57 research outputs found
Good Computational Practice in the Assignment of Absolute Configurations by TDDFT Calculations of ECD Spectra
Quantum-mechanical calculations of chiroptical properties have rapidly become the most popular method for assigning absolute configurations (AC) of organic compounds, including natural products. Black-box time-dependent Density Functional Theory (TDDFT) calculations of electronic circular dichroism (ECD) spectra are nowadays readily accessible to nonexperts. However, an uncritical attitude may easily deliver a wrong answer. We present to the Chirality Forum a discussion on what can be called good computational practice in running TDDFT ECD calculations, highlighting the most crucial points with several examples from the recent literature
Mapping Microbial Response Metabolomes for Induced Natural Product Discovery
Intergeneric
microbial interactions may originate a significant
fraction of secondary metabolic gene regulation in nature. Herein,
we expose a genomically characterized <i>Nocardiopsis</i> strain, with untapped polyketide biosynthetic potential, to intergeneric
interactions via coculture with low inoculum exposure to <i>Escherichia</i>, <i>Bacillus</i>, <i>Tsukamurella</i>, and <i>Rhodococcus</i>. The challenge-induced responses of extracted
metabolites were characterized via multivariate statistical and self-organizing
map (SOM) analyses, revealing the magnitude and selectivity engendered
by the limiting case of low inoculum exposure. The collected inventory
of cocultures revealed substantial metabolomic expansion in comparison
to monocultures with nearly 14% of metabolomic features in cocultures
undetectable in monoculture conditions and many features unique to
coculture genera. One set of SOM-identified responding features was
isolated, structurally characterized by multidimensional NMR, and
revealed to comprise previously unreported polyketides containing
an unusual pyrrolidinol substructure and moderate and selective cytotoxicity.
Designated ciromicin A and B, they are detected across mixed cultures
with intergeneric preferences under coculture conditions. The structural
novelty of ciromicin A is highlighted by its ability to undergo a
diastereoselective photochemical 12-Ď€ electron rearrangement
to ciromicin B at visible wavelengths. This study shows how organizing
trends in metabolomic responses under coculture conditions can be
harnessed to characterize multipartite cultures and identify previously
silent secondary metabolism
Mapping Microbial Response Metabolomes for Induced Natural Product Discovery
Intergeneric
microbial interactions may originate a significant
fraction of secondary metabolic gene regulation in nature. Herein,
we expose a genomically characterized <i>Nocardiopsis</i> strain, with untapped polyketide biosynthetic potential, to intergeneric
interactions via coculture with low inoculum exposure to <i>Escherichia</i>, <i>Bacillus</i>, <i>Tsukamurella</i>, and <i>Rhodococcus</i>. The challenge-induced responses of extracted
metabolites were characterized via multivariate statistical and self-organizing
map (SOM) analyses, revealing the magnitude and selectivity engendered
by the limiting case of low inoculum exposure. The collected inventory
of cocultures revealed substantial metabolomic expansion in comparison
to monocultures with nearly 14% of metabolomic features in cocultures
undetectable in monoculture conditions and many features unique to
coculture genera. One set of SOM-identified responding features was
isolated, structurally characterized by multidimensional NMR, and
revealed to comprise previously unreported polyketides containing
an unusual pyrrolidinol substructure and moderate and selective cytotoxicity.
Designated ciromicin A and B, they are detected across mixed cultures
with intergeneric preferences under coculture conditions. The structural
novelty of ciromicin A is highlighted by its ability to undergo a
diastereoselective photochemical 12-Ď€ electron rearrangement
to ciromicin B at visible wavelengths. This study shows how organizing
trends in metabolomic responses under coculture conditions can be
harnessed to characterize multipartite cultures and identify previously
silent secondary metabolism
Structuring Microbial Metabolic Responses to Multiplexed Stimuli via Self-Organizing Metabolomics Maps
SummarySecondary metabolite biosynthesis in microorganisms responds to discrete chemical and biological stimuli; however, untargeted identification of these responses presents a significant challenge. Herein we apply multiplexed stimuli to Streptomyces coelicolor and collect the resulting response metabolomes via ion mobility-mass spectrometric analysis. Self-organizing map (SOM) analytics adapted for metabolomic data demonstrate efficient characterization of the subsets of primary and secondary metabolites that respond similarly across stimuli. Over 60% of all metabolic features inventoried from responses are either not observed under control conditions or produced at greater than 2-fold increase in abundance in response to at least one of the multiplexing conditions, reflecting how metabolites encode phenotypic changes in an organism responding to multiplexed challenges. Using abundance as an additional filter, each of 16 known S. coelicolor secondary metabolites is prioritized via SOM and observed at increased levels (1.2- to 22-fold compared with unperturbed) in response to one or more challenge conditions
Structural Mass Spectrometry: Rapid Methods for Separation and Analysis of Peptide Natural Products
A significant challenge in natural product discovery
is the initial
discrimination of discrete secondary metabolites alongside functionally
similar primary metabolic cellular components within complex biological
samples. A property that has yet to be fully exploited for natural
product identification and characterization is the gas-phase collision
cross section, or, more generally, the mobility–mass correlation.
Peptide natural products possess many of the properties that distinguish
natural products, as they are frequently characterized by a high degree
of intramolecular bonding and possess extended and compact conformations
among other structural modifications. This report describes a rapid
structural mass spectrometry technique based on ion mobility–mass
spectrometry for the comparison of peptide natural products to their
primary metabolic congeners using mobility–mass correlation.
This property is empirically determined using ion mobility–mass
spectrometry, applied to the analysis of linear versus modified peptides,
and used to discriminate peptide natural products in a crude microbial
extract. Complementary computational approaches are utilized to understand
the structural basis for the separation of primary metabolism derived
linear peptides from secondary metabolite cyclic and modified cyclic
species. These findings provide a platform for enhancing the identification
of secondary metabolic peptides with distinct mobility–mass
ratios within complex biological samples
Structure and Stereochemical Determination of Hypogeamicins from a Cave-Derived Actinomycete
Culture extracts from the cave-derived
actinomycete <i>Nonomuraea
specus</i> were investigated, resulting in the discovery of a
new S-bridged pyronaphthoquinone dimer and its monomeric progenitors
designated hypogeamicins A–D (<b>1</b>–<b>4</b>). The structures were elucidated using NMR spectroscopy, and the
relative stereochemistries of the pyrans were inferred using NOE and
comparison to previously reported compounds. Absolute stereochemistry
was determined using quantum chemical calculations of specific rotation
and vibrational and electronic circular dichroism spectra, after an
extensive conformational search and including solute–solvent
polarization effects, and comparing with the corresponding experimental
data for the monomeric congeners. Interestingly, the dimeric hypogeamicin
A (<b>1</b>) was found to be cytotoxic to the colon cancer derived
cell line TCT-1 at low micromolar ranges, but not bacteria, whereas
the monomeric precursors possessed antibiotic activity but no significant
TCT-1 cytotoxicity
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