Cyclic Depsipeptide Research Articles

Exploring the Biosynthetic Potential of Tistrella Species for Producing Didemnin Antitumor Agents.

Didemnins are a class of cyclic depsipeptides derived from sea tunicates that exhibit potent anticancer, antiviral, and immunosuppressive properties. Although certain Tistrella species can produce didemnins, their complete biosynthetic potential remains largely unexplored. In this study, we utilize feature-based molecular networking to analyze the metabolomics of Tistrella mobilis and Tistrella bauzanensis, focusing on the production of didemnin natural products. In addition to didemnin B, we identify nordidemnin B and [hysp2]didemnin B, as well as several minor didemnin analogs. Heterologous expression of the didemnin biosynthetic gene cluster in a Streptomyces host results in the production of only didemnin B and nordidemnin B in limited quantities. Isotope-labeling studies reveal that the substrate promiscuity of the adenylation domains during biosynthesis leads to the accumulation of nordidemnin B and [hysp2]didemnin B. Additionally, precursor-directed biosynthesis is applied to generate eight novel didemnin derivatives by supplementing the culture with structurally related amino acids. Furthermore, we increased the titers of nordidemnin B and [hysp2]didemnin B by supplementing the fermentation medium with l-valine and l-isoleucine, respectively. Finally, both compounds undergo side-chain oxidation to enhance their biological activity, with their anticancer properties found to be as potent as plitidepsin.

Concise and Stereospecific Total Synthesis of Arenastatin A and Its Segment B Analogs.

A novel and concise synthetic method for arenastatin A, a cytotoxic cyclic depsipeptide of marine origin, was developed in this study. The convergent assembly of the four segments, including the cross-metathesis reaction, gave a cyclization precursor, and Fmoc deprotection caused simultaneous macrocyclization. The Corey-Chaykovsky reaction using a chiral sulfur ylide afforded arenastatin A with complete stereoselectivity in the longest linear sequence of seven reaction steps from the known compound. Using this synthetic method, some analogs of segment B were prepared through a late-stage diversification strategy. The simple SN2 reaction of the thiolate toward the tosylate precursor, prepared using almost the same synthetic method as described above, provided the desired sulfide analogs.

Wajeepeptin, a Cytotoxic and Antitrypanosomal Cyclic Depsipeptide from a Marine Moorena sp. Cyanobacterium.

Here, we report wajeepeptin (1), a new cyclic depsipeptide isolated from a marine Moorena sp. cyanobacterium. The structure was elucidated by a combination of spectroscopic analyses, X-ray diffraction analysis, and degradation reactions. Wajeepeptin (1) showed moderate cytotoxicity (IC50 = 3.7 μM against HeLa cells) and potent antitrypanosomal activity (IC50 = 0.73 ± 0.14 μM against Trypanosoma brucei rhodesiense).

Backbone-Determined Antiarrhythmic Structure-Activity Relationships for a Mirror Image, Oligomeric Depsipeptide Natural Product.

Cyclic oligomeric depsipeptides (COD) are a structural class within naturally occurring compounds with a wide range of biological activity. Verticilide is a COD (24-membered ring) that was identified by its inhibition of insect ryanodine receptor (RyR). We have since found that the enantiomer of verticilide (ent-verticilide, 1) is a potent inhibitor of mammalian RyR2, a cardiac calcium channel, and therefore a potential antiarrhythmic agent. Oddly, nat-verticilide does not inhibit RyR2. To further develop ent-verticilide as an antiarrhythmic, we explored potential SAR through systematic modification of the ester's functionality to both N-H and N-Me amides. The syntheses of these ent-verticilide-inspired analogs are detailed using a monomer-based platform enabled by enantioselective catalysis. Two analogs among 23 exhibited measurable reduction of calcium sparks in a functional assay of RyR2 activity. These findings illustrate the value of natural product-inspired therapeutic development, but the less-studied approach where the non-natural enantiomeric series harbors important SAR.

Isolation and Total Synthesis of PM170453, a New Cyclic Depsipeptide Isolated from Lyngbya sp.

