Aaptolines A and B,Two New Quinoline Alkaloids from the Marine Sponge Aaptos aaptos

Two new quinoline alkaloids, aaptolines A and B, were isolated from the marine sponge Aaptos aaptos. Their structures were determined by HR‐ESI‐MS data, NMR analysis, and X‐ray crystallography. Structurally, aaptoline A is characterized as having a quinoline skeleton fused with a 1,4‐dioxane motif at the C(7)?C(8) position, whereas aaptoline B possessed an intriguing 1H‐pyrrolo[2,3‐g]quinoline moiety. The cytotoxic assay of these compounds showed no cytotoxicity towards HepG2, A549, and PC9 cancer cell lines and had IC₅₀ values greater than 20 μm .     

New Indole Diketopiperazine Alkaloids from Soft Coral‐Associated Epiphytic Fungus Aspergillus sp. EGF 15‐0‐3

Three new indole diketopiperazine alkaloids, 11‐methylneoechinulin E and variecolorin M, and (+)‐variecolorin G, along with 12 known analogs, were isolated from a soft coral‐associated epiphytic fungus Aspergillus sp. EGF 15‐0‐3. The structures of the new compounds were unambiguously established by extensive spectroscopic analyses including HR‐ESI‐MS, 1D and 2D NMR spectroscopy and optical rotation measurements. The absolute configurations of (+)‐ and (?)‐variecolorin G were determined by experimental and quantum‐chemical ECD investigations and single‐crystal X‐ray diffraction analysis. Variecolorin G is a pair of enantiomeric mixtures with a ratio of 1 : 2. Moreover, (+)‐neoechinulin A is firstly reported as a natural product. The cytotoxic activities of all the isolated compounds against NCI‐H1975 gefitinib resistance (NCI‐H1975/GR) cell lines were preliminarily evaluated by MTT method.     

A comparative analysis of the equilibrium dynamics of a designed protein inferred from NMR,X‐ray,and computations

A detailed analysis of high‐resolution structural data and computationally predicted dynamics was carried out for a designed sugar‐binding protein. The mean‐square deviations in the positions of residues derived from nuclear magnetic resonance (NMR) models and those inferred from X‐ray crystallographic B‐factors for two different crystal forms were compared with the predictions based on the Gaussian Network Model (GNM) and the results from molecular dynamics (MD) simulations. GNM systematically yielded a higher correlation than MD, with experimental data, suggesting that the lack of atomistic details in the coarse‐grained GNM is more than compensated for by the mathematically exact evaluation of fluctuations using the native contacts topology. Evidence is provided that particular loop motions are curtailed by intermolecular contacts in the crystal environment causing a discrepancy between theory and experiments. Interestingly, the information conveyed by X‐ray crystallography becomes more consistent with NMR models and computational predictions when ensembles of X‐ray models are considered. Less precise (broadly distributed) ensembles indeed appear to describe the accessible conformational space under native state conditions better than B‐factors. Our results highlight the importance of using multiple conformations obtained by alternative experimental methods, and analyzing results from both coarse‐grained models and atomic simulations, for accurate assessment of motions accessible to proteins under native state conditions. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Sesquiterpenes from the Leaves of Magnolia delavayi Franch. and Their Cytotoxic Activities

Thirteen sesquiterpenes including eight new ones, magnodelavins A?H ( 1 – 8 ), were obtained from the 95 % ethanolic extract of the leaves of Magnolia delavayi Franch . The structures of the new compounds were determined by exhaustive ¹H‐, ¹³C‐, 2D‐NMR, UV, IR, and HR‐ESI‐MS data, as well as X‐ray crystallographic analysis. Compounds 9 and 10 showed potent cytotoxic activities against HL‐60, A‐549, SMMC‐7721, MCF‐7, and SW480 human cancer cell lines in vitro using MTS assay.     

New Acetophenone Derivatives from Acronychia oligophlebia and Their Anti‐inflammatory and Antioxidant Activities

Seven new acetophenone derivatives (acroliones A – G, 1  –  7 ) and three known ones ( 8  –  10 ) were isolated from the leaves of Acronychia oligophlebia. Their structures were elucidated based on extensive spectroscopic analyses (IR, UV, HR‐ESI‐MS, 1D‐ and 2D‐NMR), X‐ray diffraction and comparison with literature data. The anti‐inflammatory and antioxidant activities of all isolates were evaluated.     

