Molecular basis for DarT ADP-ribosylation of a DNA base.

ADP-ribosyltransferases use NAD+ to catalyse substrate ADP-ribosylation1, and thereby regulate cellular pathways or contribute to toxin-mediated pathogenicity of bacteria2-4. Reversible ADP-ribosylation has traditionally been considered a protein-specific modification5, but recent in vitro studies have suggested nucleic acids as targets6-9. Here we present evidence that specific, reversible ADP-ribosylation of DNA on thymidine bases occurs in cellulo through the DarT-DarG toxin-antitoxin system, which is found in a variety of bacteria (including global pathogens such as Mycobacterium tuberculosis, enteropathogenic Escherichia coli and Pseudomonas aeruginosa)10. We report the structure of DarT, which identifies this protein as a diverged member of the PARP family. We provide a set of high-resolution structures of this enzyme in ligand-free and pre- and post-reaction states, which reveals a specialized mechanism of catalysis that includes a key active-site arginine that extends the canonical ADP-ribosyltransferase toolkit. Comparison with PARP-HPF1, a well-established DNA repair protein ADP-ribosylation complex, offers insights into how the DarT class of ADP-ribosyltransferases evolved into specific DNA-modifying enzymes. Together, our structural and mechanistic data provide details of this PARP family member and contribute to a fundamental understanding of the ADP-ribosylation of nucleic acids. We also show that thymine-linked ADP-ribose DNA adducts reversed by DarG antitoxin (functioning as a noncanonical DNA repair factor) are used not only for targeted DNA damage to induce toxicity, but also as a signalling strategy for cellular processes. Using M. tuberculosis as an exemplar, we show that DarT-DarG regulates growth by ADP-ribosylation of DNA at the origin of chromosome replication.

Spectroscopic studies reveal details of substrate-induced conformational changes distant from the active site in isopenicillin N synthase.

Isopenicillin N synthase (IPNS) catalyzes formation of the ß-lactam and thiazolidine rings of isopenicillin N from its linear tripeptide l-δ-(α-aminoadipoyl)-l-cysteinyl-d-valine (ACV) substrate in an iron- and dioxygen (O2)-dependent four-electron oxidation without precedent in current synthetic chemistry. Recent X-ray free-electron laser studies including time-resolved serial femtosecond crystallography show that binding of O2 to the IPNS-Fe(II)-ACV complex induces unexpected conformational changes in α-helices on the surface of IPNS, in particular in α3 and α10. However, how substrate binding leads to conformational changes away from the active site is unknown. Here, using detailed 19F NMR and electron paramagnetic resonance experiments with labeled IPNS variants, we investigated motions in α3 and α10 induced by binding of ferrous iron, ACV, and the O2 analog nitric oxide, using the less mobile α6 for comparison. 19F NMR studies were carried out on singly and doubly labeled α3, α6, and α10 variants at different temperatures. In addition, double electron-electron resonance electron paramagnetic resonance analysis was carried out on doubly spin-labeled variants. The combined spectroscopic and crystallographic results reveal that substantial conformational changes in regions of IPNS including α3 and α10 are induced by binding of ACV and nitric oxide. Since IPNS is a member of the structural superfamily of 2-oxoglutarate-dependent oxygenases and related enzymes, related conformational changes may be of general importance in nonheme oxygenase catalysis.

Counterion-Mediated Enantioconvergent Synthesis of Axially Chiral Medium Rings.

There are few enantioconvergent reactions in which racemic substrates bearing multiple stereochemical features are converted into products with high levels of diastereo- and enantiocontrol. Here, we disclose a process for the highly enantio- and diastereoselective syntheses of medium ring lactams via an intramolecular counterion-directed C-alkylation reaction. The treatment of racemic biaryl anilides that exist as a complex mixture of enantiomers and diastereoisomeric conformers by virtue of multiple axes of restricted rotation with a quinidine-derived ammonium salt under basic conditions affords medium ring lactams bearing elements of both axial and point chirality via an enolate-driven configurational relaxation process. Thermal equilibration of the syn- and anti-product diasteroisomers has demonstrated that the barriers to bowl inversion are >124 kJ mol-1. We propose that the chiral ammonium salt differentiates between a complex and rapidly equilibrating mixture of enolate and rotational isomers, ultimately leading to highly enantioselective alkylative ring closure. This dynamic and enantioconvergent process offers an operationally simple approach to the synthesis of valuable chiral medium ring lactams for which there are few catalytic and enantioselective approaches.

