Bioactivity-driven fungal metabologenomics identifies antiproliferative stemphone analogs and their biosynthetic gene cluster.

INTRODUCTION: Fungi biosynthesize chemically diverse secondary metabolites with a wide range of biological activities. Natural product scientists have increasingly turned towards bioinformatics approaches, combining metabolomics and genomics to target secondary metabolites and their biosynthetic machinery. We recently applied an integrated metabologenomics workflow to 110 fungi and identified more than 230 high-confidence linkages between metabolites and their biosynthetic pathways. OBJECTIVES: To prioritize the discovery of bioactive natural products and their biosynthetic pathways from these hundreds of high-confidence linkages, we developed a bioactivity-driven metabologenomics workflow combining quantitative chemical information, antiproliferative bioactivity data, and genome sequences. METHODS: The 110 fungi from our metabologenomics study were tested against multiple cancer cell lines to identify which strains produced antiproliferative natural products. Three strains were selected for further study, fractionated using flash chromatography, and subjected to an additional round of bioactivity testing and mass spectral analysis. Data were overlaid using biochemometrics analysis to predict active constituents early in the fractionation process following which their biosynthetic pathways were identified using metabologenomics. RESULTS: We isolated three new-to-nature stemphone analogs, 19-acetylstemphones G (1), B (2) and E (3), that demonstrated antiproliferative activity ranging from 3 to 5 µM against human melanoma (MDA-MB-435) and ovarian cancer (OVACR3) cells. We proposed a rational biosynthetic pathway for these compounds, highlighting the potential of using bioactivity as a filter for the analysis of integrated-Omics datasets. CONCLUSIONS: This work demonstrates how the incorporation of biochemometrics as a third dimension into the metabologenomics workflow can identify bioactive metabolites and link them to their biosynthetic machinery.

Wheldone Revisited: Structure Revision Via DFT-GIAO Chemical Shift Calculations, 1,1-HD-ADEQUATE NMR Spectroscopy, and X-ray Crystallography Studies.

Wheldone is a fungal metabolite isolated from the coculture of Aspergillus fischeri and Xylaria flabelliformis, displaying cytotoxic activity against breast, melanoma, and ovarian cancer cell lines. Initially, its structure was characterized as an unusual 5-methyl-bicyclo[5.4.0]undeca-3,5-diene scaffold with a 2-hydroxy-1-propanone side chain and a 3-(2-(1-hydroxyethyl)-2-methyl-2,5-dihydrofuran-3-yl)acrylic acid moiety. Upon further examination, minor inconsistencies in the data suggested the need for the structure to be revisited. Thus, the structure of wheldone has been revised using an orthogonal experimental-computational approach, which combines 1,1-HD-ADEQUATE NMR experiments, DFT-GIAO chemical shift calculations, and single-crystal X-ray diffraction (SCXRD) analysis of a semisynthetic p-bromobenzylamide derivative, formed via a Steglich-type reaction. The summation of these data now permits the unequivocal assignment of both the structure and absolute configuration of the natural product.

A State of Independents: Rationalizing the High Z' Crystal Structures of Shikimate Esters.

Z' is a parameter used to denote the number of symmetry-independent molecules in the asymmetric unit of a crystal structure. High Z' (>1) crystal structures are relatively uncommon and are thought to arise through competition between intermolecular interactions of similar strength. As such high Z' crystal structures are challenging to predict and new examples are valuable in improving understanding in the field. Herein, we report the X-ray crystal structures of a series of shikimate esters, the asymmetric units of which exhibit high Z' values. Of special interest is the crystal structure of methyl shikimate, the asymmetric unit of which comprises 12 independent molecules; Z' = 12. This uncommonly large Z' value arises through a combination of factors, including the intrinsic homochirality of the molecule, the conformational inflexibility of the cyclohexene ring, the presence of multiple hydrogen bonding motifs, and both the cis- and trans-conformers of the ester moiety. Comparison of the X-ray crystal structures of shikimic acid, methyl shikimate, ethyl shikimate, and iso-propyl shikimate suggests that instances of high Z' in this series correlate with specific hydrogen bonding motifs influenced by the steric bulk of the ester. The results of this study provide important insights into factors that influence the formation of organic crystal structures where the value of Z' is greater than 1.

High-throughput nanoscale crystallization of dihydropyridine active pharmaceutical ingredients.