Five New C19‐Diterpenoid Alkaloids from Delphinium tianshanicum W.T.Wang

Five new diterpenoid alkaloids, tianshanitines A‐E ( 1  –  5 ), along with ten known compounds ( 6  –  15 ), were isolated from the EtOH extracts of the whole plant of Delphinium tianshanicum W.T.Wang . Their structures were determined based on extensive spectroscopic analyses, including 1D‐ and 2D‐NMR, HR‐ESI‐MS, and the structure of tianshanitine C ( 3 ) was confirmed by X‐ray diffraction analysis. Tianshanitine A ( 1 ) is the first example of natural diterpenoid alkaloid containing a benzoyl group at C(1) position. Tianshanitine B ( 2 ) is a rare natural diterpenoid alkaloid bearing a OH group at C(16) position. Compounds 1  –  5 , 6 , 8 , 10 , 12 and 14 were evaluated for cytotoxicity against HCT116, MCF‐7 and HepG2 human cancer cell lines.     

Solution and solid state conformational preferences of a family of cyclic disulphide bridged tetrapeptides

A set of cyclic tetrapeptides of the general form cyclo (Boc‐Cys‐Pro‐ X ‐Cys‐OMe) with X being L‐ / D‐Ala , L‐ / D‐Val , and L‐ / D‐Trp was synthesized. These peptides serve as model systems for structure elucidation in solution and feature a variety of structural motifs — namely a β‐turn with intramolecular hydrogen bonding interactions, cis/trans isomerism, and a disulphide bond. In this work, we performed a comprehensive structural analysis focussing on their β‐turn conformational preferences using NMR, VCD, and Raman spectroscopy. Our results provide evidence for a strong influence of a single stereocenter on the structures of the peptides whereas solvent polarity does not significantly affect them. Additionally, the solid state conformational preferences were studied by crystal structure analysis. Overall, a general trend for the conformational preferences of this set of peptides can be concluded from the results of the complementary investigations.     

Cytotoxic (9βH)‐Pimarane and (9βH)‐17‐Norpimarane Diterpenes from the Tuber of Icacina trichantha

Three (9βH)‐pimaranes, 1, 2 , and 3 , and two (9βH)‐17‐norpimaranes, 4 and 5 , belonging to a rare compound class in nature, were obtained from the tubers of Icacina trichantha for the first time. Compound 1 is a new natural product, and 2 – 5 have been previously reported. The structures were elucidated based on NMR and MS data, and optical rotation values. The absolute configurations of (9βH)‐pimaranes were unambiguously established based on X‐ray crystallographic analysis. Full NMR signal assignments for the known compounds 2, 4 , and 5 , which were not available in previous publications, are also reported. All five isolates displayed cytotoxic activities on MDA‐MB‐435 cells (IC₅₀ 0.66–6.44 μM ), while 2, 3 , and 4 also exhibited cytotoxicities on HT‐29 cells (IC₅₀ 3.00–4.94 μM ).     

Rapid screening of lignans from Phyllanthus myrtifolius and stilbenoids from Syagrus romanzoffiana by HPLC-SPE-NMR

Introduction – Application of on‐line solid‐phase extraction (SPE) as an interface between HPLC and NMR has gained great improvement in solving sensitivity problems and signal interferences by the eluents. Objective – Rapid analysis and characterisation by HPLC‐SPE‐NMR and LC/MS of the arylnaphthalene‐type lignans present in Phyllanthus myrtifolius and the minor stilbenoids present in the polyphenol‐rich fraction from the ethanol extract of the seeds of Syagrus romanzoffiana. Methodology – Pretreatment of fractions by liquid–liquid partitioning, followed by Sephadex LH‐20 fractionation, was found very useful to facilitate the focusing and analysis of the polyphenolic fraction. HPLC‐DAD‐SPE‐NMR (400 MHz and 600 MHz) analysis was carried out using an Agilent 1100 liquid chromatography, followed by a Prospekt 2 automated solid‐phase extraction unit, containing 96 HySphere‐Resin GP cartridges (10 × 2 mm, 10–12 µm), which was connected to a 120 or 60 µL LC probe. Results – Seven arylnaphthalene‐type lignans from the chloroform‐soluble fraction of P. myrtifolius and nine stilbenoids from a polyphenol‐rich butanol‐soluble fraction of the seeds of S. romanzoffiana were characterised. Conclusion – HPLC‐SPE‐NMR associated with HR‐ESI/MS, which consumed only analytical amounts of partially purified mixtures, was demonstrated to be a good tool for rapid screening of both known and new natural products. Copyright © 2011 John Wiley & Sons, Ltd.     