Modular Pulse Program Generation for NMR Supersequences.

NMR supersequences allow multiple 2D NMR data sets to be acquired in greatly reduced experiment durations through tailored detection of NMR responses within concatenated modules. In NOAH (NMR by Ordered Acquisition using 1H detection) experiments, up to five modules can be combined (or even more when parallel modules are employed), which in theory leads to thousands of plausible supersequences. However, constructing a pulse program for a supersequence is highly time-consuming, requires specialized knowledge, and is error-prone due to its complexity; this has prevented the true potential of the NOAH concept from being fully realized. We introduce here an online tool named GENESIS (GENEration of Supersequences In Silico), available via https://nmr-genesis.co.uk, which systematically generates pulse programs for arbitrary NOAH supersequences compatible with Bruker spectrometers. The GENESIS website provides a unified "one-stop" interface where users may obtain customized supersequences for specific applications, together with all associated acquisition and processing scripts, as well as detailed instructions for running NOAH experiments. Furthermore, it enables the rapid dissemination of new developments in NOAH sequences, such as new modules or improvements to existing modules. Here, we present several such enhancements, including options for solvent suppression, new modules based on pure shift NMR, and improved artifact reduction in HMBC and HMQC modules.

Polyyne [3]Rotaxanes: Synthesis via Dicobalt Carbonyl Complexes and Enhanced Stability.

New strategies for synthesizing polyyne polyrotaxanes are being developed as an approach to stable carbyne "insulated molecular wires". Here we report an active metal template route to polyyne [3]rotaxanes, using dicobalt carbonyl masked alkyne equivalents. We synthesized two [3]rotaxanes, both with the same C28 polyyne dumbbell component, one with a phenanthroline-based macrocycle and one using a 2,6-pyridyl cycloparaphenylene nanohoop. The thermal stabilities of the two rotaxanes were compared with that of the naked polyyne dumbbell in decalin at 80 °C, and the nanohoop rotaxane was found to be 4.5 times more stable.

Clerodane Diterpenoids from an Edible Plant Justicia insularis: Discovery, Cytotoxicity, and Apoptosis Induction in Human Ovarian Cancer Cells.

OBJECTIVES: The toxicity of chemotherapeutic anticancer drugs is a serious issue in clinics. Drug discovery from edible and medicinal plants represents a promising approach towards finding safer anticancer therapeutics. Justicia insularis T. Anderson (Acanthaceae) is an edible and medicinal plant in Nigeria. This study aims to discover cytotoxic compounds from this rarely explored J. insularis and investigate their underlying mechanism of action. METHODS: The cytotoxicity of the plant extract was evaluated in human ovarian cancer cell lines and normal human ovarian surface epithelia (HOE) cells using a sulforhodamine B assay. Bioassay-guided isolation was carried out using column chromatography including HPLC, and the isolated natural products were characterized using GC-MS, LC-HRMS, and 1D/2D NMR techniques. Induction of apoptosis was evaluated using Caspase 3/7, 8, and 9, and Annexin V and PI based flow cytometry assays. SwissADME and SwissTargetPrediction web tools were used to predict the molecular properties and possible protein targets of identified active compounds. Key finding: The two cytotoxic compounds were identified as clerodane diterpenoids: 16(α/ß)-hydroxy-cleroda-3,13(14)Z-dien-15,16-olide (1) and 16-oxo-cleroda-3,13(14)E-dien-15-oic acid (2) from the Acanthaceous plant for the first time. Compound 1 was a very abundant compound (0.7% per dry weight of plant material) and was shown to be more potent than compound 2 with IC50 values in the micromolar range against OVCAR-4 and OVCAR-8 cancer cells. Compounds 1 and 2 were less cytotoxic to HOE cell line. Both compounds induced apoptosis by increasing caspase 3/7 activities in a concentration dependent manner. Compound 1 further increased caspase 8 and 9 activities and apoptosis cell populations. Compounds 1 and 2 are both drug like, and compound 1 may target various proteins including a kinase. CONCLUSIONS: Clerodane diterpenoids (1 and 2) in J. insularis were identified as cytotoxic to ovarian cancer cells via the induction of apoptosis, providing an abundant and valuable source of hit compounds for the treatment of ovarian cancer.