Single-crystal X-ray diffraction analysis of small molecule active pharmaceutical ingredients is a key technique in the confirmation of molecular connectivity, including absolute stereochemistry, as well as the solid-state form. However, accessing single crystals suitable for X-ray diffraction analysis of an active pharmaceutical ingredient can be experimentally laborious, especially considering the potential for multiple solid-state forms (solvates, hydrates and polymorphs). In recent years, methods for the exploration of experimental crystallization space of small molecules have undergone a `step-change', resulting in new high-throughput techniques becoming available. Here, the application of high-throughput encapsulated nanodroplet crystallization to a series of six dihydropyridines, calcium channel blockers used in the treatment of hypertension related diseases, is described. This approach allowed 288 individual crystallization experiments to be performed in parallel on each molecule, resulting in rapid access to crystals and subsequent crystal structures for all six dihydropyridines, as well as revealing a new solvate polymorph of nifedipine (1,4-dioxane solvate) and the first known solvate of nimodipine (DMSO solvate). This work further demonstrates the power of modern high-throughput crystallization methods in the exploration of the solid-state landscape of active pharmaceutical ingredients to facilitate crystal form discovery and structural analysis by single-crystal X-ray diffraction.

Improving the Conductivity of Amide-Based Small Molecules through Enhanced Molecular Packing and Their Application as Hole Transport Mediators in Perovskite Solar Cells.

Organic-inorganic hybrid halide perovskite solar cells (PSCs) have attracted substantial attention from the photovoltaic research community, with the power conversion efficiency (PCE) already exceeding 26%. Current state-of-the-art devices rely on Spiro-OMeTAD as the hole-transporting material (HTM); however, Spiro-OMeTAD is costly due to its complicated synthesis and expensive product purification, while its low conductivity ultimately limits the achievable device efficiency. In this work, we build upon our recently introduced family of low-cost amide-based small molecules and introduce a molecule (termed TPABT) that results in high conductivity values (∼10-5 S cm-1 upon addition of standard ionic additives), outperforming our previous amide-based material (EDOT-Amide-TPA, ∼10-6 S cm-1) while only costing an estimated $5/g. We ascribe the increased optoelectronic properties to favorable molecular packing, as shown by single-crystal X-ray diffraction, which results in close spacing between the triphenylamine blocks. This, in turn, results in a short hole-hopping distance between molecules and therefore good mobility and conductivity. In addition, TPABT exhibits a higher bandgap and is as a result more transparent in the visible range of the solar spectrum, leading to lower parasitic absorption losses than Spiro-OMeTAD, and has increased moisture stability. We applied the molecule in perovskite solar cells and obtained good efficiency values in the ∼15% range. Our approach shows that engineering better molecular packing may be the key to developing high-efficiency, low-cost HTMs for perovskite solar cells.

Soft Hydrogen-Bonded Organic Frameworks Constructed Using a Flexible Organic Cage Hinge.

Soft porous crystals combine flexibility and porosity, allowing them to respond structurally to external physical and chemical environments. However, striking the right balance between flexibility and sufficient rigidity for porosity is challenging, particularly for molecular crystals formed by using weak intermolecular interactions. Here, we report a flexible oxygen-bridged prismatic organic cage molecule, Cage-6-COOH, which has three pillars that exhibit "hinge-like" rotational motion in the solid state. Cage-6-COOH can form a range of hydrogen-bonded organic frameworks (HOFs) where the "hinge" can accommodate a remarkable 67° dihedral angle range between neighboring units. This stems both from flexibility in the noncovalent hydrogen-bonding motifs in the HOFs and the molecular flexibility in the oxygen-linked cage hinge itself. The range of structures for Cage-6-COOH includes two topologically complex interpenetrated HOFs, CageHOF-2α and CageHOF-2ß. CageHOF-2α is nonporous, while CageHOF-2ß has permanent porosity and a surface area of 458 m2 g-1. The flexibility of Cage-6-COOH allows this molecule to rapidly transform from a low-crystallinity solid into the two crystalline interpenetrated HOFs, CageHOF-2α and CageHOF-2ß, under mild conditions simply by using acetonitrile or ethanol vapor, respectively. This self-healing behavior was selective, with the CageHOF-2ß structure exhibiting structural memory behavior.

Reversible Pressure-Magnetic Modulation in a Tetrathiafulvalene-Based Dyad Piezochromic Dysprosium Single-Molecule Magnet.