In our continuing search for biologically active new chemical entities from marine organisms, we have isolated a new cyclic depsipeptide, PM170453 (1), from a cyanobacterium of the genus Lyngbya sp., collected in the Indo-Pacific Ocean. Structure elucidation of the isolated compound was determined by spectroscopic methods including MS, 1H, 13C and 2D-NMR. To solve the supply problem for 1 and progress pharmaceutical development, the total synthesis of 1 that involves a total of 20 chemical steps in a convergent process was carried out. Its in vitro cytotoxic activity against four human tumor cell lines, as well as the inhibition of the interaction between the programmed cell death protein 1 PD-1 and its ligand PD-L1 were also evaluated.

Anti-cancer properties of Sansalvamide A, its derivatives, and analogs: an updated review.

As peptide-based therapies gain recognition for their potential anti-cancer activity, cyclic peptides like Sansalvamide A, a marine-derived cyclic depsipeptide, have emerged as a potential anti-cancer agent due to their potent activity against various cancer types in preclinical studies. This review offers a comprehensive overview of Sansalvamide A, including its sources, structure-activity relationship, and semi-synthetic derivatives. The review also aims to outline the mechanisms through which Sansalvamide A and its analogs exert their anti-proliferative effects and to discuss the need for enhancements in pharmacokinetic profiles for better clinical utility. An extensive literature search was conducted, focusing on studies that detailed the anti-cancer activity of Sansalvamide A, its pharmacokinetics, and mechanistic pathways. Data from both in vitro and in vivo studies were collated and analyzed. Sansalvamide A and its analogs demonstrated significant anti-cancer activity across various cancer models, mediated through Hsp 90 inhibition, Topoisomerase inhibition, and G0/G1 cell cycle arrest. However, their pharmacokinetic properties were identified as a significant limitation, requiring improvement for effective clinical translation. Despite its notable anti-cancer effects, the utility of Sansalvamide A is currently limited by its pharmacokinetic characteristics. Therefore, while Sansalvamide A exhibits promise as an anti-cancer agent, there is a compelling need for further clinical and toxicological studies and optimization of its pharmacokinetic profile to fully exploit its therapeutic potential alongside modern cancer therapies.

Computational Design of Cyclic Peptide Inhibitors of a Bacterial Membrane Lipoprotein Peptidase.

There remains a critical need for new antibiotics against multi-drug-resistant Gram-negative bacteria, a major global threat that continues to impact mortality rates. Lipoprotein signal peptidase II is an essential enzyme in the lipoprotein biosynthetic pathway of Gram-negative bacteria, making it an attractive target for antibacterial drug discovery. Although natural inhibitors of LspA have been identified, such as the cyclic depsipeptide globomycin, poor stability and production difficulties limit their use in a clinical setting. We harness computational design to generate stable de novo cyclic peptide analogues of globomycin. Only 12 peptides needed to be synthesized and tested to yield potent inhibitors, avoiding costly preparation of large libraries and screening campaigns. The most potent analogues showed comparable or better antimicrobial activity than globomycin in microdilution assays against ESKAPE-E pathogens. This work highlights computational design as a general strategy to combat antibiotic resistance.

Serratiomycins D1-D3, Antibacterial Cyclic Peptides from a Serratia sp. and Structure Revision of Serratiomycin.

Serratiomycin (1) is an antibacterial cyclic depsipeptide, first discovered from a Eubacterium culture in 1998. This compound was initially reported to contain l-Leu, l-Ser, l-allo-Thr, d-Phe, d-Ile, and hydroxydecanoic acid. In the present study, 1 and three new derivatives, serratiomycin D1-D3 (2-4), were isolated from a Serratia sp. strain isolated from the exoskeleton of a long-horned beetle. The planar structures of 1-4 were elucidated by using mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. Comparison of the NMR chemical shifts and the physicochemical data of 1 to those of previously reported serratiomycin indeed identified 1 as serratiomycin. The absolute configurations of the amino units in compounds 1-4 were determined by the advanced Marfey's method, 2,3,4,6-tetra-O-acetyl-β-d-glucopyranosyl isothiocyanate derivatization, and liquid chromatography-mass spectrometric (LC-MS) analysis. Additionally, methanolysis and the modified Mosher's method were used to determine the absolute configuration of (3R)-hydroxydecanoic acid in 1. Consequently, the revised structure of 1 was found to possess d-Leu, l-Ser, l-Thr, d-Phe, l-allo-Ile, and d-hydroxydecanoic acid. In comparison with the previously published structure of serratiomycin, l-Leu, l-allo-Thr, and d-Ile in serratiomycin were revised to d-Leu, l-Thr, and l-allo-Ile. The new members of the serratiomycin family, compounds 2 and 3, showed considerably higher antibacterial activities against Staphylococcus aureus and Salmonella enterica than compound 1.

