The utility of metabolomics in natural product and biomarker characterization

BackgroundMetabolomics is a well-established rapidly developing research field involving quantitative and qualitative metabolite assessment within biological systems. Recent improvements in metabolomics technologies reveal the unequivocal value of metabolomics tools in natural products discovery, gene-function analysis, systems biology and diagnostic platforms.Scope of reviewWe review here some of the prominent metabolomics methodologies employed in data acquisition and analysis of natural products and disease-related biomarkers.Major conclusionsThis review demonstrates that metabolomics represents a highly adaptable technology with diverse applications ranging from environmental toxicology to disease diagnosis. Metabolomic analysis is shown to provide a unique snapshot of the functional genetic status of an organism by examining its biochemical profile, with relevance toward resolving phylogenetic associations involving horizontal gene transfer and distinguishing subgroups of genera possessing high genetic homology, as well as an increasing role in both elucidating biosynthetic transformations of natural products and detecting preclinical biomarkers of numerous disease states.General significanceThis review expands the interest in multiplatform combinatorial metabolomic analysis. The applications reviewed range from phylogenetic assignment, biosynthetic transformations of natural products, and the detection of preclinical biomarkers.     

Survey of marine natural product structure revisions: a synergy of spectroscopy and chemical synthesis

The structural assignment of new natural product molecules supports research in a multitude of disciplines that may lead to new therapeutic agents and or new understanding of disease biology. However, reports of numerous structural revisions, even of recently elucidated natural products, inspired the present survey of techniques used in structural misassignments and subsequent revisions in the context of constitutional or configurational errors. Given the comparatively recent development of marine natural products chemistry, coincident with modern spectroscopy, it is of interest to consider the relative roles of spectroscopy and chemical synthesis in the structure elucidation and revision of those marine natural products that were initially misassigned. Thus, a tabulated review of all marine natural product structural revisions from 2005 to 2010 is organized according to structural motif revised. Misassignments of constitution are more frequent than perhaps anticipated by reliance on HMBC and other advanced NMR experiments, especially when considering the full complement of all natural products. However, these techniques also feature prominently in structural revisions, specifically of marine natural products. Nevertheless, as is the case for revision of relative and absolute configuration, total synthesis is a proven partner for marine, as well as terrestrial, natural products structure elucidation. It also becomes apparent that considerable 'detective work' remains in structure elucidation, in spite of the spectacular advances in spectroscopic techniques.     

Genome‐guided investigation of plant natural product biosynthesis

The medicinal plant Madagascar periwinkle, Catharanthus roseus (L.) G. Don, produces hundreds of biologically active monoterpene‐derived indole alkaloid (MIA) metabolites and is the sole source of the potent, expensive anti‐cancer compounds vinblastine and vincristine. Access to a genome sequence would enable insights into the biochemistry, control, and evolution of genes responsible for MIA biosynthesis. However, generation of a near‐complete, scaffolded genome is prohibitive to small research communities due to the expense, time, and expertise required. In this study, we generated a genome assembly for C. roseus that provides a near‐comprehensive representation of the genic space that revealed the genomic context of key points within the MIA biosynthetic pathway including physically clustered genes, tandem gene duplication, expression sub‐functionalization, and putative neo‐functionalization. The genome sequence also facilitated high resolution co‐expression analyses that revealed three distinct clusters of co‐expression within the components of the MIA pathway. Coordinated biosynthesis of precursors and intermediates throughout the pathway appear to be a feature of vinblastine/vincristine biosynthesis. The C. roseus genome also revealed localization of enzyme‐rich genic regions and transporters near known biosynthetic enzymes, highlighting how even a draft genome sequence can empower the study of high‐value specialized metabolites.     

Inhibition of eukaryotic translation initiation by the marine natural product pateamine A

Translation initiation in eukaryotes is accomplished through the coordinated and orderly action of a large number of proteins, including the eIF4 initiation factors. Herein, we report that pateamine A (PatA), a potent antiproliferative and proapoptotic marine natural product, inhibits cap-dependent eukaryotic translation initiation. PatA bound to and enhanced the intrinsic enzymatic activities of eIF4A, yet it inhibited eIF4A-eIF4G association and promoted the formation of a stable ternary complex between eIF4A and eIF4B. These changes in eIF4A affinity for its partner proteins upon binding to PatA caused the stalling of initiation complexes on mRNA in vitro and induced stress granule formation in vivo. These results suggest that PatA will be a valuable molecular probe for future studies of eukaryotic translation initiation and may serve as a lead compound for the development of anticancer agents.     

A novel class of H3 antagonists derived from the natural product guided synthesis of unnatural analogs of the marine bromopyrrole alkaloid dispyrin

This Letter describes the natural product guided synthesis of unnatural analogs of the marine bromopyrrole alkaloid dispyrin, and the resulting SAR of H₃ antagonism. Multiple rounds of iterative parallel synthesis improved human H₃ IC₅₀ ～33-fold, and afforded a new class of H₃ antagonists based on the novel bromotyramine core of dispyrin.     