The extreme sensitivity of trivalent lanthanide ions to crystal field variations led to the emergence of single-molecule magnetic switching under various stimuli. The use of pressure as an external stimulus instead of classic light irradiation, oxidation or any chemical reactions allows a fine tuning of the magnetic modulation. Here the well-known pure isotopically enriched [162 Dy(tta)3 (L)]⋅C6 H14 (162 Dy) Single-Molecule Magnet (SMM) (tta- =2-2-thenoyltrifluoroacetonate and L=4,5-bis(propylthio)-tetrathiafulvalene-2-(2-pyridyl)benzimidazole-methyl-2-pyridine) was experimentally investigated by single-crystal diffraction and squid magnetometry under high applied pressures. Both reversible piezochromic properties and pressure modulation of the slow magnetic relaxation behavior were demonstrated and supported by ab initio calculations. The magnetic study of the diluted sample [162 Dy0.05 Y0.95 (tta)3 (L)]⋅C6 H14 (162 Dy@Y) indicated that variations in the electronic structure have mainly intermolecular origin with weak intramolecular contribution. Quantitative magnetic interpretation concludes to a deterioration of the Orbach process for the benefit of both Raman and QTM mechanisms under applied pressure.

Conductivity in Thin Films of Transition Metal Coordination Complexes.

Two coordination complexes have been made by combining the dithiolene complexes [M(mnt)2]2- (mnt = maleonitriledithiolate; M = Ni2+ or Cu2+) as anion, with the copper(II) coordination complex [Cu(Stetra)] (Stetra = 6,6'-bis(4,5-dihydrothiazol-2-yl)-2,2'-bipyri-dine) as cation. The variation of the metal centers leads to a dramatic change in the conductivity of the materials, with the M = Cu2+ variant (Cu-Cu) displaying semiconductor behavior with a conductivity of approximately 2.5 × 10-8 S cm-1, while the M = Ni2+ variant (Ni-Cu) displayed no observable conductivity. Computational studies found Cu-Cu enables a minimization of reorganization energy losses and, as a result, a lower barrier to the charge transfer process, resulting in the reported higher conductivity.

The structure of a pentachromium(II) extended metal atom chain at 3 K: Cotton's conjecture proven.

We provide definitive experimental proof that the archetypal string-like compound [Cr5(tpda)4(NCS)2] has alternating long and short Cr-Cr separations in the solid state, as conjectured by F. A. Cotton, rather than essentially equally spaced Cr atoms, as initially claimed (H2tpda = N2,N6-di(pyridin-2-yl)pyridine-2,6-diamine). Single-crystal X-ray data collected from 292 to 3 K revealed that the misinterpretation is caused by pseudo-merohedral twinning and that bond length alternation is enhanced at low temperature.

Discovery, isolation, heterologous expression and mode-of-action studies of the antibiotic polyketide tatiomicin from Amycolatopsis sp. DEM30355.

A genomic and bioactivity informed analysis of the metabolome of the extremophile Amycolatopsis sp. DEM30355 has allowed for the discovery and isolation of the polyketide antibiotic tatiomicin. Identification of the biosynthetic gene cluster was confirmed by heterologous expression in Streptomyces coelicolor M1152. Structural elucidation, including absolute stereochemical assignment, was performed using complementary crystallographic, spectroscopic and computational methods. Tatiomicin shows antibiotic activity against Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA). Cytological profiling experiments suggest a putative antibiotic mode-of-action, involving membrane depolarisation and chromosomal decondensation of the target bacteria.

Spontaneous Decomposition of an Extraordinarily Twisted and Trans-Bent Fully-Phosphanyl-Substituted Digermene to an Unusual GeI Cluster.

Ditetrelenes R2 E=ER2 (E=Si, Ge, Sn, Pb) substituted by multiple N/P/O/S-donor groups are extremely rare due to their propensity to disaggregate into their tetrylene monomers R2 E. We report the synthesis of the first fully phosphanyl-substituted digermene {(Mes)2 P}2 Ge=Ge{P(Mes)2 }2 (3, Mes=2,4,6-Me3 C6 H2 ), which adopts a highly unusual structure in the solid state, that is both strongly trans-bent and highly twisted. Variable-temperature 31 P{1 H} NMR spectroscopy suggests that 3 persists in solution, but is subject to a dynamic equilibrium between two conformations, which have different geometries about the Ge=Ge bond (twisted/non-twisted) due to a difference in the nature of their π-stacking interactions. Compound 3 undergoes unprecedented, spontaneous decomposition in solution to give a unique GeI cluster {(Mes)2 P}4 Ge4 ⋅5 CyMe (7).

Differentiable Formation of Chiroptical Lanthanide Heterometallic Lnn Ln'4-n (L6 ) (n=0-4) Tetrahedra with C2 -Symmetrical Bis(tridentate) Ligands.

