R. Thomas Williamson

Biosynthesis and Structures of Cyclomarins and Cyclomarazines, Prenylated Cyclic Peptides of Marine Actinobacterial Origin

Two new diketopiperazine dipeptides, cyclomarazines A and B, were isolated and characterized along with the new cyclic heptapeptide cyclomarin D from the marine bacterium Salinispora arenicola CNS-205. These structurally related cyclic peptides each contain modified amino acid residues, including derivatives of N-(1,1-dimethylallyl)-tryptophan and delta-hydroxyleucine, which are common in the di- and heptapeptide series. Stable isotope incorporation studies in Streptomyces sp. CNB-982, which was first reported to produce the cyclomarin anti-inflammatory agents, illuminated the biosynthetic building blocks associated with the major metabolite cyclomarin A, signifying that this marine microbial peptide is nonribosomally derived largely from nonproteinogenic amino acid residues. DNA sequence analysis of the 5.8 Mb S. arenicola circular genome and PCR-targeted gene inactivation experiments identified the 47 kb cyclomarin/cyclomarazine biosynthetic gene cluster (cym) harboring 23 open reading frames. The cym locus is dominated by the 23 358 bp cymA, which encodes a 7-module nonribosomal peptide synthetase (NRPS) responsible for assembly of the full-length cyclomarin heptapeptides as well as the truncated cyclomarazine dipeptides. The unprecedented biosynthetic feature of the megasynthetase CymA to synthesize differently sized peptides in vivo may be triggered by the level of beta oxidation of the priming tryptophan residue, which is oxidized in the cyclomarin series and unoxidized in the cyclomarazines. Biosynthesis of the N-(1,1-dimethyl-2,3-epoxypropyl)-beta-hydroxytryptophan residue of cyclomarin A was further illuminated through gene inactivation experiments, which suggest that the tryptophan residue is reverse prenylated by CymD prior to release of the cyclic peptide from the CymA megasynthetase, whereas the cytochrome P450 CymV installs the epoxide group on the isoprene of cyclomarin C post-NRPS assembly. Last, the novel amino acid residue 2-amino-3,5-dimethylhex-4-enoic acid in the cyclomarin series was shown by bioinformatics and stable isotope experiments to derive from a new pathway involving condensation of isobutyraldehyde and pyruvate followed by S-adenosylmethionine methylation. Assembly of this unsaturated, branched amino acid is unexpectedly related to the degradation of the environmental pollutant 3-(3-hydroxyphenyl)propionic acid.

Biosynthetic Pathway and Origin of the Chlorinated Methyl Group in Barbamide and Dechlorobarbamide, Metabolites from the Marine Cyanobacterium Lyngbya majuscula

Abstract Structural and biosynthetic studies have been conducted on the barbamide class of molluscicidal agent. Dechlorobarbamide was isolated from a Curacao collection of the marine cyanobacterium Lyngbya majuscula and its structure determined through spectroscopic analysis and comparisons with barbamide. The absolute stereochemistry of the dolaphenine moiety of barbamide was determined to be S , defining the absolute configuration of barbamide as 2 S ,7 S . Stable isotope feeding experiments conducted with cultured L. majuscula have provided clear evidence that barbamide biosynthesis involves chlorination of the unactivated pro - R methyl group of leucine. Experiments with l -[ 2 H 10 ]leucine demonstrated that chlorination of the pro- R methyl occurs without detectable activation via the leucine-catabolic pathway. Moreover, an extremely high level of incorporation of fed [2- 13 C]-5,5,5-trichloroleucine into barbamide indicates that leucine is the probable substrate for the chlorination reaction. Incorporations of [1,2- 13 C 2 ]acetate and [1- 13 C, 1- 18 O]acetate confirmed the origins of C-5 and C-6 whereas incorporation of l -[3- 13 C]phenylalanine supported the hypothesis that the phenyl group and its three carbon side-chain in barbamide (C-7, C-8 and C-10–C-16) arise from phenylalanine. The thiazole ring (C-17–C-18) of 1 was shown to likely arise from cysteine through a [2- 13 C, 15 N]glycine feeding experiment. Detection of intact 13 C– 15 N bond was observed by application of a new GHNMBC NMR experiment. Results from this latter feeding experiment also indicated that the N–CH 3 and O–CH 3 groups of 1 originate from the C 1 pool; this was supported by enrichment in these methyl groups when cultures were provided with l -[methyl- 13 C]methionine.

LR-HSQMBC: a sensitive NMR technique to probe very long-range heteronuclear coupling pathways.