Synthesis of a Potential Precursor (Northern Fragment) for the Cyclic Depsipeptides Vioprolides A and C

AbstractThe synthesis of a potential northern fragment for the cyclic depsipeptides vioprolide A and vioprolide C is accomplished. The prepared compound is a pentapeptide and displays the non-canonical amino acid dehydrobutyrine (Dhb) at its C-terminal end. The central position is taken by another non-canonical amino acid, (2S,4R)-4-methylazetidine carboxylic acid (Maz). A route to enantiopure N-Boc-protected Maz (N-Boc-Maz) is developed from l-pyroglutamic acid, and this building block is taken into thiopeptide formation at its C-terminal end by successively coupling serine and threonine fragments. The C-terminal threonine is dehydrated to Dhb before attaching a d-Leu-Ala dipeptide to the N-terminal site of Maz. Several intermediates are directly telescoped into the next reaction step. Starting from N-Boc-Maz, the assembly of the pentapeptide is complete in eight steps with an overall yield of 16%.

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.

Mechanistic insight into human androgen receptor-mediated endocrine disrupting potential of cyclic depsipeptide mycotoxin, beauvericin, and influencing environmental factors for its biosynthesis in Fusarium oxysporum KFCC 11363P on rice cereal

In current study, Fusarium mycotoxin, beauvericin (BEA), has endocrine disrupting potential through suppressing the exogenous androgen receptor (AR)-mediated transcriptional activation. BEA was classified as an AR antagonist, with IC30 and IC50 values indicating that it suppressed AR dimerization in the cytosol. BEA suppress the translocation of cytosolic activated ARs to the nucleus via exogenous androgens. Furthermore, we investigated the impact of environmental conditions for BEA production on rice cereal using response surface methodology. The environmental factors affecting the production of BEA, namely temperature, initial moisture content, and growth time were optimized at 20.28 °C, 42.79 % (w/w), and 17.31 days, respectively. To the best of our knowledge, this is the first report showing that BEA has endocrine disrupting potential through suppressing translocation of cytosolic ARs to nucleus, and temperature, initial moisture content, and growth time are important influencing environmental factors for its biosynthesis in Fusarium strains on cereal.

Beauvericin, produced by Fusarium oxysporum inhibits bisphenol A-induced proliferation of human breast cancer cell line by regulating ERα/p38 pathway

Beauvericin (BEA) is a cyclic depsipeptide secondary metabolite of Fusarium species. It causes chemical hazards in food products and exists in an environment containing soil and various food types. On the other hand, the purified BEA has various biological activities and is regarded as a potential candidate for pharmaceutical research. This study was performed to assess the anti-proliferation activity of BEA against human breast cancer cells by regulating the estrogen receptor-alpha (ERα)/p38 pathway. TA and BA assays verified that BEA is a completed ER antagonist. Additionally, BEA suppressed cell proliferation in the anti-proliferation assay involving ER-positive human breast cancer cells co-treated with BPA and BEA. In respect to an anti-proliferation activity, the BPA-induced phosphorylation of p38 protein was inhibited in the presence of BEA. These results suggested that BEA exerts inhibitory potentials on endocrine disrupting effect and possibly acts as a natural therapeutic material for human estrogen hormonal health.

A Semisynthesis Platform for the Efficient Production and Exploration of Didemnin-Based Drugs.

