Natural Product Bis-Intercalator Depsipeptides as a New Class of Payloads for Antibody-Drug Conjugates.

A potent class of DNA-damaging agents, natural product bis-intercalator depsipeptides (NPBIDs), was evaluated as ultrapotent payloads for use in antibody-drug conjugates (ADCs). Detailed investigation of potency (both in cells and via biophysical characterization of DNA binding), chemical tractability, and in vitro and in vivo stability of the compounds in this class eliminated a number of potential candidates, greatly reducing the complexity and resources required for conjugate preparation and evaluation. This effort yielded a potent, stable, and efficacious ADC, PF-06888667, consisting of the bis-intercalator, SW-163D, conjugated via an N-acetyl-lysine-valine-citrulline- p-aminobenzyl alcohol- N, N-dimethylethylenediamine (AcLysValCit-PABC-DMAE) linker to an engineered variant of the anti-Her2 mAb, trastuzumab, catalyzed by transglutaminase.

Incorporation of [H]-(1R,2R)- and [H]-(1S,2R)-glycerols into the antibiotic nucleocidin in Streptomyces calvus.

Deuterium incorporations from [H]-(1R,2R) and [H]-(1S,2R) glycerols into the fluorine containing antibiotic nucleocidin, in Streptomyces calvus indicate that one deuterium atom is incorporated at the C-5' site of nucleocidin from each of these isotopomers of glycerol. Two deuteriums become incorporated at C-5' of nucleocidin after a feeding experiment with [H]-glycerol. These observations indicate that there is no obligate oxidation of the pro-R hydroxymethyl group of glycerol as it progresses through the pentose phosphate pathway and becomes incorporated into the fluorinated antibiotic.

Fluorometabolite biosynthesis: isotopically labelled glycerol incorporations into the antibiotic nucleocidin in Streptomyces calvus.

Deuterium and carbon-13 labelled glycerols have been fed to Streptomyces calvus fermentations and isotope incorporation into the fluorine containing antibiotic nucleocidin have been evaluated by F-NMR. A single deuterium atom was incorporated from [H]- and (R)-[H]-glycerol into C-5' of the antibiotic, suggesting that an oxidation occurs at this carbon after ribose ring assembly from glycerol (pentose phosphate pathway), during nucleocidin biosynthesis.

Isolation of pyrrolocins A-C: cis- and trans-decalin tetramic acid antibiotics from an endophytic fungal-derived pathway.

Three new decalin-type tetramic acid analogues, pyrrolocins A (1), B (2), and C (3), were defined as products of a metabolic pathway from a fern endophyte, NRRL 50135, from Papua New Guinea. NRRL 50135 initially produced 1 but ceased its production before chemical or biological evaluation could be completed. Upon transfer of the biosynthetic pathway to a model host, 1-3 were produced.

Native promoter strategy for high-yielding synthesis and engineering of fungal secondary metabolites.

Strategies are needed for the robust production of cryptic, silenced, or engineered secondary metabolites in fungi. The filamentous fungus Fusarium heterosporum natively synthesizes the polyketide equisetin at >2 g L(-1) in a controllable manner. We hypothesized that this production level was achieved by regulatory elements in the equisetin pathway, leading to the prediction that the same regulatory elements would be useful in producing other secondary metabolites.

Cytotoxic Spliceostatins from Burkholderia sp. and Their Semisynthetic Analogues.

The spliceostatin class of natural products was reported to be potent cytotoxic agents via inhibition of the spliceosome, a key protein complex in the biosynthesis of mature mRNA. As part of an effort to discover novel leads for cancer chemotherapy, we re-examined this class of compounds from several angles, including fermentation of the producing strains, isolation and structure determination of new analogues, and semisynthetic modification. Accordingly, a group of spliceostatins were isolated from a culture broth of Burkholderia sp.

Spliceostatin hemiketal biosynthesis in Burkholderia spp. is catalyzed by an iron/α-ketoglutarate-dependent dioxygenase.