HMBC is one of the most often used and vital NMR experiments for the structure elucidation of organic and inorganic molecules. We have developed a new, high sensitivity NMR pulse sequence that overcomes the typical (2,3)JCH limitation of HMBC by extending the visualization of long-range correlation data to 4-, 5-, and even 6-bond long-range (n)JCH heteronuclear couplings. This technique should prove to be an effective experiment to complement HMBC for probing the structure of proton-deficient molecules. The LR-HSQMBC NMR experiment can, in effect, extend the range of HMBC to provide data similar to that afforded by 1,n-ADEQUATE even in sample-limited situations. This is accomplished by optimizing responses for very small (n)JCH coupings as opposed to relying on the markedly less sensitive detection of long-range coupled (13)C-(13)C homonuclear pairs at natural abundance. DFT calculations were employed to determine whether the very long-range correlations observed for cervinomycin A2 were reasonable on the basis of the calculated long-range couplings.

Determination of Relative Configuration from Residual Chemical Shift Anisotropy

Determination of relative configuration is frequently a rate-limiting step in the characterization of small organic molecules. Solution NMR-based nuclear Overhauser effect and scalar J-coupling constants can provide useful spatial information but often fail when stereocenters are separated by more than 4-5 Å. Residual dipolar couplings (RDCs) can provide a means of assigning relative configuration without limits of distance between stereocenters. However, sensitivity limits their application. Chemical shift is the most readily measured NMR parameter, and partial molecular alignment can reveal the anisotropic component of the chemical shift tensor, manifested as residual chemical shift anisotropy (RCSA). Hence, (13)C RCSAs provide information on the relative orientations of specific structural moieties including nonprotonated carbons and can be used for stereochemical assignment. Herein, we present two robust and sensitive methods to accurately measure and apply (13)C RCSAs for stereochemical assignment. The complementary techniques are demonstrated with five molecules representing differing structural classes.

Bruchins—Mitogenic 3-(Hydroxypropanoyl) Esters of Long Chain Diols from Weevils of the Bruchidae

Abstract Mono- and bis 3-(hydroxypropanoyl) esters of long chain, unsaturated diols have been isolated and identified from two genera of the family Bruchidae, and have been shown to be responsible for the mitogenic activity observed on pea pods resulting from oviposition by the pea weevil, Bruchus pisorum . The mitogenic compounds have been characterized and synthesized.

Homodimericin A: A Complex Hexacyclic Fungal Metabolite

Microbes sense and respond to their environment with small molecules, and discovering these molecules and identifying their functions informs chemistry, biology, and medicine. As part of a study of molecular exchanges between termite-associated actinobacteria and pathogenic fungi, we uncovered a remarkable fungal metabolite, homodimericin A, which is strongly upregulated by the bacterial metabolite bafilomycin C1. Homodimericin A is a hexacyclic polyketide with a carbon backbone containing eight contiguous stereogenic carbons in a C20 hexacyclic core. Only half of its carbon atoms have an attached hydrogen, which presented a significant challenge for NMR-based structural analysis. In spite of its microbial production and rich stereochemistry, homodimericin A occurs naturally as a racemic mixture. A plausible nonenzymatic reaction cascade leading from two identical achiral monomers to homodimericin A is presented, and homodimericin A’s formation by this path, a six-electron oxidation, could be a response to oxidative stress triggered by bafilomycin C1.

Homodecoupled 1,1‐ and 1,n‐ADEQUATE: Pivotal NMR Experiments for the Structure Revision of Cryptospirolepine

Cryptospirolepine is the most structurally complex alkaloid discovered and characterized thus far from any Cryptolepis specie. Characterization of several degradants of the original, sealed NMR sample a decade after the initial report called the validity of the originally proposed structure in question. We now report the development of improved, homodecoupled variants of the 1,1- and 1,n-ADEQUATE (HD-ADEQUATE) NMR experiments; utilization of these techniques was critical to successfully resolving long-standing structural questions associated with crytospirolepine.

Biosynthesis of the marine cyanobacterial metabolite barbamide. 2: Elucidation of the origin of the thiazole ring by application of a new GHNMBC experiment

A new NMR experiment is presented for the detection of intact 13C15N units in biosynthetic studies. Its use is demonstrated through a feeding experiment utilizing [2-13C, 15N] glycine which confirmed the origin of the thiazole ring in the marine cyanobacterial metabolite barbamide as originating from cysteine.