Plitidepsin (or dehydrodidemnin B), an approved anticancer drug, belongs to the didemnin family of cyclic depsipeptides, which are found in limited quantities in marine tunicate extracts. Herein, we introduce a new approach that integrates microbial and chemical synthesis to generate plitidepsin and its analogues. We screened a Tistrella strain library to identify a potent didemnin B producer, and then introduced a second copy of the didemnin biosynthetic gene cluster into its genome, resulting in a didemnin B titer of approximately 75 mg/L. Next, we developed two straightforward chemical strategies to convert didemnin B into plitidepsin, one of which involved a one-step synthetic route giving over 90 % overall yield. Furthermore, we synthesized 13 new didemnin derivatives and three didemnin probes, enabling research into structure-activity relationships and interactions between didemnin and proteins. Our study highlights the synergistic potential of biosynthesis and chemical synthesis in overcoming the challenge of producing complex natural products sustainably and at scale.

In Vitro Module Editing Of NRPS Enables Production Of Highly Potent Gq‐Signaling Inhibitor FR900359 Derived From Unculturable Plant Symbiont

AbstractHeterotrimeric G proteins are key mediators in the signaling of G protein‐coupled receptors (GPCR) that are involved in a plethora of important physiological processes and thus major targets of pharmaceutical drugs. The cyclic depsipeptides YM‐254890 and FR900359 are strong and selective inhibitors of the Gq subfamily of G proteins. FR900359 was first reported to be produced by unculturable plant symbiont, however, a culturable FR900359 producer was discovered recently by the standard strategy, screening of the producing strain from the environment. As another strategy, we introduce herein the different way to supply natural compounds of unculturable microorganism origin. We therefore embarked on constructing an artificial biosynthetic gene cluster (BGC) for FR900359 with YM‐254890 BGC as a template using “in vitro module editing” technology, first developed for the modification of type‐I PKS BGCs, to edit YM‐254890 BGC. The resulting artificial BGCs coding FR900359 were heterologously expressed in the Pseudomonas putida KT2440 host strain.

In Vitro Module Editing Of NRPS Enables Production Of Highly Potent Gq -Signaling Inhibitor FR900359 Derived From Unculturable Plant Symbiont.

Heterotrimeric G proteins are key mediators in the signaling of G protein-coupled receptors (GPCR) that are involved in a plethora of important physiological processes and thus major targets of pharmaceutical drugs. The cyclic depsipeptides YM-254890 and FR900359 are strong and selective inhibitors of the Gq subfamily of G proteins. FR900359 was first reported to be produced by unculturable plant symbiont, however, a culturable FR900359 producer was discovered recently by the standard strategy, screening of the producing strain from the environment. As another strategy, we introduce herein the different way to supply natural compounds of unculturable microorganism origin. We therefore embarked on constructing an artificial biosynthetic gene cluster (BGC) for FR900359 with YM-254890 BGC as a template using "in vitro module editing" technology, first developed for the modification of type-I PKS BGCs, to edit YM-254890 BGC. The resulting artificial BGCs coding FR900359 were heterologously expressed in the Pseudomonas putida KT2440 host strain.

Metabolites with Anti-acetylcholinesterase Activities from Marine Mesophotic Zone Halichondria Sponge-associated Fungus Chaetomium sp. NBUF152

Background: Mesophotic coral ecosystems (MCEs) are light-dependent ecosystems found from 30 to 150 m in depth that are highly diverse and relatively understudied worldwide. Methods: One new indole alkaloid, chaetoid A (1), one known analog, indigodole B (2), and one known β-carboline type alkaloid 1-acetyl-β-carboline (3), along with three known cyclic depsipeptides, turnagainolide A (4), turnagainolide B (5), arthroamide (6)—were isolated from cultures of fungus Chaetomium sp. NBUF152 is associated with a 66 m deep mesophotic zone Halichondria sponge. Their structures were determined by analysis of spectroscopic data (NMR, HRESIMS, UV, IR, optical rotation, and ECD). The in vitro bioassay results showed that compounds 1-6 exhibited moderate inhibition against acetylcholinesterase (AchE). Results: The results showed that these compounds displayed moderate anti-AchE activities with IC50 values of 25.97 μmol/L, 25.80 μmol/L, 21.07 μmol/L, 23.49 μmol/L and 21.28 μmol/L, 25.3 μmol/L. Conclusion: This work could lead to additional investigation into the potential of marine organisms in MCEs as a source for discovering natural products with interesting structures and bioactivities.