Spliceostatins are potent spliceosome inhibitors biosynthesized by a hybrid nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS) system of the trans-acyl transferase (AT) type. Burkholderia sp. FERM BP-3421 produces hemiketal spliceostatins, such as FR901464, as well as analogs containing a terminal carboxylic acid.

Discovery of the lomaiviticin biosynthetic gene cluster in .

The lomaiviticins are a family of cytotoxic marine natural products that have captured the attention of both synthetic and biological chemists due to their intricate molecular scaffolds and potent biological activities. Here we describe the identification of the gene cluster responsible for lomaiviticin biosynthesis in strains DPJ-0016 and DPJ-0019 using a combination of molecular approaches and genome sequencing. The link between the gene cluster and lomaiviticin production was confirmed using bacterial genetics, and subsequent analysis and annotation of this cluster revealed the biosynthetic basis for the core polyketide scaffold.

Isolation of lomaiviticins C-E, transformation of lomaiviticin C to lomaiviticin A, complete structure elucidation of lomaiviticin A, and structure-activity analyses.

We describe the isolation of (-)-lomaiviticins C-E (6-8), elucidation of the complete absolute and relative stereochemistry of (-)-lomaiviticin A (1), the synthetic conversion of (-)-lomaiviticin C (6) to (-)-lomaiviticin A (1), and the first evidence that the dimeric diazofluorene of (-)-lomaiviticin A (1) plays a defining and critical role in antiproliferative activity.

Discovery and assembly-line biosynthesis of the lymphostin pyrroloquinoline alkaloid family of mTOR inhibitors in Salinispora bacteria.

The pyrroloquinoline alkaloid family of natural products, which includes the immunosuppressant lymphostin, has long been postulated to arise from tryptophan. We now report the molecular basis of lymphostin biosynthesis in three marine Salinispora species that maintain conserved biosynthetic gene clusters harboring a hybrid nonribosomal peptide synthetase-polyketide synthase that is central to lymphostin assembly. Through a series of experiments involving gene mutations, stable isotope profiling, and natural product discovery, we report the assembly-line biosynthesis of lymphostin and nine new analogues that exhibit potent mTOR inhibitory activity.

Biosynthetic potential of phylogenetically unique endophytic actinomycetes from tropical plants.

The culturable diversity of endophytic actinomycetes associated with tropical, native plants is essentially unexplored. In this study, 123 endophytic actinomycetes were isolated from tropical plants collected from several locations in Papua New Guinea and Mborokua Island, Solomon Islands. Isolates were found to be prevalent in roots but uncommon in leaves.

Evaluating indole-related derivatives as precursors in the directed biosynthesis of diazepinomicin analogues.

The effectiveness of precursor-directed biosynthesis to generate diazepinomicin (1) analogues with varied ring-A substitutents was investigated by feeding commercially available, potential ring-A precursors such as fluorinated tryptophans, halogenated anthranilates, and various substituted indoles into growing actinomycete culture DPJ15 (genus Micromonospora). Two new monofluorinated diazepinomicin analogues (2 and 3) were identified and characterized by spectroscopic methods. Both derivatives showed modest antibacterial activity against the Gram-positive coccus Staphylococcus aureus with MIC values in the range 8-32 microg/mL.

Probing natural product biosynthetic pathways using Fourier transform ion cyclotron resonance mass spectrometry.

Two natural products, diazepinomicin (1) and dioxapyrrolomycin (2), containing stable isotopic labels of (15)N or deuterium, were used to demonstrate the utility of Fourier transform ion cyclotron resonance mass spectrometry for probing natural product biosynthetic pathways. The isotopic fine structures of significant ions were resolved and subsequently assigned elemental compositions on the basis of highly accurate mass measurements. In most instances the mass measurement accuracy is less than one part per million (ppm), which typically makes the identification of stable-isotope labeling unambiguous.