X‐ray vs. NMR structures as templates for computational protein design

Certain protein‐design calculations involve using an experimentally determined high‐resolution structure as a template to identify new sequences that can adopt the same fold. This approach has led to the successful design of many novel, well‐folded, native‐like proteins. Although any atomic‐resolution structure can serve as a template in such calculations, most successful designs have used high‐resolution crystal structures. Because there are many proteins for which crystal structures are not available, it is of interest whether nuclear magnetic resonance (NMR) templates are also appropriate. We have analyzed differences between using X‐ray and NMR templates in side‐chain repacking and design calculations. We assembled a database of 29 proteins for which both a high‐resolution X‐ray structure and an ensemble of NMR structures are available. Using these pairs, we compared the rotamericity, χ₁‐angle recovery, and native‐sequence recovery of X‐ray and NMR templates. We carried out design using RosettaDesign on both types of templates, and compared the energies and packing qualities of the resulting structures. Overall, the X‐ray structures were better templates for use with Rosetta. However, for ～20% of proteins, a member of the reported NMR ensemble gave rise to designs with similar properties. Re‐evaluating RosettaDesign structures with other energy functions indicated much smaller differences between the two types of templates. Ultimately, experiments are required to confirm the utility of particular X‐ray and NMR templates. But our data suggest that the lack of a high‐resolution X‐ray structure should not preclude attempts at computational design if an NMR ensemble is available. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures

Statistical potentials that embody torsion angle probability densities in databases of high‐quality X‐ray protein structures supplement the incomplete structural information of experimental nuclear magnetic resonance (NMR) datasets. By biasing the conformational search during the course of structure calculation toward highly populated regions in the database, the resulting protein structures display better validation criteria and accuracy. Here, a new statistical torsion angle potential is developed using adaptive kernel density estimation to extract probability densities from a large database of more than 10⁶ quality‐filtered amino acid residues. Incorporated into the Xplor‐NIH software package, the new implementation clearly outperforms an older potential, widely used in NMR structure elucidation, in that it exhibits simultaneously smoother and sharper energy surfaces, and results in protein structures with improved conformation, nonbonded atomic interactions, and accuracy.     

Limited proteolysis analysis of the ribosome is affected by subunit association

Our understanding of the structural organization of ribosome assembly intermediates, in particular those intermediates that result from misfolding leading to their eventual degradation within the cell, is limited because of the lack of methods available to characterize assembly intermediate structures. Because conventional structural approaches, such as NMR, X‐ray crystallography, and cryo‐EM, are not ideally suited to characterize the structural organization of these flexible and sometimes heterogeneous assembly intermediates, we have set out to develop an approach combining limited proteolysis with matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) that might be applicable to ribonucleoprotein complexes as large as the ribosome. This study focuses on the limited proteolysis behavior of appropriately assembled ribosome subunits. Isolated subunits were analyzed using limited proteolysis and MALDI‐MS and the results were compared with previous data obtained from 70S ribosomes. Generally, ribosomal proteins were found to be more stable in 70S ribosomes than in their isolated subunits, consistent with a reduction in conformational flexibility on subunit assembly. This approach demonstrates that limited proteolysis combined with MALDI‐MS can reveal structural changes to ribosomes on subunit assembly or disassembly, and provides the appropriate benchmark data from 30S, 50S, and 70S proteins to enable studies of ribosome assembly intermediates. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 410–422, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Structural elucidation of novel degradation product of brotizolam

When the drug product of brotizolam (1) is decomposed according to the interview form and patent, hydrolysate (2) is obtained, but its physicochemical data are still missing. To elucidate the structure based on a spectroscopic approach, the above-mentioned degradation product was isolated and applied to the structural analysis. As a result, the structure of decomposed product was found to be different from that of 2. In this report, its isolation and structure elucidation by NMR and MS spectra are described.     

Structure Elucidation of the Main Tetrahydroxyxanthones of Hypericum Seeds and Investigations into the Testa Structure

Seeds from Hypericum species have recently been identified as an interesting source of xanthone derivatives. Extraction of seeds from H. perforatum with MeOH and subsequent concentration via polyamide adsorption yielded a fraction enriched in tetrahydroxyxanthones (THX), which were further semipurified by silica gel chromatography. Based on tentative structure assignment of the two main THX X1 and X2 by NMR a total synthesis was performed for both compounds (THX 1 and 2 , respectively), starting with an Ullmann ether synthesis. The synthesized 1 and 2 were characterized via 1D‐ and 2D‐NMR methods as well as by LC/HR‐MS analysis and proven to be 1,4,6,7‐THX ( 1 ) and 1,2,6,7‐THX ( 2 ). Final structure assignment of the natural Hypericum THX constituents was accomplished by comparing chromatographic and spectroscopic data (LC/MSⁿ and GC/MS) with those of 1 and 2 which were obtained by synthesis. Beyond, investigations into the seeds of H. perforatum and H. tetrapterum by scanning electron microscopy (SEM) provided insights of the structure of the testa (seed coat), which is established by two cell layers, with the lignified sclerenchyma presumably being the depository of the xanthones.     