Molecular Selectivity in the Binding of Alkali Metals, Alkaline Earth Metals, First-Row Transition Metals, and Lanthanides with Cyclic Depsipeptides.

Beauvericin (BEA) and enniatins (ENN) are cyclic hexadepsipeptide mycotoxins known for their ionophoric activities across cell membranes. While their ability to selectively bind alkali ions to form binary complexes has been studied, their interaction with multivalent metal ions to form higher-order complexes remains less explored. We report the unique characteristics of the 1:2, Mn+:BEA or ENN complexes with monovalent, divalent, and trivalent metal ions. A thorough IMS-MS analysis underscores the substantial interplay among ionic radii, coordination numbers, and their impact on conformational selection within higher-order complexes that is pertinent to ion transport. Transition metals offer insights into the effects of ion radii and ligand side chains on conformational selection, while lanthanide complexes enable a direct evaluation of coordination chemistry. An intriguing finding concerning the lanthanide complexes involves an unexpected C-H bond activation, wherein water ligands may catalyze the deprotonation of the cyclic peptides.

Mebamamide C, a deoxy analogue of mebamamides in Bryopsis marine green algae and Elysia sacoglossan mollusks.

Kahalalides, originally isolated from the sacoglossan mollusk Elysia rufescens, have been found in various Elysia and Bryopsis species, with over 20 variants identified to date. These compounds are biosynthesized by Candidatus Endobryopsis kahalalidefaciens within Bryopsis species. In this study, we report the isolation and structural determination of a new cyclic depsipeptide, mebamamide C (1), from Bryopsis sp. The planar structure was determined by spectroscopic data analyses, and the absolute configurations were determined using Marfey's method and modified Mosher's method. Additionally, our study explores the chemical relationship between Bryopsis algae and Elysia mollusks. The individual chemical profiles of these marine organisms highlight a fascinating aspect of marine chemical ecology. The distinct, species-specific chemical profiles observed in Elysia species imply the possibility of a symbiotic relationship with the kahalalide-producing bacteria.

Isolation and structure determination of a new depsipeptide crocapeptin C from the myxobacterium Melittangium boletus

A new cyclic depsipeptide, crocapeptin C (1), containing 3-amino-6-hydroxy-2-piperidone (Ahp) was isolated from the methanol extract of the myxobacterium Melittangium boletus. The chemical structure of crocapeptin C (1) was determined through NMR and ESI-MS analysis. The stereochemistries of the constituent amino acids in crocapeptin C (1) were determined using the advanced Marfey’s method and ROESY spectrum data. Crocapeptin C (1) exhibited potent inhibitory activity against chymotrypsin with an IC50 value of 0.5 µM.

The backbone constitution drives passive permeability independent of side chains in depsipeptide and peptide macrocycles inspired by ent-verticilide.

The number of peptide-like scaffolds found in late-stage drug development is increasing, but a critical unanswered question in the field is whether substituents (side chains) or the backbone drive passive permeability. The backbone is scrutinized in this study. Five series of macrocyclic peptidic compounds were prepared, and their passive permeability was determined (PAMPA, Caco-2), to delineate structure-permeability relationships. Each series was based on the cell-permeable antiarrhythmic compound ent-verticilide, a cyclic oligomeric depsipeptide (COD) containing repeating ester/N-Me amide didepsipeptide monomers. One key finding is that native lipophilic ester functionality can impart a favorable level of permeability, but ester content alone is not the final determinant - the analog with highest P app was discovered by a single ester-to-N-H amide replacement. Furthermore, the relative composition of esters and N-Me amides in a series had more nuanced permeability behavior. Overall, a systematic approach to structure-permeability correlations suggests that a combinatorial-like investigation of functionality in peptidic or peptide-like compounds could better identify leads with optimal passive permeability, perhaps prior to modification of side chains.