A database of natural products and chemical entities from marine habitat

Marine compound database consists of marine natural products and chemical entities, collected from various literature sources, which are known to possess bioactivity against human diseases. The database is constructed using html code. The 12 categories of 182 compounds are provided with the source, compound name, 2-dimensional structure, bioactivity and clinical trial information. The database is freely available online and can be accessed at http://www.progenebio.in/mcdb/index.htm     

Role of natural product diversity in chemical biology

Through the natural selection process, natural products possess a unique and vast chemical diversity and have been evolved for optimal interactions with biological macromolecules. Owing to their diversity, target affinity, and specificity, natural products have demonstrated enormous potential as modulators of biomolecular function, been an essential source for drug discovery, and provided design principles for combinatorial library development.     

Antitumor activity of the marine natural product dibromophakellstatin in vitro

The pyrrole-imidazole alkaloid rac-dibromophakellstatin displayed selective antitumor activity in vitro when tested in 36 cell lines in a cell survival and proliferation assay. The ovarian cancer cell line OVXF 899L proved to be most sensitive (0.60 microM, IC50), followed by the glioblastoma cell line CNXF 498NL (0.93 microM), the non-small lung cancer cell line LXF 529L (0.96 microM), and the uterus cancer cell line UXF 1138L (1.21 microM). The selectivity profile of rac-dibromophakellstatin may be indicative for a novel mechanism of action. Separation of the enantiomers on a chiral HPLC column revealed that only the naturally occurring (-)-dibromophakellstatin is antitumor active. Debromination of the pyrrole moiety leads to complete loss of activity.     

自然生态空间格局构建与规划理论研究

广义的生态空间是指具有自然属性,以提供生态系统服务为主导功能的空间,包括自然生态空间、城镇生态空间和农业生态空间。自然生态空间是指与城镇空间、农业空间并列的,分布在城镇空间与农业空间之外的国土空间,在分布上具有完整性和连续性。探讨了自然生态空间的定义、内涵以及自然生态空间格局构建的理论和技术要点,提出以重要生态功能维护格局、人居环境屏障格局和生物多样性保护格局为主体,构建自然生态空间格局体系的思路。自然生态空间格局构建的最终目的是对国土空间开发行为进行管控,理顺保护与发展的关系,最终达到保护重要生态空间及促进区域可持续发展的目的。在落实生态文明战略、维护国家生态安全的背景下,构建自然生态空间格局对于优化国土空间开发格局,指导生态保护与建设具有重要意义。     

Construction of a microbial natural product library for chemical biology studies

The RIKEN Natural Products Depository (NPDepo) is a public depository of small molecules. Currently, the NPDepo chemical library contains 39,200 pure compounds, half of which are natural products and their derivatives. In order to reinforce the uniqueness of our chemical library, we have improved our strategies for the collection of microbial natural products. Firstly, a microbial metabolite fraction library coupled with an MP (microbial products) plot database provides a powerful resource for the efficient isolation of microbial metabolites. Secondly, biosynthetic studies of microbial metabolites have enabled us to not only access ingenious biosynthetic machineries, but also obtain a variety of biosynthetic intermediates. Our chemical library contributes to the discovery of molecular probes for increasing our understanding of complex biological processes and for eventually developing new drug leads.     

Culturable rare Actinomycetes: diversity, isolation and marine natural product discovery

Rare Actinomycetes from underexplored marine environments are targeted in drug discovery studies due to the Actinomycetes’ potentially huge resource of structurally diverse natural products with unusual biological activity. Of all marine bacteria, 10 % are Actinomycetes, which have proven an outstanding and fascinating resource for new and potent bioactive molecules. Past and present efforts in the isolation of rare Actinomycetes from underexplored diverse natural habitats have resulted in the isolation of about 220 rare Actinomycete genera of which more than 50 taxa have been reported to be the producers of 2,500 bioactive compounds. That amount represents greater than 25 % of the total Actinomycetes metabolites, demonstrating that selective isolation methods are being developed and extensively applied. Due to the high rediscovery rate of known compounds from Actinomycetes, a renewed interest in the development of new antimicrobial agents from rare and novel Actinomycetes is urgently required to combat the increasing number of multidrug-resistant human pathogens. To facilitate that discovery, this review updates all selective isolation media including pretreatment and enrichment methods for the isolation of marine rare Actinomycetes. In addition, this review demonstrates that discovering new compounds with novel scaffolds can be increased by intensive efforts in isolating and screening rare marine genera of Actinomycetes. Between 2007 and mid-2013, 80 new rare Actinomycete species were reported from marine habitats. They belong to 23 rare families, of which three are novel, and 20 novel genera. Of them, the family Micromonosporaceae is dominant as a producer of promising chemical diversity.     