Penicamedine A,a Highly Oxygenated Hexacyclic Indole Alkaloid from Penicillium camemberti

A highly oxygenated hexacyclic indole alkaloid, penicamedine A ( 1 ), bearing a rare furan ring, was isolated from the culture broth of Penicillium camemberti, together with two known analogs, iso‐α‐cyclopiazonic acid ( 2 ) and cyclopiazonic acid ( 3 ). The structure of 1 was elucidated by comprehensive spectroscopic analyses including NMR and HR‐ESI‐MS. Its absolute configuration was further confirmed unambiguously by single‐crystal X‐ray diffraction analysis. Compound 1 was evaluated for anti‐HIV activity with p24 assays and tested for cytotoxic activities against five human cancer cell lines, including HL‐60, SMMC‐7721, A‐549, MCF‐7, SW480, and the immortalized non‐cancerous human pulmonary epithelial cell line BEAS‐2B by MTS method.     

Hypofolins A – L,ent‐Labdane Diterpenoids from the Roots of Hypoestes phyllostachya ‘Pink Splash’

Twelve new ent‐labdane diterpenoids, hypofolins A – F ( 1 – 6 ) and hypofolins G – L ( 7a / 7b , 8a / 8b , and 9a / 9b ), were isolated from the roots of Hypoestes phyllostachya ‘Pink Splash’. Their structures were elucidated by extensive 1D‐ and 2D‐NMR spectroscopic and HR‐MS data. The absolute configurations of 1 , 2 , 5 , and 7a / 7b were determined by single crystal X‐ray diffraction and ECD analysis, as well as chemical transformations. Compounds 7a / 7b , 8a / 8b , and 9a / 9b were isolated as three pairs of interconverting mixture of two isomers between ketone and hemiketal types. Compound 1 showed weak cytotoxicity against SMMC‐7721 cell line with IC₅₀ value of 31.40 μm .     

Measuring membrane protein bond orientations in nanodiscs via residual dipolar couplings

Membrane proteins are involved in numerous vital biological processes. To understand membrane protein functionality, accurate structural information is required. Usually, structure determination and dynamics of membrane proteins are studied in micelles using either solution state NMR or X‐ray crystallography. Even though invaluable information has been obtained by this approach, micelles are known to be far from ideal mimics of biological membranes often causing the loss or decrease of membrane protein activity. Recently, nanodiscs, which are composed of a lipid bilayer surrounded by apolipoproteins, have been introduced as a more physiological alternative than micelles for NMR investigations on membrane proteins. Here, we show that membrane protein bond orientations in nanodiscs can be obtained by measuring residual dipolar couplings (RDCs) with the outer membrane protein OmpX embedded in nanodiscs using Pf1 phage as an alignment medium. The presented collection of membrane protein RDCs in nanodiscs represents an important step toward more comprehensive structural and dynamical NMR‐based investigations of membrane proteins in a natural bilayer environment.     

Racemic crystallography of synthetic protein enantiomers used to determine the X‐ray structure of plectasin by direct methods

We describe the use of racemic crystallography to determine the X‐ray structure of the natural product plectasin, a potent antimicrobial protein recently isolated from fungus. The protein enantiomers L ‐plectasin and D ‐plectasin were prepared by total chemical synthesis; interestingly, L ‐plectasin showed the expected antimicrobial activity, while D ‐plectasin was devoid of such activity. The mirror image proteins were then used for racemic crystallization. Synchrotron X‐ray diffraction data were collected to atomic resolution from a racemic plectasin crystal; the racemate crystallized in the achiral centrosymmetric space group P1 with one L ‐plectasin molecule and one D ‐plectasin molecule forming the unit cell. Dimer‐like intermolecular interactions between the protein enantiomers were observed, which may account for the observed extremely low solvent content (13%–15%) and more highly ordered nature of the racemic crystals. The structure of the plectasin molecule was well defined for all 40 amino acids and was generally similar to the previously determined NMR structure, suggesting minimal impact of the crystal packing on the plectasin conformation.     

Parallel screening and optimization of protein constructs for structural studies

A major challenge in structural biology remains the identification of protein constructs amenable to structural characterization. Here, we present a simple method for parallel expression, labeling, and purification of protein constructs (up to 80 kDa) combined with rapid evaluation by NMR spectroscopy. Our approach, which is equally applicable for manual or automated implementation, offers an efficient way to identify and optimize protein constructs for NMR or X‐ray crystallographic investigations.     

NMR studies of dextromethorphan in both isotropic and anisotropic states

Herein, we present the solution‐state NMR studies on dextromethorphan ( 1 ) under both isotropic and anisotropic conditions. From the measurement of 22 residual dipolar couplings using a stretched polystyrene gel (PS), we show that accurate and detailed structural information is readily determined including the relative stereochemical assignments of chiral centers, validation of diastereomer configuration, and the stereospecific assignment of the seven pairs of prochiral protons. This utility of PS gels is thus showcased to obtain rapid, accurate conformational, and relative configuration information in this important class of compounds without recourse to X‐ray analysis. Chirality 2010. © 2009 Wiley‐Liss, Inc.