Construction of lanthanide heterometallic complex is important for engineering multifunction molecular containers. However, it remains a challenge because of the similar ionic radii of lanthanides. Herein we attempt to prepare chiral lanthanide heterometallic tetrahedra. Upon crystallization with a mixture of [Eu2 L3 ] and [Ln2 L3 ] (Ln=Gd, Tb and Dy) helicates, a mixture of heterometallic Eun Ln'4-n (L6 ) (n=0-4) tetrahedra was prepared. Selective formation of heterometallic tetrahedron was observed as MS deconvolution results deviated from statistical results. The formation of heterometallic tetrahedron was found to be sensitive to ionic radii as well as the ratio of the two helicates used in the crystallization.

The Role of the Fused Ring in Bicyclic Triazolium Organocatalysts: Kinetic, X-ray, and DFT Insights.

Bicyclic triazolium scaffolds are widely employed in N-heterocyclic carbene (NHC) organocatalysis. While the incorporation of a fused ring was initially for synthetic utility in accessing chiral, modular triazolyl scaffolds, recent results highlight the potential for impact upon reaction outcome with the underpinning origins unclear. The common first step to all triazolium-catalyzed transformations is C(3)-H deprotonation to form the triazolylidene NHC. Herein, we report an analysis of the impact of size of the fused (5-, 6-, and 7-membered, n = 1, 2, and 3, respectively) ring on the C(3) proton transfer reactions of a series of bicyclic triazolium salts. Rate constants for the deuteroxide-catalyzed C(3)-H/D-exchange of triazolium salts, kDO, were significantly influenced by the size of the adjacent fused ring, with the kinetic acidity trend, or protofugalities, following the order kDO (n = 1) > kDO (n = 2) ≈ kDO (n = 3). Detailed analyses of X-ray diffraction (XRD) data for 20 triazolium salts (including 16 new structures) and of computational data for the corresponding triazolylidene NHCs provide insight on structural effects of alteration of fused ring size. In particular, changes in internal triazolyl NCN angle and positioning of the most proximal CH2 with variation in fused ring size are proposed to influence the experimental protofugality order.

Structural Diversity of Perylenequinones Is Driven by Their Redox Behavior.

Hypocrellins and hypomycins are two subclasses of fungal perylenequinones with unique structural, biological, and photochemical properties. With the growing interest in these naturally occurring photosensitizers, more studies were warranted to better understand the structural relationships between these two subclasses of perylenequinones. In this study, the long-postulated biosynthetic precursor (7) of class B fungal perylenequinones was isolated and characterized from a Shiraia-like sp. (strain MSX60519). Furthermore, the electrochemical and chemical redox behaviors of hypocrellins and hypomycins were investigated under aerobic and anaerobic conditions. These studies served to define the structural relationship within hypocrellins (1-3), which was further supported by X-ray crystallography, and between hypocrellins and hypomycins (4-6). Chemical reductions of hypocrellins under anaerobic conditions identified the origin of hypomycin A (4), hypomycin C (5), and hypomycin E (6), which in turn served to confirm 4 and revise the absolute configurations of 5 and 6. Hypocrellins were shown to undergo reversible reduction and reoxidation under aerobic conditions, while in an anaerobic environment and longer time scale, the fully reduced form can, to some extent, undergo an intramolecular ring closing metathesis. This may impart a means of reductive pathway for self-protection against these phototoxins and explain the chemical diversity observed in the fungal metabolites.

Low temperature insights into the crystal and magnetic structure of a neutral radical ferromagnet.

The crystal structure of the radical ferromagnet 1a at 2 K reveals a contraction in the unit cell c constant which, at the molecular level, translates into a decrease in slippage of the radical π-stacks and an increase in ferromagnetic exchange interactions along the stacking axis. The results of BS-DFT calculations using long-range corrected functionals are consistent with an overall ferromagnetic topology.

Structural investigations into a new polymorph of F4TCNQ: towards enhanced semiconductor properties.

During the course of research into the structure of 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ), C12F4N4, an important compound in charge-transfer and organic semiconductor research, a previously unreported polymorph of F4TCNQ was grown concomitantly with the known polymorph from a saturated solution of dichloromethane. The structure was elucidated using single-crystal X-ray diffraction and it was found that the new polymorph packs with molecules in parallel layers, in a similar manner to the layered structure of F2TCNQ. The structure was analysed using Hirshfeld surface analysis, fingerprint plots and pairwise interaction energies, and compared to existing data. The structure of a toluene solvate of F4TCNQ is also reported.

Helicate-to-tetrahedron transformation of chiral lanthanide supramolecular complexes induced by ionic radii effect and linker length.