Cytoskyrins and cytosporones produced by Cytospora sp. CR200: taxonomy, fermentation and biological activities.

In screening endophytic fungi from Costa Rica for bioactivity, fungal culture CR200, isolated from a buttonwood tree, was found to contain compounds that initiate DNA damage in a test strain of E. coli (Biochemical Induction Assay, BIA) and inhibit growth of Gram-positive bacteria, including antibiotic-resistant strains. Two new bisanthraquinones (cytoskyrins A and B) and five new related octaketides (cytosporones A-E) were isolated from fermentation broths of this fungus.

Septocylindrins A and B: peptaibols produced by the terrestrial fungus Septocylindrium sp. LL-Z1518.

Two new peptaibols, septocylindrin A (1) and septocylindrin B (2), related to the well-studied membrane-channel-forming peptaibol alamethicin, were obtained from a terrestrial isolate of the fungus Septocylindrium sp. Both 1 and 2 are linear 19-amino acid peptides with a modified phenylalanine C-terminus. Analysis of the HRMS data indicated that they differ only in the 18th residue, where 1 contains Glu and 2 contains Gln.

Culicinin D, an antitumor peptaibol produced by the fungus Culicinomyces clavisporus, strain LL-12I252.

A group of new 10mer linear peptides, designated culicinins A-D (1-4), was isolated from the fermentation broth of the entomopathogenic fungus Culicinomyces clavisporus, strain LL-12I252. The structures of the culicinins were determined by a combination of 2D NMR and MS analysis. The major compound, culicinin D (4), exhibited selective inhibitory activity against PTEN-negative MDA468 tumor cells.

Penicillium dravuni, a new marine-derived species from an alga in Fiji.

Penicillium dravuni is a new monoverticillate, sclerotium-forming species that was isolated from the alga Dictyosphaeria versluyii collected in Dravuni, Fiji. This species morphologically is similar to P. turbatum in the P.

Dictyosphaeric acids A and B: new decalactones from an undescribed Penicillium sp. obtained from the alga Dictyosphaeria versluyii.

Fungal isolate F01V25 was obtained from the alga Dictyosphaeria versluyii collected near Dravuni, Fiji, in 2001 and represented a previously undescribed Penicillium sp. Fermentation of isolate F01V25 resulted in the production of two new polyketides, dictyosphaeric acids A and B, along with the known anthraquinone carviolin. The relative stereochemistry of dictyosphaeric acids A and B was determined using the J-based configuration analysis method in conjunction with ROE and NOE correlations.

Novel alpha-pyrones produced by a marine Pseudomonas sp. F92S91: taxonomy and biological activities.

Inhibitors of the enzymes involved in fatty acid biosynthesis (FAB) have been reported as antibacterial agents. These include thiolactomycin, cerulenin, triclosan, diazoborine, naphthyridinones, aminopyridines and pyridoindoles. Our search for new FAB inhibitors, using a lacZ reporter cell-based screen, led to several confirmed hits.

Cytosporacin, a highly unsaturated polyketide: application of the ACCORD-ADEQUATE experiment to the structural determination of natural products.

Cytosporacin (1), a novel antibacterial polyketide containing naphthopyranone and isochromandione moieties, was isolated from the fermentation broth of the fungus Cytospora rhizophorae. A (1)H-detected ACCORD-ADEQUATE pulse sequence that distinguished (2)J(CH) from (3)J(CH) correlations provided critical information for structural determination. NOE studies established the relative configuration and revealed the presence of two rotamers.

Brocaenols A-C: novel polyketides from a marine derived Penicillium brocae.

Chemical investigation of a Penicillium brocae, obtained from a tissue sample of a Fijian Zyzyya sp. sponge, yielded two known diketopiperazines and three novel cytotoxic polyketides, brocaenols A-C. The brocaenols contain an unusual enolized oxepine lactone ring system that to the best of our knowledge is unprecedented in the literature.