Automated identification of depsipeptide natural products by an informatic search algorithm.

Nonribosomal depsipeptides are a class of potent microbial natural products, which include several clinically approved pharmaceutical agents. Genome sequencing has revealed a large number of uninvestigated natural-product biosynthetic gene clusters. However, while novel informatic search methods to access these gene clusters have been developed to identify peptide natural products, depsipeptide detection has proven challenging. Herein, we present an improved version of our informatic search algorithm for natural products (iSNAP), which facilitates the detection of known and genetically predicted depsipeptides in complex microbial culture extracts. We validated this technology by identifying several depsipeptides from novel producers, and located a large number of novel depsipeptide gene clusters for future study. This approach highlights the value of chemoinformatic search methods for the discovery of genetically encoded metabolites by targeting specific areas of chemical space.

Nonribosomal assembly of natural lipocyclocarbamate lipoprotein-associated phospholipase inhibitors.

EXPANDING OUR KNOWLEDGE: Natural lipocyclocarbamate natural products have provided the inspiration for the first-in-class synthetic phospholipase inhibitor darapladib, currently in phase III clinical trials for the treatment of atherosclerosis. Here, we discuss their biosynthesis by a nonribosomal peptide synthetase.

Structures and biosynthesis of 12-membered macrocyclic depsipeptides from Streptomyces sp. ML55.

Two novel depsipeptides (1-2) were isolated from Streptomyces sp. ML55 together with two known analogues (3-4). Their structures were elucidated using a combination of NMR experiments, as well as detailed MS/MS experiments. The biosynthetic pathway of isolated compounds was dissected by genome sequencing data analysis for a hybrid nonribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) assembly line.

Chemical variation from the neoantimycin depsipeptide assembly line.

Here we report the biosynthetic pathway for the neoantimycin and present three novel neoantimycin analogues, neoantimycin D (1), E (2) and F (3), from this assembly system from Streptoverticillium orinoci. Identification of these novel neoantimycin variants was achieved by selective MS/MS interrogation of natural product extracts using diagnostic fragments of the known neoantimycins. Their structures, including the absolute configurations, were elucidated using a combination of NMR experiments, detailed MS/MS experiments and the advanced Marfey's method. The biosynthetic pathway of neoantimycin was dissected by genome sequencing data analysis for the first time, which includes a hybrid nonribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) assembly lines.

Systems biosynthesis of secondary metabolic pathways within the oral human microbiome member Streptococcus mutans.

Streptococcus mutans, a Gram-positive human commensal and pathogen, is commonly recognized as a primary causative agent in dental caries. Metabolic activity of this strain results in the creation of acids and secreted products are recognized as pathogenic factors and agents that promote immunomodulation by stimulating the release of pro-inflammatory cytokines. Products of secondary metabolic pathways of microorganisms from the human microbiome are increasingly investigated for their immunomodulatory functions. In this study, we sought to explore the metabolomic output of nonribosomal peptide pathways within the model S. mutans strain, S. mutans UA159, using a systems metabolomic approach to gain in-depth analysis on products created by this organism and probe these molecules for their immunomodulatory function. Comparative metabolomics and biosynthetic studies using wild-type and nonribosomal peptide deletion strains (within the mutanobactin biosynthetic locus), precursor feedings (fatty acid derivatives) led to the identification of 58 metabolites, 13 of which were structurally elucidated. In addition to these, an assembly line derailment product, mutanamide, was also identified and used to assess immunomodulatory properties of mutanobactins and actions relating to their previously reported functions describing hyphal inhibitory profiles in Candida albicans. The results of this study demonstrate both the complexity and the divergent roles of products stemming from this unique biosynthetic assembly line.

Small molecule immunomodulins from cultures of the human microbiome member Lactobacillus plantarum.

Lactobacillus plantarum strains are noted for their presence in the human gastrointestinal tract and are distinguished for their immunomodulatory actions and therapeutic applications. Despite the uncertainty in the underlining molecular mechanisms, recent evidence suggests that L. plantarum secretes immunomodulatory agents that alter immunological signaling cascades. Elaboration of these metabolic products from L. plantarum strain WCFS1 was demonstrated previously to correlate with the mid-log-stationary transition, perhaps consistent with secondary metabolite expression. Here, we present the metabolomic shifts revealed by principal component analysis that correspond to the mid-log-stationary transition of L. plantarum, and identify pyroglutamic (pyro) dipeptides within this transition as correlative with the immunomodulatory actions. Four of these (pyro-phenylalanine, pyro-leucine, pyro-isoleucine, pyro-tryptophan) were characterized and the two dominant members, pyro-phenylalanine and pyro-tryptophan, were directly interrogated for immunomodulatory activity through in vivo administration using C57BL/6 mice. Administration of these compounds resulted in decreased production of pro-inflammatory cytokine interferon (IFN)-gamma, which is of noted importance in gastrointestinal immune homeostasis.

Chemical and biosynthetic evolution of the antimycin-type depsipeptides.

Evolution of natural products, and particularly those resulting from microbial assembly line-like enzymes, such as polyketide (PK) and nonribosomal peptides (NRP), has resulted in a variety of pharmaceutically important and chemically diverse families of molecules. The antimycin-type depsipeptides are one such grouping, with a significant level of diversity and members that have noted activities against key targets governing human cellular apoptosis (e.g. Bcl-xL and GRP78). Chemical variance originates from ring size, with 9-, 12-, 15-, and 18-membered classes, and we show that such distinctions influence their molecular targeting. Further, we present here a systematic interrogation of the chemistry and assembly line evolution of antimycin-type analogues by conducting metabolomic profiling and biosynthetic gene cluster comparative analysis of the depsipeptide assembly lines for each member of the antimycin-group. Natural molecular evolution principles of such studies should assist in artificial re-combinatorializing of PK and NRP assembly lines.