Global Aromaticity in a Partially Fused 8-Porphyrin Nanoring.

Template-directed synthesis has been used to prepare a fully π-conjugated cyclic porphyrin octamer, composed of both ß,meso,ß-edge-fused porphyrin tape units and butadiyne-linked porphyrins. The UV-vis-NIR spectra of this partially fused nanoring show that π-conjugation extends around the whole macrocycle, and that it has a smaller HOMO-LUMO gap than its all-butadiyne-linked analogue, as predicted by TD-DFT calculations. The 1H NMR shifts of the bound templates confirm the disrupted aromaticity of the edge-fused porphyrins in the neutral nanoring. NMR oxidation titrations reveal the presence of a global paratropic ring current in its 4+ and 8+ oxidation states and of a global diatropic ring current in the 6+ state of the partially fused ring. The paratropic ring current in the 4+ oxidation state is about four times stronger than that in the all-butadiyne-linked cyclic octamer complex, whereas the diatropic current in the 6+ state is about 40% weaker. Two isomeric K-shaped tetrapyridyl templates with trifluoromethyl substituents at different positions were used to probe the distribution of the ring current in the 4+, 6+, and 8+ oxidation states by 19F NMR, demonstrating that the ring currents are global and homogeneous.

Reliable, high-quality suppression of NMR signals arising from water and macromolecules: application to bio-fluid analysis.

Analysis of metabolites in biofluids using nuclear magnetic resonance often requires the suppression of obscuring signals arising from water and macromolecules. This paper analyses the limitations of the pulse sequence most commonly used to achieve such suppression (presat-CPMG) and proposes new pulse sequences that do not share those limitations. The utility of these improved pulse sequences is demonstrated in a metabolomic study of multiple sclerosis (MS) patients.

Triplet NOAH supersequences optimised for small molecule structure characterisation.

A series of NMR supersequences are presented for the time-efficient structure characterisation of small molecules in the solution state. These triplet sequences provide HMBC, HSQC, and one homonuclear correlation experiment of choice according to the NMR by Ordered Acquisition using 1 H detection principle. The experiments are demonstrated to be compatible with non-uniform sampling schemes and may be acquired and processed under full automation.

Template-Directed Synthesis of a Conjugated Zinc Porphyrin Nanoball.

We report the template-directed synthesis of a π-conjugated 14-porphyrin nanoball. This structure consists of two intersecting nanorings containing six and 10 porphyrin units. Fluorescence upconversion spectroscopy experiments demonstrate that electronic excitation delocalizes over the whole three-dimensional π system in less than 0.3 ps if the nanoball is bound to its templates or over 2 ps if the nanoball is empty.

NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.

Even though NMR has found countless applications in the field of small molecule characterization, there is no standard file format available for the NMR data relevant to structure characterization of small molecules. A new format is therefore introduced to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure. These NMR parameters, which we shall call NMReDATA (for nuclear magnetic resonance extracted data), include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times, and diffusion rates. The file format is an extension of the existing Structure Data Format, which is compatible with the commonly used MOL format. The association of an NMReDATA file with the raw and spectral data from which it originates constitutes an NMR record. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, allowing automatic verification of published results, and for assisting the constitution of highly needed open-source structural databases.

Measuring Spin Relaxation Rates Using Satellite Exchange NMR Spectroscopy.

An approach to the indirect measurement of nuclear spin relaxation rates of low-magnetogyric ratio (γ) nuclei using the process of satellite exchange is described. The method does not require the observation of, or even the ability to provide radio-frequency pulses to, the low-γ nucleus, but requires this to be scalar coupled to an NMR observable nucleus, such as 31 P or 1 H, making it especially attractive for the study of diamagnetic transition metals. In situations where spin relaxation is dominated by chemical shift anisotropy (CSA), the determination of the longitudinal spin relaxation time constant (T1 ) of the metal becomes possible, as illustrated for 195 Pt and 107/109 Ag.