Suppression of phase and amplitude J(HH) modulations in HSQC experiments

The amplitude and the phase of cross peaks in conventional 2D HSQC experiments are modulated by both proton–proton, J(HH), and proton–carbon, 1J(CH), coupling constants. It is shown by spectral simulation and experimentally that J(HH) interferences are suppressed in a novel perfect‐HSQC pulse scheme that incorporates perfect‐echo INEPT periods. The improved 2D spectra afford pure in‐phase cross peaks with respect to 1J(CH) and J(HH), irrespective of the experiment delay optimization. In addition, peak volumes are not attenuated by the influence of J(HH), rendering practical issues such as phase correction, multiplet analysis, and signal integration more appropriate. Copyright

Unequivocal determination of complex molecular structures using anisotropic NMR measurements

Picking structures out of a lineup Pharmaceutical research relies critically on determining the correct structures of numerous complex molecules. When well-ordered crystals are not available for x-ray analysis, nuclear magnetic resonance (NMR) spectroscopy is the most common structure-elucidation method. However, sometimes it is hard to distinguish isomers with similar spectra. Liu et al. showcase a protocol that combines computer modeling with anisotropic NMR data acquired using gel-aligned samples. Because of its uniform sensitivity to relative bond orientations across the whole molecular framework, the method overcomes common pitfalls that can lead to invalid structure assignments. Science, this issue p. eaam5349 A nuclear magnetic resonance method applied to aligned molecules helps to elucidate their complex structures. INTRODUCTION Single-crystal x-ray diffraction studies represent the gold standard for unequivocal establishment of molecular structure and configuration. For molecules that will not crystallize or that form poorly-diffracting crystals, alternative methods must be used. Crystalline sponges and atomic force microscopy are techniques with increasing potential, although nuclear magnetic resonance (NMR) spectroscopy methods provide the primary viable alternative means to determine molecular structures. However, misinterpretation of NMR data—as a result of poor data quality, inappropriate experiment selection, or investigator bias—has led to burgeoning numbers of structure revision reports. Clearly, the development of a method to more effectively use NMR data and simultaneously quell reports of incorrect structures would be highly beneficial. RATIONALE Combining computer-assisted structure elucidation (CASE) algorithms and density functional theory (DFT) calculations with measured anisotropic NMR parameters, specifically residual dipolar coupling (RDC), and residual chemical shift anisotropy (RCSA) holds strong promise as an effective alternative means of assigning three-dimensional (3D) molecular structures. Anisotropic NMR data provide a spatial view of the relative orientations between bonds (RDCs) and chemical shielding tensors (RCSAs), regardless of the separation between the bonds and atoms, respectively. Hence, these data are sensitive reporters of global structural validity. The combination of DFT calculations and anisotropic NMR data represents an orthogonal approach to conventional NMR data interpretation that is not subject to the interpretational biases of human investigators and, as such, mitigates the risk of incorrect structure assignments. RESULTS Anisotropic NMR data can be used directly to evaluate the validity of investigator-proposed structures or can be combined with a CASE program in conjunction with DFT calculations for both structural proposal and validation. The RDC data are typically used to structurally define C-H bond vectors, whereas the RCSA data report on the chemical shift tensors of both protonated and nonprotonated carbons, the latter only accessible by long-range RDC data that are difficult to measure and interpret. These data are used to evaluate a given structure proposal on the basis of the agreement between the experimentally measured data and theoretical values calculated for the corresponding 3D DFT models. When structures generated by a CASE program are being considered, the method only requires a multidimensional NMR data set of sufficient quality and sophistication to allow the CASE program to generate a set of proposals that contains the correct structure of the molecule. The molecules being studied should also be amenable to modern DFT calculations for 3D model building. The CASE program output is sorted on the basis of cumulative error between experimental and calculated 13C data for the ensemble of structures generated, and the best-fitting molecules are subsequently subjected to DFT calculation for analysis. Results obtained using the proposed method demonstrate its applicability to a diverse range of complex molecules, each of which challenged the investigators originally reporting the structures. CONCLUSION The technique described here represents a potential paradigm shift from conventional NMR data interpretation and can provide an unequivocal and unbiased confirmation of interatomic connectivity and relative configuration for organic and natural product structures. The principle of residual dipolar coupling (RDC)–based model differentiation is shown using aquatolide as an example. The revised structure of aquatolide is shown on the top left, with the originally reported structure shown on the bottom left. The selected C-H bond vectors in the two structures have different orientations, as is evident after translating them to the same origin in the middle diagrams. Theoretical RDC values associated with these vectors can be calculated for each model on the basis of the experimentally determined alignment tensor. Correlation data are shown for only the four highlighted CH groups, although the alignment tensor was actually determined using all available data. The originally proposed (incorrect) structure clearly shows poorer agreement between the calculated and experimental data. Assignment of complex molecular structures from nuclear magnetic resonance (NMR) data can be prone to interpretational mistakes. Residual dipolar couplings and residual chemical shift anisotropy provide a spatial view of the relative orientations between bonds and chemical shielding tensors, respectively, regardless of separation. Consequently, these data constitute a reliable reporter of global structural validity. Anisotropic NMR parameters can be used to evaluate investigators’ structure proposals or structures generated by computer-assisted structure elucidation. Application of the method to several complex structure assignment problems shows promising results that signal a potential paradigm shift from conventional NMR data interpretation, which may be of particular utility for compounds not amenable to x-ray crystallography.