Synthesis and antitumor activity of indolylpyrimidines: marine natural product meridianin D analogues

Marine indole alkaloid meridianin D analogues have been synthesized starting from the appropriate 3-cyanoacetyl indole. A facile two-step conversion of 3-cyanoacetyl indole to the corresponding cyano meridianin D analogue by treatment with dimethylformamide-dimethylacetal and further cyclization of the resulting enaminonitrile with aminoguanidine is described. Then, alkaline hydrolysis of cyano meridianin D afforded the carboxylic acid analogue. The treatment of acid with 75% H(2)SO(4) afforded the desired 6-debromomeridianin D. Simply treatment of cyano meridianin D analogue with hydrazine hydrate afforded the amidrazone analogue. The biological evaluation indicated that cyano analogue showed good cytotoxic activity with IC(50) values of 0.85 and 2.65microg (against MCF7 and HeLa, respectively), but acid and amidrazone analogues showed high cytotoxicity with IC(50) values of 0.75 and 0.25microg, respectively (against MCF7).     

Building and deploying a cyberinfrastructure for the data-driven design of chemical systems and the exploration of chemical space

Abstract

The use of modern data science has recently emerged as a promising new path to tackling the complex challenges involved in the creation of next-generation chemistry and materials. However, despite the appeal of this potentially transformative development, the chemistry community has yet to incorporate it as a central tool in every-day work. Our research program is designed to enable and advance this emerging research approach. It is centred around the creation of a software ecosystem that brings together physics-based modelling, high-throughput in silico screening and data analytics (i.e. the use of machine learning and informatics for the validation, mining and modelling of chemical data). This cyberinfrastructure is devised to offer a comprehensive set of data science techniques and tools as well as a general-purpose scope to make it as versatile and widely applicable as possible. It also emphasises user-friendliness to make it accessible to the community at large. It thus provides the means for the large-scale exploration of chemical space and for a better understanding of the hidden mechanisms that determine the properties of complex chemical systems. Such insights can dramatically accelerate, streamline and ultimately transform the way chemical research is conducted. Aside from serving as a production-level tool, our cyberinfrastructure is also designed to facilitate and assess methodological innovation. Both the software and method development work are driven by concrete molecular design problems, which also allow us to assess the efficacy of the overall cyberinfrastructure.     

Quantal analysis indicates an alpha-toxin-like block by lophotoxin, a non-ionic marine natural product

The effects of a structurally novel paralytic substance (lophotoxin) on quantal transmission parameters and the time course of synaptic potentials have been examined. This substance completely abolished potentials by reducing quantal size without affecting the release of quanta. Nerve conduction, membrane potential, and the passive electrical properties of the muscle end-plate remained unaffected. Lophotoxin appears to act directly on the acetylcholine receptor-channel complex, although perhaps not the cholinoreceptive site itself, as suggested by the unusual chemistry and onset kinetics of this toxin.     

Distribution and diversity of natural product genes in marine and freshwater cyanobacterial cultures and genomes

Natural products are a functionally diverse class of biochemically synthesized compounds, which include antibiotics, toxins, and siderophores. In this paper, we describe both the detection of natural product activities and the sequence identification of gene fragments from two molecular systems that have previously been implicated in natural product production, i.e., nonribosomal peptide synthetases (NRPSs) and modular polyketide synthases (PKSs), in diverse marine and freshwater cyanobacterial cultures. Using degenerate PCR and the sequencing of cloned products, we show that NRPSs and PKSs are common among the cyanobacteria tested. Our molecular data, when combined with genomic searches of finished and progressing cyanobacterial genomes, demonstrate that not all cyanobacteria contain NRPS and PKS genes and that the filamentous and heterocystous cyanobacteria are the richest sources of these genes and the most likely sources of novel natural products within the phylum. In addition to validating the use of degenerate primers for the identification of PKS and NRPS genes in cyanobacteria, this study also defines numerous gene fragments that will be useful as probes for future studies of the synthesis of natural products in cyanobacteria. Phylogenetic analyses of the cyanobacterial NRPS and PKS fragments sequenced in this study, as well as those from the cyanobacterial genome projects, demonstrate that there is remarkable diversity and likely novelty of these genes within the cyanobacteria. These results underscore the potential variety of novel products being produced by these ubiquitous organisms.     

Exciton coupling circular dichroism of an allylic N-imidazolyl group in amaranzole A, a marine natural product from Phorbas amaranthus

A new steroidal alkaloid amaranzole A (10) with a C24-imidazolyl group displays an unusually large split-CD spectrum at short wavelengths that we assign to exciton coupled circular dichroism (ECCD) between the polarized pi-pi* transitions of the C25 C=C double bond and the imidazolyl group. A model 4,5-disubstituted imidazole 11, prepared from optically pure (R)-(-)-2-aminobutanol, exhibited similar ECCD and solvent and pH-dependence consistent with changes in the protonation state of the imidazole ring. Calculations and CD measurement of 12 (the dihydro-derivative of 11) suggest that the 4-hydroxyphenyl group is not strongly conjugated to the imidazole group in 10, and the observed ECCD is entirely accounted for by coupling between the C=C double bond and isolated imidazole pi-pi* transitions.