NOAH: NMR Supersequences for Small Molecule Analysis and Structure Elucidation.

Nested NMR experiments combining up to five conventional NMR pulse sequences into one supersequence are introduced. The core 2D NMR techniques routinely employed in small molecule NMR spectroscopy, such as HSQC, HMQC, HMBC, COSY, NOESY, TOCSY, and similar, can be recorded in a single measurement. In this way the data collection time may be dramatically reduced and sample throughput increased for basic NMR applications, such as structure elucidation and verification in synthetic, medicinal, and natural product chemistry.

Self-Assembly of Russian Doll Concentric Porphyrin Nanorings.

Electronic communication between concentric macrocycles with wave functions that extend around their circumferences can lead to remarkable behavior, as illustrated by multiwalled carbon nanotubes and photosynthetic chlorophyll arrays. However, it is difficult to hold one π-conjugated molecular ring inside another. Here, we show that ring-in-ring complexes, consisting of a 6-porphyrin ring locked inside a 12-porphyrin ring, can be assembled by placing different metals in the two rings (zinc and aluminum). A bridging ligand with carboxylate and imidazole binding sites forms spokes between the two rings, resulting in a highly cooperative supramolecular self-assembly process. Excitation is transferred from the inner 6-ring to the outer 12-ring of this Russian doll complex within 40 ps. These complexes lead to a form of template-directed synthesis in which one nanoring promotes formation of a larger concentric homologous ring; here, the effective template is an eight-component noncovalent assembly. Russian doll templating provides a new approach to amplifying the size of a covalent nanostructure.

Caterpillar track complexes in template-directed synthesis and correlated molecular motion.

Small alterations to the structure of a star-shaped template totally change its mode of operation. The hexapyridyl template directs the conversion of a porphyrin dimer to the cyclic hexamer, but deleting one pyridine site changes the product to the cyclic decamer, while deleting two binding sites changes the product to the cyclic octamer. This surprising switch in selectivity is explained by the formation of 2:1 caterpillar track complexes, in which two template wheels bind inside the nanoring. Caterpillar track complexes can also be prepared by binding the hexapyridyl template inside the 8- and 10-porphyrin nanorings. NMR exchange spectroscopy (EXSY) experiments show that these complexes exhibit correlated motion, in which the conrotatory rotation of the two template wheels is coupled to rotation of the nanoring track. In the case of the 10-porphyrin system, the correlated motion can be locked by binding palladium(II) dichloride between the two templates.

The NOAH HSQC-COSY module revisited: A theoretical and practical comparison of pulse sequences.

NMR supersequences, as exemplified by the NOAH (NMR by Ordered Acquisition using 1H detection) technique, are a powerful way of acquiring multiple 2D data sets in much shorter durations. This is accomplished through targeted excitation and detection of the magnetisation belonging to specific isotopologues ('magnetisation pools'). Separately, the HSQC-COSY experiment has recently seen an increase in popularity due to the high signal dispersion in the indirect dimension and the removal of ambiguity traditionally associated with HSQC-TOCSY experiments. Here, we describe how the HSQC-COSY experiment can be integrated as a 'module' within NOAH supersequences. The benefits and drawbacks of several different pulse sequence implementations are discussed, with a particular focus on how sensitivities of other modules in the same supersequence are affected.

A discrete three-layer stack aggregate of a linear porphyrin tetramer: solution-phase structure elucidation by NMR and X-ray scattering.

Formation of stacked aggregates can dramatically alter the properties of aromatic π-systems, yet the solution-phase structure elucidation of these aggregates is often impossible because broad distributions of species are formed, giving uninformative spectroscopic data. Here, we show that a butadiyne-linked zinc porphyrin tetramer forms a remarkably well-defined aggregate, consisting of exactly three molecules, in a parallel stacked arrangement (in chloroform at room temperature; concentration 1 mM-0.1 µM). The aggregate has a mass of 14.7 kDa. Unlike most previously reported aggregates, it gives sharp NMR resonances and aggregation is in slow exchange on the NMR time scale. The structure was elucidated using a range of NMR techniques, including diffusion-editing, (1)H-(29)Si HMBC, (1)H-(1)H COSY, TOCSY and NOESY, and (1)H-(13)C edited HSQC spectroscopy. Surprisingly, the (1)H-(1)H COSY spectrum revealed many long-range residual dipolar couplings (RDCs), and detailed analysis of magnetic field-induced (1)H-(13)C RDCs provided further evidence for the structural model. The size and shape of the aggregate is supported by small-angle X-ray scattering (SAXS) data. It adopts a geometry that maximizes van der Waals contact between the porphyrins, while avoiding clashes between side chains. The need for interdigitation of the side chains prevents formation of stacks consisting of more than three layers. Although a detailed analysis has only been carried out for one compound (the tetramer), comparison with the NMR spectra of other oligomers indicates that they form similar three-layer stacks. In all cases, aggregation can be prevented by addition of pyridine, although at low pyridine concentrations, disaggregation takes many hours to reach equilibrium.

