyces genomes were obtained and carried out into comparative genomic analysis, which revealed their high genetic diversity due to pan-genomes owning 123,302 orthologous clusters. Phylogenomic analysis indicated that the majority of Marine Streptomyces were classified into three clades named Clade I, II, and III, containing 23, 38, and 22 strains, respectively. Genomic annotations revealed that SMBGCs in the genomes of marine Streptomyces ranged from 16 to 84. Statistical analysis pointed out that phylotypes and ecotypes were both associated with SMBGCs distribution patterns. The Clade I and marine sediment-derived Streptomyces harbored more specific SMBGCs, which consisted of several common ones; whereas the Clade II and marine invertebrate-derived Streptomyces have more SMBGCs, acting as more plentiful resources for mining secondary metabolites. This study is beneficial for broadening our knowledge about SMBGC distribution patterns in marine Streptomyces and developing their secondary metabolites in the future.

Structural Simplification of Natural Products

Natural products (NPs) are important sources of clinical drugs due to their structural diversity and biological prevalidation. However, the structural complexity of NPs leads to synthetic difficulties, unfavorable pharmacokinetic profiles, and poor drug-likeness. Structural simplification by truncating unnecessary substructures is a powerful strategy for overcoming these limitations and improving the efficiency and success rate of NP-based drug development. Herein, we will provide a comprehensive review of the structural simplification of NPs with a focus on design strategies, case studies, and new technologies. In particular, a number of successful examples leading to marketed drugs or drug candidates will be discussed in detail to illustrate how structural simplification is applied in lead optimization of NPs.

Syntheses and anti-pancreatic cancer activities of rakicidin A analogues

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignant tumor and resistant to most therapies. Pancreatic cancer stem cells (PCSCs) had critical role in regulating PDAC progression, metastasis, and drug resistance. Therefore, targeting PCSCs is considered to be a promising strategy for treatment of PDAC. However, there is no effective drug that can selectively ablate PCSCs. A series of twenty rakicidin A analogues were synthesized via a combinatorial strategy and evaluated for their anti-PDAC activities, and the structure-activity relationship was also discussed. Compound 32g was prepared in 14 linear steps with 5.05% overall yield, which is much more efficient than our previously reported total synthesis of rakicidin A (19 linear steps with 0.19% yield). In a highly metastatic pancreatic cancer cell line ASPC-1, compound 32g showed about 4 times higher potency (IC₅₀ = 0.022 μM) than rakicidin A (IC₅₀ = 0.082 μM) at hypoxia condition, and 12 folds of hypoxia selectivity (IC₅₀ = 0.27 μM at nomoxia condition). In contrast, the activity of adriamycin in the same hypoxic condition decreased. The percentage of PCSCs (with CD24⁺CD44⁺ESA⁺ biomarker), activity of ALDH, and the number of tumorspheres in PANC-1 cells were greatly reduced after treatment of 32g. More importantly, the tumor-initiating frequency was reduced by 19 folds after the treatment of 32g, which is better than that of rakicidin A (reduction of 4.7 folds).

Determination of the Absolute Configurations of Microtermolides A and B

Absolute configurations of the three consecutive chiral centers in the cyclic depsipeptide microtermolide A have been tentatively assigned as 2‴R, 3‴R, and 4‴R. However, on the basis of a structural comparison with vinylamycin, another depsipeptide with a unique 4-amino-2,4-pentadienolate structure, the chiral centers could also be assigned as 2‴R, 3‴R, and 4‴S. Here, the first total synthesis of microtermolide A is reported and the configurations of the three consecutive chiral centers were confirmed to be 2‴R, 3‴R, and 4‴S. A similar approach was used to determine the analogous centers in microtermolide B as 2‴R, 3‴R, and 4‴S.

The amido-pentadienoate-functionality of the rakicidins is a thiol reactive electrophile – development of a general synthetic strategy

An Npys-mediated elimination method allows facile construction of the trademark functionality of the rakicidins – a new class of biologically-relevant Michael-acceptors.