Controlled formation of desired lanthanide supramolecular complexes is challenging because of the difficulties in predicting coordination geometry, as well as a labile coordination number. Herein, we explore the effect of ionic radii and linker length on supramolecular species formation. A helicate-to-tetrahedron transformation occurred between [Ln2L13] and [Ln4L16] (Ln = La, Sm, Eu, Gd, Tb and Lu). For six lanthanide ions, the unfavored tetrahedron [La4L16] can only be observed in a concentrated mixture with the helicate [La2L13] where no pure [La4L16] species was isolated via crystallization. For Sm, Eu, Gd, Tb, the [Ln4L16] supramolecular tetrahedron can be isolated via crystallization from diisopropyl ether. A similar result was also observed for Lu, but the tetrahedral structure was found to be relatively stable and transformed back to [Lu2L13] much slower upon dissolution.  No tetrahedron formation was observed with L3 giving rise to only [Ln2L33] species, in which L3 contains a longer and more flexible linker compared with that of L1. Results show that the supramolecular transformation in these systems is governed by both the ionic radii as well as the ligand design. Special focus is on both [Eu2L13] and [Eu4L16] which form chiral entities and exhibit interesting circular polarized luminescence.

Minimizing Polymorphic Risk through Cooperative Computational and Experimental Exploration.

We combine state-of-the-art computational crystal structure prediction (CSP) techniques with a wide range of experimental crystallization methods to understand and explore crystal structure in pharmaceuticals and minimize the risk of unanticipated late-appearing polymorphs. Initially, we demonstrate the power of CSP to rationalize the difficulty in obtaining polymorphs of the well-known pharmaceutical isoniazid and show that CSP provides the structure of the recently obtained, but unsolved, Form III of this drug despite there being only a single resolved form for almost 70 years. More dramatically, our blind CSP study predicts a significant risk of polymorphism for the related iproniazid. Employing a wide variety of experimental techniques, including high-pressure experiments, we experimentally obtained the first three known nonsolvated crystal forms of iproniazid, all of which were successfully predicted in the CSP procedure. We demonstrate the power of CSP methods and free energy calculations to rationalize the observed elusiveness of the third form of iproniazid, the success of high-pressure experiments in obtaining it, and the ability of our synergistic computational-experimental approach to "de-risk" solid form landscapes.

Encapsulated Nanodroplet Crystallization of Organic-Soluble Small Molecules.

Single-crystal X-ray diffraction analysis (SCXRD) constitutes a universal approach for the elucidation of molecular structure and the study of crystalline forms. However, the discovery of viable crystallization conditions remains both experimentally challenging and resource intensive in both time and the quantity of analyte(s). We report a robot-assisted, high-throughput method for the crystallization of organic-soluble small molecules in which we employ only micrograms of analyte per experiment. This allows hundreds of crystallization conditions to be screened in parallel with minimal overall sample requirements. Crystals suitable for SCXRD are grown from nanoliter droplets of a solution of analyte in organic solvent(s), each of which is encapsulated within an inert oil to control the rate of solvent loss. This encapsulated nanodroplet crystallization methodology can also be used to search for new crystal forms, as exemplified through both our discovery of a new (13th) polymorph of the olanzapine precursor ROY and SCXRD analysis of the "uncrystallizable" agrochemical dithianon.

Trigonal to Pentagonal Bipyramidal Coordination Switching in a Co(II) Single-Ion Magnet.

In molecular magnetism and single-ion magnets in particular, the observation of slow relaxation of the magnetization is intimately linked to the coordination environment of the metal center. Such systems typically have blocking temperatures well below that of liquid nitrogen, and therefore detailed magnetic characterization is usually carried out at very low temperatures. Despite this, there has been little advantage taken of ultralow temperature single-crystal X-ray diffraction techniques that could provide a full understanding of the crystal structure in the same temperature regime where slow magnetic relaxation occurs. Here, we present a systematic variable temperature single crystal X-ray diffraction study of [CoII(NO3)3(H2O)(HDABCO)] (1) {DABCO = 1,4-diazabicyclo[2.2.2]octane} conducted between 295 to 4 K. A reversible and robust disorder-to-order, single-crystal to single-crystal phase transition was identified, which accompanied a switching of the coordination geometry around the central Co(II) from 5- to 7-coordinate below 140 K. The magnetic properties were investigated, revealing slow relaxation of the magnetization arising from a large easy-plane magnetic anisotropy (+D) in the Co(II) pentagonal bipyramidal environment observed at low temperatures. This study highlights the importance of conducting thorough low temperature crystallographic studies, particularly where magnetic characterization is carried out at such low temperatures.