A general scheme for generating NMR supersequences combining high- and low-sensitivity experiments.

NOAH supersequences are a way of collecting multiple 2D NMR experiments in a single measurement. So far, this approach has been limited to experiments with comparable sensitivity. Here, we propose a scheme which overcomes this limitation, combining experiments with very different sensitivities such as 1,1-ADEQUATE, 15N HMBC, and 13C HSQC.

Cyclic peptides target the aromatic cage of a PHD-finger reader domain to modulate epigenetic protein function.

Plant homeodomain fingers (PHD-fingers) are a family of reader domains that can recruit epigenetic proteins to specific histone modification sites. Many PHD-fingers recognise methylated lysines on histone tails and play crucial roles in transcriptional regulation, with their dysregulation linked to various human diseases. Despite their biological importance, chemical inhibitors for targeting PHD-fingers are very limited. Here we report a potent and selective de novo cyclic peptide inhibitor (OC9) targeting the Nε-trimethyllysine-binding PHD-fingers of the KDM7 histone demethylases, developed using mRNA display. OC9 disrupts PHD-finger interaction with histone H3K4me3 by engaging the Nε-methyllysine-binding aromatic cage through a valine, revealing a new non-lysine recognition motif for the PHD-fingers that does not require cation-π interaction. PHD-finger inhibition by OC9 impacted JmjC-domain mediated demethylase activity at H3K9me2, leading to inhibition of KDM7B (PHF8) but stimulation of KDM7A (KIAA1718), representing a new approach for selective allosteric modulation of demethylase activity. Chemoproteomic analysis showed selective engagement of OC9 with KDM7s in T cell lymphoblastic lymphoma SUP T1 cells. Our results highlight the utility of mRNA-display derived cyclic peptides for targeting challenging epigenetic reader proteins to probe their biology, and the broader potential of this approach for targeting protein-protein interactions.

Fluorescent charge-assisted halogen-bonding macrocyclic halo-imidazolium receptors for anion recognition and sensing in aqueous media.

The synthesis and anion binding properties of a new family of fluorescent halogen bonding (XB) macrocyclic halo-imidazolium receptors are described. The receptors contain chloro-, bromo-, and iodo-imidazolium motifs incorporated into a cyclic structure using naphthalene spacer groups. The large size of the iodine atom substituents resulted in the isolation of anti and syn conformers of the iodo-imidazoliophane, whereas the chloro- and bromo-imidazoliophane analogues exhibit solution dynamic conformational behavior. The syn iodo-imidazoliophane isomer forms novel dimeric isostructural XB complexes of 2:2 stoichiometry with bromide and iodide anions in the solid state. Solution phase DOSY NMR experiments indicate iodide recognition takes place via cooperative convergent XB-iodide 1:1 stoichiometric binding in aqueous solvent mixtures. (1)H NMR and fluorescence spectroscopic titration experiments with a variety of anions in the competitive CD(3)OD/D(2)O (9:1) aqueous solvent mixture demonstrated the bromo- and syn iodo-imidazoliophane XB receptors to bind selectively iodide and bromide respectively, and sense these halide anions exclusively via a fluorescence response. The protic-, chloro-, and anti iodo-imidazoliophane receptors proved to be ineffectual anion complexants in this aqueous methanolic solvent mixture. Computational DFT and molecular dynamics simulations corroborate the experimental observations that bromo- and syn iodo-imidazoliophane XB receptors form stable cooperative convergent XB associations with bromide and iodide.